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Conserved domains on  [gi|70980549|ref|NP_055791|]
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protein RRP5 homolog isoform 2 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
80-176 1.04e-39

S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 142.74  E-value: 1.04e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   80 LCEGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQVTQEQ---PLKDLLHLPELFSPGMLVRCVVSSL 156
Cdd:cd05693    1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEeedDEEELPDLEDLFSVGQLVRCKVVSL 80
                         90       100
                 ....*....|....*....|
gi 70980549  157 GITDRGKKSVKLSLNPKNVN 176
Cdd:cd05693   81 DKSKSGKKRIELSLEPELVN 100
S1_Rrp5_repeat_hs7 cd05699
S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
636-707 1.12e-38

S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240204 [Multi-domain]  Cd Length: 72  Bit Score: 138.76  E-value: 1.12e-38
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 70980549  636 GQLVDVKVLEKTKDGLEVAVLPHNIRAFLPTSHLSDHVANGPLLHHWLQAGDILHRVLCLSQSEGRVLLCRK 707
Cdd:cd05699    1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLSNYKGRIILTKK 72
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
715-797 3.54e-38

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 137.72  E-value: 3.54e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  715 EGGQDPKNFSEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRML 794
Cdd:cd04461    1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80

                 ...
gi 70980549  795 LSL 797
Cdd:cd04461   81 LSL 83
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
1321-1394 4.95e-37

S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240210 [Multi-domain]  Cd Length: 74  Bit Score: 134.06  E-value: 4.95e-37
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70980549 1321 IKEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1394
Cdd:cd05705    1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
1227-1298 1.99e-35

S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 129.39  E-value: 1.99e-35
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 70980549 1227 LEEGEVAMGRVVKVTPNEGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILSTADNVLTLSLR 1298
Cdd:cd05704    1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDGKYQLSLR 72
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
542-611 3.85e-35

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 128.50  E-value: 3.85e-35
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  542 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 611
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_hs10 cd05701
S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
925-993 4.20e-32

S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240206  Cd Length: 69  Bit Score: 119.99  E-value: 4.20e-32
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549  925 GSEHQAIVQHLEKSFAIASLVETGHLAAFSLTSHLNDTFRFDSEKLQVGQGVSLTLKTTEPGVTGLLLA 993
Cdd:cd05701    1 DSRHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNCLAGGPLLA 69
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
453-521 4.64e-31

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 116.95  E-value: 4.64e-31
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTL 521
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
1036-1105 9.74e-30

S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 113.07  E-value: 9.74e-30
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1036 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEGTSPTTKLKVGKTVTARVIGGRDMKTFKYLP 1105
Cdd:cd05702    1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
183-263 3.51e-28

S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240199 [Multi-domain]  Cd Length: 74  Bit Score: 108.88  E-value: 3.51e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  183 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYirqknkgAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEV 262
Cdd:cd05694    1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73

                 .
gi 70980549  263 S 263
Cdd:cd05694   74 S 74
S1_Rrp5_repeat_hs4 cd05696
S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
365-435 8.20e-28

S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240201 [Multi-domain]  Cd Length: 71  Bit Score: 107.73  E-value: 8.20e-28
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 70980549  365 GAVLDDVPVQGFFKKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSL 435
Cdd:cd05696    1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
846-910 1.30e-27

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member cd05700:

Pssm-ID: 471952  Cd Length: 65  Bit Score: 107.25  E-value: 1.30e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549  846 GMFLDLVVQEVLEDGSVVFSGGPVPDLVLKASRYHRAGQEVESGQKKKVVILNVDLLKLEVHVSL 910
Cdd:cd05700    1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
1149-1223 7.00e-26

S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 102.27  E-value: 7.00e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549 1149 GQTVTCFLKKYNVVKKWLEveIAPDIRGRIPLLLTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTLLCLSLTG 1223
Cdd:cd05703    1 GQEVTGFVNNVSKEFVWLT--ISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
S1_Rrp5_repeat_hs3 cd05695
S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
281-344 1.04e-25

S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240200 [Multi-domain]  Cd Length: 66  Bit Score: 101.58  E-value: 1.04e-25
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 70980549  281 GLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKA--GTYFSNQAVRACILCVHPRTRVVHLS 344
Cdd:cd05695    1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSskSTYKEGQKVRARILYVDPSTKVVGLS 66
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
1600-1860 6.89e-17

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 82.85  E-value: 6.89e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1600 RQPESA-DDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfREEQEKLnvwvALLNLENMYGSQESLT 1678
Cdd:COG2956   22 GQPDKAiDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYLKAGLLD 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1679 K---VFERAVQYNEP-LKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEC 1754
Cdd:COG2956   94 RaeeLLEKLLELDPDdAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL 173
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1755 LPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLAPKRMKFF 1834
Cdd:COG2956  174 DP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA--LELDPSDDLLL 249
                        250       260
                 ....*....|....*....|....*.
gi 70980549 1835 FKRYLdYEKQHGTEKdVQAVKAKALE 1860
Cdd:COG2956  250 ALADL-LERKEGLEA-ALALLERQLR 273
PTZ00121 super family cl31754
MAEBL; Provisional
1402-1593 6.24e-04

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 45.13  E-value: 6.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1402 KPDVLSASLEgQLTKQEERKTEAEERDQKGEKKNQKRNEKKN----QKGQEEVempsKEKQQPQKPQAQKRGGRECRESG 1477
Cdd:PTZ00121 1379 KADAAKKKAE-EKKKADEAKKKAEEDKKKADELKKAAAAKKKadeaKKKAEEK----KKADEAKKKAEEAKKADEAKKKA 1453
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1478 SEQERVSKKPKKAGLSEEDDSLVDvyYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAwnvglDSLTPAlpplAESS 1557
Cdd:PTZ00121 1454 EEAKKAEEAKKKAEEAKKADEAKK--KAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKA-----DEAKKA----EEAK 1522
                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 70980549  1558 DSEEDEKPHQAtiKKSKKERELEKQKAEKELSRIEE 1593
Cdd:PTZ00121 1523 KADEAKKAEEA--KKADEAKKAEEKKKADELKKAEE 1556
 
Name Accession Description Interval E-value
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
80-176 1.04e-39

S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 142.74  E-value: 1.04e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   80 LCEGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQVTQEQ---PLKDLLHLPELFSPGMLVRCVVSSL 156
Cdd:cd05693    1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEeedDEEELPDLEDLFSVGQLVRCKVVSL 80
                         90       100
                 ....*....|....*....|
gi 70980549  157 GITDRGKKSVKLSLNPKNVN 176
Cdd:cd05693   81 DKSKSGKKRIELSLEPELVN 100
S1_Rrp5_repeat_hs7 cd05699
S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
636-707 1.12e-38

S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240204 [Multi-domain]  Cd Length: 72  Bit Score: 138.76  E-value: 1.12e-38
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 70980549  636 GQLVDVKVLEKTKDGLEVAVLPHNIRAFLPTSHLSDHVANGPLLHHWLQAGDILHRVLCLSQSEGRVLLCRK 707
Cdd:cd05699    1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLSNYKGRIILTKK 72
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
715-797 3.54e-38

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 137.72  E-value: 3.54e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  715 EGGQDPKNFSEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRML 794
Cdd:cd04461    1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80

                 ...
gi 70980549  795 LSL 797
Cdd:cd04461   81 LSL 83
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
1321-1394 4.95e-37

S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240210 [Multi-domain]  Cd Length: 74  Bit Score: 134.06  E-value: 4.95e-37
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70980549 1321 IKEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1394
Cdd:cd05705    1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
1227-1298 1.99e-35

S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 129.39  E-value: 1.99e-35
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 70980549 1227 LEEGEVAMGRVVKVTPNEGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILSTADNVLTLSLR 1298
Cdd:cd05704    1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDGKYQLSLR 72
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
542-611 3.85e-35

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 128.50  E-value: 3.85e-35
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  542 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 611
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_hs10 cd05701
S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
925-993 4.20e-32

S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240206  Cd Length: 69  Bit Score: 119.99  E-value: 4.20e-32
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549  925 GSEHQAIVQHLEKSFAIASLVETGHLAAFSLTSHLNDTFRFDSEKLQVGQGVSLTLKTTEPGVTGLLLA 993
Cdd:cd05701    1 DSRHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNCLAGGPLLA 69
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
453-521 4.64e-31

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 116.95  E-value: 4.64e-31
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTL 521
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
1036-1105 9.74e-30

S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 113.07  E-value: 9.74e-30
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1036 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEGTSPTTKLKVGKTVTARVIGGRDMKTFKYLP 1105
Cdd:cd05702    1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
364-798 6.74e-29

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 123.31  E-value: 6.74e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    364 LGAVLDDVPVQG-FFKKAGATFRLK-DGVLAYARLSHlSDSKNVFNPEAFKpGNTHKCRIIDYSQMDELALLSlRTSIIE 441
Cdd:TIGR00717   95 EKAYEEGSIVEGkIVGKVKGGFIVDlNGVEAFLPGSQ-VDVKPIKDLDSLI-GKTLKFKIIKLDQKRNNIVVS-RRAYLE 171
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    442 AQYLRYHD-----IEPGAVVKGTVLTIKSYGMLVKVGeQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKK 516
Cdd:TIGR00717  172 EERSQAREellenLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGR 250
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    517 LMMTLKKTL------IESKLPvitcyadakPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTG 589
Cdd:TIGR00717  251 ISLSLKQLGedpweaIEKKFP---------VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKG 321
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    590 QVVKVVVLNCEPSKERMLLSFKlSSDPEP-----KKEPAGhSQKKGKAINIGQLVDVKVLEKTKDGLevavlphnirafl 664
Cdd:TIGR00717  322 DEVEVMILDIDPERRRLSLGLK-QCKANPweqfeEKHPVG-DRVTGKIKKITDFGAFVELEGGIDGL------------- 386
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    665 ptSHLSD--HVANGPLLHHWLQAGDILHR-VLCLSQSEGRVLLCRKPALVSTVEggqdpkNFSEIHP-GMLLIGFVKSIK 740
Cdd:TIGR00717  387 --IHLSDisWDKDGREADHLYKKGDEIEAvVLAVDKEKKRISLGVKQLTENPWE------KFAAKYKvGSVVKGKVTEIK 458
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 70980549    741 DYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:TIGR00717  459 DFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
183-263 3.51e-28

S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240199 [Multi-domain]  Cd Length: 74  Bit Score: 108.88  E-value: 3.51e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  183 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYirqknkgAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEV 262
Cdd:cd05694    1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73

                 .
gi 70980549  263 S 263
Cdd:cd05694   74 S 74
S1_Rrp5_repeat_hs4 cd05696
S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
365-435 8.20e-28

S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240201 [Multi-domain]  Cd Length: 71  Bit Score: 107.73  E-value: 8.20e-28
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 70980549  365 GAVLDDVPVQGFFKKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSL 435
Cdd:cd05696    1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71
S1_Rrp5_repeat_hs9 cd05700
S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
846-910 1.30e-27

S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240205  Cd Length: 65  Bit Score: 107.25  E-value: 1.30e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549  846 GMFLDLVVQEVLEDGSVVFSGGPVPDLVLKASRYHRAGQEVESGQKKKVVILNVDLLKLEVHVSL 910
Cdd:cd05700    1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
1149-1223 7.00e-26

S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 102.27  E-value: 7.00e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549 1149 GQTVTCFLKKYNVVKKWLEveIAPDIRGRIPLLLTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTLLCLSLTG 1223
Cdd:cd05703    1 GQEVTGFVNNVSKEFVWLT--ISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
S1_Rrp5_repeat_hs3 cd05695
S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
281-344 1.04e-25

S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240200 [Multi-domain]  Cd Length: 66  Bit Score: 101.58  E-value: 1.04e-25
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 70980549  281 GLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKA--GTYFSNQAVRACILCVHPRTRVVHLS 344
Cdd:cd05695    1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSskSTYKEGQKVRARILYVDPSTKVVGLS 66
rpsA PRK06299
30S ribosomal protein S1; Reviewed
450-798 1.73e-25

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 113.72  E-value: 1.73e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   450 IEPGAVVKGTVLTIKSYGMLVKVGeQMRGLVppmHLADILMK---NPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL- 525
Cdd:PRK06299  199 LEEGQVVEGVVKNITDYGAFVDLG-GVDGLL---HITDISWKrvnHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGe 274
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   526 -----IESKLPVitcyadakpglqthGFIIRVK-----DYGCIVKFYNNVQGLVpkH--ELS-TEYIPDPERVFYTGQVV 592
Cdd:PRK06299  275 dpweaIEKKYPV--------------GSKVKGKvtnitDYGAFVELEEGIEGLV--HvsEMSwTKKNKHPSKVVSVGQEV 338
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   593 KVVVLNCEPSKERMLLSFK-LSSDPE---PKKEPAGhSQKKGKAINIgqlvdvkvlekTKDGLEVAvLPHNIRAFLptsH 668
Cdd:PRK06299  339 EVMVLEIDEEKRRISLGLKqCKENPWeefAEKYPVG-DVVEGKVKNI-----------TDFGAFVG-LEGGIDGLV---H 402
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   669 LSD--HVANG--PLLHhwLQAGDILH-RVLCLSQSEGRVLLCRKPALvstveggQDP-KNFSEIHP-GMLLIGFVKSIKD 741
Cdd:PRK06299  403 LSDisWDKKGeeAVEL--YKKGDEVEaVVLKVDVEKERISLGIKQLE-------EDPfEEFAKKHKkGSIVTGTVTEVKD 473
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 70980549   742 YGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK06299  474 KGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
180-611 3.26e-22

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 100.12  E-value: 3.26e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  180 SAEALKPGMLLTGTVSSLEDHGYLVDIG--VDGtraFLPLlkaqEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSv 257
Cdd:COG0539   12 SLKELKEGDIVKGTVVSIDDDEVLVDIGykSEG---IIPL----SEFSDEPGELEVKVGDEVEVYVEKVEDGEGEIVLS- 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  258 ghsevsTAIATEQQSWN-----LNNllpGLVVKAQVQKVTPFGLTlnfltfftgvVDFMHldpkkagtyfsnqaVRAcil 332
Cdd:COG0539   84 ------KKKADREKAWEeleeaFEN---GEPVEGKVKGVVKGGLI----------VDIGG--------------VRA--- 127
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  333 cvhprtrvvhlslrpiFLqPGrpltrlscqnlgavlddvpvqgffkkagatfrlkdgvlayarlSHLsDSKNVFNPEAFK 412
Cdd:COG0539  128 ----------------FL-PA-------------------------------------------SQV-DVRPVRDLDEYV 146
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  413 pGNTHKCRIIDYSQMDELALLSlRTSIIEAQYLR-----YHDIEPGAVVKGTVLTIKSYGMLVKVGEqMRGLVppmHLAD 487
Cdd:COG0539  147 -GKTLEFKIIKLDRKRNNVVVS-RRAVLEEEREEkreelLEKLEEGDVVEGTVKNITDFGAFVDLGG-VDGLL---HISE 220
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  488 IL---MKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL------IESKLPVitcyadakpGLQTHGFIIRVKDYGCI 558
Cdd:COG0539  221 ISwgrVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQLQpdpwenIAEKYPV---------GDVVKGKVTRLTDFGAF 291
                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....
gi 70980549  559 VKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 611
Cdd:COG0539  292 VELEPGVEGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
1600-1860 6.89e-17

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 82.85  E-value: 6.89e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1600 RQPESA-DDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfREEQEKLnvwvALLNLENMYGSQESLT 1678
Cdd:COG2956   22 GQPDKAiDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYLKAGLLD 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1679 K---VFERAVQYNEP-LKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEC 1754
Cdd:COG2956   94 RaeeLLEKLLELDPDdAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL 173
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1755 LPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLAPKRMKFF 1834
Cdd:COG2956  174 DP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA--LELDPSDDLLL 249
                        250       260
                 ....*....|....*....|....*.
gi 70980549 1835 FKRYLdYEKQHGTEKdVQAVKAKALE 1860
Cdd:COG2956  250 ALADL-LERKEGLEA-ALALLERQLR 273
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
451-522 4.93e-16

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 74.18  E-value: 4.93e-16
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 70980549     451 EPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 522
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
728-798 3.82e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 71.87  E-value: 3.82e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 70980549     728 PGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
540-611 5.81e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 71.10  E-value: 5.81e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 70980549     540 KPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 611
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1035-1094 8.95e-11

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 59.54  E-value: 8.95e-11
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    1035 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1094
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVK--DPEEVLKVGDEVKVKVLS 59
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
547-609 1.05e-09

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 56.14  E-value: 1.05e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 70980549    547 GFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 609
Cdd:pfam00575    9 GEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILS 71
PRK08059 PRK08059
general stress protein 13; Validated
450-524 1.62e-09

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 57.36  E-value: 1.62e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549   450 IEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKT 524
Cdd:PRK08059    5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRAT 79
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1228-1298 2.12e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 52.61  E-value: 2.12e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 70980549    1228 EEGEVAMGRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILS--TADNVLTLSLR 1298
Cdd:smart00316    1 EVGDVVEGTVTEITPG-GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSvdEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1322-1395 4.45e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 51.84  E-value: 4.45e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70980549    1322 KEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKalyNKHLPEGKLLTARVLRLNHQKNLVELSF 1395
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDP---EEVLKVGDEVKVKVLSVDEEKGRIILSL 71
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
451-517 1.36e-07

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 50.36  E-value: 1.36e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 70980549    451 EPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKL 517
Cdd:pfam00575    2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRI 68
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
729-797 2.83e-07

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 49.59  E-value: 2.83e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549    729 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSL 797
Cdd:pfam00575    4 GDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
728-798 4.31e-07

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 53.29  E-value: 4.31e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70980549   728 PGMLLIGFVKSIKDYGVFI---QFPsGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK03987    8 EGELVVGTVKEVKDFGAFVtldEYP-GKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
185-256 1.54e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.21  E-value: 1.54e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 70980549     185 KPGMLLTGTVSSLEDHGYLVDIGvDGTRAFLPLLKAQEYiRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 256
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLG-NGVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
378-436 6.19e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 45.67  E-value: 6.19e-06
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549     378 KKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSLR 436
Cdd:smart00316   14 TPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1147-1221 2.49e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.75  E-value: 2.49e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549    1147 QAGQTVTCFLKkyNVVKKWLEVEIAPDIRGRIPLllTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTLLCLSL 1221
Cdd:smart00316    1 EVGDVVEGTVT--EITPGGAFVDLGNGVEGLIPI--SELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
82-170 2.64e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.75  E-value: 2.64e-05
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549      82 EGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQvtqeqplkdllhlpelFSPGMLVRCVVSSLgitDR 161
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEV----------------LKVGDEVKVKVLSV---DE 62

                    ....*....
gi 70980549     162 GKKSVKLSL 170
Cdd:smart00316   63 EKGRIILSL 71
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
449-508 3.48e-05

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 45.17  E-value: 3.48e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 70980549  449 DIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVppmH---LADILMKNPEKKYHIGDEVKCRVL 508
Cdd:COG1098    2 SIEVGDIVEGKVTGITPFGAFVELPEGTTGLV---HiseIADGYVKDINDYLKVGDEVKVKVL 61
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
634-707 5.79e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.98  E-value: 5.79e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549     634 NIGQLVDVKVLEKTKDGLEVAvLPHNIRAFLPTSHLSDHvaNGPLLHHWLQAGDILH-RVLCLSQSEGRVLLCRK 707
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVD-LGNGVEGLIPISELSDK--RVKDPEEVLKVGDEVKvKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
280-346 5.96e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.98  E-value: 5.96e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 70980549     280 PGLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKAG----TYFSNQAVRACILCVHPRTRVVHLSLR 346
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKdpeeVLKVGDEVKVKVLSVDEEKGRIILSLK 72
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
547-629 8.68e-05

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 44.01  E-value: 8.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  547 GFIIRVKDYGCIVKFYNNVQGLVpkH--ELSTEYIPDPERVFYTGQVVKVVVLNCEPSKeRMLLSFK-LSSDPEPKKEPA 623
Cdd:COG1098   11 GKVTGITPFGAFVELPEGTTGLV--HisEIADGYVKDINDYLKVGDEVKVKVLSIDEDG-KISLSIKqAEEKPKRPPRPR 87

                 ....*.
gi 70980549  624 GHSQKK 629
Cdd:COG1098   88 RNSRPK 93
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
1035-1094 1.13e-04

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 42.27  E-value: 1.13e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1035 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1094
Cdd:pfam00575    3 KGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVE--DPDEVIKVGDEVKVKVLK 60
PRK08059 PRK08059
general stress protein 13; Validated
552-629 1.32e-04

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 43.50  E-value: 1.32e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549   552 VKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKLSSD-PEPKKEPAGHSQKK 629
Cdd:PRK08059   18 IQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEaPEAKRKKGKILIPN 96
Suf pfam05843
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ...
1727-1869 1.42e-04

Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster Suppressor of forked [Su(f)] protein shares homology with the yeast RNA14 protein and the 77-kDa subunit of human cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilization and an important role of the GU-rich sequence for this regulation to occur.


Pssm-ID: 428647 [Multi-domain]  Cd Length: 291  Bit Score: 45.83  E-value: 1.42e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1727 VWIKYGAFLlRRSQAAASHR-VLQRALEclpsKEHV--DVIAKFAQLEFQLG-DAERAKAIFENTLSTYPKRTDVWSVYI 1802
Cdd:pfam05843    3 VWIQYMRAM-RRAEGIKGARkVFKKARK----RPRLtyHVYVASALMEYYCSkDPAVAFKIFELGLKLFPEDEEFVLKYL 77
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 70980549   1803 DMTIKHGSQKDVRDIFERVIHlSLAPKRM-KFFFKRYLDYEKQHGTEKDVQAVKAKALEYVEAKSSVL 1869
Cdd:pfam05843   78 DYLISLNDDNNARVLFERVLT-RLAQEKEaKPLWKKFISYESTFGDLASILKLEKRMAELFPEDPPLA 144
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
1033-1093 2.59e-04

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 42.38  E-value: 2.59e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549  1033 LSIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHI----LDDVPEgtspttKLKVGKTVTARVI 1093
Cdd:PRK07252    1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIktgfIDNIHQ------LLKVGEEVLVQVV 59
PTZ00121 PTZ00121
MAEBL; Provisional
1402-1593 6.24e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 45.13  E-value: 6.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1402 KPDVLSASLEgQLTKQEERKTEAEERDQKGEKKNQKRNEKKN----QKGQEEVempsKEKQQPQKPQAQKRGGRECRESG 1477
Cdd:PTZ00121 1379 KADAAKKKAE-EKKKADEAKKKAEEDKKKADELKKAAAAKKKadeaKKKAEEK----KKADEAKKKAEEAKKADEAKKKA 1453
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1478 SEQERVSKKPKKAGLSEEDDSLVDvyYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAwnvglDSLTPAlpplAESS 1557
Cdd:PTZ00121 1454 EEAKKAEEAKKKAEEAKKADEAKK--KAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKA-----DEAKKA----EEAK 1522
                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 70980549  1558 DSEEDEKPHQAtiKKSKKERELEKQKAEKELSRIEE 1593
Cdd:PTZ00121 1523 KADEAKKAEEA--KKADEAKKAEEKKKADELKKAEE 1556
rpsA PRK06676
30S ribosomal protein S1; Reviewed
170-307 8.97e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 43.71  E-value: 8.97e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   170 LNPKNVNRVLSAEA----------------LKPGMLLTGTVSSLEDHGYLVDIG-VDGtraflpLLKAQE--YIRQKNKG 230
Cdd:PRK06676  160 LDPEKNRVILSRRAvveeeraakkeellssLKEGDVVEGTVARLTDFGAFVDIGgVDG------LVHISElsHERVEKPS 233
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549   231 AKLKVGQYLNCIVEKVKGNGGVVSLSVGhsevstaiATEQQSWNL--NNLLPGLVVKAQVQKVTPFGLtlnFLTFFTGV 307
Cdd:PRK06676  234 EVVSVGQEVEVKVLSIDWETERISLSLK--------DTLPGPWEGveEKLPEGDVIEGTVKRLTDFGA---FVEVLPGV 301
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
1499-1793 1.55e-03

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 43.53  E-value: 1.55e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1499 LVDVYYREGKEEaEETNVLPKEKQTKPAE-APRLQLSSGFawnVGLDSLTPALPPLAESSDseedekphqatIKKSKKER 1577
Cdd:TIGR02917  539 LAGLYLRTGNEE-EAVAWLEKAAELNPQEiEPALALAQYY---LGKGQLKKALAILNEAAD-----------AAPDSPEA 603
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1578 ELEKQKAEKELSRIEEALmdpgrqpesaDDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTIS-FREEQE 1656
Cdd:TIGR02917  604 WLMLGRAQLAAGDLNKAV----------SSFKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRALELKPdNTEAQI 673
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1657 KLnvwVALLNLENMYGSQESLTKVFEraVQYNEPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVwIKYGAFLL 1736
Cdd:TIGR02917  674 GL---AQLLLAAKRTESAKKIAKSLQ--KQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKRAPSSQNA-IKLHRALL 747
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1737 RRSQAAASHRVLQRALeclpsKEHV-DVIAKFAQLEFQLGDAERAKAI--FENTLSTYPK 1793
Cdd:TIGR02917  748 ASGNTAEAVKTLEAWL-----KTHPnDAVLRTALAELYLAQKDYDKAIkhYQTVVKKAPD 802
DUF612 pfam04747
Protein of unknown function, DUF612; This family includes several uncharacterized proteins ...
1399-1598 3.83e-03

Protein of unknown function, DUF612; This family includes several uncharacterized proteins from Caenorhabditis elegans.


Pssm-ID: 282585 [Multi-domain]  Cd Length: 511  Bit Score: 41.97  E-value: 3.83e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1399 DTGKPDVLSASLEGQLTKQEERKTEAEERDQKGEKKNQKRNEKKNQKGQEEVEMPSKEKQQPQKPQAQkrggRECRESGS 1478
Cdd:pfam04747   49 DQRKEAFASLELTEQPQQVEKVKKSEKKKAQKQIAKDHEAEQKVNAKKAAEKEARRAEAEAKKRAAQE----EEHKQWKA 124
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1479 EQERVSKKPKKaglseEDDSLVDVYYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAWNVGLD-SLTPA-LPPLAES 1556
Cdd:pfam04747  125 EQERIQKEQEK-----KEADLKKLQAEKKKEKAVKAEKAEKAEKTKKASTPAPVEEEIVVKKVANDrSAAPApEPKTPTN 199
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 70980549   1557 SDSEEDEKPHQATIKKSKKERELEKQKAEKELSRIEEALMDP 1598
Cdd:pfam04747  200 TPAEPAEQVQEITGKKNKKNKKKSESEATAAPASVEQVVEQP 241
 
Name Accession Description Interval E-value
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
80-176 1.04e-39

S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 142.74  E-value: 1.04e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   80 LCEGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQVTQEQ---PLKDLLHLPELFSPGMLVRCVVSSL 156
Cdd:cd05693    1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEeedDEEELPDLEDLFSVGQLVRCKVVSL 80
                         90       100
                 ....*....|....*....|
gi 70980549  157 GITDRGKKSVKLSLNPKNVN 176
Cdd:cd05693   81 DKSKSGKKRIELSLEPELVN 100
S1_Rrp5_repeat_hs7 cd05699
S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
636-707 1.12e-38

S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240204 [Multi-domain]  Cd Length: 72  Bit Score: 138.76  E-value: 1.12e-38
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 70980549  636 GQLVDVKVLEKTKDGLEVAVLPHNIRAFLPTSHLSDHVANGPLLHHWLQAGDILHRVLCLSQSEGRVLLCRK 707
Cdd:cd05699    1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLSNYKGRIILTKK 72
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
715-797 3.54e-38

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 137.72  E-value: 3.54e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  715 EGGQDPKNFSEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRML 794
Cdd:cd04461    1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80

                 ...
gi 70980549  795 LSL 797
Cdd:cd04461   81 LSL 83
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
1321-1394 4.95e-37

S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240210 [Multi-domain]  Cd Length: 74  Bit Score: 134.06  E-value: 4.95e-37
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70980549 1321 IKEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1394
Cdd:cd05705    1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
1227-1298 1.99e-35

S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 129.39  E-value: 1.99e-35
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 70980549 1227 LEEGEVAMGRVVKVTPNEGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILSTADNVLTLSLR 1298
Cdd:cd05704    1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDGKYQLSLR 72
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
542-611 3.85e-35

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 128.50  E-value: 3.85e-35
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  542 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 611
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_hs10 cd05701
S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
925-993 4.20e-32

S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240206  Cd Length: 69  Bit Score: 119.99  E-value: 4.20e-32
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549  925 GSEHQAIVQHLEKSFAIASLVETGHLAAFSLTSHLNDTFRFDSEKLQVGQGVSLTLKTTEPGVTGLLLA 993
Cdd:cd05701    1 DSRHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNCLAGGPLLA 69
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
453-521 4.64e-31

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 116.95  E-value: 4.64e-31
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTL 521
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
1036-1105 9.74e-30

S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 113.07  E-value: 9.74e-30
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1036 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEGTSPTTKLKVGKTVTARVIGGRDMKTFKYLP 1105
Cdd:cd05702    1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
364-798 6.74e-29

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 123.31  E-value: 6.74e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    364 LGAVLDDVPVQG-FFKKAGATFRLK-DGVLAYARLSHlSDSKNVFNPEAFKpGNTHKCRIIDYSQMDELALLSlRTSIIE 441
Cdd:TIGR00717   95 EKAYEEGSIVEGkIVGKVKGGFIVDlNGVEAFLPGSQ-VDVKPIKDLDSLI-GKTLKFKIIKLDQKRNNIVVS-RRAYLE 171
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    442 AQYLRYHD-----IEPGAVVKGTVLTIKSYGMLVKVGeQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKK 516
Cdd:TIGR00717  172 EERSQAREellenLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGR 250
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    517 LMMTLKKTL------IESKLPvitcyadakPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTG 589
Cdd:TIGR00717  251 ISLSLKQLGedpweaIEKKFP---------VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKG 321
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    590 QVVKVVVLNCEPSKERMLLSFKlSSDPEP-----KKEPAGhSQKKGKAINIGQLVDVKVLEKTKDGLevavlphnirafl 664
Cdd:TIGR00717  322 DEVEVMILDIDPERRRLSLGLK-QCKANPweqfeEKHPVG-DRVTGKIKKITDFGAFVELEGGIDGL------------- 386
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    665 ptSHLSD--HVANGPLLHHWLQAGDILHR-VLCLSQSEGRVLLCRKPALVSTVEggqdpkNFSEIHP-GMLLIGFVKSIK 740
Cdd:TIGR00717  387 --IHLSDisWDKDGREADHLYKKGDEIEAvVLAVDKEKKRISLGVKQLTENPWE------KFAAKYKvGSVVKGKVTEIK 458
                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 70980549    741 DYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:TIGR00717  459 DFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
183-263 3.51e-28

S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240199 [Multi-domain]  Cd Length: 74  Bit Score: 108.88  E-value: 3.51e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  183 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYirqknkgAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEV 262
Cdd:cd05694    1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73

                 .
gi 70980549  263 S 263
Cdd:cd05694   74 S 74
S1_Rrp5_repeat_hs4 cd05696
S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
365-435 8.20e-28

S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240201 [Multi-domain]  Cd Length: 71  Bit Score: 107.73  E-value: 8.20e-28
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 70980549  365 GAVLDDVPVQGFFKKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSL 435
Cdd:cd05696    1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71
S1_Rrp5_repeat_hs9 cd05700
S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
846-910 1.30e-27

S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240205  Cd Length: 65  Bit Score: 107.25  E-value: 1.30e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549  846 GMFLDLVVQEVLEDGSVVFSGGPVPDLVLKASRYHRAGQEVESGQKKKVVILNVDLLKLEVHVSL 910
Cdd:cd05700    1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
1149-1223 7.00e-26

S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 102.27  E-value: 7.00e-26
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549 1149 GQTVTCFLKKYNVVKKWLEveIAPDIRGRIPLLLTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTLLCLSLTG 1223
Cdd:cd05703    1 GQEVTGFVNNVSKEFVWLT--ISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
S1_Rrp5_repeat_hs3 cd05695
S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
281-344 1.04e-25

S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240200 [Multi-domain]  Cd Length: 66  Bit Score: 101.58  E-value: 1.04e-25
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 70980549  281 GLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKA--GTYFSNQAVRACILCVHPRTRVVHLS 344
Cdd:cd05695    1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSskSTYKEGQKVRARILYVDPSTKVVGLS 66
rpsA PRK06299
30S ribosomal protein S1; Reviewed
450-798 1.73e-25

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 113.72  E-value: 1.73e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   450 IEPGAVVKGTVLTIKSYGMLVKVGeQMRGLVppmHLADILMK---NPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL- 525
Cdd:PRK06299  199 LEEGQVVEGVVKNITDYGAFVDLG-GVDGLL---HITDISWKrvnHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGe 274
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   526 -----IESKLPVitcyadakpglqthGFIIRVK-----DYGCIVKFYNNVQGLVpkH--ELS-TEYIPDPERVFYTGQVV 592
Cdd:PRK06299  275 dpweaIEKKYPV--------------GSKVKGKvtnitDYGAFVELEEGIEGLV--HvsEMSwTKKNKHPSKVVSVGQEV 338
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   593 KVVVLNCEPSKERMLLSFK-LSSDPE---PKKEPAGhSQKKGKAINIgqlvdvkvlekTKDGLEVAvLPHNIRAFLptsH 668
Cdd:PRK06299  339 EVMVLEIDEEKRRISLGLKqCKENPWeefAEKYPVG-DVVEGKVKNI-----------TDFGAFVG-LEGGIDGLV---H 402
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   669 LSD--HVANG--PLLHhwLQAGDILH-RVLCLSQSEGRVLLCRKPALvstveggQDP-KNFSEIHP-GMLLIGFVKSIKD 741
Cdd:PRK06299  403 LSDisWDKKGeeAVEL--YKKGDEVEaVVLKVDVEKERISLGIKQLE-------EDPfEEFAKKHKkGSIVTGTVTEVKD 473
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 70980549   742 YGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK06299  474 KGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
180-611 3.26e-22

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 100.12  E-value: 3.26e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  180 SAEALKPGMLLTGTVSSLEDHGYLVDIG--VDGtraFLPLlkaqEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSv 257
Cdd:COG0539   12 SLKELKEGDIVKGTVVSIDDDEVLVDIGykSEG---IIPL----SEFSDEPGELEVKVGDEVEVYVEKVEDGEGEIVLS- 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  258 ghsevsTAIATEQQSWN-----LNNllpGLVVKAQVQKVTPFGLTlnfltfftgvVDFMHldpkkagtyfsnqaVRAcil 332
Cdd:COG0539   84 ------KKKADREKAWEeleeaFEN---GEPVEGKVKGVVKGGLI----------VDIGG--------------VRA--- 127
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  333 cvhprtrvvhlslrpiFLqPGrpltrlscqnlgavlddvpvqgffkkagatfrlkdgvlayarlSHLsDSKNVFNPEAFK 412
Cdd:COG0539  128 ----------------FL-PA-------------------------------------------SQV-DVRPVRDLDEYV 146
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  413 pGNTHKCRIIDYSQMDELALLSlRTSIIEAQYLR-----YHDIEPGAVVKGTVLTIKSYGMLVKVGEqMRGLVppmHLAD 487
Cdd:COG0539  147 -GKTLEFKIIKLDRKRNNVVVS-RRAVLEEEREEkreelLEKLEEGDVVEGTVKNITDFGAFVDLGG-VDGLL---HISE 220
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  488 IL---MKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL------IESKLPVitcyadakpGLQTHGFIIRVKDYGCI 558
Cdd:COG0539  221 ISwgrVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQLQpdpwenIAEKYPV---------GDVVKGKVTRLTDFGAF 291
                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....
gi 70980549  559 VKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 611
Cdd:COG0539  292 VELEPGVEGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
182-611 2.80e-20

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 96.73  E-value: 2.80e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    182 EALKPGMLLTGTVSSLEDHGYLVDIGvdGTRAFLPlLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHse 261
Cdd:TIGR00717  183 ENLKEGDVVKGVVKNITDFGAFVDLG--GVDGLLH-ITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQ-- 257
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    262 vstaiaTEQQSWN--LNNLLPGLVVKAQVQKVTPFGltlnfltfftgvvdfmhldpkkagtyfsnqavracilcvhprtr 339
Cdd:TIGR00717  258 ------LGEDPWEaiEKKFPVGDKITGRVTNLTDYG-------------------------------------------- 287
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    340 vvhlslrpIFLQpgrpltrlscqnlgavlddvpvqgffkkagatfrLKDGVLAYARLSHLSDSKNVFNP-EAFKPGNTHK 418
Cdd:TIGR00717  288 --------VFVE----------------------------------IEEGIEGLVHVSEMSWVKKNSHPsKVVKKGDEVE 325
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    419 CRIIDYSQMDELALLSLRT------SIIEAQYlryhdiEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVppmHLADIL--- 489
Cdd:TIGR00717  326 VMILDIDPERRRLSLGLKQckanpwEQFEEKH------PVGDRVTGKIKKITDFGAFVELEGGIDGLI---HLSDISwdk 396
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    490 -MKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKtLIESKLPVITcyADAKPGLQTHGFIIRVKDYGCIVKFYNNVQGL 568
Cdd:TIGR00717  397 dGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQ-LTENPWEKFA--AKYKVGSVVKGKVTEIKDFGAFVELPGGVEGL 473
                          410       420       430       440
                   ....*....|....*....|....*....|....*....|...
gi 70980549    569 VPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 611
Cdd:TIGR00717  474 IRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
427-798 4.29e-20

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 96.94  E-value: 4.29e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   427 MDELALLSLRTSIIEAQYLRYHDIEP--GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVK 504
Cdd:PRK00087  275 MSELDNMEEVEENEQLEYMNELEKQIrrGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIE 354
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   505 CRVLLCD------------PEAKKLMMTLKKTLiESKLPVItcyadakpglqthGFIIRVKDYGCIVKfYNNVQGLVPKH 572
Cdd:PRK00087  355 VKVLKLEdedgyvvlskkeADREKAWKELEEAF-ENGEPVK-------------GKVKEVVKGGLLVD-YGGVRAFLPAS 419
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   573 ELSTEYIPDPERvfYTGQVVKVVVLNCEPSKERMLLsfkLSSDPEPKKEPAGHSQKKGKAINIGQLVDVKVLEKTKDGLE 652
Cdd:PRK00087  420 HVELGYVEDLSE--YKGQELEVKIIEFNRKRRKKVV---LSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAF 494
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   653 VAVlpHNIRAFLPTSHLSDHVANGPLLHhwLQAGDILH-RVLCLSQSEGRVLLCRKPALvstveggQDP-KNFSEIHP-G 729
Cdd:PRK00087  495 VDI--GGVDGLLHVSEISWGRVEKPSDV--LKVGDEIKvYILDIDKENKKLSLSLKKLL-------PDPwENVEEKYPvG 563
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549   730 MLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK00087  564 SIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIK 632
rpsA PRK06299
30S ribosomal protein S1; Reviewed
179-671 4.71e-19

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 93.31  E-value: 4.71e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   179 LSAEALKPGMLLTGTVSSLEDHGYLVDIG--VDGtraFLPLlkaqEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 256
Cdd:PRK06299   23 LKESETREGSIVKGTVVAIDKDYVLVDVGlkSEG---RIPL----EEFKNEQGELEVKVGDEVEVYVERIEDGFGETVLS 95
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   257 VghsevstAIATEQQSWN-LNNLL-PGLVVKAQVQKVTPFGLT--LNfltfftGVVDFM---HLD--PKKAGTYFSNQAV 327
Cdd:PRK06299   96 R-------EKAKRLEAWDkLEKAFeNGEIVEGVINGKVKGGFTvdLN------GVEAFLpgsQVDvrPVRDTDPLEGKEL 162
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   328 RACILCVHPRTRVVHLSLRPIF--------------LQPGrpltrlscqnlgavldDVpVQGFFKKA---GATFRLK--D 388
Cdd:PRK06299  163 EFKVIKLDKKRNNIVVSRRAVLeeeraeereellenLEEG----------------QV-VEGVVKNItdyGAFVDLGgvD 225
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   389 GVLAYARLSHlsdsKNVFNP-EAFKPGNTHKCRIIDYSQmdELALLSLrtSI----------IEAQYlryhdiEPGAVVK 457
Cdd:PRK06299  226 GLLHITDISW----KRVNHPsEVVNVGDEVKVKVLKFDK--EKKRVSL--GLkqlgedpweaIEKKY------PVGSKVK 291
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   458 GTVLTIKSYGMLVKVGEQMRGLVppmHLADI----LMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL------IE 527
Cdd:PRK06299  292 GKVTNITDYGAFVELEEGIEGLV---HVSEMswtkKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKenpweeFA 368
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   528 SKLPVitcyadakpGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERM 606
Cdd:PRK06299  369 EKYPV---------GDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERI 439
                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 70980549   607 LLSFK-LSSDPepkkepAGHSQKKGKainIGQLVDVKVLEKTKDGLEVAvLPHNIRAFLPTSHLSD 671
Cdd:PRK06299  440 SLGIKqLEEDP------FEEFAKKHK---KGSIVTGTVTEVKDKGAFVE-LEDGVEGLIRASELSR 495
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
567-798 1.91e-18

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 88.95  E-value: 1.91e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  567 GLVPKHELSTEyipdPERVFYT-GQVVKVVVLNCEPSKERMLLSfklssdpepkKEPAGhsQKKG-----KAINIGQLVD 640
Cdd:COG0539   44 GIIPLSEFSDE----PGELEVKvGDEVEVYVEKVEDGEGEIVLS----------KKKAD--REKAweeleEAFENGEPVE 107
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  641 VKVLEKTKDGLEVAVlpHNIRAFLPTSHLSDH-VAN-GPLLHHWLQAgdilhRVLCLSQSEGRVLLCRKPALVSTVEGGQ 718
Cdd:COG0539  108 GKVKGVVKGGLIVDI--GGVRAFLPASQVDVRpVRDlDEYVGKTLEF-----KIIKLDRKRNNVVVSRRAVLEEEREEKR 180
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  719 DpKNFSEIHPGMLLIGFVKSIKDYGVFIQFPsGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:COG0539  181 E-ELLEKLEEGDVVEGTVKNITDFGAFVDLG-GVDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLK 258
rpsA PRK06676
30S ribosomal protein S1; Reviewed
565-798 2.04e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 89.55  E-value: 2.04e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   565 VQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKLSsdpepkKEPAGHSQKKGKAINiGQLVDVKVL 644
Cdd:PRK06676   42 VEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRL------EAEKAWDKLEEKFEE-GEVVEVKVT 114
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   645 EKTKDGLEVAVlpHNIRAFLPTSHLSDH-VANgpllHHWLQAGDILHRVLCLSQSEGRVLLCRKpALVSTVEGGQDPKNF 723
Cdd:PRK06676  115 EVVKGGLVVDV--EGVRGFIPASLISTRfVED----FSDFKGKTLEVKIIELDPEKNRVILSRR-AVVEEERAAKKEELL 187
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549   724 SEIHPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK06676  188 SSLKEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLK 261
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
1600-1860 6.89e-17

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 82.85  E-value: 6.89e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1600 RQPESA-DDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfREEQEKLnvwvALLNLENMYGSQESLT 1678
Cdd:COG2956   22 GQPDKAiDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYLKAGLLD 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1679 K---VFERAVQYNEP-LKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEC 1754
Cdd:COG2956   94 RaeeLLEKLLELDPDdAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL 173
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1755 LPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLAPKRMKFF 1834
Cdd:COG2956  174 DP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA--LELDPSDDLLL 249
                        250       260
                 ....*....|....*....|....*.
gi 70980549 1835 FKRYLdYEKQHGTEKdVQAVKAKALE 1860
Cdd:COG2956  250 ALADL-LERKEGLEA-ALALLERQLR 273
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
451-522 4.93e-16

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 74.18  E-value: 4.93e-16
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 70980549     451 EPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 522
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA PRK06676
30S ribosomal protein S1; Reviewed
405-621 8.52e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 81.46  E-value: 8.52e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   405 VFNPEAFKpGNTHKCRIIDYSQMDELALLSlRTSIIEAQYLRYHD-----IEPGAVVKGTVLTIKSYGMLVKVGEqMRGL 479
Cdd:PRK06676  142 VEDFSDFK-GKTLEVKIIELDPEKNRVILS-RRAVVEEERAAKKEellssLKEGDVVEGTVARLTDFGAFVDIGG-VDGL 218
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   480 VppmHLADI---LMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL------IESKLPVitcyadakpGLQTHGFII 550
Cdd:PRK06676  219 V---HISELsheRVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLpgpwegVEEKLPE---------GDVIEGTVK 286
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 70980549   551 RVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKlSSDPEPKKE 621
Cdd:PRK06676  287 RLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIK-ALEEAPAEE 356
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
729-798 9.35e-16

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 73.41  E-value: 9.35e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  729 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
566-1094 2.78e-15

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 80.93  E-value: 2.78e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    566 QGLVPKHElsteyIPDPERVFYTGQVVKVVVLNCEPSKERMLLSfklssdpepkKEPAGHSQKKGK---AINIGQLVDVK 642
Cdd:TIGR00717   43 EGRIPKEE-----FLDAPLEIQVGDEVEVYLDRVEDRFGETVLS----------REKAQRHELWIKlekAYEEGSIVEGK 107
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    643 VLEKTKDGLEVAVlpHNIRAFLPTSHLSDHVANGPLLHhwlQAGDILHRVLCLSQSEGRVLLCRKPALVSTVEGGQDpKN 722
Cdd:TIGR00717  108 IVGKVKGGFIVDL--NGVEAFLPGSQVDVKPIKDLDSL---IGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQARE-EL 181
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    723 FSEIHPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLRLSDc 802
Cdd:TIGR00717  182 LENLKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLG- 259
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    803 glGD--LAItsllllnqclEELQGVRSLMSNRdsvliqtLAEMTP-GMFLDLV--------VQEVLEDGSVVfsggpvpd 871
Cdd:TIGR00717  260 --EDpwEAI----------EKKFPVGDKITGR-------VTNLTDyGVFVEIEegieglvhVSEMSWVKKNS-------- 312
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    872 lvlKASRYHRAGQEVEsgqkkkVVILNVDLLKLEVHVSLHQDLVN---RKARKLRKGSEHQAIVQHLEKSFAIASLVE-- 946
Cdd:TIGR00717  313 ---HPSKVVKKGDEVE------VMILDIDPERRRLSLGLKQCKANpweQFEEKHPVGDRVTGKIKKITDFGAFVELEGgi 383
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    947 TGHLaafsltsHLNDTFRFDSEKlqvgqgVSLTLKTTEPGVTGLLLAVEGPAAKRTMRPTQKDSETVDEDEEVDPaltvg 1026
Cdd:TIGR00717  384 DGLI-------HLSDISWDKDGR------EADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYK----- 445
                          490       500       510       520       530       540
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 70980549   1027 tikkhtlsIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1094
Cdd:TIGR00717  446 --------VGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDE--DKTDEIKVGDEVEAKVVD 503
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
527-610 2.97e-15

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 72.62  E-value: 2.97e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  527 ESKLPviTCYADAKPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERM 606
Cdd:cd04461    2 EGTLP--TNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRF 79

                 ....
gi 70980549  607 LLSF 610
Cdd:cd04461   80 LLSL 83
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
728-798 3.82e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 71.87  E-value: 3.82e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 70980549     728 PGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
540-611 5.81e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 71.10  E-value: 5.81e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 70980549     540 KPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 611
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
631-1094 8.47e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 79.82  E-value: 8.47e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   631 KAINIGQLVDVKVLEKTKDGLEVAVlpHNIRAFLPTSHLS-----DHvanGPLLHHWLQAgdilhRVLCLSQSEGRVLLC 705
Cdd:PRK06299  110 KAFENGEIVEGVINGKVKGGFTVDL--NGVEAFLPGSQVDvrpvrDT---DPLEGKELEF-----KVIKLDKKRNNIVVS 179
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   706 RKpALVSTVEGGQDPKNFSEIHPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTN 785
Cdd:PRK06299  180 RR-AVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDL-GGVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLK 257
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   786 VDEEKQRMLLSLRLsdcgLGD---LAITsllllnqclEELQgVRSLMSNRDSVLiqtlaemTP-GMFLDlvvqevLEDGs 861
Cdd:PRK06299  258 FDKEKKRVSLGLKQ----LGEdpwEAIE---------KKYP-VGSKVKGKVTNI-------TDyGAFVE------LEEG- 309
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   862 vvfsggpVPDLV-----------LKASRYHRAGQEVEsgqkkkVVILNVDLLKLEVHVSLHQDLVN---RKARKLRKGSE 927
Cdd:PRK06299  310 -------IEGLVhvsemswtkknKHPSKVVSVGQEVE------VMVLEIDEEKRRISLGLKQCKENpweEFAEKYPVGDV 376
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   928 HQAivqhleksfAIASLVETGhlaAFsltshlndtfrfdseklqvgqgVSLtlkttEPGVTGLL----LA--VEGPAAKR 1001
Cdd:PRK06299  377 VEG---------KVKNITDFG---AF----------------------VGL-----EGGIDGLVhlsdISwdKKGEEAVE 417
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1002 TMRptqKDSE------TVDEDEE----------VDPALTVgtIKKHTlsIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHA 1065
Cdd:PRK06299  418 LYK---KGDEveavvlKVDVEKErislgikqleEDPFEEF--AKKHK--KGSIVTGTVTEVKDKGAFVELEDGVEGLIRA 490
                         490       500
                  ....*....|....*....|....*....
gi 70980549  1066 SHILDDvpEGTSPTTKLKVGKTVTARVIG 1094
Cdd:PRK06299  491 SELSRD--RVEDATEVLKVGDEVEAKVIN 517
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
1628-1860 3.96e-14

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 74.77  E-value: 3.96e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1628 FHLQATEIEKARAVAERALKtisfrEEQEKLNVWVALLNLENMYGSQESLTKVFERAVQYNEP-LKVFLHLADIYAKSEK 1706
Cdd:COG2956   17 NYLLNGQPDKAIDLLEEALE-----LDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLERDPDrAEALLELAQDYLKAGL 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1707 FQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPSKEHVDVIAkfAQLEFQLGDAERAKAIFEN 1786
Cdd:COG2956   92 LDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCEL--AELYLEQGDYDEAIEALEK 169
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70980549 1787 TLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLAPKRMKFFFKRYLDYEKQHGTEKDVQAVKaKALE 1860
Cdd:COG2956  170 ALKLDPDCARALLLLAELYLEQGDYEEAIAALERA--LEQDPDYLPALPRLAELYEKLGDPEEALELLR-KALE 240
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
1576-1791 7.83e-13

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 70.91  E-value: 7.83e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1576 ERELEKQKAEKELSRIeeaLMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfrEEQ 1655
Cdd:COG2956   70 ERDPDRAEALLELAQD---YLKAGLLDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLK-----LGP 141
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1656 EKLNVWVALLNLENMYGSQESLTKVFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAF 1734
Cdd:COG2956  142 ENAHAYCELAELYLEQGDYDEAIEALEKALKLDpDCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAEL 221
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 70980549 1735 LLRRSQAAASHRVLQRALECLPSkehVDVIAKFAQLEFQLGDAERAKAIFENTLSTY 1791
Cdd:COG2956  222 YEKLGDPEEALELLRKALELDPS---DDLLLALADLLERKEGLEAALALLERQLRRH 275
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
732-796 9.80e-13

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 64.71  E-value: 9.80e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549  732 LIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 796
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
456-520 1.15e-12

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 64.32  E-value: 1.15e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549  456 VKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMT 520
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
rpsA PRK06676
30S ribosomal protein S1; Reviewed
449-798 1.18e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 71.83  E-value: 1.18e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   449 DIEPGAVVKGTVLTIKSYGMLVKV-GEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIE 527
Cdd:PRK06676   14 EVEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAE 93
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   528 ---SKLpvITCYADAKPglqthgFIIRVKDY---GCIVKFyNNVQGLVPKHELSTEYIPDPERvfYTGQVVKVVVLNCEP 601
Cdd:PRK06676   94 kawDKL--EEKFEEGEV------VEVKVTEVvkgGLVVDV-EGVRGFIPASLISTRFVEDFSD--FKGKTLEVKIIELDP 162
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   602 SKERMLLSFK--LSSDPEPKKEPAGHSqkkgkaINIGQLVDVKVLEKTK----------DGLevavlphnirafLPTSHL 669
Cdd:PRK06676  163 EKNRVILSRRavVEEERAAKKEELLSS------LKEGDVVEGTVARLTDfgafvdiggvDGL------------VHISEL 224
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   670 S-DHVANgpllhhwlqAGDILH-------RVLCLSQSEGRVLLCRKPALVSTVEGGQDpknfsEIHPGMLLIGFVKSIKD 741
Cdd:PRK06676  225 ShERVEK---------PSEVVSvgqevevKVLSIDWETERISLSLKDTLPGPWEGVEE-----KLPEGDVIEGTVKRLTD 290
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 70980549   742 YGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK06676  291 FGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIK 347
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
1679-1793 8.05e-12

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 64.44  E-value: 8.05e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1679 KVFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPs 1757
Cdd:COG4783   25 ALLEKALELDpDNPEAFALLGEILLQLGDLDEAIVLLHEALELDPDEPEARLNLGLALLKAGDYDEALALLEKALKLDP- 103
                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 70980549 1758 kEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPK 1793
Cdd:COG4783  104 -EHPEAYLRLARAYRALGRPDEAIAALEKALELDPD 138
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
450-798 8.36e-12

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 69.76  E-value: 8.36e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    450 IEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPpmhLADILmkNPEKKYHIGDEVKCRVLLCDP-EAKKLMMTLKKTLIES 528
Cdd:TIGR00717   16 TRPGSIVKGTVVAINKDTVFVDVGLKSEGRIP---KEEFL--DAPLEIQVGDEVEVYLDRVEDrFGETVLSREKAQRHEL 90
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    529 KLPVITCYADAKPglqTHGFIIRVKDYGCIVKFyNNVQGLVPKHELSTEYIPDPERvfYTGQVVKVVVLNCEPSKERMLL 608
Cdd:TIGR00717   91 WIKLEKAYEEGSI---VEGKIVGKVKGGFIVDL-NGVEAFLPGSQVDVKPIKDLDS--LIGKTLKFKIIKLDQKRNNIVV 164
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    609 SFKLSSDPEPKKEpaghSQKKGKAINIGQLVDVKVLEKTKDGleVAVLPHNIRAFLPTSHLS-DHVANgPllHHWLQAGD 687
Cdd:TIGR00717  165 SRRAYLEEERSQA----REELLENLKEGDVVKGVVKNITDFG--AFVDLGGVDGLLHITDMSwKRVKH-P--SEYVKVGQ 235
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    688 ILH-RVLCLSQSEGRVLLCRKpalvstvEGGQDP-KNFSEIHP-GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMS-D 763
Cdd:TIGR00717  236 EVKvKVIKFDKEKGRISLSLK-------QLGEDPwEAIEKKFPvGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwV 308
                          330       340       350
                   ....*....|....*....|....*....|....*
gi 70980549    764 KFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:TIGR00717  309 KKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
546-609 1.00e-11

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 62.01  E-value: 1.00e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70980549  546 HGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 609
Cdd:cd00164    2 TGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1035-1094 8.95e-11

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 59.54  E-value: 8.95e-11
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    1035 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1094
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVK--DPEEVLKVGDEVKVKVLS 59
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
729-798 1.17e-10

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 58.84  E-value: 1.17e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  729 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKqRMLLSLR 798
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARG-RISLSIK 69
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
727-800 1.80e-10

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 58.49  E-value: 1.80e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549  727 HPGMLLIGFVKSIKDYGVFIQF-PSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLRLS 800
Cdd:cd05708    1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75
rpsA PRK13806
30S ribosomal protein S1; Provisional
401-687 2.09e-10

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 65.52  E-value: 2.09e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   401 DSKNVFNPEAFKpGNTHKCRIIDYSQ------MDELALLSLRTSIIEAQYLRyhDIEPGAVVKGTVLTIKSYGMLVKVGE 474
Cdd:PRK13806  148 DLRYVEDPESYV-GQTFQFLITRVEEngrnivVSRRALLEREQKEALEAFME--TVKEGDVVEGTVTRLAPFGAFVELAP 224
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   475 QMRGLVppmHLADI---LMKNPEKKYHIGDEVKCRVLLCDPEAK----KLMMTLKKTlieSKLPVITCYADAKPGLQTHG 547
Cdd:PRK13806  225 GVEGMV---HISELswsRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIKQA---GGDPWDTVGDRLKAGDKVTG 298
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   548 FIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKlssdpEPKKEP-AGH 625
Cdd:PRK13806  299 KVVRLAPFGAFVEILPGIEGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLR-----DAEGDPwADV 373
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 70980549   626 SQKkgkaINIGQLVDVKVLEKTKDGLEVAVLPhNIRAFLPTSHLSDhvANGPLLHHWLQAGD 687
Cdd:PRK13806  374 AER----FAPGTTVTGTVEKRAQFGLFVNLAP-GVTGLLPASVISR--AGKPATYEKLKPGD 428
rpsA PRK13806
30S ribosomal protein S1; Provisional
537-796 5.01e-10

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 63.98  E-value: 5.01e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   537 ADAKPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKE----RMLLSFK- 611
Cdd:PRK13806  198 ETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIKq 277
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   612 LSSDPepkkepaghSQKKGKAINIGQLVDVKVLEKTKDGLEVAVLPhNIRAFLPTSHLSdHV--ANGPllHHWLQAGDIL 689
Cdd:PRK13806  278 AGGDP---------WDTVGDRLKAGDKVTGKVVRLAPFGAFVEILP-GIEGLVHVSEMS-WTrrVNKP--EDVVAPGDAV 344
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   690 H-RVLCLSQSEGRVLLCRKPAlvstvEGgqDP-KNFSE-IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFV 766
Cdd:PRK13806  345 AvKIKDIDPAKRRISLSLRDA-----EG--DPwADVAErFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGK 417
                         250       260       270
                  ....*....|....*....|....*....|
gi 70980549   767 TSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 796
Cdd:PRK13806  418 PATYEKLKPGDSVTLVVEEIDTAKRKISLA 447
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
453-522 1.04e-09

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 56.08  E-value: 1.04e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 522
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
547-609 1.05e-09

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 56.14  E-value: 1.05e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 70980549    547 GFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 609
Cdd:pfam00575    9 GEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILS 71
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
1681-1800 1.46e-09

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 57.71  E-value: 1.46e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1681 FERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskE 1759
Cdd:COG4235    6 LRQALAANpNDAEGWLLLGRAYLRLGRYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEELLERALALDP--D 83
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 70980549 1760 HVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSV 1800
Cdd:COG4235   84 NPEALYLLGLAAFQQGDYAEAIAAWQKLLALLPADAPARLL 124
PRK08059 PRK08059
general stress protein 13; Validated
450-524 1.62e-09

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 57.36  E-value: 1.62e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549   450 IEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKT 524
Cdd:PRK08059    5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRAT 79
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
453-798 1.75e-09

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 61.60  E-value: 1.75e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  453 GAVVKGTVL-TIKSyGMLVKVGEqMRGLVPPMHLADILMKNPEKkyHIGDEVKCRVLLCDPEAKKL-----------MMT 520
Cdd:COG0539  103 GEPVEGKVKgVVKG-GLIVDIGG-VRAFLPASQVDVRPVRDLDE--YVGKTLEFKIIKLDRKRNNVvvsrravleeeREE 178
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  521 LKKTLIEsKLpvitcyadaKPGLQTHGFIIRVKDYGCIVKFyNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCE 600
Cdd:COG0539  179 KREELLE-KL---------EEGDVVEGTVKNITDFGAFVDL-GGVDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKID 247
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  601 PSKERMLLSFK-LSSDPepkkepaghsqkkgkainigqlvdvkvlektkdglevavlphniraflptshlsdhvangpll 679
Cdd:COG0539  248 REKERISLSLKqLQPDP--------------------------------------------------------------- 264
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  680 hhWLQAGDilhrvlclsqsegrvllcrkpalvstveggqdpknfsEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKA 759
Cdd:COG0539  265 --WENIAE-------------------------------------KYPVGDVVKGKVTRLTDFGAFVELEPGVEGLVHIS 305
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|
gi 70980549  760 IMS-DKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:COG0539  306 EMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
1689-1825 2.07e-09

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 57.51  E-value: 2.07e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1689 EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskEHVDVIAKFA 1768
Cdd:COG4783    2 ACAEALYALAQALLLAGDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALELDP--DEPEARLNLG 79
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 70980549 1769 QLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVIHLS 1825
Cdd:COG4783   80 LALLKAGDYDEALALLEKALKLDPEHPEAYLRLARAYRALGRPDEAIAALEKALELD 136
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
453-527 7.61e-09

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 60.73  E-value: 7.61e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549   453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIE 527
Cdd:PRK00087  563 GSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEE 637
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
37-346 8.93e-09

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 60.13  E-value: 8.93e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549     37 TEEGSTKRKKSQKGPAKTKKLKIEKRESSKSAREKFEilsvESLCEGMRILGCVKEVNELELVISLPNGLQGFVQVTEIc 116
Cdd:TIGR00717  231 VKVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIE----KKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEM- 305
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    117 dAYTKKLNeqvtqeqplkdllHLPELFSPGMLVRCVVssLGItDRGKKSVKLSLNPKNVNRVLSAEALKP-GMLLTGTVS 195
Cdd:TIGR00717  306 -SWVKKNS-------------HPSKVVKKGDEVEVMI--LDI-DPERRRLSLGLKQCKANPWEQFEEKHPvGDRVTGKIK 368
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    196 SLEDHGYLVDIGvDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHsevstaiATEQQSWNL 275
Cdd:TIGR00717  369 KITDFGAFVELE-GGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQ-------LTENPWEKF 440
                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 70980549    276 NNLLP-GLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHL----DPKKAGTYFSNQAVRACILCVHPRTRVVHLSLR 346
Cdd:TIGR00717  441 AAKYKvGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELsenrDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
rpsA PRK06299
30S ribosomal protein S1; Reviewed
182-553 1.23e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 59.79  E-value: 1.23e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   182 EALKPGMLLTGTVSSLEDHGYLVDI-GVDGtraflpLLKAQE--YIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVG 258
Cdd:PRK06299  197 ENLEEGQVVEGVVKNITDYGAFVDLgGVDG------LLHITDisWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLK 270
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   259 hsevstaiATEQQSW-NLNNLLP-GLVVKAQVQKVTPFGLtlnFLTFFTGVVDFMHL-------DPKKAGTYFS-NQAVR 328
Cdd:PRK06299  271 --------QLGEDPWeAIEKKYPvGSKVKGKVTNITDYGA---FVELEEGIEGLVHVsemswtkKNKHPSKVVSvGQEVE 339
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   329 ACILCVHPRTRVVHLSLRPifLQPgRPLTRLSCQ-NLGAVlddvpVQGFFK---KAGATFRLKDGVLAYARLSHLSDSKN 404
Cdd:PRK06299  340 VMVLEIDEEKRRISLGLKQ--CKE-NPWEEFAEKyPVGDV-----VEGKVKnitDFGAFVGLEGGIDGLVHLSDISWDKK 411
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   405 VFNP-EAFKPGNTHKCRIIDYSQMDELALLSLR------TSIIEAQYlryhdiEPGAVVKGTVLTIKSYGMLVKVGEQMR 477
Cdd:PRK06299  412 GEEAvELYKKGDEVEAVVLKVDVEKERISLGIKqleedpFEEFAKKH------KKGSIVTGTVTEVKDKGAFVELEDGVE 485
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 70980549   478 GLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIESKLPVITCYADAKPGLQTHGFIIRVK 553
Cdd:PRK06299  486 GLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEAEEKEAIAEYNSASDSKTTLGDLLKAA 561
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
381-611 1.24e-08

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 60.11  E-value: 1.24e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   381 GATFRLKDGVLAYARLSHLSDSKNVFNP-EAFKPGNTHKCRIIDYSQMDELALLSLRTSI------IEAQYlryhdiEPG 453
Cdd:PRK12269  593 GAFIELAEGIEGLAHISEFSWVKKTSKPsDMVKIGDEVECMILGYDIQAGRVSLGLKQVTanpweeIEARY------PVG 666
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   454 AVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNP-EKKYHIGDEVKCRVLLCDPEAKKLMMTLKKtLIESKLPV 532
Cdd:PRK12269  667 ARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPaDHELEVGKEIECMVIECDPQARRIRLGVKQ-LSDNPWQV 745
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   533 itcYADA-KPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPE---RVFYTGQVVKVVVLNCEPSKERMLL 608
Cdd:PRK12269  746 ---FANAyGVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPGealRKYAVGDRVKAVIVDMNVKDRKVAF 822

                  ...
gi 70980549   609 SFK 611
Cdd:PRK12269  823 SVR 825
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
1039-1101 1.38e-08

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 52.77  E-value: 1.38e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 70980549 1039 VTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIGGRDMKTF 1101
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVK--DPSEVFKVGDEVEVKVLEVDPEKGR 61
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1228-1298 2.12e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 52.61  E-value: 2.12e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 70980549    1228 EEGEVAMGRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILS--TADNVLTLSLR 1298
Cdd:smart00316    1 EVGDVVEGTVTEITPG-GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSvdEEKGRIILSLK 72
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1663-1820 4.44e-08

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 56.17  E-value: 4.44e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1663 ALLNLENMYGSQESLTK---VFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRR 1738
Cdd:COG0457   10 AYNNLGLAYRRLGRYEEaieDYEKALELDpDDAEALYNLGLAYLRLGRYEEALADYEQALELDPDDAEALNNLGLALQAL 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1739 SQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIF 1818
Cdd:COG0457   90 GRYEEALEDYDKALELDP--DDAEALYNLGLALLELGRYDEAIEAYERALELDPDDADALYNLGIALEKLGRYEEALELL 167

                 ..
gi 70980549 1819 ER 1820
Cdd:COG0457  168 EK 169
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1322-1395 4.45e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 51.84  E-value: 4.45e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70980549    1322 KEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKalyNKHLPEGKLLTARVLRLNHQKNLVELSF 1395
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDP---EEVLKVGDEVKVKVLSVDEEKGRIILSL 71
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
1327-1394 7.07e-08

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 50.84  E-value: 7.07e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 70980549 1327 LRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQhspSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1394
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSD---KFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
729-795 8.76e-08

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 50.96  E-value: 8.76e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 70980549  729 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMS-DKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLL 795
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
1030-1394 1.14e-07

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 56.67  E-value: 1.14e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1030 KHTLSIGDMVTGTVKSIKPTHVVVTLeDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIGGRDMKTFKYLPISHp 1109
Cdd:TIGR00717  182 LENLKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVK--HPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQ- 257
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1110 rfvrTIPElsvrpseledghtalnthsvsPMEKI-KQYQAGQTVTCflKKYNVVKKWLEVEIAPDIRGRIPLLLTSLSFK 1188
Cdd:TIGR00717  258 ----LGED---------------------PWEAIeKKFPVGDKITG--RVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKK 310
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1189 VlKHPDKKFRVGQALRATVVGPDSSKTLLCLSL--TGPHKLEE-------GEVAMGRVVKVTpNEGLTVSFPFGKIGTVS 1259
Cdd:TIGR00717  311 N-SHPSKVVKKGDEVEVMILDIDPERRRLSLGLkqCKANPWEQfeekhpvGDRVTGKIKKIT-DFGAFVELEGGIDGLIH 388
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1260 IFHMS-DSYSETPLEDFVPQKVVRCYILStadnvltLSLRSSRTNPETKSKVEDPEINSIQDIKEGQLLRGYVGSIQPHG 1338
Cdd:TIGR00717  389 LSDISwDKDGREADHLYKKGDEIEAVVLA-------VDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKDFG 461
                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 70980549   1339 VFFRLGPSVVGLARYSHVSQHSPSKKALynkHLPEGKLLTARVLRLNHQKNLVELS 1394
Cdd:TIGR00717  462 AFVELPGGVEGLIRNSELSENRDEDKTD---EIKVGDEVEAKVVDIDKKNRKVSLS 514
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
451-517 1.36e-07

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 50.36  E-value: 1.36e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 70980549    451 EPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKL 517
Cdd:pfam00575    2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRI 68
rpsA PRK13806
30S ribosomal protein S1; Provisional
381-609 1.72e-07

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 55.89  E-value: 1.72e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   381 GATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSLRTSIIEAQYLRYHDI----EPGAVV 456
Cdd:PRK13806  217 GAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVgdrlKAGDKV 296
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   457 KGTVLTIKSYGMLVKVGEQMRGLVppmHLADI----LMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIESKLPV 532
Cdd:PRK13806  297 TGKVVRLAPFGAFVEILPGIEGLV---HVSEMswtrRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADV 373
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 70980549   533 ITCYAdakPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 609
Cdd:PRK13806  374 AERFA---PGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLA 447
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
729-796 1.75e-07

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 49.92  E-value: 1.75e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 70980549  729 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 796
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
1700-1792 1.82e-07

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 52.66  E-value: 1.82e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1700 IYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQLGDAER 1779
Cdd:COG5010   63 LYNKLGDFEESLALLEQALQLDPNNPELYYNLALLYSRSGDKDEAKEYYEKALALSP--DNPNAYSNLAALLLSLGQDDE 140
                         90
                 ....*....|...
gi 70980549 1780 AKAIFENTLSTYP 1792
Cdd:COG5010  141 AKAALQRALGTSP 153
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
1697-1861 2.14e-07

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 54.35  E-value: 2.14e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1697 LADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEclPSKEHVDVIAKFAQLEFQLGD 1776
Cdd:COG2956   14 KGLNYLLNGQPDKAIDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE--RDPDRAEALLELAQDYLKAGL 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1777 AERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVIHLSlaPKRMKFFFKRYLDYEKQHGTEKDVQAVKa 1856
Cdd:COG2956   92 LDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLG--PENAHAYCELAELYLEQGDYDEAIEALE- 168

                 ....*
gi 70980549 1857 KALEY 1861
Cdd:COG2956  169 KALKL 173
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
728-796 2.22e-07

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 49.55  E-value: 2.22e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549  728 PGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 796
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
729-797 2.83e-07

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 49.59  E-value: 2.83e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549    729 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSL 797
Cdd:pfam00575    4 GDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
1700-1793 3.80e-07

Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 49.78  E-value: 3.80e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1700 IYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRvLQRALECLPskEHVDVIAKFAQLEFQLGDAER 1779
Cdd:COG3063    1 LYLKLGDLEEAEEYYEKALELDPDNADALNNLGLLLLEQGRYDEAIA-LEKALKLDP--NNAEALLNLAELLLELGDYDE 77
                         90
                 ....*....|....
gi 70980549 1780 AKAIFENTLSTYPK 1793
Cdd:COG3063   78 ALAYLERALELDPS 91
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
728-798 4.31e-07

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 53.29  E-value: 4.31e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70980549   728 PGMLLIGFVKSIKDYGVFI---QFPsGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK03987    8 EGELVVGTVKEVKDFGAFVtldEYP-GKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80
rpsA PRK06676
30S ribosomal protein S1; Reviewed
1033-1431 9.46e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 53.34  E-value: 9.46e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1033 LSIGDMVTGTVKSIKPTHVVVTLEDGII-GCIHASHILDDVPEGTSPTtkLKVGKTVTARVIGGRDMKtfKYLpishprf 1111
Cdd:PRK06676   15 VEVGDVVTGEVLKVEDKQVFVNIEGYKVeGVIPISELSNDHIEDINDV--VKVGDELEVYVLKVEDGE--GNL------- 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1112 vrtipELSVRPSELEDGHTALNthsvspmekiKQYQAGQTVTCFLKKynVVKKWLEVEIApDIRGRIPLLLTSLSFKvlk 1191
Cdd:PRK06676   84 -----LLSKRRLEAEKAWDKLE----------EKFEEGEVVEVKVTE--VVKGGLVVDVE-GVRGFIPASLISTRFV--- 142
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1192 hPDKKFRVGQALRATVVGPDSSKTLLCLSltgpHK-----------------LEEGEVAMGRVVKVTPnegltvsfpFG- 1253
Cdd:PRK06676  143 -EDFSDFKGKTLEVKIIELDPEKNRVILS----RRavveeeraakkeellssLKEGDVVEGTVARLTD---------FGa 208
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1254 --KIGTVS-IFHMSD-SYS--ETPLEDFVPQKVVRCYILStAD---NVLTLSLRSsrTNPETKSKVEdpeinsiQDIKEG 1324
Cdd:PRK06676  209 fvDIGGVDgLVHISElSHErvEKPSEVVSVGQEVEVKVLS-IDwetERISLSLKD--TLPGPWEGVE-------EKLPEG 278
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1325 QLLRGYVGSIQPHGVFFRLGPSVVGLArysHVSQHSpskkalyNKH-------LPEGKLLTARVLRLNHQKNLVELSflp 1397
Cdd:PRK06676  279 DVIEGTVKRLTDFGAFVEVLPGVEGLV---HISQIS-------HKHiatpsevLEEGQEVKVKVLEVNEEEKRISLS--- 345
                         410       420       430
                  ....*....|....*....|....*....|....
gi 70980549  1398 gdtgKPDVLSASLEGQLTKQEERKTEAEErDQKG 1431
Cdd:PRK06676  346 ----IKALEEAPAEEEDRREEYRQYELPE-EETG 374
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1593-1782 1.01e-06

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 51.93  E-value: 1.01e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1593 EALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisfreeqeKLNVWVALLNLENMYG 1672
Cdd:COG0457   16 LAYRRLGRYEEAIEDYEKALELDPDDAEALYNLGLAYLRLGRYEEALADYEQALEL--------DPDDAEALNNLGLALQ 87
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1673 SQESLTK---VFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVL 1748
Cdd:COG0457   88 ALGRYEEaleDYDKALELDpDDAEALYNLGLALLELGRYDEAIEAYERALELDPDDADALYNLGIALEKLGRYEEALELL 167
                        170       180       190
                 ....*....|....*....|....*....|....
gi 70980549 1749 QRALECLPSKEHVDVIAKFAQLEFQLGDAERAKA 1782
Cdd:COG0457  168 EKLEAAALAALLAAALGEAALALAAAEVLLALLL 201
PRK08059 PRK08059
general stress protein 13; Validated
724-798 1.16e-06

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 49.27  E-value: 1.16e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549   724 SEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK08059    3 SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
449-521 1.19e-06

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 47.97  E-value: 1.19e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 70980549  449 DIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTL 521
Cdd:cd04461   11 DLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
542-611 1.21e-06

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 47.67  E-value: 1.21e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  542 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPsKERMLLSFK 611
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK 69
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
1317-1395 1.32e-06

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 47.97  E-value: 1.32e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549 1317 SIQDIKEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKalyNKHLPEGKLLTARVLRLNHQKNLVELSF 1395
Cdd:cd04461    8 NFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDP---SFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
185-256 1.54e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.21  E-value: 1.54e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 70980549     185 KPGMLLTGTVSSLEDHGYLVDIGvDGTRAFLPLLKAQEYiRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 256
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLG-NGVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
453-522 1.90e-06

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 47.32  E-value: 1.90e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 70980549  453 GAVVKGTVLTIKSYGMLVKV-GEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 522
Cdd:cd05708    3 GQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
378-434 2.22e-06

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 46.60  E-value: 2.22e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 70980549  378 KKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLS 434
Cdd:cd00164    9 TKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
729-798 2.62e-06

S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein.


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 46.81  E-value: 2.62e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 70980549  729 GMLLIGFVKSIKDYGVFI---QFPsGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:cd04452    4 GELVVVTVKSIADMGAYVsllEYG-NIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK 75
RNA14 COG5107
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ...
1608-1868 2.96e-06

Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification];


Pssm-ID: 227438 [Multi-domain]  Cd Length: 660  Bit Score: 52.33  E-value: 2.96e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1608 FDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALK---TISFR-EEQEKLNvwvalLNLENMYGSQESLTKVFER 1683
Cdd:COG5107  291 HNQILDYFYYAEEVWFDYSEYLIGISDKQKALKTVERGIEmspSLTMFlSEYYELV-----NDEEAVYGCFDKCTQDLKR 365
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1684 AVQYNEplkvflhlADIYAKSE-KFQEAGELynrMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEcLPSKEHvD 1762
Cdd:COG5107  366 KYSMGE--------SESASKVDnNFEYSKEL---LLKRINKLTFVFCVHLNYVLRKRGLEAARKLFIKLRK-EGIVGH-H 432
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1763 VIAKFAQLEFQ-LGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVIHlSLAPKRMKFFFKRYLDY 1841
Cdd:COG5107  433 VYIYCAFIEYYaTGDRATAYNIFELGLLKFPDSTLYKEKYLLFLIRINDEENARALFETSVE-RLEKTQLKRIYDKMIEY 511
                        250       260
                 ....*....|....*....|....*..
gi 70980549 1842 EKQHGTEKDVQAVKAKALEYVEAKSSV 1868
Cdd:COG5107  512 ESMVGSLNNVYSLEERFRELVPQENLI 538
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
182-524 4.45e-06

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 50.81  E-value: 4.45e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  182 EALKPGMLLTGTVSSLEDHGYLVDIGvdGTRAFLPLlkAQEYIRQKNKGAKLkVGQYLNCIVEKV--KGNGGVVSlsvgH 259
Cdd:COG0539   98 EAFENGEPVEGKVKGVVKGGLIVDIG--GVRAFLPA--SQVDVRPVRDLDEY-VGKTLEFKIIKLdrKRNNVVVS----R 168
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  260 SEVSTAIATEQQSWNLNNLLPGLVVKAQVQKVTPFGLTLNFltfftGVVDFMhldpkkagtyfsnqavracilcvhprtr 339
Cdd:COG0539  169 RAVLEEEREEKREELLEKLEEGDVVEGTVKNITDFGAFVDL-----GGVDGL---------------------------- 215
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  340 vVHLSlrpiflqpgrpltrlscqnlgavlDdvpvqgffkkagatfrlkdgvLAYARLSHLSdsknvfnpEAFKPGNTHKC 419
Cdd:COG0539  216 -LHIS------------------------E---------------------ISWGRVKHPS--------EVLKVGDEVEV 241
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  420 RIIDYSQMDELALLSLRT------SIIEAQYlryhdiEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVppmHLADILM--- 490
Cdd:COG0539  242 KVLKIDREKERISLSLKQlqpdpwENIAEKY------PVGDVVKGKVTRLTDFGAFVELEPGVEGLV---HISEMSWtkr 312
                        330       340       350
                 ....*....|....*....|....*....|....*
gi 70980549  491 -KNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKT 524
Cdd:COG0539  313 vAHPSDVVKVGDEVEVKVLDIDPEERRISLSIKQL 347
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
454-618 5.67e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 50.57  E-value: 5.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   454 AVVKGTVLTIKSYGMLVKVgEQMRGLVPPMHLAdilmKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIESKLPVI 533
Cdd:PRK07400  120 ATVRSEVFATNRGGALVRI-EGLRGFIPGSHIS----TRKPKEELVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRL 194
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   534 tcyadaKPGLQTHGFIIRVKDYGCIVKFyNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKlS 613
Cdd:PRK07400  195 ------EVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTK-Q 266

                  ....*
gi 70980549   614 SDPEP 618
Cdd:PRK07400  267 LEPEP 271
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
378-436 6.19e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 45.67  E-value: 6.19e-06
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549     378 KKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSLR 436
Cdd:smart00316   14 TPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
726-796 6.68e-06

S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240210 [Multi-domain]  Cd Length: 74  Bit Score: 45.47  E-value: 6.68e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70980549  726 IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTS---DHFVEGQTVAAKVTNVDEEKQRMLLS 796
Cdd:cd05705    1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSlynKYLPEGKLLTAKVLSVNSEKNLVELS 74
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
80-170 9.87e-06

S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 45.04  E-value: 9.87e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   80 LCEGMRILGCVKEVNELE-LVISLPNGLQGFVQVTEICDAYTkklneqvtqEQPLKDllhlpelFSPGMLVRCVVSSlgi 158
Cdd:cd05704    1 LEEGAVTLGMVTKVIPHSgLTVQLPFGKTGLVSIFHLSDSYT---------ENPLEG-------FKPGKIVRCCILS--- 61
                         90
                 ....*....|..
gi 70980549  159 tdRGKKSVKLSL 170
Cdd:cd05704   62 --KKDGKYQLSL 71
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
729-796 1.31e-05

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 44.59  E-value: 1.31e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 70980549  729 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 796
Cdd:cd05707    1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
rpsA PRK06676
30S ribosomal protein S1; Reviewed
626-900 1.65e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 49.49  E-value: 1.65e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   626 SQKKGKAINIGQLVDVKVLEKTKDGLEVAVLPHNIRAFLPTSHLS-DHVANGPLLhhwLQAGDILH-RVLCLSQSEGRVL 703
Cdd:PRK06676    8 SLNSVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSnDHIEDINDV---VKVGDELEvYVLKVEDGEGNLL 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   704 LCRKPALVStveggqdpKNFSEI----HPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDhFVeGQTV 779
Cdd:PRK06676   85 LSKRRLEAE--------KAWDKLeekfEEGEVVEVKVTEVVKGGLVVDV-EGVRGFIPASLISTRFVEDFSD-FK-GKTL 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   780 AAKVTNVDEEKQRMLLSLRlsdcglgdlAItsllllnqcLEElqgvrSLMSNRDSVLiQTLAEmtpGMFLDLVVQEVLED 859
Cdd:PRK06676  154 EVKIIELDPEKNRVILSRR---------AV---------VEE-----ERAAKKEELL-SSLKE---GDVVEGTVARLTDF 206
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 70980549   860 GSVVFSGGpVPDLV----LKASRYHRAGQEVESGQKKKVVILNVD 900
Cdd:PRK06676  207 GAFVDIGG-VDGLVhiseLSHERVEKPSEVVSVGQEVEVKVLSID 250
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
1234-1297 2.02e-05

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 43.91  E-value: 2.02e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70980549 1234 MGRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILSTADNVLTLSL 1297
Cdd:cd00164    2 TGKVVSITKF-GVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISL 64
COG4700 COG4700
Uncharacterized conserved protein ECs_4300, contains TPR-like domain [Function unknown];
1682-1838 2.24e-05

Uncharacterized conserved protein ECs_4300, contains TPR-like domain [Function unknown];


Pssm-ID: 443735 [Multi-domain]  Cd Length: 249  Bit Score: 47.95  E-value: 2.24e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1682 ERAVQYNEPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVwIKYGA----FLLRRSQAAASHrvLQRALECLPS 1757
Cdd:COG4700   80 EKALEFADTVQNRVRLADALLELGRYDEAIELYEEALTGIFADDPH-ILLGLaqalFELGRYAEALET--LEKLIAKNPD 156
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1758 KEHVDVIAKFAQ-LEfQLGDAERAKAIFENTLSTYPKRtDVWSVYIDMTIKHGSQKDVRDIFERVIHLSlapKRMKFFFK 1836
Cdd:COG4700  157 FKSSDAHLLYARaLE-ALGDLEAAEAELEALARRYSGP-EARYRYAKFLARQGRTAEAKELLEEILDEA---KHMPKHYR 231

                 ..
gi 70980549 1837 RY 1838
Cdd:COG4700  232 RL 233
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
44-346 2.24e-05

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 49.56  E-value: 2.24e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    44 RKKSQKGPAKTKKLKIEKRESSKSAREKFEilsveslcEGMRILGCVKEVNELELVISLpNGLQGFVQVTEICDAYTKKL 123
Cdd:PRK00087  359 KLEDEDGYVVLSKKEADREKAWKELEEAFE--------NGEPVKGKVKEVVKGGLLVDY-GGVRAFLPASHVELGYVEDL 429
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   124 NEQVTQEQPLKDLLhlpelFSPGMLVRCVVSslgitdrgKKSVKLSLNPKNVNRVLsaEALKPGMLLTGTVSSLEDHGYL 203
Cdd:PRK00087  430 SEYKGQELEVKIIE-----FNRKRRKKVVLS--------RKAILEEEKEKKKEETW--NSLEEGDVVEGEVKRLTDFGAF 494
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   204 VDI-GVDGtraflpLLKAQE--YIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSvghsevstaiateqqswnLNNLLP 280
Cdd:PRK00087  495 VDIgGVDG------LLHVSEisWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLS------------------LKKLLP 550
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   281 ------------GLVVKAQVQKVTPFGLtlnFLTFFTGVVDFMHLD---------PKKAgtYFSNQAVRACILCVHPRTR 339
Cdd:PRK00087  551 dpwenveekypvGSIVLGKVVRIAPFGA---FVELEPGVDGLVHISqiswkridkPEDV--LSEGEEVKAKILEVDPEEK 625

                  ....*..
gi 70980549   340 VVHLSLR 346
Cdd:PRK00087  626 RIRLSIK 632
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1147-1221 2.49e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.75  E-value: 2.49e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549    1147 QAGQTVTCFLKkyNVVKKWLEVEIAPDIRGRIPLllTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTLLCLSL 1221
Cdd:smart00316    1 EVGDVVEGTVT--EITPGGAFVDLGNGVEGLIPI--SELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
82-170 2.64e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.75  E-value: 2.64e-05
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549      82 EGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQvtqeqplkdllhlpelFSPGMLVRCVVSSLgitDR 161
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEV----------------LKVGDEVKVKVLSV---DE 62

                    ....*....
gi 70980549     162 GKKSVKLSL 170
Cdd:smart00316   63 EKGRIILSL 71
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
1032-1388 2.93e-05

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 48.50  E-value: 2.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1032 TLSIGDMVTGTVKSIKPTHVVVTL---EDGIIgciHASHILDDvpegtSPTTKLKVGKTVTARVIGGRDmktfkylpish 1108
Cdd:COG0539   15 ELKEGDIVKGTVVSIDDDEVLVDIgykSEGII---PLSEFSDE-----PGELEVKVGDEVEVYVEKVED----------- 75
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1109 pRFVRTIpeLSVRPSELEDGhtalnthsvspMEKIKQ-YQAGQTVTCFLKkyNVVKKWLEVEIApDIRGRIP-------- 1179
Cdd:COG0539   76 -GEGEIV--LSKKKADREKA-----------WEELEEaFENGEPVEGKVK--GVVKGGLIVDIG-GVRAFLPasqvdvrp 138
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1180 ------LLLTSLSFKVLKHPDKKFRVgqalratVVgpdSSKTLL----------CLSltgphKLEEGEVAMGRVVKVTpN 1243
Cdd:COG0539  139 vrdldeYVGKTLEFKIIKLDRKRNNV-------VV---SRRAVLeeereekreeLLE-----KLEEGDVVEGTVKNIT-D 202
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1244 EGLTVSFPfGKIGTVsifHMSD-SYS--ETPlEDFVpqKV---VRCYILS--TADNVLTLSLrssrtnpetKSKVEDPEI 1315
Cdd:COG0539  203 FGAFVDLG-GVDGLL---HISEiSWGrvKHP-SEVL--KVgdeVEVKVLKidREKERISLSL---------KQLQPDPWE 266
                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 70980549 1316 NSIQDIKEGQLLRGYVGSIQPHGVFFRLGPSVVGLArysHVSQHSPSKKalyNKH----LPEGKLLTARVLRLNHQK 1388
Cdd:COG0539  267 NIAEKYPVGDVVKGKVTRLTDFGAFVELEPGVEGLV---HISEMSWTKR---VAHpsdvVKVGDEVEVKVLDIDPEE 337
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
449-508 3.48e-05

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 45.17  E-value: 3.48e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 70980549  449 DIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVppmH---LADILMKNPEKKYHIGDEVKCRVL 508
Cdd:COG1098    2 SIEVGDIVEGKVTGITPFGAFVELPEGTTGLV---HiseIADGYVKDINDYLKVGDEVKVKVL 61
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
724-798 5.05e-05

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 48.12  E-value: 5.05e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549   724 SEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDeEKQRMLLSLR 798
Cdd:PRK11824  617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRLSRK 690
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
1036-1093 5.38e-05

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 43.00  E-value: 5.38e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 70980549 1036 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPegTSPTTKLKVGKTVTARVI 1093
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRL--KHPEKKFKPGLKVKCRVL 56
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
634-707 5.79e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.98  E-value: 5.79e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549     634 NIGQLVDVKVLEKTKDGLEVAvLPHNIRAFLPTSHLSDHvaNGPLLHHWLQAGDILH-RVLCLSQSEGRVLLCRK 707
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVD-LGNGVEGLIPISELSDK--RVKDPEEVLKVGDEVKvKVLSVDEEKGRIILSLK 72
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
453-522 5.90e-05

S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 43.03  E-value: 5.90e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 522
Cdd:cd05691    1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
280-346 5.96e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.98  E-value: 5.96e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 70980549     280 PGLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKAG----TYFSNQAVRACILCVHPRTRVVHLSLR 346
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKdpeeVLKVGDEVKVKVLSVDEEKGRIILSLK 72
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
1593-1720 6.14e-05

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 44.80  E-value: 6.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1593 EALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisFREEQEklnVWVALLNLENMYG 1672
Cdd:COG4783   12 QALLLAGDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALEL--DPDEPE---ARLNLGLALLKAG 86
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 70980549 1673 SQESLTKVFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKR 1720
Cdd:COG4783   87 DYDEALALLEKALKLDpEHPEAYLRLARAYRALGRPDEAIAALEKALEL 135
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
1322-1397 6.93e-05

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 42.70  E-value: 6.93e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 70980549 1322 KEGQLLRGYVGSIQPHGVFFRL-GPSVVGLArysHVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELSFLP 1397
Cdd:cd05708    1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLC---HKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKA 74
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
547-629 8.68e-05

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 44.01  E-value: 8.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  547 GFIIRVKDYGCIVKFYNNVQGLVpkH--ELSTEYIPDPERVFYTGQVVKVVVLNCEPSKeRMLLSFK-LSSDPEPKKEPA 623
Cdd:COG1098   11 GKVTGITPFGAFVELPEGTTGLV--HisEIADGYVKDINDYLKVGDEVKVKVLSIDEDG-KISLSIKqAEEKPKRPPRPR 87

                 ....*.
gi 70980549  624 GHSQKK 629
Cdd:COG1098   88 RNSRPK 93
CpoB COG1729
Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane ...
1699-1793 1.01e-04

Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane constriction [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441335 [Multi-domain]  Cd Length: 113  Bit Score: 43.44  E-value: 1.01e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1699 DIYAKSEKFQEAGELYNRMLKRFRQEK---AVWIKYGAFLLRRSQAAASHRVLQRALECLP-SKEHVDVIAKFAQLEFQL 1774
Cdd:COG1729    1 KALLKAGDYDEAIAAFKAFLKRYPNSPlapDALYWLGEAYYALGDYDEAAEAFEKLLKRYPdSPKAPDALLKLGLSYLEL 80
                         90
                 ....*....|....*....
gi 70980549 1775 GDAERAKAIFENTLSTYPK 1793
Cdd:COG1729   81 GDYDKARATLEELIKKYPD 99
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
452-517 1.04e-04

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 42.23  E-value: 1.04e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549  452 PGAVVKGTVLTIKSYGMLVKVGeQMRGLVppmHLADIL---MKNPEKKYHIGDEVKCRVLLCDPEAKKL 517
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDLG-GVDGLL---HISDMSwgrVKHPSEVVNVGDEVEVKVLKIDKERKRI 65
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
453-508 1.08e-04

S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 42.19  E-value: 1.08e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 70980549  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVppmHLADIL-----MKNPEKKYHIGDEVKCRVL 508
Cdd:cd05702    1 GDLVKAKVKSVKPTQLNVQLADNVHGRI---HVSEVFdewpdGKNPLSKFKIGQKIKARVI 58
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
726-801 1.12e-04

S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 42.97  E-value: 1.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  726 IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVT-------------------STSDHFVEGQTVAAKVTNV 786
Cdd:cd05693    1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTErleeldeeseeeddeeelpDLEDLFSVGQLVRCKVVSL 80
                         90
                 ....*....|....*...
gi 70980549  787 DEE---KQRMLLSLRLSD 801
Cdd:cd05693   81 DKSksgKKRIELSLEPEL 98
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
1035-1094 1.13e-04

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 42.27  E-value: 1.13e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1035 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1094
Cdd:pfam00575    3 KGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVE--DPDEVIKVGDEVKVKVLK 60
PRK08059 PRK08059
general stress protein 13; Validated
552-629 1.32e-04

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 43.50  E-value: 1.32e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549   552 VKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKLSSD-PEPKKEPAGHSQKK 629
Cdd:PRK08059   18 IQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEaPEAKRKKGKILIPN 96
Suf pfam05843
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ...
1727-1869 1.42e-04

Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster Suppressor of forked [Su(f)] protein shares homology with the yeast RNA14 protein and the 77-kDa subunit of human cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilization and an important role of the GU-rich sequence for this regulation to occur.


Pssm-ID: 428647 [Multi-domain]  Cd Length: 291  Bit Score: 45.83  E-value: 1.42e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1727 VWIKYGAFLlRRSQAAASHR-VLQRALEclpsKEHV--DVIAKFAQLEFQLG-DAERAKAIFENTLSTYPKRTDVWSVYI 1802
Cdd:pfam05843    3 VWIQYMRAM-RRAEGIKGARkVFKKARK----RPRLtyHVYVASALMEYYCSkDPAVAFKIFELGLKLFPEDEEFVLKYL 77
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 70980549   1803 DMTIKHGSQKDVRDIFERVIHlSLAPKRM-KFFFKRYLDYEKQHGTEKDVQAVKAKALEYVEAKSSVL 1869
Cdd:pfam05843   78 DYLISLNDDNNARVLFERVLT-RLAQEKEaKPLWKKFISYESTFGDLASILKLEKRMAELFPEDPPLA 144
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
453-517 1.48e-04

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 41.71  E-value: 1.48e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVppmHLADI----LMKNPEKKYHIGDEVKCRVLLCDPEAKKL 517
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLV---HISDIswtqRVRHPSEIYKKGQEVEAVVLNIDVERERI 66
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
447-507 1.69e-04

S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.


Pssm-ID: 239919 [Multi-domain]  Cd Length: 77  Bit Score: 41.82  E-value: 1.69e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 70980549  447 YHDIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLvppMHLADILMknpekKYHIGDEVKCRV 507
Cdd:cd04473   11 MEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGL---IHRSNLLR-----DYEVGDEVIVQV 63
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
547-613 1.71e-04

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 41.93  E-value: 1.71e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 70980549  547 GFIIRVKDYGCIVKFYN-NVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKLS 613
Cdd:cd05708    8 GTVRRVEDYGVFIDIDGtNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
453-515 1.78e-04

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 41.50  E-value: 1.78e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 70980549  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAK 515
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGR 63
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
1036-1094 1.90e-04

S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 41.49  E-value: 1.90e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549 1036 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1094
Cdd:cd05691    1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVE--DATERFKVGDEVEAKITN 57
rpsA PRK13806
30S ribosomal protein S1; Provisional
446-798 2.20e-04

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 45.87  E-value: 2.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   446 RYHDIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPmhlADILMKNPEKKYHIGDEVKCRVLLCDPEAKKL-------- 517
Cdd:PRK13806   28 RKTELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDR---AELLDADGELTVAVGDEVELYVVSVNGQEIRLskalsgqg 104
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   518 -MMTLKKTLiESKLPVITCYADAKPGlqthGFIIRV--KDYGCivkfynnvqglvPKHELSTEYIPDPERvfYTGQVVKV 594
Cdd:PRK13806  105 gAAMLEEAY-ENGVPVEGKVTGTCKG----GFNVEVlgRRAFC------------PVSQIDLRYVEDPES--YVGQTFQF 165
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   595 VVLNCEPSKERMLLSFKLSSDPEPKKEPAGHSQKkgkaINIGQLVDVKVLEKTKDGLEVAVLPhNIRAFLPTSHLSDHVA 674
Cdd:PRK13806  166 LITRVEENGRNIVVSRRALLEREQKEALEAFMET----VKEGDVVEGTVTRLAPFGAFVELAP-GVEGMVHISELSWSRV 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   675 NGPllHHWLQAGDILH-RVLCLSQSEG----RVLLCRKPAlvstvegGQDPKNF--SEIHPGMLLIGFVKSIKDYGVFIQ 747
Cdd:PRK13806  241 QKA--DEAVSVGDTVRvKVLGIERAKKgkglRISLSIKQA-------GGDPWDTvgDRLKAGDKVTGKVVRLAPFGAFVE 311
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 70980549   748 FPSGLSGLAPKAIMS-DKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK13806  312 ILPGIEGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLR 363
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
453-520 2.47e-04

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 41.13  E-value: 2.47e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 70980549  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMT 520
Cdd:cd05707    1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
1033-1093 2.59e-04

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 42.38  E-value: 2.59e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549  1033 LSIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHI----LDDVPEgtspttKLKVGKTVTARVI 1093
Cdd:PRK07252    1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIktgfIDNIHQ------LLKVGEEVLVQVV 59
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
1227-1288 2.76e-04

S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 41.82  E-value: 2.76e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1227 LEEGEVAMGRVVKVTPNEgLTVSFPFGKIGTVSIFHMSDSYS-----------------ETP-LED-FVPQKVVRCYILS 1287
Cdd:cd05693    1 LSEGMLVLGQVKEITKLD-LVISLPNGLTGYVPITNISDAYTerleeldeeseeeddeeELPdLEDlFSVGQLVRCKVVS 79

                 .
gi 70980549 1288 T 1288
Cdd:cd05693   80 L 80
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
1605-1756 2.80e-04

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 43.41  E-value: 2.80e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1605 ADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTISFREEQEKLNVWVALLNLENMygsQESLtKVFERA 1684
Cdd:COG5010    5 EGFDRLPLYLLLLTKLRTLVEKYEAALAGANNTKEDELAAAGRDKLAKAFAIESPSDNLYNKLGDF---EESL-ALLEQA 80
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 70980549 1685 VQYNEPL-KVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLP 1756
Cdd:COG5010   81 LQLDPNNpELYYNLALLYSRSGDKDEAKEYYEKALALSPDNPNAYSNLAALLLSLGQDDEAKAALQRALGTSP 153
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
734-798 3.35e-04

S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 40.72  E-value: 3.35e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549  734 GFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:cd05691    6 GKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
547-597 3.44e-04

S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 40.60  E-value: 3.44e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 70980549  547 GFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVL 597
Cdd:cd04472    6 GKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVI 56
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
547-609 3.45e-04

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 40.74  E-value: 3.45e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 70980549  547 GFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 609
Cdd:cd05707    6 GFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
726-798 3.85e-04

S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240211 [Multi-domain]  Cd Length: 73  Bit Score: 40.70  E-value: 3.85e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 70980549  726 IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:cd05706    1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
186-256 3.91e-04

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 40.30  E-value: 3.91e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70980549  186 PGMLLTGTVSSLEDHGYLVDIG-VDGtraflpLLKAQE--YIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 256
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDLGgVDG------LLHISDmsWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
1036-1094 3.94e-04

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 40.35  E-value: 3.94e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549 1036 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDvpEGTSPTTKLKVGKTVTARVIG 1094
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHK--RVKDVKDVLKEGDKVKVKVLS 57
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1035-1093 4.64e-04

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 44.94  E-value: 4.64e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549  1035 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVI 1093
Cdd:PRK00087  562 VGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRID--KPEDVLSEGEEVKAKIL 618
PRK08582 PRK08582
RNA-binding protein S1;
726-789 5.64e-04

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 41.94  E-value: 5.64e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70980549   726 IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEE 789
Cdd:PRK08582    3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDD 66
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
542-608 6.20e-04

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 39.78  E-value: 6.20e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 70980549  542 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLL 608
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
1160-1220 6.23e-04

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 39.67  E-value: 6.23e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 70980549 1160 NVVKKWLEVEIAPDIRGRIPLllTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTLLCLS 1220
Cdd:cd00164    7 SITKFGVFVELEDGVEGLVHI--SELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
PTZ00121 PTZ00121
MAEBL; Provisional
1402-1593 6.24e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 45.13  E-value: 6.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1402 KPDVLSASLEgQLTKQEERKTEAEERDQKGEKKNQKRNEKKN----QKGQEEVempsKEKQQPQKPQAQKRGGRECRESG 1477
Cdd:PTZ00121 1379 KADAAKKKAE-EKKKADEAKKKAEEDKKKADELKKAAAAKKKadeaKKKAEEK----KKADEAKKKAEEAKKADEAKKKA 1453
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1478 SEQERVSKKPKKAGLSEEDDSLVDvyYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAwnvglDSLTPAlpplAESS 1557
Cdd:PTZ00121 1454 EEAKKAEEAKKKAEEAKKADEAKK--KAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKA-----DEAKKA----EEAK 1522
                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 70980549  1558 DSEEDEKPHQAtiKKSKKERELEKQKAEKELSRIEE 1593
Cdd:PTZ00121 1523 KADEAKKAEEA--KKADEAKKAEEKKKADELKKAEE 1556
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
453-517 6.69e-04

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 39.91  E-value: 6.69e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 70980549  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKL 517
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRI 65
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
729-797 6.71e-04

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 39.91  E-value: 6.71e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549  729 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSL 797
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
PTZ00121 PTZ00121
MAEBL; Provisional
1413-1594 8.10e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 44.75  E-value: 8.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1413 QLTKQEERKTEAEERDQKGEKKNQKRNEKKNQKGQEEVEMPSKEKQQPQKPQAQKRGGRECRESGSEQERVSKKPKKAgl 1492
Cdd:PTZ00121 1435 EAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKA-- 1512
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1493 seedDSLVDVYYREGKEEAEETNVLPKEKQTKPAEAPRlqlssgfawnvGLDSLTPAlpplAESSDSEEDEKPHQAtiKK 1572
Cdd:PTZ00121 1513 ----DEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKK-----------KADELKKA----EELKKAEEKKKAEEA--KK 1571
                         170       180
                  ....*....|....*....|..
gi 70980549  1573 SKKERELEKQKAEkELSRIEEA 1594
Cdd:PTZ00121 1572 AEEDKNMALRKAE-EAKKAEEA 1592
PTZ00121 PTZ00121
MAEBL; Provisional
1402-1610 8.66e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 44.36  E-value: 8.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1402 KPDVLSASLEGQLTKQEERKTEAEERDQKGEKKNQKRNE--KKNQKGQEEVEMPSKEKQQPQKPQAQKRGGRECRESGSE 1479
Cdd:PTZ00121 1634 KVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEdkKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAE 1713
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1480 QERVSKKPKKAglSEEDDSLVDVYYREGKEE---AEETNVLPKEK----QTKPAEAPRLQLSSGFAWNV---GLDSLTPA 1549
Cdd:PTZ00121 1714 EKKKAEELKKA--EEENKIKAEEAKKEAEEDkkkAEEAKKDEEEKkkiaHLKKEEEKKAEEIRKEKEAVieeELDEEDEK 1791
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 70980549  1550 LPPLAESsdSEEDEKPHQATIKKSKKERELE-KQKAEKELSRIEEALMDPGRQPESADDFDR 1610
Cdd:PTZ00121 1792 RRMEVDK--KIKDIFDNFANIIEGGKEGNLViNDSKEMEDSAIKEVADSKNMQLEEADAFEK 1851
rpsA PRK06676
30S ribosomal protein S1; Reviewed
170-307 8.97e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 43.71  E-value: 8.97e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   170 LNPKNVNRVLSAEA----------------LKPGMLLTGTVSSLEDHGYLVDIG-VDGtraflpLLKAQE--YIRQKNKG 230
Cdd:PRK06676  160 LDPEKNRVILSRRAvveeeraakkeellssLKEGDVVEGTVARLTDFGAFVDIGgVDG------LVHISElsHERVEKPS 233
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549   231 AKLKVGQYLNCIVEKVKGNGGVVSLSVGhsevstaiATEQQSWNL--NNLLPGLVVKAQVQKVTPFGLtlnFLTFFTGV 307
Cdd:PRK06676  234 EVVSVGQEVEVKVLSIDWETERISLSLK--------DTLPGPWEGveEKLPEGDVIEGTVKRLTDFGA---FVEVLPGV 301
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
728-798 9.45e-04

S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 39.64  E-value: 9.45e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 70980549  728 PGMLLIGFV-KSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVtnVDEEKQRMLLSLR 798
Cdd:cd05704    3 EGAVTLGMVtKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCI--LSKKDGKYQLSLR 72
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
540-798 1.10e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 43.93  E-value: 1.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   540 KPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTeyipdPERvfyTGQVVKVVVLNCEPSKERMllsFKLSSDPEPK 619
Cdd:PRK12269  320 EPGSVRMGTVVQVNAGTVFVDIGGKSEGRVPVEEFEA-----PPK---AGDGVRVYVERVTPYGPEL---SKTKADRLGL 388
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   620 KEPAGHSQKKGKAINiGQLVDvkvLEKTKDGLEVAvLPHNIRAFLPTSHLSDHVANGPLLHHWLQAGDILHRVLCLSQSE 699
Cdd:PRK12269  389 KVKLRDAERDGTPVE-GRIVR---LTEKKSGFEVD-LGAGMMAFLPISQSDCQKVDAPESLIGLTSKFYIERISQSKQHR 463
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   700 GR--VLLCRKPALVSTVEGGQDpKNFSEIHPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQ 777
Cdd:PRK12269  464 GNdnIVINRRRYLEERARQARE-EFFNSVHIEDSVSGVVKSFTSFGAFIDL-GGFDGLLHVNDMSWGHVARPREFVKKGQ 541
                         250       260
                  ....*....|....*....|.
gi 70980549   778 TVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK12269  542 TIELKVIRLDQAEKRINLSLK 562
rpsA PRK13806
30S ribosomal protein S1; Provisional
1168-1350 1.12e-03

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 43.56  E-value: 1.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1168 VEIAPDIRGRIPLllTSLSFKVLKHPDKKFRVGQALRATVVGPDSSK----TLLCLSL---------TGPHKLEEGEVAM 1234
Cdd:PRK13806  220 VELAPGVEGMVHI--SELSWSRVQKADEAVSVGDTVRVKVLGIERAKkgkgLRISLSIkqaggdpwdTVGDRLKAGDKVT 297
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1235 GRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFV-PQKVVRCYI--LSTADNVLTLSLRSSRTnpetkskve 1311
Cdd:PRK13806  298 GKVVRLAPF-GAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVaPGDAVAVKIkdIDPAKRRISLSLRDAEG--------- 367
                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 70980549  1312 DPEINSIQDIKEGQLLRGYVGSIQPHGVFFRLGPSVVGL 1350
Cdd:PRK13806  368 DPWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGL 406
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
1695-1825 1.39e-03

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 41.10  E-value: 1.39e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1695 LHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQL 1774
Cdd:COG5010   24 VEKYEAALAGANNTKEDELAAAGRDKLAKAFAIESPSDNLYNKLGDFEESLALLEQALQLDP--NNPELYYNLALLYSRS 101
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 70980549 1775 GDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVIHLS 1825
Cdd:COG5010  102 GDKDEAKEYYEKALALSPDNPNAYSNLAALLLSLGQDDEAKAALQRALGTS 152
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1594-1782 1.41e-03

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 42.30  E-value: 1.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1594 ALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisfreeqeKLNVWVALLNLENMYGS 1673
Cdd:COG0457   51 AYLRLGRYEEALADYEQALELDPDDAEALNNLGLALQALGRYEEALEDYDKALEL--------DPDDAEALYNLGLALLE 122
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1674 QESLTK---VFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNrmlKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQ 1749
Cdd:COG0457  123 LGRYDEaieAYERALELDpDDADALYNLGIALEKLGRYEEALELLE---KLEAAALAALLAAALGEAALALAAAEVLLAL 199
                        170       180       190
                 ....*....|....*....|....*....|...
gi 70980549 1750 RALECLPSKEHVDVIAKFAQLEFQLGDAERAKA 1782
Cdd:COG0457  200 LLALEQALRKKLAILTLAALAELLLLALALLLA 232
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
88-169 1.41e-03

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 38.90  E-value: 1.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   88 GCVKEVNELELVISLPNGLQGFVQVTEICDAYTKklneqvtqeqplkdllHLPELFSPGMLVRCVVSSLgitDRGKKSVK 167
Cdd:cd00164    3 GKVVSITKFGVFVELEDGVEGLVHISELSDKFVK----------------DPSEVFKVGDEVEVKVLEV---DPEKGRIS 63

                 ..
gi 70980549  168 LS 169
Cdd:cd00164   64 LS 65
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
190-256 1.49e-03

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 38.90  E-value: 1.49e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 70980549  190 LTGTVSSLEDHGYLVDIGvDGTRAFLPLLKAQEYiRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 256
Cdd:cd00164    1 VTGKVVSITKFGVFVELE-DGVEGLVHISELSDK-FVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
1499-1793 1.55e-03

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 43.53  E-value: 1.55e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1499 LVDVYYREGKEEaEETNVLPKEKQTKPAE-APRLQLSSGFawnVGLDSLTPALPPLAESSDseedekphqatIKKSKKER 1577
Cdd:TIGR02917  539 LAGLYLRTGNEE-EAVAWLEKAAELNPQEiEPALALAQYY---LGKGQLKKALAILNEAAD-----------AAPDSPEA 603
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1578 ELEKQKAEKELSRIEEALmdpgrqpesaDDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTIS-FREEQE 1656
Cdd:TIGR02917  604 WLMLGRAQLAAGDLNKAV----------SSFKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRALELKPdNTEAQI 673
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1657 KLnvwVALLNLENMYGSQESLTKVFEraVQYNEPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVwIKYGAFLL 1736
Cdd:TIGR02917  674 GL---AQLLLAAKRTESAKKIAKSLQ--KQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKRAPSSQNA-IKLHRALL 747
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1737 RRSQAAASHRVLQRALeclpsKEHV-DVIAKFAQLEFQLGDAERAKAI--FENTLSTYPK 1793
Cdd:TIGR02917  748 ASGNTAEAVKTLEAWL-----KTHPnDAVLRTALAELYLAQKDYDKAIkhYQTVVKKAPD 802
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
90-134 1.72e-03

S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 38.73  E-value: 1.72e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 70980549   90 VKEVNELELVISLPNGLQGFVQVTEICDAYTkklneqvTQEQPLK 134
Cdd:cd05702    8 VKSVKPTQLNVQLADNVHGRIHVSEVFDEWP-------DGKNPLS 45
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1032-1394 1.82e-03

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 43.01  E-value: 1.82e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1032 TLSIGDMVTGTVKSIKPTHVVVTL---EDGIIGCIHASHilddvPEGTSPTTKLKVGKTVTARVIGGRDmktfkylpish 1108
Cdd:PRK00087  299 QIRRGDIVKGTVVSVNENEVFVDVgykSEGVIPLRELTL-----DEISSLKESVKVGDEIEVKVLKLED----------- 362
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1109 prfvrtipelsvrpselEDGHTALN---THSVSPMEKIKQ-YQAGQTVTCFLKKynVVKKWLEVEIApDIRGRIPLLLTS 1184
Cdd:PRK00087  363 -----------------EDGYVVLSkkeADREKAWKELEEaFENGEPVKGKVKE--VVKGGLLVDYG-GVRAFLPASHVE 422
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1185 LSFKvlkhPDKKFRVGQALRATVVGPD---------SSKTLLCLSLTGPHK-----LEEGEVAMGRVVKVTPNeGLtvsf 1250
Cdd:PRK00087  423 LGYV----EDLSEYKGQELEVKIIEFNrkrrkkvvlSRKAILEEEKEKKKEetwnsLEEGDVVEGEVKRLTDF-GA---- 493
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1251 pFGKIGTVS-IFHMSD---SYSETPLEDFVPQKVVRCYILSTADNVLTLSLrsSRtnpetKSKVEDPEINSIQDIKEGQL 1326
Cdd:PRK00087  494 -FVDIGGVDgLLHVSEiswGRVEKPSDVLKVGDEIKVYILDIDKENKKLSL--SL-----KKLLPDPWENVEEKYPVGSI 565
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 70980549  1327 LRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQH---SPSKKalynkhLPEGKLLTARVLRLNHQKNLVELS 1394
Cdd:PRK00087  566 VLGKVVRIAPFGAFVELEPGVDGLVHISQISWKridKPEDV------LSEGEEVKAKILEVDPEEKRIRLS 630
rpsA PRK07899
30S ribosomal protein S1; Reviewed
443-523 2.35e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 42.72  E-value: 2.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   443 QYLRYHDIepGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 522
Cdd:PRK07899  286 QFARTHAI--GQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLK 363

                  .
gi 70980549   523 K 523
Cdd:PRK07899  364 Q 364
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
1629-1720 2.36e-03

Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 39.00  E-value: 2.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1629 HLQATEIEKARAVAERALKTisfreeqeKLNVWVALLNLENMYGSQESltkvFERAVQYNEPLK-------VFLHLADIY 1701
Cdd:COG3063    2 YLKLGDLEEAEEYYEKALEL--------DPDNADALNNLGLLLLEQGR----YDEAIALEKALKldpnnaeALLNLAELL 69
                         90
                 ....*....|....*....
gi 70980549 1702 AKSEKFQEAGELYNRMLKR 1720
Cdd:COG3063   70 LELGDYDEALAYLERALEL 88
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
636-707 2.64e-03

S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 239911 [Multi-domain]  Cd Length: 67  Bit Score: 38.21  E-value: 2.64e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70980549  636 GQLVDVKVLEKTKDGLEVAVlpHNIRAFLPTSHLSD-HVAN-GPLLHHWLQAgdilhRVLCLSQSEGRVLLCRK 707
Cdd:cd04465    1 GEIVEGKVTEKVKGGLIVDI--EGVRAFLPASQVDLrPVEDlDEYVGKELKF-----KIIEIDRERNNIVLSRR 67
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
1748-1829 3.21e-03

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 39.60  E-value: 3.21e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1748 LQRALECLPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLA 1827
Cdd:COG4235    6 LRQALAANP--NDAEGWLLLGRAYLRLGRYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEELLERA--LALD 81

                 ..
gi 70980549 1828 PK 1829
Cdd:COG4235   82 PD 83
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
542-608 3.23e-03

S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240194 [Multi-domain]  Cd Length: 72  Bit Score: 37.94  E-value: 3.23e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 70980549  542 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLL 608
Cdd:cd05689    4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDwTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISL 71
rpsA PRK13806
30S ribosomal protein S1; Provisional
66-306 3.27e-03

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 42.02  E-value: 3.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549    66 KSAREKFeilsVESLCEGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQVtqeqplkdllhlpelfSP 145
Cdd:PRK13806  190 KEALEAF----METVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAV----------------SV 249
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   146 GMLVRcvVSSLGITDRGK-KSVKLSLNPKNV-----NRVlsAEALKPGMLLTGTVSSLEDHGYLVDI--GVDGtrafLPL 217
Cdd:PRK13806  250 GDTVR--VKVLGIERAKKgKGLRISLSIKQAggdpwDTV--GDRLKAGDKVTGKVVRLAPFGAFVEIlpGIEG----LVH 321
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   218 LKAQEYIRQKNK-GAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEVSTAIATEQQswnlnnLLPGLVVKAQVQKVTPFGL 296
Cdd:PRK13806  322 VSEMSWTRRVNKpEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAER------FAPGTTVTGTVEKRAQFGL 395
                         250
                  ....*....|
gi 70980549   297 TLNFLTFFTG 306
Cdd:PRK13806  396 FVNLAPGVTG 405
PTZ00121 PTZ00121
MAEBL; Provisional
1416-1725 3.47e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 42.44  E-value: 3.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1416 KQEERKTEAEERDQKGE--KKNQKRNEKKNQKGQEEVEMPSKEKQQPQKPQAQKRGGRECRESGSEQERVSKKPKKAglS 1493
Cdd:PTZ00121 1323 KAEEAKKKADAAKKKAEeaKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKK--A 1400
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1494 EEDDSLVDVYYR--EGKEEAEETNVLPKEK------QTKPAEAPRLQLSSGFAWNVgldSLTPALPPLAESSDSEEDEKP 1565
Cdd:PTZ00121 1401 EEDKKKADELKKaaAAKKKADEAKKKAEEKkkadeaKKKAEEAKKADEAKKKAEEA---KKAEEAKKKAEEAKKADEAKK 1477
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1566 HQATIKKS---KKERELEKQKAEkELSRIEEA--LMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARA 1640
Cdd:PTZ00121 1478 KAEEAKKAdeaKKKAEEAKKKAD-EAKKAAEAkkKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEE 1556
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549  1641 V--AERALKTISFREEQEKlnvwvallnlENMYGSQESLTKVFERAvQYNEPLKVFLHLADIYAKSEKFQEAGELYNRML 1718
Cdd:PTZ00121 1557 LkkAEEKKKAEEAKKAEED----------KNMALRKAEEAKKAEEA-RIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEEL 1625

                  ....*..
gi 70980549  1719 KRFRQEK 1725
Cdd:PTZ00121 1626 KKAEEEK 1632
PRK08582 PRK08582
RNA-binding protein S1;
450-508 3.63e-03

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 39.63  E-value: 3.63e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549   450 IEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVL 508
Cdd:PRK08582    3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVL 61
DUF612 pfam04747
Protein of unknown function, DUF612; This family includes several uncharacterized proteins ...
1399-1598 3.83e-03

Protein of unknown function, DUF612; This family includes several uncharacterized proteins from Caenorhabditis elegans.


Pssm-ID: 282585 [Multi-domain]  Cd Length: 511  Bit Score: 41.97  E-value: 3.83e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1399 DTGKPDVLSASLEGQLTKQEERKTEAEERDQKGEKKNQKRNEKKNQKGQEEVEMPSKEKQQPQKPQAQkrggRECRESGS 1478
Cdd:pfam04747   49 DQRKEAFASLELTEQPQQVEKVKKSEKKKAQKQIAKDHEAEQKVNAKKAAEKEARRAEAEAKKRAAQE----EEHKQWKA 124
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1479 EQERVSKKPKKaglseEDDSLVDVYYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAWNVGLD-SLTPA-LPPLAES 1556
Cdd:pfam04747  125 EQERIQKEQEK-----KEADLKKLQAEKKKEKAVKAEKAEKAEKTKKASTPAPVEEEIVVKKVANDrSAAPApEPKTPTN 199
                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 70980549   1557 SDSEEDEKPHQATIKKSKKERELEKQKAEKELSRIEEALMDP 1598
Cdd:pfam04747  200 TPAEPAEQVQEITGKKNKKNKKKSESEATAAPASVEQVVEQP 241
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
1571-1793 4.97e-03

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 41.99  E-value: 4.97e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1571 KKSKKERELEKQ--------KAEKELSRIEealMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVA 1642
Cdd:TIGR02917  480 DLAKAREAFEKAlsiepdffPAAANLARID---IQEGNPDDAIQRFEKVLTIDPKNLRAILALAGLYLRTGNEEEAVAWL 556
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1643 ERALKTISfREEQEKLNVWVALLNLENMygsQESLTKVFERAVQYNEPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFR 1722
Cdd:TIGR02917  557 EKAAELNP-QEIEPALALAQYYLGKGQL---KKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQP 632
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 70980549   1723 QEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPK 1793
Cdd:TIGR02917  633 DSALALLLLADAYAVMKNYAKAITSLKRALELKP--DNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQHPK 701
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
1324-1394 5.36e-03

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 37.27  E-value: 5.36e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 70980549 1324 GQLLRGYVGSIQPHGVFFRLGPSVVGLARyshVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1394
Cdd:cd05707    1 GDVVRGFVKNIANNGVFVTLGRGVDARVR---VSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
1576-1833 5.64e-03

Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443119 [Multi-domain]  Cd Length: 658  Bit Score: 41.52  E-value: 5.64e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1576 ERELEKQKAEKELSRIEEALMDPGRQPESADDFDRLVLSSPNSSILWLqYMAFHLQATE-IEKARAVAERALKtisfree 1654
Cdd:COG3914   69 AAAAALLLLAALLELAALLLQALGRYEEALALYRRALALNPDNAEALF-NLGNLLLALGrLEEALAALRRALA------- 140
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1655 qeklnvwvalLNLENmygsqesltkvferavqynepLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAF 1734
Cdd:COG3914  141 ----------LNPDF---------------------AEAYLNLGEALRRLGRLEEAIAALRRALELDPDNAEALNNLGNA 189
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1735 LLRRSQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQLGDAERAkAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDV 1814
Cdd:COG3914  190 LQDLGRLEEAIAAYRRALELDP--DNADAHSNLLFALRQACDWEVY-DRFEELLAALARGPSELSPFALLYLPDDDPAEL 266
                        250       260
                 ....*....|....*....|..
gi 70980549 1815 RDI---FERVIHLSLAPKRMKF 1833
Cdd:COG3914  267 LALaraWAQLVAAAAAPELPPP 288
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
1609-1792 6.09e-03

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 41.61  E-value: 6.09e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1609 DRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisfreEQEKLNvwvALLNLENMYGSQESL---TKVFERAV 1685
Cdd:TIGR02917  455 KKLEKKQPDNASLHNLLGAIYLGKGDLAKAREAFEKALSI-----EPDFFP---AAANLARIDIQEGNPddaIQRFEKVL 526
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   1686 QYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLP-SKEHVDV 1763
Cdd:TIGR02917  527 TIDpKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAADAAPdSPEAWLM 606
                          170       180
                   ....*....|....*....|....*....
gi 70980549   1764 IAKfAQLefQLGDAERAKAIFENTLSTYP 1792
Cdd:TIGR02917  607 LGR-AQL--AAGDLNKAVSSFKKLLALQP 632
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
1226-1297 6.38e-03

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 37.57  E-value: 6.38e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70980549 1226 KLEEGEVAMGRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILS--TADNVLTLSL 1297
Cdd:cd04461   11 DLKPGMVVHGYVRNITPY-GVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSvdEEKQRFLLSL 83
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
660-796 6.69e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 40.94  E-value: 6.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549   660 IRAFLPTSHLSDHVANGPLLHHWLQAgdilhRVLCLSQSEGRVLLCRKPALVStveggqdpKNFSEIHPGMLLIGFVKSI 739
Cdd:PRK07400  141 LRGFIPGSHISTRKPKEELVGEELPL-----KFLEVDEERNRLVLSHRRALVE--------RKMNRLEVGEVVVGTVRGI 207
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 70980549   740 KDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 796
Cdd:PRK07400  208 KPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLS 263
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
1679-1766 6.98e-03

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 38.45  E-value: 6.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70980549 1679 KVFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPS 1757
Cdd:COG4235   38 AAYEKALRLDpDNADALLDLAEALLAAGDTEEAEELLERALALDPDNPEALYLLGLAAFQQGDYAEAIAAWQKLLALLPA 117

                 ....*....
gi 70980549 1758 KEHVDVIAK 1766
Cdd:COG4235  118 DAPARLLEA 126
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
732-798 8.04e-03

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 38.14  E-value: 8.04e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 70980549   732 LIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK07252    7 LKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLR 73
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
1033-1093 8.81e-03

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 37.18  E-value: 8.81e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 70980549 1033 LSIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPegTSPTTKLKVGKTVTARVI 1093
Cdd:cd04461   12 LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFV--TDPSFGFKKGQSVTAKVT 70
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
541-609 9.00e-03

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 36.45  E-value: 9.00e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 70980549  541 PGLQTHGFIIRVKDYGCIVKFyNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 609
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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