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Conserved domains on  [gi|2462517970|ref|XP_054221245|]
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protein RRP5 homolog isoform X4 [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 ...
 140-236 6.45e-40

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: 143.51  E-value: 6.45e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  140 LCEGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQVTQEQ---PLKDLLHLPELFSPGMLVRCVVSSL 216
Cdd:cd05693      1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEeedDEEELPDLEDLFSVGQLVRCKVVSL 80

                           90       100
                   ....*....|....*....|
gi 2462517970  217 GITDRGKKSVKLSLNPKNVN 236
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 ...
 696-767 1.09e-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: 1.09e-38
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517970  696 GQLVDVKVLEKTKDGLEVAVLPHNIRAFLPTSHLSDHVANGPLLHHWLQAGDILHRVLCLSQSEGRVLLCRK 767
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 ...
 775-857 2.98e-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: 138.10  E-value: 2.98e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  775 EGGQDPKNFSEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRML 854
Cdd:cd04461      1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                   ...
gi 2462517970  855 LSL 857
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 ...
 1381-1454 3.74e-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: 134.45  E-value: 3.74e-37
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517970 1381 IKEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1454
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 ...
 1287-1358 1.93e-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: 129.78  E-value: 1.93e-35
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517970 1287 LEEGEVAMGRVVKVTPNEGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILSTADNVLTLSLR 1358
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 ...
 602-671 2.97e-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: 128.88  E-value: 2.97e-35
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  602 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 671
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 ...
 985-1053 4.13e-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: 4.13e-32
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  985 GSEHQAIVQHLEKSFAIASLVETGHLAAFSLTSHLNDTFRFDSEKLQVGQGVSLTLKTTEPGVTGLLLA 1053
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 ...
 513-581 4.10e-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: 117.34  E-value: 4.10e-31
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  513 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTL 581
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 ...
 1096-1165 8.20e-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: 113.45  E-value: 8.20e-30
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1096 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEGTSPTTKLKVGKTVTARVIGGRDMKTFKYLP 1165
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 ...
 243-323 2.66e-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: 109.26  E-value: 2.66e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  243 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYirqknkgAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEV 322
Cdd:cd05694      1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73


                   .
gi 2462517970  323 S 323
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 ...
 425-495 7.17e-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: 108.12  E-value: 7.17e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517970  425 GAVLDDVPVQGFFKKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSL 495
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 ...
 906-970 9.27e-28

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: 107.63  E-value: 9.27e-28
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970  906 GMFLDLVVQEVLEDGSVVFSGGPVPDLVLKASRYHRAGQEVESGQKKKVVILNVDLLKLEVHVSL 970
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 ...
 1209-1283 5.29e-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: 102.65  E-value: 5.29e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970 1209 GQTVTCFLKKYNVVKKWLEveIAPDIRGRIPLLLTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTFLCLSLTG 1283
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 ...
 341-404 8.53e-26

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: 101.97  E-value: 8.53e-26
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462517970  341 GLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKA--GTYFSNQAVRACILCVHPRTRVVHLS 404
Cdd:cd05695      1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSskSTYKEGQKVRARILYVDPSTKVVGLS 66
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1660-1920 3.81e-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: 83.63  E-value: 3.81e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1660 RQPESA-DDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfREEQEKLnvwvALLNLENMYGSQESLT 1738
Cdd:COG2956     22 GQPDKAiDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYLKAGLLD 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1739 K---VFERAVQYNEP-LKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEC 1814
Cdd:COG2956     94 RaeeLLEKLLELDPDdAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL 173

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1815 LPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLAPKRMKFF 1894
Cdd:COG2956    174 DP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA--LELDPSDDLLL 249

                          250       260
                   ....*....|....*....|....*.
gi 2462517970 1895 FKRYLdYEKQHGTEKdVQAVKAKALE 1920
Cdd:COG2956    250 ALADL-LERKEGLEA-ALALLERQLR 273
PTZ00121 super family cl31754
MAEBL; Provisional
 1462-1653 4.46e-04

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 45.52  E-value: 4.46e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1462 KPDVLSASLEgQLTKQEERKTEAEERDQKGEKKNQKRNEKKN----QKGQEEVempsKEKQQPQKPQAQKRGGRECRESG 1537
Cdd:PTZ00121  1379 KADAAKKKAE-EKKKADEAKKKAEEDKKKADELKKAAAAKKKadeaKKKAEEK----KKADEAKKKAEEAKKADEAKKKA 1453

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1538 SEQERVSKKPKKAGLSEEDDSLVDvyYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAwnvglDSLTPAlpplAESS 1617
Cdd:PTZ00121  1454 EEAKKAEEAKKKAEEAKKADEAKK--KAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKA-----DEAKKA----EEAK 1522

                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 2462517970 1618 DSEEDEKPHQAtiKKSKKERELEKQKAEKELSRIEE 1653
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 ...
 140-236 6.45e-40

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: 143.51  E-value: 6.45e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  140 LCEGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQVTQEQ---PLKDLLHLPELFSPGMLVRCVVSSL 216
Cdd:cd05693      1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEeedDEEELPDLEDLFSVGQLVRCKVVSL 80

                           90       100
                   ....*....|....*....|
gi 2462517970  217 GITDRGKKSVKLSLNPKNVN 236
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 ...
 696-767 1.09e-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: 1.09e-38
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517970  696 GQLVDVKVLEKTKDGLEVAVLPHNIRAFLPTSHLSDHVANGPLLHHWLQAGDILHRVLCLSQSEGRVLLCRK 767
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 ...
 775-857 2.98e-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: 138.10  E-value: 2.98e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  775 EGGQDPKNFSEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRML 854
Cdd:cd04461      1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                   ...
gi 2462517970  855 LSL 857
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 ...
 1381-1454 3.74e-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: 134.45  E-value: 3.74e-37
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517970 1381 IKEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1454
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 ...
 1287-1358 1.93e-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: 129.78  E-value: 1.93e-35
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517970 1287 LEEGEVAMGRVVKVTPNEGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILSTADNVLTLSLR 1358
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 ...
 602-671 2.97e-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: 128.88  E-value: 2.97e-35
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  602 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 671
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 ...
 985-1053 4.13e-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: 4.13e-32
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  985 GSEHQAIVQHLEKSFAIASLVETGHLAAFSLTSHLNDTFRFDSEKLQVGQGVSLTLKTTEPGVTGLLLA 1053
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 ...
 513-581 4.10e-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: 117.34  E-value: 4.10e-31
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  513 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTL 581
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 ...
 1096-1165 8.20e-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: 113.45  E-value: 8.20e-30
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1096 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEGTSPTTKLKVGKTVTARVIGGRDMKTFKYLP 1165
Cdd:cd05702      1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 424-858 2.75e-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: 124.85  E-value: 2.75e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  424 LGAVLDDVPVQG-FFKKAGATFRLK-DGVLAYARLSHlSDSKNVFNPEAFKpGNTHKCRIIDYSQMDELALLSlRTSIIE 501
Cdd:TIGR00717   95 EKAYEEGSIVEGkIVGKVKGGFIVDlNGVEAFLPGSQ-VDVKPIKDLDSLI-GKTLKFKIIKLDQKRNNIVVS-RRAYLE 171

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  502 AQYLRYHD-----IEPGAVVKGTVLTIKSYGMLVKVGeQMRGLVppmHLADIL---MKNPEKKYHIGDEVKCRVLLCDPE 573
Cdd:TIGR00717  172 EERSQAREellenLKEGDVVKGVVKNITDFGAFVDLG-GVDGLL---HITDMSwkrVKHPSEYVKVGQEVKVKVIKFDKE 247

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  574 AKKLMMTLKKTL------IESKLPvitcyadakPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVF 646
Cdd:TIGR00717  248 KGRISLSLKQLGedpweaIEKKFP---------VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVV 318

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  647 YTGQVVKVVVLNCEPSKERMLLSFKlSSDPEP-----KKEPAGhSQKKGKAINIGQLVDVKVLEKTKDGLevavlphnir 721
Cdd:TIGR00717  319 KKGDEVEVMILDIDPERRRLSLGLK-QCKANPweqfeEKHPVG-DRVTGKIKKITDFGAFVELEGGIDGL---------- 386

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  722 aflptSHLSD--HVANGPLLHHWLQAGDILHR-VLCLSQSEGRVLLCRKPALVSTVEggqdpkNFSEIHP-GMLLIGFVK 797
Cdd:TIGR00717  387 -----IHLSDisWDKDGREADHLYKKGDEIEAvVLAVDKEKKRISLGVKQLTENPWE------KFAAKYKvGSVVKGKVT 455

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517970  798 SIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:TIGR00717  456 EIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 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 ...
 243-323 2.66e-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: 109.26  E-value: 2.66e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  243 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYirqknkgAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEV 322
Cdd:cd05694      1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73


                   .
gi 2462517970  323 S 323
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 ...
 425-495 7.17e-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: 108.12  E-value: 7.17e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517970  425 GAVLDDVPVQGFFKKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSL 495
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 ...
 906-970 9.27e-28

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: 107.63  E-value: 9.27e-28
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970  906 GMFLDLVVQEVLEDGSVVFSGGPVPDLVLKASRYHRAGQEVESGQKKKVVILNVDLLKLEVHVSL 970
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 ...
 1209-1283 5.29e-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: 102.65  E-value: 5.29e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970 1209 GQTVTCFLKKYNVVKKWLEveIAPDIRGRIPLLLTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTFLCLSLTG 1283
Cdd:cd05703      1 GQEVTGFVNNVSKEFVWLT--ISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 510-858 7.13e-26

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 114.88  E-value: 7.13e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  510 IEPGAVVKGTVLTIKSYGMLVKVGeQMRGLVppmHLADILMK---NPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL- 585
Cdd:PRK06299   199 LEEGQVVEGVVKNITDYGAFVDLG-GVDGLL---HITDISWKrvnHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGe 274

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  586 -----IESKLPVitcyadakpglqthGFIIRVK-----DYGCIVKFYNNVQGLVpkH--ELS-TEYIPDPERVFYTGQVV 652
Cdd:PRK06299   275 dpweaIEKKYPV--------------GSKVKGKvtnitDYGAFVELEEGIEGLV--HvsEMSwTKKNKHPSKVVSVGQEV 338

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  653 KVVVLNCEPSKERMLLSFK-LSSDPE---PKKEPAGhSQKKGKAINIgqlvdvkvlekTKDGLEVAvLPHNIRAFLptsH 728
Cdd:PRK06299   339 EVMVLEIDEEKRRISLGLKqCKENPWeefAEKYPVG-DVVEGKVKNI-----------TDFGAFVG-LEGGIDGLV---H 402

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  729 LSD--HVANG--PLLHhwLQAGDILH-RVLCLSQSEGRVLLCRKPALvstveggQDP-KNFSEIHP-GMLLIGFVKSIKD 801
Cdd:PRK06299   403 LSDisWDKKGeeAVEL--YKKGDEVEaVVLKVDVEKERISLGIKQLE-------EDPfEEFAKKHKkGSIVTGTVTEVKD 473

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517970  802 YGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:PRK06299   474 KGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
S1_Rrp5_repeat_hs3 cd05695
S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 341-404 8.53e-26

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: 101.97  E-value: 8.53e-26
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462517970  341 GLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKA--GTYFSNQAVRACILCVHPRTRVVHLS 404
Cdd:cd05695      1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSskSTYKEGQKVRARILYVDPSTKVVGLS 66
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 240-671 1.28e-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: 101.66  E-value: 1.28e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  240 SAEALKPGMLLTGTVSSLEDHGYLVDIG--VDGtraFLPLlkaqEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSv 317
Cdd:COG0539     12 SLKELKEGDIVKGTVVSIDDDEVLVDIGykSEG---IIPL----SEFSDEPGELEVKVGDEVEVYVEKVEDGEGEIVLS- 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  318 ghsevsTAIATEQQSWN-----LNNllpGLVVKAQVQKVTPFGLTlnfltfftgvVDFMHldpkkagtyfsnqaVRAcil 392
Cdd:COG0539     84 ------KKKADREKAWEeleeaFEN---GEPVEGKVKGVVKGGLI----------VDIGG--------------VRA--- 127

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  393 cvhprtrvvhlslrpiFLqPGrpltrlscqnlgavlddvpvqgffkkagatfrlkdgvlayarlSHLsDSKNVFNPEAFK 472
Cdd:COG0539    128 ----------------FL-PA-------------------------------------------SQV-DVRPVRDLDEYV 146

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  473 pGNTHKCRIIDYSQMDELALLSlRTSIIEAQYLR-----YHDIEPGAVVKGTVLTIKSYGMLVKVGEqMRGLVppmHLAD 547
Cdd:COG0539    147 -GKTLEFKIIKLDRKRNNVVVS-RRAVLEEEREEkreelLEKLEEGDVVEGTVKNITDFGAFVDLGG-VDGLL---HISE 220

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  548 IL---MKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL------IESKLPVitcyadakpGLQTHGFIIRVKDYGCI 618
Cdd:COG0539    221 ISwgrVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQLQpdpwenIAEKYPV---------GDVVKGKVTRLTDFGAF 291

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2462517970  619 VKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 671
Cdd:COG0539    292 VELEPGVEGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1660-1920 3.81e-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: 83.63  E-value: 3.81e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1660 RQPESA-DDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfREEQEKLnvwvALLNLENMYGSQESLT 1738
Cdd:COG2956     22 GQPDKAiDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYLKAGLLD 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1739 K---VFERAVQYNEP-LKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEC 1814
Cdd:COG2956     94 RaeeLLEKLLELDPDdAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL 173

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1815 LPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLAPKRMKFF 1894
Cdd:COG2956    174 DP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA--LELDPSDDLLL 249

                          250       260
                   ....*....|....*....|....*.
gi 2462517970 1895 FKRYLdYEKQHGTEKdVQAVKAKALE 1920
Cdd:COG2956    250 ALADL-LERKEGLEA-ALALLERQLR 273
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
511-582 3.48e-16

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 74.95  E-value: 3.48e-16
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517970   511 EPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 582
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
788-858 2.62e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 72.25  E-value: 2.62e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517970   788 PGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
600-671 3.98e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 71.87  E-value: 3.98e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517970   600 KPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 671
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1095-1154 6.32e-11

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 59.92  E-value: 6.32e-11
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  1095 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1154
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 ...
 607-669 8.51e-10

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: 56.53  E-value: 8.51e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517970  607 GFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 669
Cdd:pfam00575    9 GEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILS 71
PRK08059 PRK08059
general stress protein 13; Validated
 510-584 1.37e-09

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 57.75  E-value: 1.37e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970  510 IEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKT 584
Cdd:PRK08059     5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRAT 79
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1288-1358 1.51e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 52.99  E-value: 1.51e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517970  1288 EEGEVAMGRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILS--TADNVLTLSLR 1358
Cdd:smart00316    1 EVGDVVEGTVTEITPG-GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSvdEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1382-1455 3.46e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 52.22  E-value: 3.46e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517970  1382 KEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKalyNKHLPEGKLLTARVLRLNHQKNLVELSF 1455
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 ...
 511-577 1.10e-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: 50.75  E-value: 1.10e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517970  511 EPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKL 577
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 ...
 789-857 2.36e-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: 49.59  E-value: 2.36e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  789 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSL 857
Cdd:pfam00575    4 GDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 788-858 3.48e-07

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 53.67  E-value: 3.48e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517970  788 PGMLLIGFVKSIKDYGVFI---QFPsGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:PRK03987     8 EGELVVGTVKEVKDFGAFVtldEYP-GKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
245-316 1.21e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.60  E-value: 1.21e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517970   245 KPGMLLTGTVSSLEDHGYLVDIGvDGTRAFLPLLKAQEYiRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 316
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLG-NGVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
438-496 5.00e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 46.06  E-value: 5.00e-06
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970   438 KKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSLR 496
Cdd:smart00316   14 TPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1207-1281 8.75e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 45.29  E-value: 8.75e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970  1207 QAGQTVTCFLKkyNVVKKWLEVEIAPDIRGRIPLllTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTFLCLSL 1281
Cdd:smart00316    1 EVGDVVEGTVT--EITPGGAFVDLGNGVEGLIPI--SELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
142-230 1.93e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 44.13  E-value: 1.93e-05
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970   142 EGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQvtqeqplkdllhlpelFSPGMLVRCVVSSLgitDR 221
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEV----------------LKVGDEVKVKVLSV---DE 62


                    ....*....
gi 2462517970   222 GKKSVKLSL 230
Cdd:smart00316   63 EKGRIILSL 71
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 509-568 2.85e-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: 45.56  E-value: 2.85e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517970  509 DIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVppmH---LADILMKNPEKKYHIGDEVKCRVL 568
Cdd:COG1098      2 SIEVGDIVEGKVTGITPFGAFVELPEGTTGLV---HiseIADGYVKDINDYLKVGDEVKVKVL 61
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
694-767 4.37e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.36  E-value: 4.37e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970   694 NIGQLVDVKVLEKTKDGLEVAvLPHNIRAFLPTSHLSDHvaNGPLLHHWLQAGDILH-RVLCLSQSEGRVLLCRK 767
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVD-LGNGVEGLIPISELSDK--RVKDPEEVLKVGDEVKvKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
340-406 4.77e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.36  E-value: 4.77e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517970   340 PGLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKAG----TYFSNQAVRACILCVHPRTRVVHLSLR 406
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKdpeeVLKVGDEVKVKVLSVDEEKGRIILSLK 72
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 607-689 7.12e-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: 44.40  E-value: 7.12e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  607 GFIIRVKDYGCIVKFYNNVQGLVpkH--ELSTEYIPDPERVFYTGQVVKVVVLNCEPSKeRMLLSFK-LSSDPEPKKEPA 683
Cdd:COG1098     11 GKVTGITPFGAFVELPEGTTGLV--HisEIADGYVKDINDYLKVGDEVKVKVLSIDEDG-KISLSIKqAEEKPKRPPRPR 87


                   ....*.
gi 2462517970  684 GHSQKK 689
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 ...
 1095-1154 9.49e-05

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: 9.49e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1095 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1154
Cdd:pfam00575    3 KGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVE--DPDEVIKVGDEVKVKVLK 60
PRK08059 PRK08059
general stress protein 13; Validated
 612-689 1.16e-04

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 43.50  E-value: 1.16e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  612 VKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKLSSD-PEPKKEPAGHSQKK 689
Cdd:PRK08059    18 IQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEaPEAKRKKGKILIPN 96
Suf pfam05843
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ...
 1787-1929 1.51e-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: 1.51e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1787 VWIKYGAFLlRRSQAAASHR-VLQRALEclpsKEHV--DVIAKFAQLEFQLG-DAERAKAIFENTLSTYPKRTDVWSVYI 1862
Cdd:pfam05843    3 VWIQYMRAM-RRAEGIKGARkVFKKARK----RPRLtyHVYVASALMEYYCSkDPAVAFKIFELGLKLFPEDEEFVLKYL 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517970 1863 DMTIKHGSQKDVRDIFERVIHlSLAPKRM-KFFFKRYLDYEKQHGTEKDVQAVKAKALEYVEAKSSVL 1929
Cdd:pfam05843   78 DYLISLNDDNNARVLFERVLT-RLAQEKEaKPLWKKFISYESTFGDLASILKLEKRMAELFPEDPPLA 144
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
1093-1153 2.10e-04

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 42.77  E-value: 2.10e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970 1093 LSIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHI----LDDVPEgtspttKLKVGKTVTARVI 1153
Cdd:PRK07252     1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIktgfIDNIHQ------LLKVGEEVLVQVV 59
PTZ00121 PTZ00121
MAEBL; Provisional
 1462-1653 4.46e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 45.52  E-value: 4.46e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1462 KPDVLSASLEgQLTKQEERKTEAEERDQKGEKKNQKRNEKKN----QKGQEEVempsKEKQQPQKPQAQKRGGRECRESG 1537
Cdd:PTZ00121  1379 KADAAKKKAE-EKKKADEAKKKAEEDKKKADELKKAAAAKKKadeaKKKAEEK----KKADEAKKKAEEAKKADEAKKKA 1453

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1538 SEQERVSKKPKKAGLSEEDDSLVDvyYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAwnvglDSLTPAlpplAESS 1617
Cdd:PTZ00121  1454 EEAKKAEEAKKKAEEAKKADEAKK--KAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKA-----DEAKKA----EEAK 1522

                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 2462517970 1618 DSEEDEKPHQAtiKKSKKERELEKQKAEKELSRIEE 1653
Cdd:PTZ00121  1523 KADEAKKAEEA--KKADEAKKAEEKKKADELKKAEE 1556
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 230-367 6.92e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 44.10  E-value: 6.92e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  230 LNPKNVNRVLSAEA----------------LKPGMLLTGTVSSLEDHGYLVDIG-VDGtraflpLLKAQE--YIRQKNKG 290
Cdd:PRK06676   160 LDPEKNRVILSRRAvveeeraakkeellssLKEGDVVEGTVARLTDFGAFVDIGgVDG------LVHISElsHERVEKPS 233

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  291 AKLKVGQYLNCIVEKVKGNGGVVSLSVGhsevstaiATEQQSWNL--NNLLPGLVVKAQVQKVTPFGLtlnFLTFFTGV 367
Cdd:PRK06676   234 EVVSVGQEVEVKVLSIDWETERISLSLK--------DTLPGPWEGveEKLPEGDVIEGTVKRLTDFGA---FVEVLPGV 301
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1559-1853 1.40e-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: 1.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1559 LVDVYYREGKEEaEETNVLPKEKQTKPAE-APRLQLSSGFawnVGLDSLTPALPPLAESSDseedekphqatIKKSKKER 1637
Cdd:TIGR02917  539 LAGLYLRTGNEE-EAVAWLEKAAELNPQEiEPALALAQYY---LGKGQLKKALAILNEAAD-----------AAPDSPEA 603

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1638 ELEKQKAEKELSRIEEALmdpgrqpesaDDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALktisfreeQEK 1717
Cdd:TIGR02917  604 WLMLGRAQLAAGDLNKAV----------SSFKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRAL--------ELK 665

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1718 LNVWVALL---NLENMYGSQESLTKVFeRAVQYNEPLKVFLH--LADIYAKSEKFQEAGELYNRMLKRFRQEKAVwIKYG 1792
Cdd:TIGR02917  666 PDNTEAQIglaQLLLAAKRTESAKKIA-KSLQKQHPKAALGFelEGDLYLRQKDYPAAIQAYRKALKRAPSSQNA-IKLH 743

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517970 1793 AFLLRRSQAAASHRVLQRALeclpsKEHV-DVIAKFAQLEFQLGDAERAKAI--FENTLSTYPK 1853
Cdd:TIGR02917  744 RALLASGNTAEAVKTLEAWL-----KTHPnDAVLRTALAELYLAQKDYDKAIkhYQTVVKKAPD 802
DUF612 pfam04747
Protein of unknown function, DUF612; This family includes several uncharacterized proteins ...
 1459-1658 3.96e-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: 3.96e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1459 DTGKPDVLSASLEGQLTKQEERKTEAEERDQKGEKKNQKRNEKKNQKGQEEVEMPSKEKQQPQKPQAQkrggRECRESGS 1538
Cdd:pfam04747   49 DQRKEAFASLELTEQPQQVEKVKKSEKKKAQKQIAKDHEAEQKVNAKKAAEKEARRAEAEAKKRAAQE----EEHKQWKA 124

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1539 EQERVSKKPKKaglseEDDSLVDVYYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAWNVGLD-SLTPA-LPPLAES 1616
Cdd:pfam04747  125 EQERIQKEQEK-----KEADLKKLQAEKKKEKAVKAEKAEKAEKTKKASTPAPVEEEIVVKKVANDrSAAPApEPKTPTN 199

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 2462517970 1617 SDSEEDEKPHQATIKKSKKERELEKQKAEKELSRIEEALMDP 1658
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 ...
 140-236 6.45e-40

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: 143.51  E-value: 6.45e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  140 LCEGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQVTQEQ---PLKDLLHLPELFSPGMLVRCVVSSL 216
Cdd:cd05693      1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEeedDEEELPDLEDLFSVGQLVRCKVVSL 80

                           90       100
                   ....*....|....*....|
gi 2462517970  217 GITDRGKKSVKLSLNPKNVN 236
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 ...
 696-767 1.09e-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: 1.09e-38
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517970  696 GQLVDVKVLEKTKDGLEVAVLPHNIRAFLPTSHLSDHVANGPLLHHWLQAGDILHRVLCLSQSEGRVLLCRK 767
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 ...
 775-857 2.98e-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: 138.10  E-value: 2.98e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  775 EGGQDPKNFSEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRML 854
Cdd:cd04461      1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                   ...
gi 2462517970  855 LSL 857
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 ...
 1381-1454 3.74e-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: 134.45  E-value: 3.74e-37
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517970 1381 IKEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1454
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 ...
 1287-1358 1.93e-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: 129.78  E-value: 1.93e-35
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517970 1287 LEEGEVAMGRVVKVTPNEGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILSTADNVLTLSLR 1358
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 ...
 602-671 2.97e-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: 128.88  E-value: 2.97e-35
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  602 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 671
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 ...
 985-1053 4.13e-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: 4.13e-32
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  985 GSEHQAIVQHLEKSFAIASLVETGHLAAFSLTSHLNDTFRFDSEKLQVGQGVSLTLKTTEPGVTGLLLA 1053
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 ...
 513-581 4.10e-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: 117.34  E-value: 4.10e-31
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  513 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTL 581
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 ...
 1096-1165 8.20e-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: 113.45  E-value: 8.20e-30
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1096 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEGTSPTTKLKVGKTVTARVIGGRDMKTFKYLP 1165
Cdd:cd05702      1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 424-858 2.75e-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: 124.85  E-value: 2.75e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  424 LGAVLDDVPVQG-FFKKAGATFRLK-DGVLAYARLSHlSDSKNVFNPEAFKpGNTHKCRIIDYSQMDELALLSlRTSIIE 501
Cdd:TIGR00717   95 EKAYEEGSIVEGkIVGKVKGGFIVDlNGVEAFLPGSQ-VDVKPIKDLDSLI-GKTLKFKIIKLDQKRNNIVVS-RRAYLE 171

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  502 AQYLRYHD-----IEPGAVVKGTVLTIKSYGMLVKVGeQMRGLVppmHLADIL---MKNPEKKYHIGDEVKCRVLLCDPE 573
Cdd:TIGR00717  172 EERSQAREellenLKEGDVVKGVVKNITDFGAFVDLG-GVDGLL---HITDMSwkrVKHPSEYVKVGQEVKVKVIKFDKE 247

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  574 AKKLMMTLKKTL------IESKLPvitcyadakPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVF 646
Cdd:TIGR00717  248 KGRISLSLKQLGedpweaIEKKFP---------VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVV 318

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  647 YTGQVVKVVVLNCEPSKERMLLSFKlSSDPEP-----KKEPAGhSQKKGKAINIGQLVDVKVLEKTKDGLevavlphnir 721
Cdd:TIGR00717  319 KKGDEVEVMILDIDPERRRLSLGLK-QCKANPweqfeEKHPVG-DRVTGKIKKITDFGAFVELEGGIDGL---------- 386

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  722 aflptSHLSD--HVANGPLLHHWLQAGDILHR-VLCLSQSEGRVLLCRKPALVSTVEggqdpkNFSEIHP-GMLLIGFVK 797
Cdd:TIGR00717  387 -----IHLSDisWDKDGREADHLYKKGDEIEAvVLAVDKEKKRISLGVKQLTENPWE------KFAAKYKvGSVVKGKVT 455

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517970  798 SIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:TIGR00717  456 EIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 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 ...
 243-323 2.66e-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: 109.26  E-value: 2.66e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  243 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYirqknkgAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEV 322
Cdd:cd05694      1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73


                   .
gi 2462517970  323 S 323
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 ...
 425-495 7.17e-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: 108.12  E-value: 7.17e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517970  425 GAVLDDVPVQGFFKKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSL 495
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 ...
 906-970 9.27e-28

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: 107.63  E-value: 9.27e-28
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970  906 GMFLDLVVQEVLEDGSVVFSGGPVPDLVLKASRYHRAGQEVESGQKKKVVILNVDLLKLEVHVSL 970
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 ...
 1209-1283 5.29e-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: 102.65  E-value: 5.29e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970 1209 GQTVTCFLKKYNVVKKWLEveIAPDIRGRIPLLLTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTFLCLSLTG 1283
Cdd:cd05703      1 GQEVTGFVNNVSKEFVWLT--ISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 510-858 7.13e-26

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 114.88  E-value: 7.13e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  510 IEPGAVVKGTVLTIKSYGMLVKVGeQMRGLVppmHLADILMK---NPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL- 585
Cdd:PRK06299   199 LEEGQVVEGVVKNITDYGAFVDLG-GVDGLL---HITDISWKrvnHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGe 274

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  586 -----IESKLPVitcyadakpglqthGFIIRVK-----DYGCIVKFYNNVQGLVpkH--ELS-TEYIPDPERVFYTGQVV 652
Cdd:PRK06299   275 dpweaIEKKYPV--------------GSKVKGKvtnitDYGAFVELEEGIEGLV--HvsEMSwTKKNKHPSKVVSVGQEV 338

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  653 KVVVLNCEPSKERMLLSFK-LSSDPE---PKKEPAGhSQKKGKAINIgqlvdvkvlekTKDGLEVAvLPHNIRAFLptsH 728
Cdd:PRK06299   339 EVMVLEIDEEKRRISLGLKqCKENPWeefAEKYPVG-DVVEGKVKNI-----------TDFGAFVG-LEGGIDGLV---H 402

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  729 LSD--HVANG--PLLHhwLQAGDILH-RVLCLSQSEGRVLLCRKPALvstveggQDP-KNFSEIHP-GMLLIGFVKSIKD 801
Cdd:PRK06299   403 LSDisWDKKGeeAVEL--YKKGDEVEaVVLKVDVEKERISLGIKQLE-------EDPfEEFAKKHKkGSIVTGTVTEVKD 473

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517970  802 YGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:PRK06299   474 KGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
S1_Rrp5_repeat_hs3 cd05695
S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 341-404 8.53e-26

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: 101.97  E-value: 8.53e-26
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462517970  341 GLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKA--GTYFSNQAVRACILCVHPRTRVVHLS 404
Cdd:cd05695      1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSskSTYKEGQKVRARILYVDPSTKVVGLS 66
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 240-671 1.28e-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: 101.66  E-value: 1.28e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  240 SAEALKPGMLLTGTVSSLEDHGYLVDIG--VDGtraFLPLlkaqEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSv 317
Cdd:COG0539     12 SLKELKEGDIVKGTVVSIDDDEVLVDIGykSEG---IIPL----SEFSDEPGELEVKVGDEVEVYVEKVEDGEGEIVLS- 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  318 ghsevsTAIATEQQSWN-----LNNllpGLVVKAQVQKVTPFGLTlnfltfftgvVDFMHldpkkagtyfsnqaVRAcil 392
Cdd:COG0539     84 ------KKKADREKAWEeleeaFEN---GEPVEGKVKGVVKGGLI----------VDIGG--------------VRA--- 127

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  393 cvhprtrvvhlslrpiFLqPGrpltrlscqnlgavlddvpvqgffkkagatfrlkdgvlayarlSHLsDSKNVFNPEAFK 472
Cdd:COG0539    128 ----------------FL-PA-------------------------------------------SQV-DVRPVRDLDEYV 146

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  473 pGNTHKCRIIDYSQMDELALLSlRTSIIEAQYLR-----YHDIEPGAVVKGTVLTIKSYGMLVKVGEqMRGLVppmHLAD 547
Cdd:COG0539    147 -GKTLEFKIIKLDRKRNNVVVS-RRAVLEEEREEkreelLEKLEEGDVVEGTVKNITDFGAFVDLGG-VDGLL---HISE 220

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  548 IL---MKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL------IESKLPVitcyadakpGLQTHGFIIRVKDYGCI 618
Cdd:COG0539    221 ISwgrVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQLQpdpwenIAEKYPV---------GDVVKGKVTRLTDFGAF 291

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2462517970  619 VKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 671
Cdd:COG0539    292 VELEPGVEGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 242-671 1.26e-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: 97.88  E-value: 1.26e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  242 EALKPGMLLTGTVSSLEDHGYLVDIGvdGTRAFLPlLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHse 321
Cdd:TIGR00717  183 ENLKEGDVVKGVVKNITDFGAFVDLG--GVDGLLH-ITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQ-- 257

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  322 vstaiaTEQQSWN--LNNLLPGLVVKAQVQKVTPFGltlnfltfftgvvdfmhldpkkagtyfsnqavracilcvhprtr 399
Cdd:TIGR00717  258 ------LGEDPWEaiEKKFPVGDKITGRVTNLTDYG-------------------------------------------- 287

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  400 vvhlslrpIFLQpgrpltrlscqnlgavlddvpvqgffkkagatfrLKDGVLAYARLSHLSDSKNVFNP-EAFKPGNTHK 478
Cdd:TIGR00717  288 --------VFVE----------------------------------IEEGIEGLVHVSEMSWVKKNSHPsKVVKKGDEVE 325

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  479 CRIIDYSQMDELALLSLRT------SIIEAQYlryhdiEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVppmHLADIL--- 549
Cdd:TIGR00717  326 VMILDIDPERRRLSLGLKQckanpwEQFEEKH------PVGDRVTGKIKKITDFGAFVELEGGIDGLI---HLSDISwdk 396

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  550 -MKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKtLIESKLPVITcyADAKPGLQTHGFIIRVKDYGCIVKFYNNVQGL 628
Cdd:TIGR00717  397 dGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQ-LTENPWEKFA--AKYKVGSVVKGKVTEIKDFGAFVELPGGVEGL 473

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|...
gi 2462517970  629 VPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 671
Cdd:TIGR00717  474 IRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
487-858 2.46e-20

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 97.71  E-value: 2.46e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  487 MDELALLSLRTSIIEAQYLRYHDIEP--GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVK 564
Cdd:PRK00087   275 MSELDNMEEVEENEQLEYMNELEKQIrrGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIE 354

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  565 CRVLLCD------------PEAKKLMMTLKKTLiESKLPVItcyadakpglqthGFIIRVKDYGCIVKfYNNVQGLVPKH 632
Cdd:PRK00087   355 VKVLKLEdedgyvvlskkeADREKAWKELEEAF-ENGEPVK-------------GKVKEVVKGGLLVD-YGGVRAFLPAS 419

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  633 ELSTEYIPDPERvfYTGQVVKVVVLNCEPSKERMLLsfkLSSDPEPKKEPAGHSQKKGKAINIGQLVDVKVLEKTKDGLE 712
Cdd:PRK00087   420 HVELGYVEDLSE--YKGQELEVKIIEFNRKRRKKVV---LSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAF 494

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  713 VAVlpHNIRAFLPTSHLSDHVANGPLLHhwLQAGDILH-RVLCLSQSEGRVLLCRKPALvstveggQDP-KNFSEIHP-G 789
Cdd:PRK00087   495 VDI--GGVDGLLHVSEISWGRVEKPSDV--LKVGDEIKvYILDIDKENKKLSLSLKKLL-------PDPwENVEEKYPvG 563

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  790 MLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:PRK00087   564 SIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIK 632
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 239-731 1.87e-19

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 94.46  E-value: 1.87e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  239 LSAEALKPGMLLTGTVSSLEDHGYLVDIG--VDGtraFLPLlkaqEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 316
Cdd:PRK06299    23 LKESETREGSIVKGTVVAIDKDYVLVDVGlkSEG---RIPL----EEFKNEQGELEVKVGDEVEVYVERIEDGFGETVLS 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  317 VghsevstAIATEQQSWN-LNNLL-PGLVVKAQVQKVTPFGLT--LNfltfftGVVDFM---HLD--PKKAGTYFSNQAV 387
Cdd:PRK06299    96 R-------EKAKRLEAWDkLEKAFeNGEIVEGVINGKVKGGFTvdLN------GVEAFLpgsQVDvrPVRDTDPLEGKEL 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  388 RACILCVHPRTRVVHLSLRPIF--------------LQPGrpltrlscqnlgavldDVpVQGFFKKA---GATFRLK--D 448
Cdd:PRK06299   163 EFKVIKLDKKRNNIVVSRRAVLeeeraeereellenLEEG----------------QV-VEGVVKNItdyGAFVDLGgvD 225

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  449 GVLAYARLSHlsdsKNVFNP-EAFKPGNTHKCRIIDYSQmdELALLSLrtSI----------IEAQYlryhdiEPGAVVK 517
Cdd:PRK06299   226 GLLHITDISW----KRVNHPsEVVNVGDEVKVKVLKFDK--EKKRVSL--GLkqlgedpweaIEKKY------PVGSKVK 291

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  518 GTVLTIKSYGMLVKVGEQMRGLVppmHLADI----LMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL------IE 587
Cdd:PRK06299   292 GKVTNITDYGAFVELEEGIEGLV---HVSEMswtkKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKenpweeFA 368

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  588 SKLPVitcyadakpGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERM 666
Cdd:PRK06299   369 EKYPV---------GDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERI 439

                          490       500       510       520       530       540
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462517970  667 LLSFK-LSSDPepkkepAGHSQKKGKainIGQLVDVKVLEKTKDGLEVAvLPHNIRAFLPTSHLSD 731
Cdd:PRK06299   440 SLGIKqLEEDP------FEEFAKKHK---KGSIVTGTVTEVKDKGAFVE-LEDGVEGLIRASELSR 495
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 627-858 1.21e-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: 89.72  E-value: 1.21e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  627 GLVPKHELSTEyipdPERVFYT-GQVVKVVVLNCEPSKERMLLSfklssdpepkKEPAGhsQKKG-----KAINIGQLVD 700
Cdd:COG0539     44 GIIPLSEFSDE----PGELEVKvGDEVEVYVEKVEDGEGEIVLS----------KKKAD--REKAweeleEAFENGEPVE 107

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  701 VKVLEKTKDGLEVAVlpHNIRAFLPTSHLSDH-VAN-GPLLHHWLQAgdilhRVLCLSQSEGRVLLCRKPALVSTVEGGQ 778
Cdd:COG0539    108 GKVKGVVKGGLIVDI--GGVRAFLPASQVDVRpVRDlDEYVGKTLEF-----KIIKLDRKRNNVVVSRRAVLEEEREEKR 180

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  779 DpKNFSEIHPGMLLIGFVKSIKDYGVFIQFPsGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:COG0539    181 E-ELLEKLEEGDVVEGTVKNITDFGAFVDLG-GVDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLK 258
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 625-858 1.26e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 90.32  E-value: 1.26e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  625 VQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKLSsdpepkKEPAGHSQKKGKAINiGQLVDVKVL 704
Cdd:PRK06676    42 VEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRL------EAEKAWDKLEEKFEE-GEVVEVKVT 114

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  705 EKTKDGLEVAVlpHNIRAFLPTSHLSDH-VANgpllHHWLQAGDILHRVLCLSQSEGRVLLCRKpALVSTVEGGQDPKNF 783
Cdd:PRK06676   115 EVVKGGLVVDV--EGVRGFIPASLISTRfVED----FSDFKGKTLEVKIIELDPEKNRVILSRR-AVVEEERAAKKEELL 187

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970  784 SEIHPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:PRK06676   188 SSLKEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLK 261
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1660-1920 3.81e-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: 83.63  E-value: 3.81e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1660 RQPESA-DDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfREEQEKLnvwvALLNLENMYGSQESLT 1738
Cdd:COG2956     22 GQPDKAiDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYLKAGLLD 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1739 K---VFERAVQYNEP-LKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEC 1814
Cdd:COG2956     94 RaeeLLEKLLELDPDdAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL 173

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1815 LPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLAPKRMKFF 1894
Cdd:COG2956    174 DP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA--LELDPSDDLLL 249

                          250       260
                   ....*....|....*....|....*.
gi 2462517970 1895 FKRYLdYEKQHGTEKdVQAVKAKALE 1920
Cdd:COG2956    250 ALADL-LERKEGLEA-ALALLERQLR 273
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
511-582 3.48e-16

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 74.95  E-value: 3.48e-16
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517970   511 EPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 582
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 465-681 5.01e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 82.23  E-value: 5.01e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  465 VFNPEAFKpGNTHKCRIIDYSQMDELALLSlRTSIIEAQYLRYHD-----IEPGAVVKGTVLTIKSYGMLVKVGEqMRGL 539
Cdd:PRK06676   142 VEDFSDFK-GKTLEVKIIELDPEKNRVILS-RRAVVEEERAAKKEellssLKEGDVVEGTVARLTDFGAFVDIGG-VDGL 218

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  540 VppmHLADI---LMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL------IESKLPVitcyadakpGLQTHGFII 610
Cdd:PRK06676   219 V---HISELsheRVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLpgpwegVEEKLPE---------GDVIEGTVK 286

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517970  611 RVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKlSSDPEPKKE 681
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 ...
 789-858 8.59e-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: 8.59e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  789 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:cd05698      1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 600-1154 1.21e-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: 82.09  E-value: 1.21e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  600 KPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHElsteyIPDPERVFYTGQVVKVVVLNCEPSKERMLLSfklssdpepk 679
Cdd:TIGR00717   17 RPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEE-----FLDAPLEIQVGDEVEVYLDRVEDRFGETVLS---------- 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  680 KEPAGHSQKKGK---AINIGQLVDVKVLEKTKDGLEVAVlpHNIRAFLPTSHLSDHVANGPLLHhwlQAGDILHRVLCLS 756
Cdd:TIGR00717   82 REKAQRHELWIKlekAYEEGSIVEGKIVGKVKGGFIVDL--NGVEAFLPGSQVDVKPIKDLDSL---IGKTLKFKIIKLD 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  757 QSEGRVLLCRKPALVSTVEGGQDpKNFSEIHPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEG 836
Cdd:TIGR00717  157 QKRNNIVVSRRAYLEEERSQARE-ELLENLKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVKHPSEYVKVG 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  837 QTVAAKVTNVDEEKQRMLLSLRLSDcglGD--LAItsllllnqclEELQGVRSLMSNRdsvliqtLAEMTP-GMFLDLV- 912
Cdd:TIGR00717  235 QEVKVKVIKFDKEKGRISLSLKQLG---EDpwEAI----------EKKFPVGDKITGR-------VTNLTDyGVFVEIEe 294

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  913 -------VQEVLEDGSVVfsggpvpdlvlKASRYHRAGQEVEsgqkkkVVILNVDLLKLEVHVSLHQDLVN---RKARKL 982
Cdd:TIGR00717  295 gieglvhVSEMSWVKKNS-----------HPSKVVKKGDEVE------VMILDIDPERRRLSLGLKQCKANpweQFEEKH 357

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  983 RKGSEHQAIVQHLEKSFAIASLVE--TGHLaafsltsHLNDTFRFDSEKlqvgqgVSLTLKTTEPGVTGLLLAVEGPAAK 1060
Cdd:TIGR00717  358 PVGDRVTGKIKKITDFGAFVELEGgiDGLI-------HLSDISWDKDGR------EADHLYKKGDEIEAVVLAVDKEKKR 424

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1061 RTMRPTQKDSETVDEDEEVDPaltvgtikkhtlsIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTT 1140
Cdd:TIGR00717  425 ISLGVKQLTENPWEKFAAKYK-------------VGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDE--DKTD 489

                          570
                   ....*....|....
gi 2462517970 1141 KLKVGKTVTARVIG 1154
Cdd:TIGR00717  490 EIKVGDEVEAKVVD 503
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 587-670 2.57e-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: 2.57e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  587 ESKLPviTCYADAKPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERM 666
Cdd:cd04461      2 EGTLP--TNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRF 79


                   ....
gi 2462517970  667 LLSF 670
Cdd:cd04461     80 LLSL 83
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
788-858 2.62e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 72.25  E-value: 2.62e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517970   788 PGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 691-1154 3.04e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 81.36  E-value: 3.04e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  691 KAINIGQLVDVKVLEKTKDGLEVAVlpHNIRAFLPTSHLS-----DHvanGPLLHHWLQAgdilhRVLCLSQSEGRVLLC 765
Cdd:PRK06299   110 KAFENGEIVEGVINGKVKGGFTVDL--NGVEAFLPGSQVDvrpvrDT---DPLEGKELEF-----KVIKLDKKRNNIVVS 179

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  766 RKpALVSTVEGGQDPKNFSEIHPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTN 845
Cdd:PRK06299   180 RR-AVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDL-GGVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLK 257

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  846 VDEEKQRMLLSLRLsdcgLGD---LAITsllllnqclEELQgVRSLMSNRDSVLiqtlaemTP-GMFLDlvvqevLEDGs 921
Cdd:PRK06299   258 FDKEKKRVSLGLKQ----LGEdpwEAIE---------KKYP-VGSKVKGKVTNI-------TDyGAFVE------LEEG- 309

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  922 vvfsggpVPDLV-----------LKASRYHRAGQEVEsgqkkkVVILNVDLLKLEVHVSLHQDLVN---RKARKLRKGSE 987
Cdd:PRK06299   310 -------IEGLVhvsemswtkknKHPSKVVSVGQEVE------VMVLEIDEEKRRISLGLKQCKENpweEFAEKYPVGDV 376

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  988 HQAivqhleksfAIASLVETGhlaAFsltshlndtfrfdseklqvgqgVSLtlkttEPGVTGLL----LA--VEGPAAKR 1061
Cdd:PRK06299   377 VEG---------KVKNITDFG---AF----------------------VGL-----EGGIDGLVhlsdISwdKKGEEAVE 417

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1062 TMRptqKDSE------TVDEDEE----------VDPALTVgtIKKHTlsIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHA 1125
Cdd:PRK06299   418 LYK---KGDEveavvlKVDVEKErislgikqleEDPFEEF--AKKHK--KGSIVTGTVTEVKDKGAFVELEDGVEGLIRA 490

                          490       500
                   ....*....|....*....|....*....
gi 2462517970 1126 SHILDDvpEGTSPTTKLKVGKTVTARVIG 1154
Cdd:PRK06299   491 SELSRD--RVEDATEVLKVGDEVEAKVIN 517
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
600-671 3.98e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 71.87  E-value: 3.98e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517970   600 KPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 671
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1688-1920 2.96e-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: 75.15  E-value: 2.96e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1688 FHLQATEIEKARAVAERALKtisfrEEQEKLNVWVALLNLENMYGSQESLTKVFERAVQYNEP-LKVFLHLADIYAKSEK 1766
Cdd:COG2956     17 NYLLNGQPDKAIDLLEEALE-----LDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLERDPDrAEALLELAQDYLKAGL 91

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1767 FQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPSKEHVDVIAkfAQLEFQLGDAERAKAIFEN 1846
Cdd:COG2956     92 LDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCEL--AELYLEQGDYDEAIEALEK 169

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517970 1847 TLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLAPKRMKFFFKRYLDYEKQHGTEKDVQAVKaKALE 1920
Cdd:COG2956    170 ALKLDPDCARALLLLAELYLEQGDYEEAIAALERA--LEQDPDYLPALPRLAELYEKLGDPEEALELLR-KALE 240
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1636-1851 5.10e-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: 71.68  E-value: 5.10e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1636 ERELEKQKAEKELSRIeeaLMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfrEEQ 1715
Cdd:COG2956     70 ERDPDRAEALLELAQD---YLKAGLLDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLK-----LGP 141

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1716 EKLNVWVALLNLENMYGSQESLTKVFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAF 1794
Cdd:COG2956    142 ENAHAYCELAELYLEQGDYDEAIEALEKALKLDpDCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAEL 221

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517970 1795 LLRRSQAAASHRVLQRALECLPSkehVDVIAKFAQLEFQLGDAERAKAIFENTLSTY 1851
Cdd:COG2956    222 YEKLGDPEEALELLRKALELDPS---DDLLLALADLLERKEGLEAALALLERQLRRH 275
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 509-858 6.67e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 72.60  E-value: 6.67e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  509 DIEPGAVVKGTVLTIKSYGMLVKV-GEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIE 587
Cdd:PRK06676    14 EVEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAE 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  588 ---SKLpvITCYADAKPglqthgFIIRVKDY---GCIVKFyNNVQGLVPKHELSTEYIPDPERvfYTGQVVKVVVLNCEP 661
Cdd:PRK06676    94 kawDKL--EEKFEEGEV------VEVKVTEVvkgGLVVDV-EGVRGFIPASLISTRFVEDFSD--FKGKTLEVKIIELDP 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  662 SKERMLLSFK--LSSDPEPKKEPAGHSqkkgkaINIGQLVDVKVLEKTK----------DGLevavlphnirafLPTSHL 729
Cdd:PRK06676   163 EKNRVILSRRavVEEERAAKKEELLSS------LKEGDVVEGTVARLTDfgafvdiggvDGL------------VHISEL 224

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  730 S-DHVANgpllhhwlqAGDILH-------RVLCLSQSEGRVLLCRKPALVSTVEGGQDpknfsEIHPGMLLIGFVKSIKD 801
Cdd:PRK06676   225 ShERVEK---------PSEVVSvgqevevKVLSIDWETERISLSLKDTLPGPWEGVEE-----KLPEGDVIEGTVKRLTD 290

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517970  802 YGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:PRK06676   291 FGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIK 347
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 792-856 7.05e-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: 65.09  E-value: 7.05e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970  792 LIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 856
Cdd:cd00164      1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 516-580 8.57e-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: 65.09  E-value: 8.57e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970  516 VKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMT 580
Cdd:cd00164      1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 510-858 4.62e-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: 70.92  E-value: 4.62e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  510 IEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPpmhLADILmkNPEKKYHIGDEVKCRVLLCDP-EAKKLMMTLKKTLIES 588
Cdd:TIGR00717   16 TRPGSIVKGTVVAINKDTVFVDVGLKSEGRIP---KEEFL--DAPLEIQVGDEVEVYLDRVEDrFGETVLSREKAQRHEL 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  589 KLPVITCYADAKPglqTHGFIIRVKDYGCIVKFyNNVQGLVPKHELSTEYIPDPERvfYTGQVVKVVVLNCEPSKERMLL 668
Cdd:TIGR00717   91 WIKLEKAYEEGSI---VEGKIVGKVKGGFIVDL-NGVEAFLPGSQVDVKPIKDLDS--LIGKTLKFKIIKLDQKRNNIVV 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  669 SFKLSSDPEPKKEpaghSQKKGKAINIGQLVDVKVLEKTKDGleVAVLPHNIRAFLPTSHLS-DHVANgPllHHWLQAGD 747
Cdd:TIGR00717  165 SRRAYLEEERSQA----REELLENLKEGDVVKGVVKNITDFG--AFVDLGGVDGLLHITDMSwKRVKH-P--SEYVKVGQ 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  748 ILH-RVLCLSQSEGRVLLCRKpalvstvEGGQDP-KNFSEIHP-GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMS-D 823
Cdd:TIGR00717  236 EVKvKVIKFDKEKGRISLSLK-------QLGEDPwEAIEKKFPvGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwV 308

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 2462517970  824 KFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:TIGR00717  309 KKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 606-669 7.72e-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: 62.01  E-value: 7.72e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517970  606 HGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 669
Cdd:cd00164      2 TGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1739-1853 8.32e-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: 8.32e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1739 KVFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPs 1817
Cdd:COG4783     25 ALLEKALELDpDNPEAFALLGEILLQLGDLDEAIVLLHEALELDPDEPEARLNLGLALLKAGDYDEALALLEKALKLDP- 103

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 2462517970 1818 kEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPK 1853
Cdd:COG4783    104 -EHPEAYLRLARAYRALGRPDEAIAALEKALELDPD 138
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1095-1154 6.32e-11

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 59.92  E-value: 6.32e-11
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  1095 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1154
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 ...
 789-858 9.78e-11

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: 59.22  E-value: 9.78e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  789 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKqRMLLSLR 858
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 ...
 787-860 1.44e-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: 58.88  E-value: 1.44e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970  787 HPGMLLIGFVKSIKDYGVFIQF-PSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLRLS 860
Cdd:cd05708      1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75
rpsA PRK13806
30S ribosomal protein S1; Provisional
 461-747 1.67e-10

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 65.90  E-value: 1.67e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  461 DSKNVFNPEAFKpGNTHKCRIIDYSQ------MDELALLSLRTSIIEAQYLRyhDIEPGAVVKGTVLTIKSYGMLVKVGE 534
Cdd:PRK13806   148 DLRYVEDPESYV-GQTFQFLITRVEEngrnivVSRRALLEREQKEALEAFME--TVKEGDVVEGTVTRLAPFGAFVELAP 224

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  535 QMRGLVppmHLADI---LMKNPEKKYHIGDEVKCRVLLCDPEAK----KLMMTLKKTlieSKLPVITCYADAKPGLQTHG 607
Cdd:PRK13806   225 GVEGMV---HISELswsRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIKQA---GGDPWDTVGDRLKAGDKVTG 298

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  608 FIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKlssdpEPKKEP-AGH 685
Cdd:PRK13806   299 KVVRLAPFGAFVEILPGIEGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLR-----DAEGDPwADV 373

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517970  686 SQKkgkaINIGQLVDVKVLEKTKDGLEVAVLPhNIRAFLPTSHLSDhvANGPLLHHWLQAGD 747
Cdd:PRK13806   374 AER----FAPGTTVTGTVEKRAQFGLFVNLAP-GVTGLLPASVISR--AGKPATYEKLKPGD 428
rpsA PRK13806
30S ribosomal protein S1; Provisional
 597-856 4.19e-10

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 64.36  E-value: 4.19e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  597 ADAKPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKE----RMLLSFK- 671
Cdd:PRK13806   198 ETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIKq 277

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  672 LSSDPepkkepaghSQKKGKAINIGQLVDVKVLEKTKDGLEVAVLPhNIRAFLPTSHLSdHV--ANGPllHHWLQAGDIL 749
Cdd:PRK13806   278 AGGDP---------WDTVGDRLKAGDKVTGKVVRLAPFGAFVEILP-GIEGLVHVSEMS-WTrrVNKP--EDVVAPGDAV 344

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  750 H-RVLCLSQSEGRVLLCRKPAlvstvEGgqDP-KNFSE-IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFV 826
Cdd:PRK13806   345 AvKIKDIDPAKRRISLSLRDA-----EG--DPwADVAErFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGK 417

                          250       260       270
                   ....*....|....*....|....*....|
gi 2462517970  827 TSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 856
Cdd:PRK13806   418 PATYEKLKPGDSVTLVVEEIDTAKRKISLA 447
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 607-669 8.51e-10

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: 56.53  E-value: 8.51e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517970  607 GFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 669
Cdd:pfam00575    9 GEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILS 71
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 513-582 9.36e-10

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: 56.47  E-value: 9.36e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  513 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 582
Cdd:cd05698      1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 513-858 1.09e-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: 62.37  E-value: 1.09e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  513 GAVVKGTVL-TIKSyGMLVKVGEqMRGLVPPMHLADILMKNPEKkyHIGDEVKCRVLLCDPEAKKL-----------MMT 580
Cdd:COG0539    103 GEPVEGKVKgVVKG-GLIVDIGG-VRAFLPASQVDVRPVRDLDE--YVGKTLEFKIIKLDRKRNNVvvsrravleeeREE 178

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  581 LKKTLIEsKLpvitcyadaKPGLQTHGFIIRVKDYGCIVKFyNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCE 660
Cdd:COG0539    179 KREELLE-KL---------EEGDVVEGTVKNITDFGAFVDL-GGVDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKID 247

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  661 PSKERMLLSFK-LSSDPepkkepaghsqkkgkainigqlvdvkvlektkdglevavlphniraflptshlsdhvangpll 739
Cdd:COG0539    248 REKERISLSLKqLQPDP--------------------------------------------------------------- 264

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  740 hhWLQAGDilhrvlclsqsegrvllcrkpalvstveggqdpknfsEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKA 819
Cdd:COG0539    265 --WENIAE-------------------------------------KYPVGDVVKGKVTRLTDFGAFVELEPGVEGLVHIS 305

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|
gi 2462517970  820 IMS-DKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:COG0539    306 EMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
PRK08059 PRK08059
general stress protein 13; Validated
 510-584 1.37e-09

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 57.75  E-value: 1.37e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970  510 IEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKT 584
Cdd:PRK08059     5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRAT 79
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1741-1860 1.51e-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: 1.51e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1741 FERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskE 1819
Cdd:COG4235      6 LRQALAANpNDAEGWLLLGRAYLRLGRYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEELLERALALDP--D 83

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2462517970 1820 HVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSV 1860
Cdd:COG4235     84 NPEALYLLGLAAFQQGDYAEAIAAWQKLLALLPADAPARLL 124
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1749-1885 2.14e-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: 2.14e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1749 EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskEHVDVIAKFA 1828
Cdd:COG4783      2 ACAEALYALAQALLLAGDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALELDP--DEPEARLNLG 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517970 1829 QLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVIHLS 1885
Cdd:COG4783     80 LALLKAGDYDEALALLEKALKLDPEHPEAYLRLARAYRALGRPDEAIAALEKALELD 136
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 97-406 5.82e-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: 60.90  E-value: 5.82e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970   97 TEEGSTKRKKSQKGPAKTKKLKIEKRESSKSAREKFEilsvESLCEGMRILGCVKEVNELELVISLPNGLQGFVQVTEIc 176
Cdd:TIGR00717  231 VKVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIE----KKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEM- 305

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  177 dAYTKKLNeqvtqeqplkdllHLPELFSPGMLVRCVVssLGItDRGKKSVKLSLNPKNVNRVLSAEALKP-GMLLTGTVS 255
Cdd:TIGR00717  306 -SWVKKNS-------------HPSKVVKKGDEVEVMI--LDI-DPERRRLSLGLKQCKANPWEQFEEKHPvGDRVTGKIK 368

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  256 SLEDHGYLVDIGvDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHsevstaiATEQQSWNL 335
Cdd:TIGR00717  369 KITDFGAFVELE-GGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQ-------LTENPWEKF 440

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462517970  336 NNLLP-GLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHL----DPKKAGTYFSNQAVRACILCVHPRTRVVHLSLR 406
Cdd:TIGR00717  441 AAKYKvGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELsenrDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
513-587 6.71e-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: 6.71e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970  513 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIE 587
Cdd:PRK00087   563 GSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEE 637
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 228-613 7.84e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 60.56  E-value: 7.84e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  228 LSLNPKNVNRVLS----------------AEALKPGMLLTGTVSSLEDHGYLVDI-GVDGtraflpLLKAQE--YIRQKN 288
Cdd:PRK06299   167 IKLDKKRNNIVVSrravleeeraeereelLENLEEGQVVEGVVKNITDYGAFVDLgGVDG------LLHITDisWKRVNH 240

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  289 KGAKLKVGQYLNCIVEKVKGNGGVVSLSVGhsevstaiATEQQSW-NLNNLLP-GLVVKAQVQKVTPFGLtlnFLTFFTG 366
Cdd:PRK06299   241 PSEVVNVGDEVKVKVLKFDKEKKRVSLGLK--------QLGEDPWeAIEKKYPvGSKVKGKVTNITDYGA---FVELEEG 309

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  367 VVDFMHL-------DPKKAGTYFS-NQAVRACILCVHPRTRVVHLSLRPifLQPgRPLTRLSCQ-NLGAVlddvpVQGFF 437
Cdd:PRK06299   310 IEGLVHVsemswtkKNKHPSKVVSvGQEVEVMVLEIDEEKRRISLGLKQ--CKE-NPWEEFAEKyPVGDV-----VEGKV 381

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  438 K---KAGATFRLKDGVLAYARLSHLSDSKNVFNP-EAFKPGNTHKCRIIDYSQMDELALLSLR------TSIIEAQYlry 507
Cdd:PRK06299   382 KnitDFGAFVGLEGGIDGLVHLSDISWDKKGEEAvELYKKGDEVEAVVLKVDVEKERISLGIKqleedpFEEFAKKH--- 458

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  508 hdiEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIE 587
Cdd:PRK06299   459 ---KKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEA 535

                          410       420
                   ....*....|....*....|....*.
gi 2462517970  588 SKLPVITCYADAKPGLQTHGFIIRVK 613
Cdd:PRK06299   536 EEKEAIAEYNSASDSKTTLGDLLKAA 561
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1099-1161 1.09e-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: 53.15  E-value: 1.09e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517970 1099 VTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIGGRDMKTF 1161
Cdd:cd00164      1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVK--DPSEVFKVGDEVEVKVLEVDPEKGR 61
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 441-671 1.28e-08

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 60.11  E-value: 1.28e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  441 GATFRLKDGVLAYARLSHLSDSKNVFNP-EAFKPGNTHKCRIIDYSQMDELALLSLRTSI------IEAQYlryhdiEPG 513
Cdd:PRK12269   593 GAFIELAEGIEGLAHISEFSWVKKTSKPsDMVKIGDEVECMILGYDIQAGRVSLGLKQVTanpweeIEARY------PVG 666

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  514 AVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNP-EKKYHIGDEVKCRVLLCDPEAKKLMMTLKKtLIESKLPV 592
Cdd:PRK12269   667 ARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPaDHELEVGKEIECMVIECDPQARRIRLGVKQ-LSDNPWQV 745

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  593 itcYADA-KPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPE---RVFYTGQVVKVVVLNCEPSKERMLL 668
Cdd:PRK12269   746 ---FANAyGVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPGealRKYAVGDRVKAVIVDMNVKDRKVAF 822


                   ...
gi 2462517970  669 SFK 671
Cdd:PRK12269   823 SVR 825
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1288-1358 1.51e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 52.99  E-value: 1.51e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517970  1288 EEGEVAMGRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILS--TADNVLTLSLR 1358
Cdd:smart00316    1 EVGDVVEGTVTEITPG-GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSvdEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1382-1455 3.46e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 52.22  E-value: 3.46e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517970  1382 KEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKalyNKHLPEGKLLTARVLRLNHQKNLVELSF 1455
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDP---EEVLKVGDEVKVKVLSVDEEKGRIILSL 71
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1723-1880 4.60e-08

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 56.17  E-value: 4.60e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1723 ALLNLENMYGSQESLTK---VFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRR 1798
Cdd:COG0457     10 AYNNLGLAYRRLGRYEEaieDYEKALELDpDDAEALYNLGLAYLRLGRYEEALADYEQALELDPDDAEALNNLGLALQAL 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1799 SQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIF 1878
Cdd:COG0457     90 GRYEEALEDYDKALELDP--DDAEALYNLGLALLELGRYDEAIEAYERALELDPDDADALYNLGIALEKLGRYEEALELL 167


                   ..
gi 2462517970 1879 ER 1880
Cdd:COG0457    168 EK 169
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1387-1454 5.60e-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: 51.23  E-value: 5.60e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517970 1387 LRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQhspSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1454
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 ...
 789-855 7.36e-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: 7.36e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517970  789 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMS-DKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLL 855
Cdd:cd05690      1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1090-1454 8.57e-08

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: 57.05  E-value: 8.57e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1090 KHTLSIGDMVTGTVKSIKPTHVVVTLeDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIGGRDMKTFKYLPISHp 1169
Cdd:TIGR00717  182 LENLKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVK--HPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQ- 257

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1170 rfvrTIPElsvrpseledghtalnthsvsPMEKI-KQYQAGQTVTCflKKYNVVKKWLEVEIAPDIRGRIPLLLTSLSFK 1248
Cdd:TIGR00717  258 ----LGED---------------------PWEAIeKKFPVGDKITG--RVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKK 310

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1249 VlKHPDKKFRVGQALRATVVGPDSSKTFLCLSL--TGPHKLEE-------GEVAMGRVVKVTpNEGLTVSFPFGKIGTVS 1319
Cdd:TIGR00717  311 N-SHPSKVVKKGDEVEVMILDIDPERRRLSLGLkqCKANPWEQfeekhpvGDRVTGKIKKIT-DFGAFVELEGGIDGLIH 388

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1320 IFHMS-DSYSETPLEDFVPQKVVRCYILStadnvltLSLRSSRTNPETKSKVEDPEINSIQDIKEGQLLRGYVGSIQPHG 1398
Cdd:TIGR00717  389 LSDISwDKDGREADHLYKKGDEIEAVVLA-------VDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKDFG 461

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462517970 1399 VFFRLGPSVVGLARYSHVSQHSPSKKALynkHLPEGKLLTARVLRLNHQKNLVELS 1454
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 ...
 511-577 1.10e-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: 50.75  E-value: 1.10e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517970  511 EPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKL 577
Cdd:pfam00575    2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRI 68
rpsA PRK13806
30S ribosomal protein S1; Provisional
 441-669 1.45e-07

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 56.27  E-value: 1.45e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  441 GATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSLRTSIIEAQYLRYHDI----EPGAVV 516
Cdd:PRK13806   217 GAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVgdrlKAGDKV 296

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  517 KGTVLTIKSYGMLVKVGEQMRGLVppmHLADI----LMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIESKLPV 592
Cdd:PRK13806   297 TGKVVRLAPFGAFVEILPGIEGLV---HVSEMswtrRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADV 373

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517970  593 ITCYAdakPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 669
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 ...
 789-856 1.66e-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: 1.66e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517970  789 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 856
Cdd:cd05685      1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1757-1921 1.72e-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: 54.74  E-value: 1.72e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1757 LADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEclPSKEHVDVIAKFAQLEFQLGD 1836
Cdd:COG2956     14 KGLNYLLNGQPDKAIDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE--RDPDRAEALLELAQDYLKAGL 91

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1837 AERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVIHLSlaPKRMKFFFKRYLDYEKQHGTEKDVQAVKa 1916
Cdd:COG2956     92 LDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLG--PENAHAYCELAELYLEQGDYDEAIEALE- 168


                   ....*
gi 2462517970 1917 KALEY 1921
Cdd:COG2956    169 KALKL 173
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 1760-1852 1.88e-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: 1.88e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1760 IYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQLGDAER 1839
Cdd:COG5010     63 LYNKLGDFEESLALLEQALQLDPNNPELYYNLALLYSRSGDKDEAKEYYEKALALSP--DNPNAYSNLAALLLSLGQDDE 140

                           90
                   ....*....|...
gi 2462517970 1840 AKAIFENTLSTYP 1852
Cdd:COG5010    141 AKAALQRALGTSP 153
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 788-856 2.08e-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: 2.08e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  788 PGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 856
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 ...
 789-857 2.36e-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: 49.59  E-value: 2.36e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  789 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSL 857
Cdd:pfam00575    4 GDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 788-858 3.48e-07

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 53.67  E-value: 3.48e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517970  788 PGMLLIGFVKSIKDYGVFI---QFPsGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:PRK03987     8 EGELVVGTVKEVKDFGAFVtldEYP-GKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
1760-1853 3.93e-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: 3.93e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1760 IYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRvLQRALECLPskEHVDVIAKFAQLEFQLGDAER 1839
Cdd:COG3063      1 LYLKLGDLEEAEEYYEKALELDPDNADALNNLGLLLLEQGRYDEAIA-LEKALKLDP--NNAEALLNLAELLLELGDYDE 77

                           90
                   ....*....|....
gi 2462517970 1840 AKAIFENTLSTYPK 1853
Cdd:COG3063     78 ALAYLERALELDPS 91
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 1093-1491 5.28e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 54.11  E-value: 5.28e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1093 LSIGDMVTGTVKSIKPTHVVVTLEDGII-GCIHASHILDDVPEGTSPTtkLKVGKTVTARVIGGRDMKtfKYLpishprf 1171
Cdd:PRK06676    15 VEVGDVVTGEVLKVEDKQVFVNIEGYKVeGVIPISELSNDHIEDINDV--VKVGDELEVYVLKVEDGE--GNL------- 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1172 vrtipELSVRPSELEDGHTALNthsvspmekiKQYQAGQTVTCFLKKynVVKKWLEVEIApDIRGRIPLLLTSLSFKvlk 1251
Cdd:PRK06676    84 -----LLSKRRLEAEKAWDKLE----------EKFEEGEVVEVKVTE--VVKGGLVVDVE-GVRGFIPASLISTRFV--- 142

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1252 hPDKKFRVGQALRATVVGPDSSKTFLCLSltgpHK-----------------LEEGEVAMGRVVKVTPnegltvsfpFG- 1313
Cdd:PRK06676   143 -EDFSDFKGKTLEVKIIELDPEKNRVILS----RRavveeeraakkeellssLKEGDVVEGTVARLTD---------FGa 208

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1314 --KIGTVS-IFHMSD-SYS--ETPLEDFVPQKVVRCYILStAD---NVLTLSLRSsrTNPETKSKVEdpeinsiQDIKEG 1384
Cdd:PRK06676   209 fvDIGGVDgLVHISElSHErvEKPSEVVSVGQEVEVKVLS-IDwetERISLSLKD--TLPGPWEGVE-------EKLPEG 278

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1385 QLLRGYVGSIQPHGVFFRLGPSVVGLArysHVSQHSpskkalyNKH-------LPEGKLLTARVLRLNHQKNLVELSflp 1457
Cdd:PRK06676   279 DVIEGTVKRLTDFGAFVEVLPGVEGLV---HISQIS-------HKHiatpsevLEEGQEVKVKVLEVNEEEKRISLS--- 345

                          410       420       430
                   ....*....|....*....|....*....|....
gi 2462517970 1458 gdtgKPDVLSASLEGQLTKQEERKTEAEErDQKG 1491
Cdd:PRK06676   346 ----IKALEEAPAEEEDRREEYRQYELPE-EETG 374
PRK08059 PRK08059
general stress protein 13; Validated
 784-858 9.33e-07

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 49.66  E-value: 9.33e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970  784 SEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:PRK08059     3 SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 602-671 1.03e-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: 1.03e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  602 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPsKERMLLSFK 671
Cdd:cd05692      1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK 69
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1653-1842 1.04e-06

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 51.93  E-value: 1.04e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1653 EALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisfreeqeKLNVWVALLNLENMYG 1732
Cdd:COG0457     16 LAYRRLGRYEEAIEDYEKALELDPDDAEALYNLGLAYLRLGRYEEALADYEQALEL--------DPDDAEALNNLGLALQ 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1733 SQESLTK---VFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVL 1808
Cdd:COG0457     88 ALGRYEEaleDYDKALELDpDDAEALYNLGLALLELGRYDEAIEAYERALELDPDDADALYNLGIALEKLGRYEEALELL 167

                          170       180       190
                   ....*....|....*....|....*....|....
gi 2462517970 1809 QRALECLPSKEHVDVIAKFAQLEFQLGDAERAKA 1842
Cdd:COG0457    168 EKLEAAALAALLAAALGEAALALAAAEVLLALLL 201
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 509-581 1.14e-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: 1.14e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517970  509 DIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTL 581
Cdd:cd04461     11 DLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
245-316 1.21e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.60  E-value: 1.21e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517970   245 KPGMLLTGTVSSLEDHGYLVDIGvDGTRAFLPLLKAQEYiRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 316
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLG-NGVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 1377-1455 1.27e-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: 1.27e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970 1377 SIQDIKEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKalyNKHLPEGKLLTARVLRLNHQKNLVELSF 1455
Cdd:cd04461      8 NFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDP---SFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 513-582 1.60e-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: 47.71  E-value: 1.60e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517970  513 GAVVKGTVLTIKSYGMLVKV-GEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 582
Cdd:cd05708      3 GQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 438-494 1.78e-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: 46.99  E-value: 1.78e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517970  438 KKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLS 494
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. ...
 789-858 2.20e-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: 47.19  E-value: 2.20e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517970  789 GMLLIGFVKSIKDYGVFI---QFPsGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:cd04452      4 GELVVVTVKSIADMGAYVsllEYG-NIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK 75
RNA14 COG5107
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ...
 1668-1928 2.50e-06

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


Pssm-ID: 227438 [Multi-domain]  Cd Length: 660  Bit Score: 52.71  E-value: 2.50e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1668 FDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALK---TISFR-EEQEKLNvwvalLNLENMYGSQESLTKVFER 1743
Cdd:COG5107    291 HNQILDYFYYAEEVWFDYSEYLIGISDKQKALKTVERGIEmspSLTMFlSEYYELV-----NDEEAVYGCFDKCTQDLKR 365

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1744 AVQYNEplkvflhlADIYAKSE-KFQEAGELynrMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEcLPSKEHvD 1822
Cdd:COG5107    366 KYSMGE--------SESASKVDnNFEYSKEL---LLKRINKLTFVFCVHLNYVLRKRGLEAARKLFIKLRK-EGIVGH-H 432

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1823 VIAKFAQLEFQ-LGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVIHlSLAPKRMKFFFKRYLDY 1901
Cdd:COG5107    433 VYIYCAFIEYYaTGDRATAYNIFELGLLKFPDSTLYKEKYLLFLIRINDEENARALFETSVE-RLEKTQLKRIYDKMIEY 511

                          250       260
                   ....*....|....*....|....*..
gi 2462517970 1902 EKQHGTEKDVQAVKAKALEYVEAKSSV 1928
Cdd:COG5107    512 ESMVGSLNNVYSLEERFRELVPQENLI 538
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 242-584 2.67e-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: 51.58  E-value: 2.67e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  242 EALKPGMLLTGTVSSLEDHGYLVDIGvdGTRAFLPLlkAQEYIRQKNKGAKLkVGQYLNCIVEKV--KGNGGVVSlsvgH 319
Cdd:COG0539     98 EAFENGEPVEGKVKGVVKGGLIVDIG--GVRAFLPA--SQVDVRPVRDLDEY-VGKTLEFKIIKLdrKRNNVVVS----R 168

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  320 SEVSTAIATEQQSWNLNNLLPGLVVKAQVQKVTPFGLTLNFltfftGVVDFMhldpkkagtyfsnqavracilcvhprtr 399
Cdd:COG0539    169 RAVLEEEREEKREELLEKLEEGDVVEGTVKNITDFGAFVDL-----GGVDGL---------------------------- 215

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  400 vVHLSlrpiflqpgrpltrlscqnlgavlDdvpvqgffkkagatfrlkdgvLAYARLSHLSdsknvfnpEAFKPGNTHKC 479
Cdd:COG0539    216 -LHIS------------------------E---------------------ISWGRVKHPS--------EVLKVGDEVEV 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  480 RIIDYSQMDELALLSLRT------SIIEAQYlryhdiEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVppmHLADILM--- 550
Cdd:COG0539    242 KVLKIDREKERISLSLKQlqpdpwENIAEKY------PVGDVVKGKVTRLTDFGAFVELEPGVEGLV---HISEMSWtkr 312

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 2462517970  551 -KNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKT 584
Cdd:COG0539    313 vAHPSDVVKVGDEVEVKVLDIDPEERRISLSIKQL 347
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
438-496 5.00e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 46.06  E-value: 5.00e-06
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970   438 KKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSLR 496
Cdd:smart00316   14 TPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 514-678 5.37e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 50.57  E-value: 5.37e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  514 AVVKGTVLTIKSYGMLVKVgEQMRGLVPPMHLAdilmKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIESKLPVI 593
Cdd:PRK07400   120 ATVRSEVFATNRGGALVRI-EGLRGFIPGSHIS----TRKPKEELVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRL 194

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  594 tcyadaKPGLQTHGFIIRVKDYGCIVKFyNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKlS 673
Cdd:PRK07400   195 ------EVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTK-Q 266


                   ....*
gi 2462517970  674 SDPEP 678
Cdd:PRK07400   267 LEPEP 271
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 786-856 6.44e-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: 45.85  E-value: 6.44e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517970  786 IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTS---DHFVEGQTVAAKVTNVDEEKQRMLLS 856
Cdd:cd05705      1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSlynKYLPEGKLLTAKVLSVNSEKNLVELS 74
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1207-1281 8.75e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 45.29  E-value: 8.75e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970  1207 QAGQTVTCFLKkyNVVKKWLEVEIAPDIRGRIPLllTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTFLCLSL 1281
Cdd:smart00316    1 EVGDVVEGTVT--EITPGGAFVDLGNGVEGLIPI--SELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 140-230 9.51e-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: 9.51e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  140 LCEGMRILGCVKEVNELE-LVISLPNGLQGFVQVTEICDAYTkklneqvtqEQPLKDllhlpelFSPGMLVRCVVSSlgi 218
Cdd:cd05704      1 LEEGAVTLGMVTKVIPHSgLTVQLPFGKTGLVSIFHLSDSYT---------ENPLEG-------FKPGKIVRCCILS--- 61

                           90
                   ....*....|..
gi 2462517970  219 tdRGKKSVKLSL 230
Cdd:cd05704     62 --KKDGKYQLSL 71
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 686-960 1.11e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 49.87  E-value: 1.11e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  686 SQKKGKAINIGQLVDVKVLEKTKDGLEVAVLPHNIRAFLPTSHLS-DHVANGPLLhhwLQAGDILH-RVLCLSQSEGRVL 763
Cdd:PRK06676     8 SLNSVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSnDHIEDINDV---VKVGDELEvYVLKVEDGEGNLL 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  764 LCRKPALVStveggqdpKNFSEI----HPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDhFVeGQTV 839
Cdd:PRK06676    85 LSKRRLEAE--------KAWDKLeekfEEGEVVEVKVTEVVKGGLVVDV-EGVRGFIPASLISTRFVEDFSD-FK-GKTL 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  840 AAKVTNVDEEKQRMLLSLRlsdcglgdlAItsllllnqcLEElqgvrSLMSNRDSVLiQTLAEmtpGMFLDLVVQEVLED 919
Cdd:PRK06676   154 EVKIIELDPEKNRVILSRR---------AV---------VEE-----ERAAKKEELL-SSLKE---GDVVEGTVARLTDF 206

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*
gi 2462517970  920 GSVVFSGGpVPDLV----LKASRYHRAGQEVESGQKKKVVILNVD 960
Cdd:PRK06676   207 GAFVDIGG-VDGLVhiseLSHERVEKPSEVVSVGQEVEVKVLSID 250
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 789-856 1.16e-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: 44.98  E-value: 1.16e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517970  789 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 856
Cdd:cd05707      1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
104-406 1.37e-05

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 49.95  E-value: 1.37e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  104 RKKSQKGPAKTKKLKIEKRESSKSAREKFEilsveslcEGMRILGCVKEVNELELVISLpNGLQGFVQVTEICDAYTKKL 183
Cdd:PRK00087   359 KLEDEDGYVVLSKKEADREKAWKELEEAFE--------NGEPVKGKVKEVVKGGLLVDY-GGVRAFLPASHVELGYVEDL 429

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  184 NEQVTQEQPLKDLlhlpElFSPGMLVRCVVSslgitdrgKKSVKLSLNPKNVNRVLsaEALKPGMLLTGTVSSLEDHGYL 263
Cdd:PRK00087   430 SEYKGQELEVKII----E-FNRKRRKKVVLS--------RKAILEEEKEKKKEETW--NSLEEGDVVEGEVKRLTDFGAF 494

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  264 VDI-GVDGtraflpLLKAQE--YIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSvghsevstaiateqqswnLNNLLP 340
Cdd:PRK00087   495 VDIgGVDG------LLHVSEisWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLS------------------LKKLLP 550

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  341 ------------GLVVKAQVQKVTPFGLtlnFLTFFTGVVDFMHLD---------PKKAgtYFSNQAVRACILCVHPRTR 399
Cdd:PRK00087   551 dpwenveekypvGSIVLGKVVRIAPFGA---FVELEPGVDGLVHISqiswkridkPEDV--LSEGEEVKAKILEVDPEEK 625


                   ....*..
gi 2462517970  400 VVHLSLR 406
Cdd:PRK00087   626 RIRLSIK 632
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1294-1357 1.65e-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: 44.29  E-value: 1.65e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517970 1294 MGRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILSTADNVLTLSL 1357
Cdd:cd00164      2 TGKVVSITKF-GVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISL 64
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 1092-1448 1.75e-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: 49.27  E-value: 1.75e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1092 TLSIGDMVTGTVKSIKPTHVVVTL---EDGIIgciHASHILDDvpegtSPTTKLKVGKTVTARVIGGRDmktfkylpish 1168
Cdd:COG0539     15 ELKEGDIVKGTVVSIDDDEVLVDIgykSEGII---PLSEFSDE-----PGELEVKVGDEVEVYVEKVED----------- 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1169 pRFVRTIpeLSVRPSELEDGhtalnthsvspMEKIKQ-YQAGQTVTCFLKkyNVVKKWLEVEIApDIRGRIP-------- 1239
Cdd:COG0539     76 -GEGEIV--LSKKKADREKA-----------WEELEEaFENGEPVEGKVK--GVVKGGLIVDIG-GVRAFLPasqvdvrp 138

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1240 ------LLLTSLSFKVLKHpDKKFR--VG----------QALRATVVGpdssktflclsltgphKLEEGEVAMGRVVKVT 1301
Cdd:COG0539    139 vrdldeYVGKTLEFKIIKL-DRKRNnvVVsrravleeerEEKREELLE----------------KLEEGDVVEGTVKNIT 201

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1302 pNEGLTVSFPfGKIGTVsifHMSD-SYS--ETPlEDFVpqKV---VRCYILS--TADNVLTLSLrssrtnpetKSKVEDP 1373
Cdd:COG0539    202 -DFGAFVDLG-GVDGLL---HISEiSWGrvKHP-SEVL--KVgdeVEVKVLKidREKERISLSL---------KQLQPDP 264

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970 1374 EINSIQDIKEGQLLRGYVGSIQPHGVFFRLGPSVVGLArysHVSQHSPSKKalyNKH----LPEGKLLTARVLRLNHQK 1448
Cdd:COG0539    265 WENIAEKYPVGDVVKGKVTRLTDFGAFVELEPGVEGLV---HISEMSWTKR---VAHpsdvVKVGDEVEVKVLDIDPEE 337
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
142-230 1.93e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 44.13  E-value: 1.93e-05
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970   142 EGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQvtqeqplkdllhlpelFSPGMLVRCVVSSLgitDR 221
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEV----------------LKVGDEVKVKVLSV---DE 62


                    ....*....
gi 2462517970   222 GKKSVKLSL 230
Cdd:smart00316   63 EKGRIILSL 71
COG4700 COG4700
Uncharacterized conserved protein ECs_4300, contains TPR-like domain [Function unknown];
1742-1898 2.32e-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: 2.32e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1742 ERAVQYNEPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVwIKYGA----FLLRRSQAAASHrvLQRALECLPS 1817
Cdd:COG4700     80 EKALEFADTVQNRVRLADALLELGRYDEAIELYEEALTGIFADDPH-ILLGLaqalFELGRYAEALET--LEKLIAKNPD 156

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1818 KEHVDVIAKFAQ-LEfQLGDAERAKAIFENTLSTYPKRtDVWSVYIDMTIKHGSQKDVRDIFERVIHLSlapKRMKFFFK 1896
Cdd:COG4700    157 FKSSDAHLLYARaLE-ALGDLEAAEAELEALARRYSGP-EARYRYAKFLARQGRTAEAKELLEEILDEA---KHMPKHYR 231


                   ..
gi 2462517970 1897 RY 1898
Cdd:COG4700    232 RL 233
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 509-568 2.85e-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: 45.56  E-value: 2.85e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517970  509 DIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVppmH---LADILMKNPEKKYHIGDEVKCRVL 568
Cdd:COG1098      2 SIEVGDIVEGKVTGITPFGAFVELPEGTTGLV---HiseIADGYVKDINDYLKVGDEVKVKVL 61
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
694-767 4.37e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.36  E-value: 4.37e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970   694 NIGQLVDVKVLEKTKDGLEVAvLPHNIRAFLPTSHLSDHvaNGPLLHHWLQAGDILH-RVLCLSQSEGRVLLCRK 767
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVD-LGNGVEGLIPISELSDK--RVKDPEEVLKVGDEVKvKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
340-406 4.77e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.36  E-value: 4.77e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517970   340 PGLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKAG----TYFSNQAVRACILCVHPRTRVVHLSLR 406
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKdpeeVLKVGDEVKVKVLSVDEEKGRIILSLK 72
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 784-858 4.97e-05

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 48.51  E-value: 4.97e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970  784 SEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDeEKQRMLLSLR 858
Cdd:PRK11824   617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRLSRK 690
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 513-582 5.06e-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: 5.06e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  513 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 582
Cdd:cd05691      1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 1096-1153 5.29e-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: 5.29e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517970 1096 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPegTSPTTKLKVGKTVTARVI 1153
Cdd:cd05697      1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRL--KHPEKKFKPGLKVKCRVL 56
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1382-1457 5.71e-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: 43.09  E-value: 5.71e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517970 1382 KEGQLLRGYVGSIQPHGVFFRL-GPSVVGLArysHVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELSFLP 1457
Cdd:cd05708      1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLC---HKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKA 74
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1653-1780 6.35e-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: 6.35e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1653 EALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisFREEQEklnVWVALLNLENMYG 1732
Cdd:COG4783     12 QALLLAGDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALEL--DPDEPE---ARLNLGLALLKAG 86

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 2462517970 1733 SQESLTKVFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKR 1780
Cdd:COG4783     87 DYDEALALLEKALKLDpEHPEAYLRLARAYRALGRPDEAIAALEKALEL 135
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 607-689 7.12e-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: 44.40  E-value: 7.12e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  607 GFIIRVKDYGCIVKFYNNVQGLVpkH--ELSTEYIPDPERVFYTGQVVKVVVLNCEPSKeRMLLSFK-LSSDPEPKKEPA 683
Cdd:COG1098     11 GKVTGITPFGAFVELPEGTTGLV--HisEIADGYVKDINDYLKVGDEVKVKVLSIDEDG-KISLSIKqAEEKPKRPPRPR 87


                   ....*.
gi 2462517970  684 GHSQKK 689
Cdd:COG1098     88 RNSRPK 93
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 786-861 9.22e-05

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: 43.36  E-value: 9.22e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  786 IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVT-------------------STSDHFVEGQTVAAKVTNV 846
Cdd:cd05693      1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTErleeldeeseeeddeeelpDLEDLFSVGQLVRCKVVSL 80

                           90
                   ....*....|....*...
gi 2462517970  847 DEE---KQRMLLSLRLSD 861
Cdd:cd05693     81 DKSksgKKRIELSLEPEL 98
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 512-577 9.34e-05

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: 9.34e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  512 PGAVVKGTVLTIKSYGMLVKVGeQMRGLVppmHLADIL---MKNPEKKYHIGDEVKCRVLLCDPEAKKL 577
Cdd:cd05688      1 EGDVVEGTVKSITDFGAFVDLG-GVDGLL---HISDMSwgrVKHPSEVVNVGDEVEVKVLKIDKERKRI 65
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1095-1154 9.49e-05

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: 9.49e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1095 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1154
Cdd:pfam00575    3 KGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVE--DPDEVIKVGDEVKVKVLK 60
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 513-568 9.91e-05

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: 9.91e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517970  513 GAVVKGTVLTIKSYGMLVKVGEQMRGLVppmHLADIL-----MKNPEKKYHIGDEVKCRVL 568
Cdd:cd05702      1 GDLVKAKVKSVKPTQLNVQLADNVHGRI---HVSEVFdewpdGKNPLSKFKIGQKIKARVI 58
CpoB COG1729
Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane ...
 1759-1853 1.05e-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: 1.05e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1759 DIYAKSEKFQEAGELYNRMLKRFRQEK---AVWIKYGAFLLRRSQAAASHRVLQRALECLP-SKEHVDVIAKFAQLEFQL 1834
Cdd:COG1729      1 KALLKAGDYDEAIAAFKAFLKRYPNSPlapDALYWLGEAYYALGDYDEAAEAFEKLLKRYPdSPKAPDALLKLGLSYLEL 80

                           90
                   ....*....|....*....
gi 2462517970 1835 GDAERAKAIFENTLSTYPK 1853
Cdd:COG1729     81 GDYDKARATLEELIKKYPD 99
PRK08059 PRK08059
general stress protein 13; Validated
 612-689 1.16e-04

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 43.50  E-value: 1.16e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  612 VKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKLSSD-PEPKKEPAGHSQKK 689
Cdd:PRK08059    18 IQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEaPEAKRKKGKILIPN 96
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 513-577 1.33e-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: 1.33e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  513 GAVVKGTVLTIKSYGMLVKVGEQMRGLVppmHLADI----LMKNPEKKYHIGDEVKCRVLLCDPEAKKL 577
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 ...
 507-567 1.43e-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: 1.43e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517970  507 YHDIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLvppMHLADILMknpekKYHIGDEVKCRV 567
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 ...
 607-673 1.48e-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: 1.48e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517970  607 GFIIRVKDYGCIVKFYN-NVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKLS 673
Cdd:cd05708      8 GTVRRVEDYGVFIDIDGtNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75
Suf pfam05843
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ...
 1787-1929 1.51e-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: 1.51e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1787 VWIKYGAFLlRRSQAAASHR-VLQRALEclpsKEHV--DVIAKFAQLEFQLG-DAERAKAIFENTLSTYPKRTDVWSVYI 1862
Cdd:pfam05843    3 VWIQYMRAM-RRAEGIKGARkVFKKARK----RPRLtyHVYVASALMEYYCSkDPAVAFKIFELGLKLFPEDEEFVLKYL 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517970 1863 DMTIKHGSQKDVRDIFERVIHlSLAPKRM-KFFFKRYLDYEKQHGTEKDVQAVKAKALEYVEAKSSVL 1929
Cdd:pfam05843   78 DYLISLNDDNNARVLFERVLT-RLAQEKEaKPLWKKFISYESTFGDLASILKLEKRMAELFPEDPPLA 144
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 513-575 1.55e-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: 1.55e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517970  513 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAK 575
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 ...
 1096-1154 1.62e-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: 41.87  E-value: 1.62e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970 1096 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1154
Cdd:cd05691      1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVE--DATERFKVGDEVEAKITN 57
rpsA PRK13806
30S ribosomal protein S1; Provisional
 506-858 1.79e-04

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 46.26  E-value: 1.79e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  506 RYHDIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPmhlADILMKNPEKKYHIGDEVKCRVLLCDPEAKKL-------- 577
Cdd:PRK13806    28 RKTELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDR---AELLDADGELTVAVGDEVELYVVSVNGQEIRLskalsgqg 104

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  578 -MMTLKKTLiESKLPVITCYADAKPGlqthGFIIRV--KDYGCivkfynnvqglvPKHELSTEYIPDPERvfYTGQVVKV 654
Cdd:PRK13806   105 gAAMLEEAY-ENGVPVEGKVTGTCKG----GFNVEVlgRRAFC------------PVSQIDLRYVEDPES--YVGQTFQF 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  655 VVLNCEPSKERMLLSFKLSSDPEPKKEPAGHSQKkgkaINIGQLVDVKVLEKTKDGLEVAVLPhNIRAFLPTSHLSDHVA 734
Cdd:PRK13806   166 LITRVEENGRNIVVSRRALLEREQKEALEAFMET----VKEGDVVEGTVTRLAPFGAFVELAP-GVEGMVHISELSWSRV 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  735 NGPllHHWLQAGDILH-RVLCLSQSEG----RVLLCRKPAlvstvegGQDPKNF--SEIHPGMLLIGFVKSIKDYGVFIQ 807
Cdd:PRK13806   241 QKA--DEAVSVGDTVRvKVLGIERAKKgkglRISLSIKQA-------GGDPWDTvgDRLKAGDKVTGKVVRLAPFGAFVE 311

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2462517970  808 FPSGLSGLAPKAIMS-DKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:PRK13806   312 ILPGIEGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLR 363
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
1093-1153 2.10e-04

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 42.77  E-value: 2.10e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970 1093 LSIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHI----LDDVPEgtspttKLKVGKTVTARVI 1153
Cdd:PRK07252     1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIktgfIDNIHQ------LLKVGEEVLVQVV 59
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 513-580 2.29e-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: 2.29e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517970  513 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMT 580
Cdd:cd05707      1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1287-1348 2.30e-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: 42.20  E-value: 2.30e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1287 LEEGEVAMGRVVKVTPNEgLTVSFPFGKIGTVSIFHMSDSYS-----------------ETP-LED-FVPQKVVRCYILS 1347
Cdd:cd05693      1 LSEGMLVLGQVKEITKLD-LVISLPNGLTGYVPITNISDAYTerleeldeeseeeddeeELPdLEDlFSVGQLVRCKVVS 79


                   .
gi 2462517970 1348 T 1348
Cdd:cd05693     80 L 80
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 794-858 2.79e-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: 41.10  E-value: 2.79e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970  794 GFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:cd05691      6 GKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 1665-1816 2.89e-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: 2.89e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1665 ADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTISFREEQEKLNVWVALLNLENMygsQESLtKVFERA 1744
Cdd:COG5010      5 EGFDRLPLYLLLLTKLRTLVEKYEAALAGANNTKEDELAAAGRDKLAKAFAIESPSDNLYNKLGDF---EESL-ALLEQA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517970 1745 VQYNEPL-KVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLP 1816
Cdd:COG5010     81 LQLDPNNpELYYNLALLYSRSGDKDEAKEYYEKALALSPDNPNAYSNLAALLLSLGQDDEAKAALQRALGTSP 153
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1220-1280 2.93e-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: 40.83  E-value: 2.93e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517970 1220 NVVKKWLEVEIAPDIRGRIPLllTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTFLCLS 1280
Cdd:cd00164      7 SITKFGVFVELEDGVEGLVHI--SELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 607-657 2.95e-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: 40.99  E-value: 2.95e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2462517970  607 GFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVL 657
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 ...
 607-669 3.23e-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: 3.23e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517970  607 GFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 669
Cdd:cd05707      6 GFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 246-316 3.35e-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: 40.69  E-value: 3.35e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517970  246 PGMLLTGTVSSLEDHGYLVDIG-VDGtraflpLLKAQE--YIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 316
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 ...
 1096-1154 3.51e-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: 40.73  E-value: 3.51e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970 1096 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDvpEGTSPTTKLKVGKTVTARVIG 1154
Cdd:cd05692      1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHK--RVKDVKDVLKEGDKVKVKVLS 57
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 786-858 3.72e-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: 3.72e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517970  786 IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
Cdd:cd05706      1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1095-1153 4.08e-04

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 45.32  E-value: 4.08e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970 1095 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVI 1153
Cdd:PRK00087   562 VGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRID--KPEDVLSEGEEVKAKIL 618
PTZ00121 PTZ00121
MAEBL; Provisional
 1462-1653 4.46e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 45.52  E-value: 4.46e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1462 KPDVLSASLEgQLTKQEERKTEAEERDQKGEKKNQKRNEKKN----QKGQEEVempsKEKQQPQKPQAQKRGGRECRESG 1537
Cdd:PTZ00121  1379 KADAAKKKAE-EKKKADEAKKKAEEDKKKADELKKAAAAKKKadeaKKKAEEK----KKADEAKKKAEEAKKADEAKKKA 1453

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1538 SEQERVSKKPKKAGLSEEDDSLVDvyYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAwnvglDSLTPAlpplAESS 1617
Cdd:PTZ00121  1454 EEAKKAEEAKKKAEEAKKADEAKK--KAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKA-----DEAKKA----EEAK 1522

                          170       180       190
                   ....*....|....*....|....*....|....*.
gi 2462517970 1618 DSEEDEKPHQAtiKKSKKERELEKQKAEKELSRIEE 1653
Cdd:PTZ00121  1523 KADEAKKAEEA--KKADEAKKAEEKKKADELKKAEE 1556
PRK08582 PRK08582
RNA-binding protein S1;
786-849 5.10e-04

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 42.33  E-value: 5.10e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517970  786 IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEE 849
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 ...
 602-668 5.75e-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: 40.17  E-value: 5.75e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517970  602 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLL 668
Cdd:cd05690      1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 513-577 6.20e-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: 6.20e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517970  513 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKL 577
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 ...
 789-857 6.34e-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: 6.34e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  789 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSL 857
Cdd:cd05697      1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
PTZ00121 PTZ00121
MAEBL; Provisional
 1473-1654 6.41e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 45.13  E-value: 6.41e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1473 QLTKQEERKTEAEERDQKGEKKNQKRNEKKNQKGQEEVEMPSKEKQQPQKPQAQKRGGRECRESGSEQERVSKKPKKAgl 1552
Cdd:PTZ00121  1435 EAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKA-- 1512

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1553 seedDSLVDVYYREGKEEAEETNVLPKEKQTKPAEAPRlqlssgfawnvGLDSLTPAlpplAESSDSEEDEKPHQAtiKK 1632
Cdd:PTZ00121  1513 ----DEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKK-----------KADELKKA----EELKKAEEKKKAEEA--KK 1571

                          170       180
                   ....*....|....*....|..
gi 2462517970 1633 SKKERELEKQKAEkELSRIEEA 1654
Cdd:PTZ00121  1572 AEEDKNMALRKAE-EAKKAEEA 1592
PTZ00121 PTZ00121
MAEBL; Provisional
 1462-1670 6.57e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 45.13  E-value: 6.57e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1462 KPDVLSASLEGQLTKQEERKTEAEERDQKGEKKNQKRNE--KKNQKGQEEVEMPSKEKQQPQKPQAQKRGGRECRESGSE 1539
Cdd:PTZ00121  1634 KVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEdkKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAE 1713

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1540 QERVSKKPKKAglSEEDDSLVDVYYREGKEE---AEETNVLPKEK----QTKPAEAPRLQLSSGFAWNV---GLDSLTPA 1609
Cdd:PTZ00121  1714 EKKKAEELKKA--EEENKIKAEEAKKEAEEDkkkAEEAKKDEEEKkkiaHLKKEEEKKAEEIRKEKEAVieeELDEEDEK 1791

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517970 1610 LPPLAESsdSEEDEKPHQATIKKSKKERELE-KQKAEKELSRIEEALMDPGRQPESADDFDR 1670
Cdd:PTZ00121  1792 RRMEVDK--KIKDIFDNFANIIEGGKEGNLViNDSKEMEDSAIKEVADSKNMQLEEADAFEK 1851
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 230-367 6.92e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 44.10  E-value: 6.92e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  230 LNPKNVNRVLSAEA----------------LKPGMLLTGTVSSLEDHGYLVDIG-VDGtraflpLLKAQE--YIRQKNKG 290
Cdd:PRK06676   160 LDPEKNRVILSRRAvveeeraakkeellssLKEGDVVEGTVARLTDFGAFVDIGgVDG------LVHISElsHERVEKPS 233

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  291 AKLKVGQYLNCIVEKVKGNGGVVSLSVGhsevstaiATEQQSWNL--NNLLPGLVVKAQVQKVTPFGLtlnFLTFFTGV 367
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 ...
 788-858 9.47e-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: 9.47e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517970  788 PGMLLIGFV-KSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVtnVDEEKQRMLLSLR 858
Cdd:cd05704      3 EGAVTLGMVtKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCI--LSKKDGKYQLSLR 72
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 148-229 1.13e-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: 39.29  E-value: 1.13e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  148 GCVKEVNELELVISLPNGLQGFVQVTEICDAYTKklneqvtqeqplkdllHLPELFSPGMLVRCVVSSLgitDRGKKSVK 227
Cdd:cd00164      3 GKVVSITKFGVFVELEDGVEGLVHISELSDKFVK----------------DPSEVFKVGDEVEVKVLEV---DPEKGRIS 63


                   ..
gi 2462517970  228 LS 229
Cdd:cd00164     64 LS 65
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 600-858 1.13e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 43.93  E-value: 1.13e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  600 KPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTeyipdPERvfyTGQVVKVVVLNCEPSKERMllsFKLSSDPEPK 679
Cdd:PRK12269   320 EPGSVRMGTVVQVNAGTVFVDIGGKSEGRVPVEEFEA-----PPK---AGDGVRVYVERVTPYGPEL---SKTKADRLGL 388

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  680 KEPAGHSQKKGKAINiGQLVDvkvLEKTKDGLEVAvLPHNIRAFLPTSHLSDHVANGPLLHHWLQAGDILHRVLCLSQSE 759
Cdd:PRK12269   389 KVKLRDAERDGTPVE-GRIVR---LTEKKSGFEVD-LGAGMMAFLPISQSDCQKVDAPESLIGLTSKFYIERISQSKQHR 463

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  760 GR--VLLCRKPALVSTVEGGQDpKNFSEIHPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQ 837
Cdd:PRK12269   464 GNdnIVINRRRYLEERARQARE-EFFNSVHIEDSVSGVVKSFTSFGAFIDL-GGFDGLLHVNDMSWGHVARPREFVKKGQ 541

                          250       260
                   ....*....|....*....|.
gi 2462517970  838 TVAAKVTNVDEEKQRMLLSLR 858
Cdd:PRK12269   542 TIELKVIRLDQAEKRINLSLK 562
rpsA PRK13806
30S ribosomal protein S1; Provisional
 1228-1410 1.20e-03

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 43.56  E-value: 1.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1228 VEIAPDIRGRIPLllTSLSFKVLKHPDKKFRVGQALRATVVGPDSSK----TFLCLSL---------TGPHKLEEGEVAM 1294
Cdd:PRK13806   220 VELAPGVEGMVHI--SELSWSRVQKADEAVSVGDTVRVKVLGIERAKkgkgLRISLSIkqaggdpwdTVGDRLKAGDKVT 297

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1295 GRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFV-PQKVVRCYI--LSTADNVLTLSLRSSRTnpetkskve 1371
Cdd:PRK13806   298 GKVVRLAPF-GAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVaPGDAVAVKIkdIDPAKRRISLSLRDAEG--------- 367

                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 2462517970 1372 DPEINSIQDIKEGQLLRGYVGSIQPHGVFFRLGPSVVGL 1410
Cdd:PRK13806   368 DPWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGL 406
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 250-316 1.26e-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: 1.26e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517970  250 LTGTVSSLEDHGYLVDIGvDGTRAFLPLLKAQEYiRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 316
Cdd:cd00164      1 VTGKVVSITKFGVFVELE-DGVEGLVHISELSDK-FVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1559-1853 1.40e-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: 1.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1559 LVDVYYREGKEEaEETNVLPKEKQTKPAE-APRLQLSSGFawnVGLDSLTPALPPLAESSDseedekphqatIKKSKKER 1637
Cdd:TIGR02917  539 LAGLYLRTGNEE-EAVAWLEKAAELNPQEiEPALALAQYY---LGKGQLKKALAILNEAAD-----------AAPDSPEA 603

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1638 ELEKQKAEKELSRIEEALmdpgrqpesaDDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALktisfreeQEK 1717
Cdd:TIGR02917  604 WLMLGRAQLAAGDLNKAV----------SSFKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRAL--------ELK 665

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1718 LNVWVALL---NLENMYGSQESLTKVFeRAVQYNEPLKVFLH--LADIYAKSEKFQEAGELYNRMLKRFRQEKAVwIKYG 1792
Cdd:TIGR02917  666 PDNTEAQIglaQLLLAAKRTESAKKIA-KSLQKQHPKAALGFelEGDLYLRQKDYPAAIQAYRKALKRAPSSQNA-IKLH 743

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517970 1793 AFLLRRSQAAASHRVLQRALeclpsKEHV-DVIAKFAQLEFQLGDAERAKAI--FENTLSTYPK 1853
Cdd:TIGR02917  744 RALLASGNTAEAVKTLEAWL-----KTHPnDAVLRTALAELYLAQKDYDKAIkhYQTVVKKAPD 802
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 1755-1885 1.43e-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: 1.43e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1755 LHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQL 1834
Cdd:COG5010     24 VEKYEAALAGANNTKEDELAAAGRDKLAKAFAIESPSDNLYNKLGDFEESLALLEQALQLDP--NNPELYYNLALLYSRS 101

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2462517970 1835 GDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVIHLS 1885
Cdd:COG5010    102 GDKDEAKEYYEKALALSPDNPNAYSNLAALLLSLGQDDEAKAALQRALGTS 152
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1654-1842 1.46e-03

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 42.30  E-value: 1.46e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1654 ALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisfreeqeKLNVWVALLNLENMYGS 1733
Cdd:COG0457     51 AYLRLGRYEEALADYEQALELDPDDAEALNNLGLALQALGRYEEALEDYDKALEL--------DPDDAEALYNLGLALLE 122

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1734 QESLTK---VFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNrmlKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQ 1809
Cdd:COG0457    123 LGRYDEaieAYERALELDpDDADALYNLGIALEKLGRYEEALELLE---KLEAAALAALLAAALGEAALALAAAEVLLAL 199

                          170       180       190
                   ....*....|....*....|....*....|...
gi 2462517970 1810 RALECLPSKEHVDVIAKFAQLEFQLGDAERAKA 1842
Cdd:COG0457    200 LLALEQALRKKLAILTLAALAELLLLALALLLA 232
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 150-194 1.68e-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: 1.68e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2462517970  150 VKEVNELELVISLPNGLQGFVQVTEICDAYTkklneqvTQEQPLK 194
Cdd:cd05702      8 VKSVKPTQLNVQLADNVHGRIHVSEVFDEWP-------DGKNPLS 45
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 696-767 2.20e-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: 2.20e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517970  696 GQLVDVKVLEKTKDGLEVAVlpHNIRAFLPTSHLSD-HVAN-GPLLHHWLQAgdilhRVLCLSQSEGRVLLCRK 767
Cdd:cd04465      1 GEIVEGKVTEKVKGGLIVDI--EGVRAFLPASQVDLrPVEDlDEYVGKELKF-----KIIEIDRERNNIVLSRR 67
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 503-583 2.24e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 42.72  E-value: 2.24e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  503 QYLRYHDIepGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 582
Cdd:PRK07899   286 QFARTHAI--GQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLK 363


                   .
gi 2462517970  583 K 583
Cdd:PRK07899   364 Q 364
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1092-1454 2.41e-03

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 42.63  E-value: 2.41e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1092 TLSIGDMVTGTVKSIKPTHVVVTL---EDGIIGCIHASHilddvPEGTSPTTKLKVGKTVTARVIGGRDmktfkylpish 1168
Cdd:PRK00087   299 QIRRGDIVKGTVVSVNENEVFVDVgykSEGVIPLRELTL-----DEISSLKESVKVGDEIEVKVLKLED----------- 362

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1169 prfvrtipelsvrpselEDGHTALN---THSVSPMEKIKQ-YQAGQTVTCFLKKynVVKKWLEVEIApDIRGRIPLLLTS 1244
Cdd:PRK00087   363 -----------------EDGYVVLSkkeADREKAWKELEEaFENGEPVKGKVKE--VVKGGLLVDYG-GVRAFLPASHVE 422

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1245 LSFKvlkhPDKKFRVGQALRATVVGPD---------SSKTFLCLSLTGPHK-----LEEGEVAMGRVVKVTPNeGLtvsf 1310
Cdd:PRK00087   423 LGYV----EDLSEYKGQELEVKIIEFNrkrrkkvvlSRKAILEEEKEKKKEetwnsLEEGDVVEGEVKRLTDF-GA---- 493

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1311 pFGKIGTVS-IFHMSD---SYSETPLEDFVPQKVVRCYILSTADNVLTLSLrsSRtnpetKSKVEDPEINSIQDIKEGQL 1386
Cdd:PRK00087   494 -FVDIGGVDgLLHVSEiswGRVEKPSDVLKVGDEIKVYILDIDKENKKLSL--SL-----KKLLPDPWENVEEKYPVGSI 565

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517970 1387 LRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQH---SPSKKalynkhLPEGKLLTARVLRLNHQKNLVELS 1454
Cdd:PRK00087   566 VLGKVVRIAPFGAFVELEPGVDGLVHISQISWKridKPEDV------LSEGEEVKAKILEVDPEEKRIRLS 630
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
1689-1780 2.44e-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: 2.44e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1689 HLQATEIEKARAVAERALKTisfreeqeKLNVWVALLNLENMYGSQESltkvFERAVQYNEPLK-------VFLHLADIY 1761
Cdd:COG3063      2 YLKLGDLEEAEEYYEKALEL--------DPDNADALNNLGLLLLEQGR----YDEAIALEKALKldpnnaeALLNLAELL 69

                           90
                   ....*....|....*....
gi 2462517970 1762 AKSEKFQEAGELYNRMLKR 1780
Cdd:COG3063     70 LELGDYDEALAYLERALEL 88
PTZ00121 PTZ00121
MAEBL; Provisional
 1476-1785 2.77e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 42.82  E-value: 2.77e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1476 KQEERKTEAEERDQKGE--KKNQKRNEKKNQKGQEEVEMPSKEKQQPQKPQAQKRGGRECRESGSEQERVSKKPKKAglS 1553
Cdd:PTZ00121  1323 KAEEAKKKADAAKKKAEeaKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKK--A 1400

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1554 EEDDSLVDVYYR--EGKEEAEETNVLPKEK------QTKPAEAPRLQLSSGFAWNVgldSLTPALPPLAESSDSEEDEKP 1625
Cdd:PTZ00121  1401 EEDKKKADELKKaaAAKKKADEAKKKAEEKkkadeaKKKAEEAKKADEAKKKAEEA---KKAEEAKKKAEEAKKADEAKK 1477

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1626 HQATIKKS---KKERELEKQKAEkELSRIEEA--LMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARA 1700
Cdd:PTZ00121  1478 KAEEAKKAdeaKKKAEEAKKKAD-EAKKAAEAkkKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEE 1556

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1701 V--AERALKTISFREEQEKlnvwvallnlENMYGSQESLTKVFERAvQYNEPLKVFLHLADIYAKSEKFQEAGELYNRML 1778
Cdd:PTZ00121  1557 LkkAEEKKKAEEAKKAEED----------KNMALRKAEEAKKAEEA-RIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEEL 1625


                   ....*..
gi 2462517970 1779 KRFRQEK 1785
Cdd:PTZ00121  1626 KKAEEEK 1632
rpsA PRK13806
30S ribosomal protein S1; Provisional
 126-366 2.78e-03

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 42.40  E-value: 2.78e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  126 KSAREKFeilsVESLCEGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQVtqeqplkdllhlpelfSP 205
Cdd:PRK13806   190 KEALEAF----METVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAV----------------SV 249

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  206 GMLVRcvVSSLGITDRGK-KSVKLSLNPKNV-----NRVlsAEALKPGMLLTGTVSSLEDHGYLVDI--GVDGtrafLPL 277
Cdd:PRK13806   250 GDTVR--VKVLGIERAKKgKGLRISLSIKQAggdpwDTV--GDRLKAGDKVTGKVVRLAPFGAFVEIlpGIEG----LVH 321

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  278 LKAQEYIRQKNK-GAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEVSTAIATEQQswnlnnLLPGLVVKAQVQKVTPFGL 356
Cdd:PRK13806   322 VSEMSWTRRVNKpEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAER------FAPGTTVTGTVEKRAQFGL 395

                          250
                   ....*....|
gi 2462517970  357 TLNFLTFFTG 366
Cdd:PRK13806   396 FVNLAPGVTG 405
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 602-668 3.24e-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: 3.24e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517970  602 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLL 668
Cdd:cd05689      4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDwTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISL 71
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1808-1889 3.32e-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: 3.32e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1808 LQRALECLPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLA 1887
Cdd:COG4235      6 LRQALAANP--NDAEGWLLLGRAYLRLGRYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEELLERA--LALD 81


                   ..
gi 2462517970 1888 PK 1889
Cdd:COG4235     82 PD 83
PRK08582 PRK08582
RNA-binding protein S1;
510-568 3.51e-03

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 39.63  E-value: 3.51e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  510 IEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVL 568
Cdd:PRK08582     3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVL 61
DUF612 pfam04747
Protein of unknown function, DUF612; This family includes several uncharacterized proteins ...
 1459-1658 3.96e-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: 3.96e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1459 DTGKPDVLSASLEGQLTKQEERKTEAEERDQKGEKKNQKRNEKKNQKGQEEVEMPSKEKQQPQKPQAQkrggRECRESGS 1538
Cdd:pfam04747   49 DQRKEAFASLELTEQPQQVEKVKKSEKKKAQKQIAKDHEAEQKVNAKKAAEKEARRAEAEAKKRAAQE----EEHKQWKA 124

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1539 EQERVSKKPKKaglseEDDSLVDVYYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAWNVGLD-SLTPA-LPPLAES 1616
Cdd:pfam04747  125 EQERIQKEQEK-----KEADLKKLQAEKKKEKAVKAEKAEKAEKTKKASTPAPVEEEIVVKKVANDrSAAPApEPKTPTN 199

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 2462517970 1617 SDSEEDEKPHQATIKKSKKERELEKQKAEKELSRIEEALMDP 1658
Cdd:pfam04747  200 TPAEPAEQVQEITGKKNKKNKKKSESEATAAPASVEQVVEQP 241
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1631-1853 4.61e-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: 4.61e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1631 KKSKKERELEKQ--------KAEKELSRIEealMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVA 1702
Cdd:TIGR02917  480 DLAKAREAFEKAlsiepdffPAAANLARID---IQEGNPDDAIQRFEKVLTIDPKNLRAILALAGLYLRTGNEEEAVAWL 556

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1703 ERALKTISfREEQEKLNVWVALLNLENMygsQESLTKVFERAVQYNEPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFR 1782
Cdd:TIGR02917  557 EKAAELNP-QEIEPALALAQYYLGKGQL---KKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQP 632

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517970 1783 QEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPK 1853
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 ...
 1384-1454 4.78e-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: 4.78e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517970 1384 GQLLRGYVGSIQPHGVFFRLGPSVVGLARyshVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1454
Cdd:cd05707      1 GDVVRGFVKNIANNGVFVTLGRGVDARVR---VSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1669-1852 5.74e-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: 5.74e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1669 DRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisfreEQEKLNvwvALLNLENMYGSQESL---TKVFERAV 1745
Cdd:TIGR02917  455 KKLEKKQPDNASLHNLLGAIYLGKGDLAKAREAFEKALSI-----EPDFFP---AAANLARIDIQEGNPddaIQRFEKVL 526

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1746 QYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLP-SKEHVDV 1823
Cdd:TIGR02917  527 TIDpKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAADAAPdSPEAWLM 606

                          170       180
                   ....*....|....*....|....*....
gi 2462517970 1824 IAKfAQLefQLGDAERAKAIFENTLSTYP 1852
Cdd:TIGR02917  607 LGR-AQL--AAGDLNKAVSSFKKLLALQP 632
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 1636-1893 5.83e-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: 5.83e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1636 ERELEKQKAEKELSRIEEALMDPGRQPESADDFDRLVLSSPNSSILWLqYMAFHLQATE-IEKARAVAERALKtisfree 1714
Cdd:COG3914     69 AAAAALLLLAALLELAALLLQALGRYEEALALYRRALALNPDNAEALF-NLGNLLLALGrLEEALAALRRALA------- 140

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1715 qeklnvwvalLNLENmygsqesltkvferavqynepLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAF 1794
Cdd:COG3914    141 ----------LNPDF---------------------AEAYLNLGEALRRLGRLEEAIAALRRALELDPDNAEALNNLGNA 189

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1795 LLRRSQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQLGDAERAkAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDV 1874
Cdd:COG3914    190 LQDLGRLEEAIAAYRRALELDP--DNADAHSNLLFALRQACDWEVY-DRFEELLAALARGPSELSPFALLYLPDDDPAEL 266

                          250       260
                   ....*....|....*....|..
gi 2462517970 1875 RDI---FERVIHLSLAPKRMKF 1893
Cdd:COG3914    267 LALaraWAQLVAAAAAPELPPP 288
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 1286-1357 6.33e-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: 6.33e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517970 1286 KLEEGEVAMGRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILS--TADNVLTLSL 1357
Cdd:cd04461     11 DLKPGMVVHGYVRNITPY-GVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSvdEEKQRFLLSL 83
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 720-856 6.40e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 40.94  E-value: 6.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970  720 IRAFLPTSHLSDHVANGPLLHHWLQAgdilhRVLCLSQSEGRVLLCRKPALVStveggqdpKNFSEIHPGMLLIGFVKSI 799
Cdd:PRK07400   141 LRGFIPGSHISTRKPKEELVGEELPL-----KFLEVDEERNRLVLSHRRALVE--------RKMNRLEVGEVVVGTVRGI 207

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517970  800 KDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 856
Cdd:PRK07400   208 KPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLS 263
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1739-1826 7.21e-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: 38.45  E-value: 7.21e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517970 1739 KVFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPS 1817
Cdd:COG4235     38 AAYEKALRLDpDNADALLDLAEALLAAGDTEEAEELLERALALDPDNPEALYLLGLAAFQQGDYAEAIAAWQKLLALLPA 117


                   ....*....
gi 2462517970 1818 KEHVDVIAK 1826
Cdd:COG4235    118 DAPARLLEA 126
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
792-858 7.40e-03

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 38.53  E-value: 7.40e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517970  792 LIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 858
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 ...
 1093-1153 8.33e-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: 8.33e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517970 1093 LSIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPegTSPTTKLKVGKTVTARVI 1153
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 ...
 601-669 8.42e-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: 36.84  E-value: 8.42e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517970  601 PGLQTHGFIIRVKDYGCIVKFyNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 669
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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