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Conserved domains on  [gi|767962239|ref|XP_011537842|]
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protein RRP5 homolog isoform X3 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S1_Rrp5_repeat_hs7 cd05699
S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 553-624 1.21e-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: 1.21e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767962239  553 GQLVDVKVLEKTKDGLEVAVLPHNIRAFLPTSHLSDHVANGPLLHHWLQAGDILHRVLCLSQSEGRVLLCRK 624
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 ...
 632-714 3.73e-38

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


:

Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 137.72  E-value: 3.73e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  632 EGGQDPKNFSEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRML 711
Cdd:cd04461     1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                  ...
gi 767962239  712 LSL 714
Cdd:cd04461    81 LSL 83
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1-93 3.98e-37

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: 135.42  E-value: 3.98e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239    1 MRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQVTQEQ---PLKDLLHLPELFSPGMLVRCVVSSLGITD 77
Cdd:cd05693     5 MLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEeedDEEELPDLEDLFSVGQLVRCKVVSLDKSK 84

                          90
                  ....*....|....*.
gi 767962239   78 RGKKSVKLSLNPKNVN 93
Cdd:cd05693    85 SGKKRIELSLEPELVN 100
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1238-1311 4.50e-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: 4.50e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767962239 1238 IKEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1311
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 ...
 1144-1215 1.90e-35

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


:

Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 129.39  E-value: 1.90e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767962239 1144 LEEGEVAMGRVVKVTPNEGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILSTADNVLTLSLR 1215
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 ...
 459-528 3.64e-35

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


:

Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 128.50  E-value: 3.64e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  459 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 528
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 ...
 842-910 4.02e-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: 4.02e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  842 GSEHQAIVQHLEKSFAIASLVETGHLAAFSLTSHLNDTFRFDSEKLQVGQGVSLTLKTTEPGVTGLLLA 910
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 ...
 370-438 5.23e-31

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


:

Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 116.95  E-value: 5.23e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  370 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTL 438
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 ...
 953-1022 8.37e-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: 8.37e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  953 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEGTSPTTKLKVGKTVTARVIGGRDMKTFKYLP 1022
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 ...
 100-180 3.36e-28

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


:

Pssm-ID: 240199 [Multi-domain]  Cd Length: 74  Bit Score: 108.88  E-value: 3.36e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  100 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYirqknkgAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEV 179
Cdd:cd05694     1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73


                  .
gi 767962239  180 S 180
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 ...
 282-352 8.80e-28

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


:

Pssm-ID: 240201 [Multi-domain]  Cd Length: 71  Bit Score: 107.73  E-value: 8.80e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767962239  282 GAVLDDVPVQGFFKKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSL 352
Cdd:cd05696     1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 763-827 1.49e-27

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


The actual alignment was detected with superfamily member cd05700:

Pssm-ID: 471952  Cd Length: 65  Bit Score: 106.86  E-value: 1.49e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239  763 GMFLDLVVQEVLEDGSVVFSGGPVPDLVLKASRYHRAGQEVESGQKKKVVILNVDLLKLEVHVSL 827
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 ...
 1066-1140 6.56e-26

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


:

Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 102.27  E-value: 6.56e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239 1066 GQTVTCFLKKYNVVKKWLEveIAPDIRGRIPLLLTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTLLCLSLTG 1140
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 ...
 198-261 1.11e-25

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


:

Pssm-ID: 240200 [Multi-domain]  Cd Length: 66  Bit Score: 101.58  E-value: 1.11e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767962239  198 GLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKA--GTYFSNQAVRACILCVHPRTRVVHLS 261
Cdd:cd05695     1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSskSTYKEGQKVRARILYVDPSTKVVGLS 66
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1518-1778 6.61e-17

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


:

Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 82.85  E-value: 6.61e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1518 RQPESA-DDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfREEQEKLnvwvALLNLENMYGSQESLT 1596
Cdd:COG2956    22 GQPDKAiDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYLKAGLLD 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1597 K---VFERAVQYNEP-LKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEC 1672
Cdd:COG2956    94 RaeeLLEKLLELDPDdAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1673 LPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLAPKRMKFF 1752
Cdd:COG2956   174 DP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA--LELDPSDDLLL 249

                         250       260
                  ....*....|....*....|....*.
gi 767962239 1753 FKRYLdYEKQHGTEKdVQAVKAKALE 1778
Cdd:COG2956   250 ALADL-LERKEGLEA-ALALLERQLR 273
PTZ00121 super family cl31754
MAEBL; Provisional
 1319-1610 6.39e-05

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 48.21  E-value: 6.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1319 KPDVLSASLEgQLTKQEERKTEAEERDQKGEKKNQKRNEKKN----QKGQEEVempsKEKQQPQKPQAQKRGGRECRESG 1394
Cdd:PTZ00121 1379 KADAAKKKAE-EKKKADEAKKKAEEDKKKADELKKAAAAKKKadeaKKKAEEK----KKADEAKKKAEEAKKADEAKKKA 1453

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1395 SEQERVSKKPKKAGLSEEDDSLVDvyYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAwnvglDSLTPA-------- 1466
Cdd:PTZ00121 1454 EEAKKAEEAKKKAEEAKKADEAKK--KAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKA-----DEAKKAeeakkade 1526

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1467 LPPLAESSDSEEDEKPHQ---ATQIKKSKKERELEKQKAEKELSRIEEALMDPGRQPESADDFDRLVLSSPNSSILWLQY 1543
Cdd:PTZ00121 1527 AKKAEEAKKADEAKKAEEkkkADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKK 1606

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767962239 1544 MAFHlQATEIEKARAVAERALKtisfrEEQEKLNVWVALLNLENMYGSQESLTKVFERAVQYNEPLK 1610
Cdd:PTZ00121 1607 MKAE-EAKKAEEAKIKAEELKK-----AEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEA 1667
 
Name Accession Description Interval E-value
S1_Rrp5_repeat_hs7 cd05699
S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 553-624 1.21e-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: 1.21e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767962239  553 GQLVDVKVLEKTKDGLEVAVLPHNIRAFLPTSHLSDHVANGPLLHHWLQAGDILHRVLCLSQSEGRVLLCRK 624
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 ...
 632-714 3.73e-38

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


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 137.72  E-value: 3.73e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  632 EGGQDPKNFSEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRML 711
Cdd:cd04461     1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                  ...
gi 767962239  712 LSL 714
Cdd:cd04461    81 LSL 83
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1-93 3.98e-37

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: 135.42  E-value: 3.98e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239    1 MRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQVTQEQ---PLKDLLHLPELFSPGMLVRCVVSSLGITD 77
Cdd:cd05693     5 MLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEeedDEEELPDLEDLFSVGQLVRCKVVSLDKSK 84

                          90
                  ....*....|....*.
gi 767962239   78 RGKKSVKLSLNPKNVN 93
Cdd:cd05693    85 SGKKRIELSLEPELVN 100
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1238-1311 4.50e-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: 4.50e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767962239 1238 IKEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1311
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 ...
 1144-1215 1.90e-35

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


Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 129.39  E-value: 1.90e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767962239 1144 LEEGEVAMGRVVKVTPNEGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILSTADNVLTLSLR 1215
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 ...
 459-528 3.64e-35

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


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 128.50  E-value: 3.64e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  459 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 528
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 ...
 842-910 4.02e-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: 4.02e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  842 GSEHQAIVQHLEKSFAIASLVETGHLAAFSLTSHLNDTFRFDSEKLQVGQGVSLTLKTTEPGVTGLLLA 910
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 ...
 370-438 5.23e-31

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


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 116.95  E-value: 5.23e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  370 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTL 438
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 ...
 953-1022 8.37e-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: 8.37e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  953 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEGTSPTTKLKVGKTVTARVIGGRDMKTFKYLP 1022
Cdd:cd05702     1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 281-715 2.86e-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: 124.46  E-value: 2.86e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   281 LGAVLDDVPVQG-FFKKAGATFRLK-DGVLAYARLSHlSDSKNVFNPEAFKpGNTHKCRIIDYSQMDELALLSlRTSIIE 358
Cdd:TIGR00717   95 EKAYEEGSIVEGkIVGKVKGGFIVDlNGVEAFLPGSQ-VDVKPIKDLDSLI-GKTLKFKIIKLDQKRNNIVVS-RRAYLE 171

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   359 AQYLRYHD-----IEPGAVVKGTVLTIKSYGMLVKVGeQMRGLVppmHLADIL---MKNPEKKYHIGDEVKCRVLLCDPE 430
Cdd:TIGR00717  172 EERSQAREellenLKEGDVVKGVVKNITDFGAFVDLG-GVDGLL---HITDMSwkrVKHPSEYVKVGQEVKVKVIKFDKE 247

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   431 AKKLMMTLKKTL------IESKLPvitcyadakPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVF 503
Cdd:TIGR00717  248 KGRISLSLKQLGedpweaIEKKFP---------VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVV 318

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   504 YTGQVVKVVVLNCEPSKERMLLSFKlSSDPEP-----KKEPAGhSQKKGKAINIGQLVDVKVLEKTKDGLevavlphnir 578
Cdd:TIGR00717  319 KKGDEVEVMILDIDPERRRLSLGLK-QCKANPweqfeEKHPVG-DRVTGKIKKITDFGAFVELEGGIDGL---------- 386

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   579 aflptSHLSD--HVANGPLLHHWLQAGDILHR-VLCLSQSEGRVLLCRKPALVSTVEggqdpkNFSEIHP-GMLLIGFVK 654
Cdd:TIGR00717  387 -----IHLSDisWDKDGREADHLYKKGDEIEAvVLAVDKEKKRISLGVKQLTENPWE------KFAAKYKvGSVVKGKVT 455

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767962239   655 SIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
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 ...
 100-180 3.36e-28

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


Pssm-ID: 240199 [Multi-domain]  Cd Length: 74  Bit Score: 108.88  E-value: 3.36e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  100 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYirqknkgAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEV 179
Cdd:cd05694     1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73


                  .
gi 767962239  180 S 180
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 ...
 282-352 8.80e-28

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


Pssm-ID: 240201 [Multi-domain]  Cd Length: 71  Bit Score: 107.73  E-value: 8.80e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767962239  282 GAVLDDVPVQGFFKKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSL 352
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 ...
 763-827 1.49e-27

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


Pssm-ID: 240205  Cd Length: 65  Bit Score: 106.86  E-value: 1.49e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239  763 GMFLDLVVQEVLEDGSVVFSGGPVPDLVLKASRYHRAGQEVESGQKKKVVILNVDLLKLEVHVSL 827
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 ...
 1066-1140 6.56e-26

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


Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 102.27  E-value: 6.56e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239 1066 GQTVTCFLKKYNVVKKWLEveIAPDIRGRIPLLLTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTLLCLSLTG 1140
Cdd:cd05703     1 GQEVTGFVNNVSKEFVWLT--ISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 367-715 9.48e-26

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 114.11  E-value: 9.48e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  367 IEPGAVVKGTVLTIKSYGMLVKVGeQMRGLVppmHLADILMK---NPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL- 442
Cdd:PRK06299  199 LEEGQVVEGVVKNITDYGAFVDLG-GVDGLL---HITDISWKrvnHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGe 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  443 -----IESKLPVitcyadakpglqthGFIIRVK-----DYGCIVKFYNNVQGLVpkH--ELS-TEYIPDPERVFYTGQVV 509
Cdd:PRK06299  275 dpweaIEKKYPV--------------GSKVKGKvtnitDYGAFVELEEGIEGLV--HvsEMSwTKKNKHPSKVVSVGQEV 338

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  510 KVVVLNCEPSKERMLLSFK-LSSDPE---PKKEPAGhSQKKGKAINIgqlvdvkvlekTKDGLEVAvLPHNIRAFLptsH 585
Cdd:PRK06299  339 EVMVLEIDEEKRRISLGLKqCKENPWeefAEKYPVG-DVVEGKVKNI-----------TDFGAFVG-LEGGIDGLV---H 402

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  586 LSD--HVANG--PLLHhwLQAGDILH-RVLCLSQSEGRVLLCRKPALvstveggQDP-KNFSEIHP-GMLLIGFVKSIKD 658
Cdd:PRK06299  403 LSDisWDKKGeeAVEL--YKKGDEVEaVVLKVDVEKERISLGIKQLE-------EDPfEEFAKKHKkGSIVTGTVTEVKD 473

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767962239  659 YGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
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 ...
 198-261 1.11e-25

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


Pssm-ID: 240200 [Multi-domain]  Cd Length: 66  Bit Score: 101.58  E-value: 1.11e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767962239  198 GLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKA--GTYFSNQAVRACILCVHPRTRVVHLS 261
Cdd:cd05695     1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSskSTYKEGQKVRARILYVDPSTKVVGLS 66
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 97-528 1.94e-22

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 100.89  E-value: 1.94e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   97 SAEALKPGMLLTGTVSSLEDHGYLVDIG--VDGtraFLPLlkaqEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSv 174
Cdd:COG0539    12 SLKELKEGDIVKGTVVSIDDDEVLVDIGykSEG---IIPL----SEFSDEPGELEVKVGDEVEVYVEKVEDGEGEIVLS- 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  175 ghsevsTAIATEQQSWN-----LNNllpGLVVKAQVQKVTPFGLTlnfltfftgvVDFMHldpkkagtyfsnqaVRAcil 249
Cdd:COG0539    84 ------KKKADREKAWEeleeaFEN---GEPVEGKVKGVVKGGLI----------VDIGG--------------VRA--- 127

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  250 cvhprtrvvhlslrpiFLqPGrpltrlscqnlgavlddvpvqgffkkagatfrlkdgvlayarlSHLsDSKNVFNPEAFK 329
Cdd:COG0539   128 ----------------FL-PA-------------------------------------------SQV-DVRPVRDLDEYV 146

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  330 pGNTHKCRIIDYSQMDELALLSlRTSIIEAQYLR-----YHDIEPGAVVKGTVLTIKSYGMLVKVGEqMRGLVppmHLAD 404
Cdd:COG0539   147 -GKTLEFKIIKLDRKRNNVVVS-RRAVLEEEREEkreelLEKLEEGDVVEGTVKNITDFGAFVDLGG-VDGLL---HISE 220

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  405 IL---MKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL------IESKLPVitcyadakpGLQTHGFIIRVKDYGCI 475
Cdd:COG0539   221 ISwgrVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQLQpdpwenIAEKYPV---------GDVVKGKVTRLTDFGAF 291

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....
gi 767962239  476 VKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 528
Cdd:COG0539   292 VELEPGVEGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1518-1778 6.61e-17

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 82.85  E-value: 6.61e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1518 RQPESA-DDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfREEQEKLnvwvALLNLENMYGSQESLT 1596
Cdd:COG2956    22 GQPDKAiDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYLKAGLLD 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1597 K---VFERAVQYNEP-LKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEC 1672
Cdd:COG2956    94 RaeeLLEKLLELDPDdAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1673 LPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLAPKRMKFF 1752
Cdd:COG2956   174 DP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA--LELDPSDDLLL 249

                         250       260
                  ....*....|....*....|....*.
gi 767962239 1753 FKRYLdYEKQHGTEKdVQAVKAKALE 1778
Cdd:COG2956   250 ALADL-LERKEGLEA-ALALLERQLR 273
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
368-439 4.27e-16

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 74.56  E-value: 4.27e-16
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767962239    368 EPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 439
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
645-715 3.28e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 71.87  E-value: 3.28e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767962239    645 PGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
457-528 5.03e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 71.48  E-value: 5.03e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767962239    457 KPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 528
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
952-1011 8.23e-11

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 59.54  E-value: 8.23e-11
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239    952 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1011
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 ...
 464-526 9.76e-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: 9.76e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767962239   464 GFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 526
Cdd:pfam00575    9 GEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILS 71
PRK08059 PRK08059
general stress protein 13; Validated
 367-441 1.25e-09

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 57.75  E-value: 1.25e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239  367 IEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKT 441
Cdd:PRK08059    5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRAT 79
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1145-1215 1.87e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 52.61  E-value: 1.87e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767962239   1145 EEGEVAMGRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILS--TADNVLTLSLR 1215
Cdd:smart00316    1 EVGDVVEGTVTEITPG-GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSvdEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1239-1312 4.09e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 51.84  E-value: 4.09e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767962239   1239 KEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKalyNKHLPEGKLLTARVLRLNHQKNLVELSF 1312
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 ...
 368-434 1.27e-07

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 50.36  E-value: 1.27e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767962239   368 EPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKL 434
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 ...
 646-714 2.60e-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: 2.60e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239   646 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSL 714
Cdd:pfam00575    4 GDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 645-715 3.36e-07

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 53.67  E-value: 3.36e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767962239  645 PGMLLIGFVKSIKDYGVFI---QFPsGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
Cdd:PRK03987    8 EGELVVGTVKEVKDFGAFVtldEYP-GKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
102-173 1.40e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.60  E-value: 1.40e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767962239    102 KPGMLLTGTVSSLEDHGYLVDIGvDGTRAFLPLLKAQEYiRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 173
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLG-NGVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
295-353 5.63e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 45.67  E-value: 5.63e-06
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239    295 KKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSLR 353
Cdd:smart00316   14 TPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1064-1138 2.24e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 44.13  E-value: 2.24e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239   1064 QAGQTVTCFLKkyNVVKKWLEVEIAPDIRGRIPLllTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTLLCLSL 1138
Cdd:smart00316    1 EVGDVVEGTVT--EITPGGAFVDLGNGVEGLIPI--SELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 366-425 2.61e-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: 2.61e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767962239  366 DIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVppmH---LADILMKNPEKKYHIGDEVKCRVL 425
Cdd:COG1098     2 SIEVGDIVEGKVTGITPFGAFVELPEGTTGLV---HiseIADGYVKDINDYLKVGDEVKVKVL 61
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
551-624 4.96e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.98  E-value: 4.96e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239    551 NIGQLVDVKVLEKTKDGLEVAvLPHNIRAFLPTSHLSDHvaNGPLLHHWLQAGDILH-RVLCLSQSEGRVLLCRK 624
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVD-LGNGVEGLIPISELSDK--RVKDPEEVLKVGDEVKvKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
197-263 5.42e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.98  E-value: 5.42e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767962239    197 PGLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKAG----TYFSNQAVRACILCVHPRTRVVHLSLR 263
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKdpeeVLKVGDEVKVKVLSVDEEKGRIILSLK 72
PTZ00121 PTZ00121
MAEBL; Provisional
 1319-1610 6.39e-05

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 48.21  E-value: 6.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1319 KPDVLSASLEgQLTKQEERKTEAEERDQKGEKKNQKRNEKKN----QKGQEEVempsKEKQQPQKPQAQKRGGRECRESG 1394
Cdd:PTZ00121 1379 KADAAKKKAE-EKKKADEAKKKAEEDKKKADELKKAAAAKKKadeaKKKAEEK----KKADEAKKKAEEAKKADEAKKKA 1453

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1395 SEQERVSKKPKKAGLSEEDDSLVDvyYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAwnvglDSLTPA-------- 1466
Cdd:PTZ00121 1454 EEAKKAEEAKKKAEEAKKADEAKK--KAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKA-----DEAKKAeeakkade 1526

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1467 LPPLAESSDSEEDEKPHQ---ATQIKKSKKERELEKQKAEKELSRIEEALMDPGRQPESADDFDRLVLSSPNSSILWLQY 1543
Cdd:PTZ00121 1527 AKKAEEAKKADEAKKAEEkkkADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKK 1606

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767962239 1544 MAFHlQATEIEKARAVAERALKtisfrEEQEKLNVWVALLNLENMYGSQESLTKVFERAVQYNEPLK 1610
Cdd:PTZ00121 1607 MKAE-EAKKAEEAKIKAEELKK-----AEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEA 1667
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 464-546 6.58e-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: 6.58e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  464 GFIIRVKDYGCIVKFYNNVQGLVpkH--ELSTEYIPDPERVFYTGQVVKVVVLNCEPSKeRMLLSFK-LSSDPEPKKEPA 540
Cdd:COG1098    11 GKVTGITPFGAFVELPEGTTGLV--HisEIADGYVKDINDYLKVGDEVKVKVLSIDEDG-KISLSIKqAEEKPKRPPRPR 87


                  ....*.
gi 767962239  541 GHSQKK 546
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 ...
 952-1011 1.05e-04

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 42.27  E-value: 1.05e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   952 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1011
Cdd:pfam00575    3 KGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVE--DPDEVIKVGDEVKVKVLK 60
PRK08059 PRK08059
general stress protein 13; Validated
 469-546 1.06e-04

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 43.50  E-value: 1.06e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  469 VKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKLSSD-PEPKKEPAGHSQKK 546
Cdd:PRK08059   18 IQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEaPEAKRKKGKILIPN 96
Suf pfam05843
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ...
 1645-1787 1.18e-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: 46.21  E-value: 1.18e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1645 VWIKYGAFLlRRSQAAASHR-VLQRALEclpsKEHV--DVIAKFAQLEFQLG-DAERAKAIFENTLSTYPKRTDVWSVYI 1720
Cdd:pfam05843    3 VWIQYMRAM-RRAEGIKGARkVFKKARK----RPRLtyHVYVASALMEYYCSkDPAVAFKIFELGLKLFPEDEEFVLKYL 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767962239  1721 DMTIKHGSQKDVRDIFERVIHlSLAPKRM-KFFFKRYLDYEKQHGTEKDVQAVKAKALEYVEAKSSVL 1787
Cdd:pfam05843   78 DYLISLNDDNNARVLFERVLT-RLAQEKEaKPLWKKFISYESTFGDLASILKLEKRMAELFPEDPPLA 144
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
950-1010 2.08e-04

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 42.77  E-value: 2.08e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239  950 LSIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHI----LDDVPEgtspttKLKVGKTVTARVI 1010
Cdd:PRK07252    1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIktgfIDNIHQ------LLKVGEEVLVQVV 59
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1-87 3.90e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 40.66  E-value: 3.90e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239      1 MRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQvtqeqplkdllhlpelFSPGMLVRCVVSSLgitDRGK 80
Cdd:smart00316    4 DVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEV----------------LKVGDEVKVKVLSV---DEEK 64


                    ....*..
gi 767962239     81 KSVKLSL 87
Cdd:smart00316   65 GRIILSL 71
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 87-224 7.06e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 44.10  E-value: 7.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   87 LNPKNVNRVLSAEA----------------LKPGMLLTGTVSSLEDHGYLVDIG-VDGtraflpLLKAQE--YIRQKNKG 147
Cdd:PRK06676  160 LDPEKNRVILSRRAvveeeraakkeellssLKEGDVVEGTVARLTDFGAFVDIGgVDG------LVHISElsHERVEKPS 233

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  148 AKLKVGQYLNCIVEKVKGNGGVVSLSVGhsevstaiATEQQSWNL--NNLLPGLVVKAQVQKVTPFGLtlnFLTFFTGV 224
Cdd:PRK06676  234 EVVSVGQEVEVKVLSIDWETERISLSLK--------DTLPGPWEGveEKLPEGDVIEGTVKRLTDFGA---FVEVLPGV 301
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1416-1711 1.24e-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: 43.92  E-value: 1.24e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1416 LVDVYYREGKEEaEETNVLPKEKQTKPAE-APRLQLSSGFawnVGLDSLTPALPPLAESSDSEEDEKphQATQIKKSKke 1494
Cdd:TIGR02917  539 LAGLYLRTGNEE-EAVAWLEKAAELNPQEiEPALALAQYY---LGKGQLKKALAILNEAADAAPDSP--EAWLMLGRA-- 610

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1495 relekQKAEKELSRIEEAlmdpgrqpesaddFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALktisfreeQE 1574
Cdd:TIGR02917  611 -----QLAAGDLNKAVSS-------------FKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRAL--------EL 664

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1575 KLNVWVALL---NLENMYGSQESLTKVFeRAVQYNEPLKVFLH--LADIYAKSEKFQEAGELYNRMLKRFRQEKAVwIKY 1649
Cdd:TIGR02917  665 KPDNTEAQIglaQLLLAAKRTESAKKIA-KSLQKQHPKAALGFelEGDLYLRQKDYPAAIQAYRKALKRAPSSQNA-IKL 742

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239  1650 GAFLLRRSQAAASHRVLQRALeclpsKEHV-DVIAKFAQLEFQLGDAERAKAI--FENTLSTYPK 1711
Cdd:TIGR02917  743 HRALLASGNTAEAVKTLEAWL-----KTHPnDAVLRTALAELYLAQKDYDKAIkhYQTVVKKAPD 802
DUF612 pfam04747
Protein of unknown function, DUF612; This family includes several uncharacterized proteins ...
 1316-1516 3.32e-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: 3.32e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1316 DTGKPDVLSASLEGQLTKQEERKTEAEERDQKGEKKNQKRNEKKNQKGQEEVEMPSKEKQQPQKPQAQkrggRECRESGS 1395
Cdd:pfam04747   49 DQRKEAFASLELTEQPQQVEKVKKSEKKKAQKQIAKDHEAEQKVNAKKAAEKEARRAEAEAKKRAAQE----EEHKQWKA 124

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1396 EQERVSKKPKKaglseEDDSLVDVYYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAWNVGLD-SLTPALPPLAESS 1474
Cdd:pfam04747  125 EQERIQKEQEK-----KEADLKKLQAEKKKEKAVKAEKAEKAEKTKKASTPAPVEEEIVVKKVANDrSAAPAPEPKTPTN 199

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 767962239  1475 DSEEDEKPHQATQIKKSKKERELEKQKAEKELSRIEEALMDP 1516
Cdd:pfam04747  200 TPAEPAEQVQEITGKKNKKNKKKSESEATAAPASVEQVVEQP 241
 
Name Accession Description Interval E-value
S1_Rrp5_repeat_hs7 cd05699
S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 553-624 1.21e-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: 1.21e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767962239  553 GQLVDVKVLEKTKDGLEVAVLPHNIRAFLPTSHLSDHVANGPLLHHWLQAGDILHRVLCLSQSEGRVLLCRK 624
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 ...
 632-714 3.73e-38

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


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 137.72  E-value: 3.73e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  632 EGGQDPKNFSEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRML 711
Cdd:cd04461     1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                  ...
gi 767962239  712 LSL 714
Cdd:cd04461    81 LSL 83
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1-93 3.98e-37

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: 135.42  E-value: 3.98e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239    1 MRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQVTQEQ---PLKDLLHLPELFSPGMLVRCVVSSLGITD 77
Cdd:cd05693     5 MLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEeedDEEELPDLEDLFSVGQLVRCKVVSLDKSK 84

                          90
                  ....*....|....*.
gi 767962239   78 RGKKSVKLSLNPKNVN 93
Cdd:cd05693    85 SGKKRIELSLEPELVN 100
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1238-1311 4.50e-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: 4.50e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767962239 1238 IKEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1311
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 ...
 1144-1215 1.90e-35

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


Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 129.39  E-value: 1.90e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767962239 1144 LEEGEVAMGRVVKVTPNEGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILSTADNVLTLSLR 1215
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 ...
 459-528 3.64e-35

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


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 128.50  E-value: 3.64e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  459 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 528
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 ...
 842-910 4.02e-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: 4.02e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  842 GSEHQAIVQHLEKSFAIASLVETGHLAAFSLTSHLNDTFRFDSEKLQVGQGVSLTLKTTEPGVTGLLLA 910
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 ...
 370-438 5.23e-31

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


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 116.95  E-value: 5.23e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  370 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTL 438
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 ...
 953-1022 8.37e-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: 8.37e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  953 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEGTSPTTKLKVGKTVTARVIGGRDMKTFKYLP 1022
Cdd:cd05702     1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 281-715 2.86e-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: 124.46  E-value: 2.86e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   281 LGAVLDDVPVQG-FFKKAGATFRLK-DGVLAYARLSHlSDSKNVFNPEAFKpGNTHKCRIIDYSQMDELALLSlRTSIIE 358
Cdd:TIGR00717   95 EKAYEEGSIVEGkIVGKVKGGFIVDlNGVEAFLPGSQ-VDVKPIKDLDSLI-GKTLKFKIIKLDQKRNNIVVS-RRAYLE 171

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   359 AQYLRYHD-----IEPGAVVKGTVLTIKSYGMLVKVGeQMRGLVppmHLADIL---MKNPEKKYHIGDEVKCRVLLCDPE 430
Cdd:TIGR00717  172 EERSQAREellenLKEGDVVKGVVKNITDFGAFVDLG-GVDGLL---HITDMSwkrVKHPSEYVKVGQEVKVKVIKFDKE 247

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   431 AKKLMMTLKKTL------IESKLPvitcyadakPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVF 503
Cdd:TIGR00717  248 KGRISLSLKQLGedpweaIEKKFP---------VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVV 318

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   504 YTGQVVKVVVLNCEPSKERMLLSFKlSSDPEP-----KKEPAGhSQKKGKAINIGQLVDVKVLEKTKDGLevavlphnir 578
Cdd:TIGR00717  319 KKGDEVEVMILDIDPERRRLSLGLK-QCKANPweqfeEKHPVG-DRVTGKIKKITDFGAFVELEGGIDGL---------- 386

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   579 aflptSHLSD--HVANGPLLHHWLQAGDILHR-VLCLSQSEGRVLLCRKPALVSTVEggqdpkNFSEIHP-GMLLIGFVK 654
Cdd:TIGR00717  387 -----IHLSDisWDKDGREADHLYKKGDEIEAvVLAVDKEKKRISLGVKQLTENPWE------KFAAKYKvGSVVKGKVT 455

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767962239   655 SIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
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 ...
 100-180 3.36e-28

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


Pssm-ID: 240199 [Multi-domain]  Cd Length: 74  Bit Score: 108.88  E-value: 3.36e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  100 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYirqknkgAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEV 179
Cdd:cd05694     1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73


                  .
gi 767962239  180 S 180
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 ...
 282-352 8.80e-28

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


Pssm-ID: 240201 [Multi-domain]  Cd Length: 71  Bit Score: 107.73  E-value: 8.80e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767962239  282 GAVLDDVPVQGFFKKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSL 352
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 ...
 763-827 1.49e-27

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


Pssm-ID: 240205  Cd Length: 65  Bit Score: 106.86  E-value: 1.49e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239  763 GMFLDLVVQEVLEDGSVVFSGGPVPDLVLKASRYHRAGQEVESGQKKKVVILNVDLLKLEVHVSL 827
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 ...
 1066-1140 6.56e-26

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


Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 102.27  E-value: 6.56e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239 1066 GQTVTCFLKKYNVVKKWLEveIAPDIRGRIPLLLTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTLLCLSLTG 1140
Cdd:cd05703     1 GQEVTGFVNNVSKEFVWLT--ISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 367-715 9.48e-26

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 114.11  E-value: 9.48e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  367 IEPGAVVKGTVLTIKSYGMLVKVGeQMRGLVppmHLADILMK---NPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL- 442
Cdd:PRK06299  199 LEEGQVVEGVVKNITDYGAFVDLG-GVDGLL---HITDISWKrvnHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGe 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  443 -----IESKLPVitcyadakpglqthGFIIRVK-----DYGCIVKFYNNVQGLVpkH--ELS-TEYIPDPERVFYTGQVV 509
Cdd:PRK06299  275 dpweaIEKKYPV--------------GSKVKGKvtnitDYGAFVELEEGIEGLV--HvsEMSwTKKNKHPSKVVSVGQEV 338

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  510 KVVVLNCEPSKERMLLSFK-LSSDPE---PKKEPAGhSQKKGKAINIgqlvdvkvlekTKDGLEVAvLPHNIRAFLptsH 585
Cdd:PRK06299  339 EVMVLEIDEEKRRISLGLKqCKENPWeefAEKYPVG-DVVEGKVKNI-----------TDFGAFVG-LEGGIDGLV---H 402

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  586 LSD--HVANG--PLLHhwLQAGDILH-RVLCLSQSEGRVLLCRKPALvstveggQDP-KNFSEIHP-GMLLIGFVKSIKD 658
Cdd:PRK06299  403 LSDisWDKKGeeAVEL--YKKGDEVEaVVLKVDVEKERISLGIKQLE-------EDPfEEFAKKHKkGSIVTGTVTEVKD 473

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767962239  659 YGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
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 ...
 198-261 1.11e-25

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


Pssm-ID: 240200 [Multi-domain]  Cd Length: 66  Bit Score: 101.58  E-value: 1.11e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767962239  198 GLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKA--GTYFSNQAVRACILCVHPRTRVVHLS 261
Cdd:cd05695     1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSskSTYKEGQKVRARILYVDPSTKVVGLS 66
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 97-528 1.94e-22

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 100.89  E-value: 1.94e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   97 SAEALKPGMLLTGTVSSLEDHGYLVDIG--VDGtraFLPLlkaqEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSv 174
Cdd:COG0539    12 SLKELKEGDIVKGTVVSIDDDEVLVDIGykSEG---IIPL----SEFSDEPGELEVKVGDEVEVYVEKVEDGEGEIVLS- 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  175 ghsevsTAIATEQQSWN-----LNNllpGLVVKAQVQKVTPFGLTlnfltfftgvVDFMHldpkkagtyfsnqaVRAcil 249
Cdd:COG0539    84 ------KKKADREKAWEeleeaFEN---GEPVEGKVKGVVKGGLI----------VDIGG--------------VRA--- 127

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  250 cvhprtrvvhlslrpiFLqPGrpltrlscqnlgavlddvpvqgffkkagatfrlkdgvlayarlSHLsDSKNVFNPEAFK 329
Cdd:COG0539   128 ----------------FL-PA-------------------------------------------SQV-DVRPVRDLDEYV 146

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  330 pGNTHKCRIIDYSQMDELALLSlRTSIIEAQYLR-----YHDIEPGAVVKGTVLTIKSYGMLVKVGEqMRGLVppmHLAD 404
Cdd:COG0539   147 -GKTLEFKIIKLDRKRNNVVVS-RRAVLEEEREEkreelLEKLEEGDVVEGTVKNITDFGAFVDLGG-VDGLL---HISE 220

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  405 IL---MKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL------IESKLPVitcyadakpGLQTHGFIIRVKDYGCI 475
Cdd:COG0539   221 ISwgrVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQLQpdpwenIAEKYPV---------GDVVKGKVTRLTDFGAF 291

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....
gi 767962239  476 VKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 528
Cdd:COG0539   292 VELEPGVEGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 99-528 1.34e-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: 1.34e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239    99 EALKPGMLLTGTVSSLEDHGYLVDIGvdGTRAFLPlLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHse 178
Cdd:TIGR00717  183 ENLKEGDVVKGVVKNITDFGAFVDLG--GVDGLLH-ITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQ-- 257

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   179 vstaiaTEQQSWN--LNNLLPGLVVKAQVQKVTPFGltlnfltfftgvvdfmhldpkkagtyfsnqavracilcvhprtr 256
Cdd:TIGR00717  258 ------LGEDPWEaiEKKFPVGDKITGRVTNLTDYG-------------------------------------------- 287

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   257 vvhlslrpIFLQpgrpltrlscqnlgavlddvpvqgffkkagatfrLKDGVLAYARLSHLSDSKNVFNP-EAFKPGNTHK 335
Cdd:TIGR00717  288 --------VFVE----------------------------------IEEGIEGLVHVSEMSWVKKNSHPsKVVKKGDEVE 325

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   336 CRIIDYSQMDELALLSLRT------SIIEAQYlryhdiEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVppmHLADIL--- 406
Cdd:TIGR00717  326 VMILDIDPERRRLSLGLKQckanpwEQFEEKH------PVGDRVTGKIKKITDFGAFVELEGGIDGLI---HLSDISwdk 396

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   407 -MKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKtLIESKLPVITcyADAKPGLQTHGFIIRVKDYGCIVKFYNNVQGL 485
Cdd:TIGR00717  397 dGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQ-LTENPWEKFA--AKYKVGSVVKGKVTEIKDFGAFVELPGGVEGL 473

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|...
gi 767962239   486 VPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 528
Cdd:TIGR00717  474 IRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
344-715 2.54e-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: 2.54e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  344 MDELALLSLRTSIIEAQYLRYHDIEP--GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVK 421
Cdd:PRK00087  275 MSELDNMEEVEENEQLEYMNELEKQIrrGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIE 354

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  422 CRVLLCD------------PEAKKLMMTLKKTLiESKLPVItcyadakpglqthGFIIRVKDYGCIVKfYNNVQGLVPKH 489
Cdd:PRK00087  355 VKVLKLEdedgyvvlskkeADREKAWKELEEAF-ENGEPVK-------------GKVKEVVKGGLLVD-YGGVRAFLPAS 419

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  490 ELSTEYIPDPERvfYTGQVVKVVVLNCEPSKERMLLsfkLSSDPEPKKEPAGHSQKKGKAINIGQLVDVKVLEKTKDGLE 569
Cdd:PRK00087  420 HVELGYVEDLSE--YKGQELEVKIIEFNRKRRKKVV---LSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAF 494

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  570 VAVlpHNIRAFLPTSHLSDHVANGPLLHhwLQAGDILH-RVLCLSQSEGRVLLCRKPALvstveggQDP-KNFSEIHP-G 646
Cdd:PRK00087  495 VDI--GGVDGLLHVSEISWGRVEKPSDV--LKVGDEIKvYILDIDKENKKLSLSLKKLL-------PDPwENVEEKYPvG 563

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  647 MLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
Cdd:PRK00087  564 SIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIK 632
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 96-588 2.52e-19

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 94.08  E-value: 2.52e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   96 LSAEALKPGMLLTGTVSSLEDHGYLVDIG--VDGtraFLPLlkaqEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 173
Cdd:PRK06299   23 LKESETREGSIVKGTVVAIDKDYVLVDVGlkSEG---RIPL----EEFKNEQGELEVKVGDEVEVYVERIEDGFGETVLS 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  174 VghsevstAIATEQQSWN-LNNLL-PGLVVKAQVQKVTPFGLT--LNfltfftGVVDFM---HLD--PKKAGTYFSNQAV 244
Cdd:PRK06299   96 R-------EKAKRLEAWDkLEKAFeNGEIVEGVINGKVKGGFTvdLN------GVEAFLpgsQVDvrPVRDTDPLEGKEL 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  245 RACILCVHPRTRVVHLSLRPIF--------------LQPGrpltrlscqnlgavldDVpVQGFFKKA---GATFRLK--D 305
Cdd:PRK06299  163 EFKVIKLDKKRNNIVVSRRAVLeeeraeereellenLEEG----------------QV-VEGVVKNItdyGAFVDLGgvD 225

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  306 GVLAYARLSHlsdsKNVFNP-EAFKPGNTHKCRIIDYSQmdELALLSLrtSI----------IEAQYlryhdiEPGAVVK 374
Cdd:PRK06299  226 GLLHITDISW----KRVNHPsEVVNVGDEVKVKVLKFDK--EKKRVSL--GLkqlgedpweaIEKKY------PVGSKVK 291

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  375 GTVLTIKSYGMLVKVGEQMRGLVppmHLADI----LMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL------IE 444
Cdd:PRK06299  292 GKVTNITDYGAFVELEEGIEGLV---HVSEMswtkKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKenpweeFA 368

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  445 SKLPVitcyadakpGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERM 523
Cdd:PRK06299  369 EKYPV---------GDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERI 439

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767962239  524 LLSFK-LSSDPepkkepAGHSQKKGKainIGQLVDVKVLEKTKDGLEVAvLPHNIRAFLPTSHLSD 588
Cdd:PRK06299  440 SLGIKqLEEDP------FEEFAKKHK---KGSIVTGTVTEVKDKGAFVE-LEDGVEGLIRASELSR 495
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 482-715 1.40e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 89.93  E-value: 1.40e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  482 VQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKLSsdpepkKEPAGHSQKKGKAINiGQLVDVKVL 561
Cdd:PRK06676   42 VEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRL------EAEKAWDKLEEKFEE-GEVVEVKVT 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  562 EKTKDGLEVAVlpHNIRAFLPTSHLSDH-VANgpllHHWLQAGDILHRVLCLSQSEGRVLLCRKpALVSTVEGGQDPKNF 640
Cdd:PRK06676  115 EVVKGGLVVDV--EGVRGFIPASLISTRfVED----FSDFKGKTLEVKIIELDPEKNRVILSRR-AVVEEERAAKKEELL 187

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239  641 SEIHPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
Cdd:PRK06676  188 SSLKEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLK 261
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 484-715 1.46e-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: 89.33  E-value: 1.46e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  484 GLVPKHELSTEyipdPERVFYT-GQVVKVVVLNCEPSKERMLLSfklssdpepkKEPAGhsQKKG-----KAINIGQLVD 557
Cdd:COG0539    44 GIIPLSEFSDE----PGELEVKvGDEVEVYVEKVEDGEGEIVLS----------KKKAD--REKAweeleEAFENGEPVE 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  558 VKVLEKTKDGLEVAVlpHNIRAFLPTSHLSDH-VAN-GPLLHHWLQAgdilhRVLCLSQSEGRVLLCRKPALVSTVEGGQ 635
Cdd:COG0539   108 GKVKGVVKGGLIVDI--GGVRAFLPASQVDVRpVRDlDEYVGKTLEF-----KIIKLDRKRNNVVVSRRAVLEEEREEKR 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  636 DpKNFSEIHPGMLLIGFVKSIKDYGVFIQFPsGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
Cdd:COG0539   181 E-ELLEKLEEGDVVEGTVKNITDFGAFVDLG-GVDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLK 258
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1518-1778 6.61e-17

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 82.85  E-value: 6.61e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1518 RQPESA-DDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfREEQEKLnvwvALLNLENMYGSQESLT 1596
Cdd:COG2956    22 GQPDKAiDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYLKAGLLD 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1597 K---VFERAVQYNEP-LKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEC 1672
Cdd:COG2956    94 RaeeLLEKLLELDPDdAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1673 LPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLAPKRMKFF 1752
Cdd:COG2956   174 DP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA--LELDPSDDLLL 249

                         250       260
                  ....*....|....*....|....*.
gi 767962239 1753 FKRYLdYEKQHGTEKdVQAVKAKALE 1778
Cdd:COG2956   250 ALADL-LERKEGLEA-ALALLERQLR 273
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
368-439 4.27e-16

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 74.56  E-value: 4.27e-16
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767962239    368 EPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 439
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 322-538 5.49e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 82.23  E-value: 5.49e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  322 VFNPEAFKpGNTHKCRIIDYSQMDELALLSlRTSIIEAQYLRYHD-----IEPGAVVKGTVLTIKSYGMLVKVGEqMRGL 396
Cdd:PRK06676  142 VEDFSDFK-GKTLEVKIIELDPEKNRVILS-RRAVVEEERAAKKEellssLKEGDVVEGTVARLTDFGAFVDIGG-VDGL 218

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  397 VppmHLADI---LMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL------IESKLPVitcyadakpGLQTHGFII 467
Cdd:PRK06676  219 V---HISELsheRVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLpgpwegVEEKLPE---------GDVIEGTVK 286

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767962239  468 RVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKlSSDPEPKKE 538
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 ...
 646-715 8.85e-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: 8.85e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  646 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 457-1011 1.26e-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: 1.26e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   457 KPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHElsteyIPDPERVFYTGQVVKVVVLNCEPSKERMLLSfklssdpepk 536
Cdd:TIGR00717   17 RPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEE-----FLDAPLEIQVGDEVEVYLDRVEDRFGETVLS---------- 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   537 KEPAGHSQKKGK---AINIGQLVDVKVLEKTKDGLEVAVlpHNIRAFLPTSHLSDHVANGPLLHhwlQAGDILHRVLCLS 613
Cdd:TIGR00717   82 REKAQRHELWIKlekAYEEGSIVEGKIVGKVKGGFIVDL--NGVEAFLPGSQVDVKPIKDLDSL---IGKTLKFKIIKLD 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   614 QSEGRVLLCRKPALVSTVEGGQDpKNFSEIHPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEG 693
Cdd:TIGR00717  157 QKRNNIVVSRRAYLEEERSQARE-ELLENLKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVKHPSEYVKVG 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   694 QTVAAKVTNVDEEKQRMLLSLRLSDcglGD--LAItsllllnqclEELQGVRSLMSNRdsvliqtLAEMTP-GMFLDLV- 769
Cdd:TIGR00717  235 QEVKVKVIKFDKEKGRISLSLKQLG---EDpwEAI----------EKKFPVGDKITGR-------VTNLTDyGVFVEIEe 294

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   770 -------VQEVLEDGSVVfsggpvpdlvlKASRYHRAGQEVEsgqkkkVVILNVDLLKLEVHVSLHQDLVN---RKARKL 839
Cdd:TIGR00717  295 gieglvhVSEMSWVKKNS-----------HPSKVVKKGDEVE------VMILDIDPERRRLSLGLKQCKANpweQFEEKH 357

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   840 RKGSEHQAIVQHLEKSFAIASLVE--TGHLaafsltsHLNDTFRFDSEKlqvgqgVSLTLKTTEPGVTGLLLAVEGPAAK 917
Cdd:TIGR00717  358 PVGDRVTGKIKKITDFGAFVELEGgiDGLI-------HLSDISWDKDGR------EADHLYKKGDEIEAVVLAVDKEKKR 424

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   918 RTMRPTQKDSETVDEDEEVDPaltvgtikkhtlsIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTT 997
Cdd:TIGR00717  425 ISLGVKQLTENPWEKFAAKYK-------------VGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDE--DKTD 489

                          570
                   ....*....|....
gi 767962239   998 KLKVGKTVTARVIG 1011
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 ...
 444-527 2.97e-15

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


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 72.24  E-value: 2.97e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  444 ESKLPviTCYADAKPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERM 523
Cdd:cd04461     2 EGTLP--TNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRF 79


                  ....
gi 767962239  524 LLSF 527
Cdd:cd04461    80 LLSL 83
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
645-715 3.28e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 71.87  E-value: 3.28e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767962239    645 PGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 548-1011 3.95e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 80.59  E-value: 3.95e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  548 KAINIGQLVDVKVLEKTKDGLEVAVlpHNIRAFLPTSHLS-----DHvanGPLLHHWLQAgdilhRVLCLSQSEGRVLLC 622
Cdd:PRK06299  110 KAFENGEIVEGVINGKVKGGFTVDL--NGVEAFLPGSQVDvrpvrDT---DPLEGKELEF-----KVIKLDKKRNNIVVS 179

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  623 RKpALVSTVEGGQDPKNFSEIHPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTN 702
Cdd:PRK06299  180 RR-AVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDL-GGVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLK 257

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  703 VDEEKQRMLLSLRLsdcgLGD---LAITsllllnqclEELQgVRSLMSNRDSVLiqtlaemTP-GMFLDlvvqevLEDGs 778
Cdd:PRK06299  258 FDKEKKRVSLGLKQ----LGEdpwEAIE---------KKYP-VGSKVKGKVTNI-------TDyGAFVE------LEEG- 309

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  779 vvfsggpVPDLV-----------LKASRYHRAGQEVEsgqkkkVVILNVDLLKLEVHVSLHQDLVN---RKARKLRKGSE 844
Cdd:PRK06299  310 -------IEGLVhvsemswtkknKHPSKVVSVGQEVE------VMVLEIDEEKRRISLGLKQCKENpweEFAEKYPVGDV 376

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  845 HQAivqhleksfAIASLVETGhlaAFsltshlndtfrfdseklqvgqgVSLtlkttEPGVTGLL----LA--VEGPAAKR 918
Cdd:PRK06299  377 VEG---------KVKNITDFG---AF----------------------VGL-----EGGIDGLVhlsdISwdKKGEEAVE 417

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  919 TMRptqKDSE------TVDEDEE----------VDPALTVgtIKKHTlsIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHA 982
Cdd:PRK06299  418 LYK---KGDEveavvlKVDVEKErislgikqleEDPFEEF--AKKHK--KGSIVTGTVTEVKDKGAFVELEDGVEGLIRA 490

                         490       500
                  ....*....|....*....|....*....
gi 767962239  983 SHILDDvpEGTSPTTKLKVGKTVTARVIG 1011
Cdd:PRK06299  491 SELSRD--RVEDATEVLKVGDEVEAKVIN 517
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
457-528 5.03e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 71.48  E-value: 5.03e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767962239    457 KPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 528
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1546-1778 3.77e-14

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 74.77  E-value: 3.77e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1546 FHLQATEIEKARAVAERALKtisfrEEQEKLNVWVALLNLENMYGSQESLTKVFERAVQYNEP-LKVFLHLADIYAKSEK 1624
Cdd:COG2956    17 NYLLNGQPDKAIDLLEEALE-----LDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLERDPDrAEALLELAQDYLKAGL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1625 FQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPSKEHVDVIAkfAQLEFQLGDAERAKAIFEN 1704
Cdd:COG2956    92 LDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCEL--AELYLEQGDYDEAIEALEK 169

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767962239 1705 TLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLAPKRMKFFFKRYLDYEKQHGTEKDVQAVKaKALE 1778
Cdd:COG2956   170 ALKLDPDCARALLLLAELYLEQGDYEEAIAALERA--LEQDPDYLPALPRLAELYEKLGDPEEALELLR-KALE 240
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1494-1709 7.52e-13

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 70.91  E-value: 7.52e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1494 ERELEKQKAEKELSRIeeaLMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfrEEQ 1573
Cdd:COG2956    70 ERDPDRAEALLELAQD---YLKAGLLDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLK-----LGP 141

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1574 EKLNVWVALLNLENMYGSQESLTKVFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAF 1652
Cdd:COG2956   142 ENAHAYCELAELYLEQGDYDEAIEALEKALKLDpDCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAEL 221

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767962239 1653 LLRRSQAAASHRVLQRALECLPSkehVDVIAKFAQLEFQLGDAERAKAIFENTLSTY 1709
Cdd:COG2956   222 YEKLGDPEEALELLRKALELDPS---DDLLLALADLLERKEGLEAALALLERQLRRH 275
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 366-715 7.92e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 72.22  E-value: 7.92e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  366 DIEPGAVVKGTVLTIKSYGMLVKV-GEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIE 444
Cdd:PRK06676   14 EVEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAE 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  445 ---SKLpvITCYADAKPglqthgFIIRVKDY---GCIVKFyNNVQGLVPKHELSTEYIPDPERvfYTGQVVKVVVLNCEP 518
Cdd:PRK06676   94 kawDKL--EEKFEEGEV------VEVKVTEVvkgGLVVDV-EGVRGFIPASLISTRFVEDFSD--FKGKTLEVKIIELDP 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  519 SKERMLLSFK--LSSDPEPKKEPAGHSqkkgkaINIGQLVDVKVLEKTK----------DGLevavlphnirafLPTSHL 586
Cdd:PRK06676  163 EKNRVILSRRavVEEERAAKKEELLSS------LKEGDVVEGTVARLTDfgafvdiggvDGL------------VHISEL 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  587 S-DHVANgpllhhwlqAGDILH-------RVLCLSQSEGRVLLCRKPALVSTVEGGQDpknfsEIHPGMLLIGFVKSIKD 658
Cdd:PRK06676  225 ShERVEK---------PSEVVSvgqevevKVLSIDWETERISLSLKDTLPGPWEGVEE-----KLPEGDVIEGTVKRLTD 290

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767962239  659 YGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
Cdd:PRK06676  291 FGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIK 347
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 649-713 9.37e-13

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


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 64.71  E-value: 9.37e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239  649 LIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 713
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 373-437 1.08e-12

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


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 64.71  E-value: 1.08e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239  373 VKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMT 437
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 367-715 4.29e-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: 4.29e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   367 IEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPpmhLADILmkNPEKKYHIGDEVKCRVLLCDP-EAKKLMMTLKKTLIES 445
Cdd:TIGR00717   16 TRPGSIVKGTVVAINKDTVFVDVGLKSEGRIP---KEEFL--DAPLEIQVGDEVEVYLDRVEDrFGETVLSREKAQRHEL 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   446 KLPVITCYADAKPglqTHGFIIRVKDYGCIVKFyNNVQGLVPKHELSTEYIPDPERvfYTGQVVKVVVLNCEPSKERMLL 525
Cdd:TIGR00717   91 WIKLEKAYEEGSI---VEGKIVGKVKGGFIVDL-NGVEAFLPGSQVDVKPIKDLDS--LIGKTLKFKIIKLDQKRNNIVV 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   526 SFKLSSDPEPKKEpaghSQKKGKAINIGQLVDVKVLEKTKDGleVAVLPHNIRAFLPTSHLS-DHVANgPllHHWLQAGD 604
Cdd:TIGR00717  165 SRRAYLEEERSQA----REELLENLKEGDVVKGVVKNITDFG--AFVDLGGVDGLLHITDMSwKRVKH-P--SEYVKVGQ 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   605 ILH-RVLCLSQSEGRVLLCRKpalvstvEGGQDP-KNFSEIHP-GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMS-D 680
Cdd:TIGR00717  236 EVKvKVIKFDKEKGRISLSLK-------QLGEDPwEAIEKKFPvGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwV 308

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 767962239   681 KFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
Cdd:TIGR00717  309 KKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1597-1711 7.68e-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: 7.68e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1597 KVFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPs 1675
Cdd:COG4783    25 ALLEKALELDpDNPEAFALLGEILLQLGDLDEAIVLLHEALELDPDEPEARLNLGLALLKAGDYDEALALLEKALKLDP- 103

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 767962239 1676 kEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPK 1711
Cdd:COG4783   104 -EHPEAYLRLARAYRALGRPDEAIAALEKALELDPD 138
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 463-526 9.49e-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: 9.49e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767962239  463 HGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 526
Cdd:cd00164     2 TGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
952-1011 8.23e-11

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 59.54  E-value: 8.23e-11
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239    952 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1011
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 ...
 646-715 1.12e-10

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


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 58.84  E-value: 1.12e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  646 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKqRMLLSLR 715
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARG-RISLSIK 69
rpsA PRK13806
30S ribosomal protein S1; Provisional
 318-604 1.49e-10

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 65.90  E-value: 1.49e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  318 DSKNVFNPEAFKpGNTHKCRIIDYSQ------MDELALLSLRTSIIEAQYLRyhDIEPGAVVKGTVLTIKSYGMLVKVGE 391
Cdd:PRK13806  148 DLRYVEDPESYV-GQTFQFLITRVEEngrnivVSRRALLEREQKEALEAFME--TVKEGDVVEGTVTRLAPFGAFVELAP 224

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  392 QMRGLVppmHLADI---LMKNPEKKYHIGDEVKCRVLLCDPEAK----KLMMTLKKTlieSKLPVITCYADAKPGLQTHG 464
Cdd:PRK13806  225 GVEGMV---HISELswsRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIKQA---GGDPWDTVGDRLKAGDKVTG 298

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  465 FIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKlssdpEPKKEP-AGH 542
Cdd:PRK13806  299 KVVRLAPFGAFVEILPGIEGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLR-----DAEGDPwADV 373

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767962239  543 SQKkgkaINIGQLVDVKVLEKTKDGLEVAVLPhNIRAFLPTSHLSDhvANGPLLHHWLQAGD 604
Cdd:PRK13806  374 AER----FAPGTTVTGTVEKRAQFGLFVNLAP-GVTGLLPASVISR--AGKPATYEKLKPGD 428
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 644-717 1.50e-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: 1.50e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239  644 HPGMLLIGFVKSIKDYGVFIQF-PSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLRLS 717
Cdd:cd05708     1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75
rpsA PRK13806
30S ribosomal protein S1; Provisional
 454-713 3.67e-10

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 64.36  E-value: 3.67e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  454 ADAKPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKE----RMLLSFK- 528
Cdd:PRK13806  198 ETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIKq 277

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  529 LSSDPepkkepaghSQKKGKAINIGQLVDVKVLEKTKDGLEVAVLPhNIRAFLPTSHLSdHV--ANGPllHHWLQAGDIL 606
Cdd:PRK13806  278 AGGDP---------WDTVGDRLKAGDKVTGKVVRLAPFGAFVEILP-GIEGLVHVSEMS-WTrrVNKP--EDVVAPGDAV 344

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  607 H-RVLCLSQSEGRVLLCRKPAlvstvEGgqDP-KNFSE-IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFV 683
Cdd:PRK13806  345 AvKIKDIDPAKRRISLSLRDA-----EG--DPwADVAErFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGK 417

                         250       260       270
                  ....*....|....*....|....*....|
gi 767962239  684 TSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 713
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 ...
 464-526 9.76e-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: 9.76e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767962239   464 GFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 526
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 ...
 370-439 9.93e-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: 56.08  E-value: 9.93e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  370 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 439
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 370-715 1.19e-09

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 61.98  E-value: 1.19e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  370 GAVVKGTVL-TIKSyGMLVKVGEqMRGLVPPMHLADILMKNPEKkyHIGDEVKCRVLLCDPEAKKL-----------MMT 437
Cdd:COG0539   103 GEPVEGKVKgVVKG-GLIVDIGG-VRAFLPASQVDVRPVRDLDE--YVGKTLEFKIIKLDRKRNNVvvsrravleeeREE 178

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  438 LKKTLIEsKLpvitcyadaKPGLQTHGFIIRVKDYGCIVKFyNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCE 517
Cdd:COG0539   179 KREELLE-KL---------EEGDVVEGTVKNITDFGAFVDL-GGVDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKID 247

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  518 PSKERMLLSFK-LSSDPepkkepaghsqkkgkainigqlvdvkvlektkdglevavlphniraflptshlsdhvangpll 596
Cdd:COG0539   248 REKERISLSLKqLQPDP--------------------------------------------------------------- 264

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  597 hhWLQAGDilhrvlclsqsegrvllcrkpalvstveggqdpknfsEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKA 676
Cdd:COG0539   265 --WENIAE-------------------------------------KYPVGDVVKGKVTRLTDFGAFVELEPGVEGLVHIS 305

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 767962239  677 IMS-DKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
Cdd:COG0539   306 EMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
PRK08059 PRK08059
general stress protein 13; Validated
 367-441 1.25e-09

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 57.75  E-value: 1.25e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239  367 IEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKT 441
Cdd:PRK08059    5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRAT 79
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1599-1718 1.39e-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: 1.39e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1599 FERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskE 1677
Cdd:COG4235     6 LRQALAANpNDAEGWLLLGRAYLRLGRYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEELLERALALDP--D 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 767962239 1678 HVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSV 1718
Cdd:COG4235    84 NPEALYLLGLAAFQQGDYAEAIAAWQKLLALLPADAPARLL 124
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1607-1743 1.98e-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: 1.98e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1607 EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskEHVDVIAKFA 1686
Cdd:COG4783     2 ACAEALYALAQALLLAGDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALELDP--DEPEARLNLG 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767962239 1687 QLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVIHLS 1743
Cdd:COG4783    80 LALLKAGDYDEALALLEKALKLDPEHPEAYLRLARAYRALGRPDEAIAALEKALELD 136
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
370-444 6.36e-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: 6.36e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239  370 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIE 444
Cdd:PRK00087  563 GSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEE 637
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 85-470 8.31e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 60.18  E-value: 8.31e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   85 LSLNPKNVNRVLS----------------AEALKPGMLLTGTVSSLEDHGYLVDI-GVDGtraflpLLKAQE--YIRQKN 145
Cdd:PRK06299  167 IKLDKKRNNIVVSrravleeeraeereelLENLEEGQVVEGVVKNITDYGAFVDLgGVDG------LLHITDisWKRVNH 240

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  146 KGAKLKVGQYLNCIVEKVKGNGGVVSLSVGhsevstaiATEQQSW-NLNNLLP-GLVVKAQVQKVTPFGLtlnFLTFFTG 223
Cdd:PRK06299  241 PSEVVNVGDEVKVKVLKFDKEKKRVSLGLK--------QLGEDPWeAIEKKYPvGSKVKGKVTNITDYGA---FVELEEG 309

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  224 VVDFMHL-------DPKKAGTYFS-NQAVRACILCVHPRTRVVHLSLRPifLQPgRPLTRLSCQ-NLGAVlddvpVQGFF 294
Cdd:PRK06299  310 IEGLVHVsemswtkKNKHPSKVVSvGQEVEVMVLEIDEEKRRISLGLKQ--CKE-NPWEEFAEKyPVGDV-----VEGKV 381

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  295 K---KAGATFRLKDGVLAYARLSHLSDSKNVFNP-EAFKPGNTHKCRIIDYSQMDELALLSLR------TSIIEAQYlry 364
Cdd:PRK06299  382 KnitDFGAFVGLEGGIDGLVHLSDISWDKKGEEAvELYKKGDEVEAVVLKVDVEKERISLGIKqleedpFEEFAKKH--- 458

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  365 hdiEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIE 444
Cdd:PRK06299  459 ---KKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEA 535

                         410       420
                  ....*....|....*....|....*.
gi 767962239  445 SKLPVITCYADAKPGLQTHGFIIRVK 470
Cdd:PRK06299  536 EEKEAIAEYNSASDSKTTLGDLLKAA 561
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 298-528 1.18e-08

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 60.11  E-value: 1.18e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  298 GATFRLKDGVLAYARLSHLSDSKNVFNP-EAFKPGNTHKCRIIDYSQMDELALLSLRTSI------IEAQYlryhdiEPG 370
Cdd:PRK12269  593 GAFIELAEGIEGLAHISEFSWVKKTSKPsDMVKIGDEVECMILGYDIQAGRVSLGLKQVTanpweeIEARY------PVG 666

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  371 AVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNP-EKKYHIGDEVKCRVLLCDPEAKKLMMTLKKtLIESKLPV 449
Cdd:PRK12269  667 ARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPaDHELEVGKEIECMVIECDPQARRIRLGVKQ-LSDNPWQV 745

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  450 itcYADA-KPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPE---RVFYTGQVVKVVVLNCEPSKERMLL 525
Cdd:PRK12269  746 ---FANAyGVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPGealRKYAVGDRVKAVIVDMNVKDRKVAF 822


                  ...
gi 767962239  526 SFK 528
Cdd:PRK12269  823 SVR 825
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 956-1018 1.30e-08

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


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 52.77  E-value: 1.30e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767962239  956 VTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIGGRDMKTF 1018
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVK--DPSEVFKVGDEVEVKVLEVDPEKGR 61
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1145-1215 1.87e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 52.61  E-value: 1.87e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767962239   1145 EEGEVAMGRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILS--TADNVLTLSLR 1215
Cdd:smart00316    1 EVGDVVEGTVTEITPG-GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSvdEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1239-1312 4.09e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 51.84  E-value: 4.09e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767962239   1239 KEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKalyNKHLPEGKLLTARVLRLNHQKNLVELSF 1312
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDP---EEVLKVGDEVKVKVLSVDEEKGRIILSL 71
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1581-1738 4.23e-08

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 56.17  E-value: 4.23e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1581 ALLNLENMYGSQESLTK---VFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRR 1656
Cdd:COG0457    10 AYNNLGLAYRRLGRYEEaieDYEKALELDpDDAEALYNLGLAYLRLGRYEEALADYEQALELDPDDAEALNNLGLALQAL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1657 SQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIF 1736
Cdd:COG0457    90 GRYEEALEDYDKALELDP--DDAEALYNLGLALLELGRYDEAIEAYERALELDPDDADALYNLGIALEKLGRYEEALELL 167


                  ..
gi 767962239 1737 ER 1738
Cdd:COG0457   168 EK 169
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1244-1311 6.75e-08

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


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 50.84  E-value: 6.75e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767962239 1244 LRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQhspSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1311
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSD---KFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 947-1311 7.03e-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: 57.44  E-value: 7.03e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   947 KHTLSIGDMVTGTVKSIKPTHVVVTLeDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIGGRDMKTFKYLPISHp 1026
Cdd:TIGR00717  182 LENLKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVK--HPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQ- 257

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1027 rfvrTIPElsvrpseledghtalnthsvsPMEKI-KQYQAGQTVTCflKKYNVVKKWLEVEIAPDIRGRIPLLLTSLSFK 1105
Cdd:TIGR00717  258 ----LGED---------------------PWEAIeKKFPVGDKITG--RVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKK 310

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1106 VlKHPDKKFRVGQALRATVVGPDSSKTLLCLSL--TGPHKLEE-------GEVAMGRVVKVTpNEGLTVSFPFGKIGTVS 1176
Cdd:TIGR00717  311 N-SHPSKVVKKGDEVEVMILDIDPERRRLSLGLkqCKANPWEQfeekhpvGDRVTGKIKKIT-DFGAFVELEGGIDGLIH 388

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1177 IFHMS-DSYSETPLEDFVPQKVVRCYILStadnvltLSLRSSRTNPETKSKVEDPEINSIQDIKEGQLLRGYVGSIQPHG 1255
Cdd:TIGR00717  389 LSDISwDKDGREADHLYKKGDEIEAVVLA-------VDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKDFG 461

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 767962239  1256 VFFRLGPSVVGLARYSHVSQHSPSKKALynkHLPEGKLLTARVLRLNHQKNLVELS 1311
Cdd:TIGR00717  462 AFVELPGGVEGLIRNSELSENRDEDKTD---EIKVGDEVEAKVVDIDKKNRKVSLS 514
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 2-263 7.15e-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: 7.15e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239     2 RILGCVKEVNELELVISLPNGLQGFVQVTEIcdAYTKKLNeqvtqeqplkdllHLPELFSPGMLVRCVVssLGItDRGKK 81
Cdd:TIGR00717  275 KITGRVTNLTDYGVFVEIEEGIEGLVHVSEM--SWVKKNS-------------HPSKVVKKGDEVEVMI--LDI-DPERR 336

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239    82 SVKLSLNPKNVNRVLSAEALKP-GMLLTGTVSSLEDHGYLVDIGvDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIV 160
Cdd:TIGR00717  337 RLSLGLKQCKANPWEQFEEKHPvGDRVTGKIKKITDFGAFVELE-GGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVV 415

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   161 EKVKGNGGVVSLSVGHsevstaiATEQQSWNLNNLLP-GLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHL----DPKKA 235
Cdd:TIGR00717  416 LAVDKEKKRISLGVKQ-------LTENPWEKFAAKYKvGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELsenrDEDKT 488

                          250       260
                   ....*....|....*....|....*...
gi 767962239   236 GTYFSNQAVRACILCVHPRTRVVHLSLR 263
Cdd:TIGR00717  489 DEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 646-712 7.97e-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: 7.97e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767962239  646 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMS-DKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLL 712
Cdd:cd05690     1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 368-434 1.27e-07

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 50.36  E-value: 1.27e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767962239   368 EPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKL 434
Cdd:pfam00575    2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRI 68
rpsA PRK13806
30S ribosomal protein S1; Provisional
 298-526 1.37e-07

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 56.27  E-value: 1.37e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  298 GATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSLRTSIIEAQYLRYHDI----EPGAVV 373
Cdd:PRK13806  217 GAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVgdrlKAGDKV 296

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  374 KGTVLTIKSYGMLVKVGEQMRGLVppmHLADI----LMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIESKLPV 449
Cdd:PRK13806  297 TGKVVRLAPFGAFVEILPGIEGLV---HVSEMswtrRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADV 373

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767962239  450 ITCYAdakPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 526
Cdd:PRK13806  374 AERFA---PGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLA 447
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 1618-1710 1.73e-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: 1.73e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1618 IYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQLGDAER 1697
Cdd:COG5010    63 LYNKLGDFEESLALLEQALQLDPNNPELYYNLALLYSRSGDKDEAKEYYEKALALSP--DNPNAYSNLAALLLSLGQDDE 140

                          90
                  ....*....|...
gi 767962239 1698 AKAIFENTLSTYP 1710
Cdd:COG5010   141 AKAALQRALGTSP 153
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 646-713 1.85e-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: 1.85e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767962239  646 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 713
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1615-1779 2.07e-07

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 54.35  E-value: 2.07e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1615 LADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEclPSKEHVDVIAKFAQLEFQLGD 1694
Cdd:COG2956    14 KGLNYLLNGQPDKAIDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE--RDPDRAEALLELAQDYLKAGL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1695 AERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVIHLSlaPKRMKFFFKRYLDYEKQHGTEKDVQAVKa 1774
Cdd:COG2956    92 LDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLG--PENAHAYCELAELYLEQGDYDEAIEALE- 168


                  ....*
gi 767962239 1775 KALEY 1779
Cdd:COG2956   169 KALKL 173
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 645-713 2.14e-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: 2.14e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  645 PGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 713
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 ...
 646-714 2.60e-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: 2.60e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239   646 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSL 714
Cdd:pfam00575    4 GDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 645-715 3.36e-07

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 53.67  E-value: 3.36e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767962239  645 PGMLLIGFVKSIKDYGVFI---QFPsGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
Cdd:PRK03987    8 EGELVVGTVKEVKDFGAFVtldEYP-GKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
1618-1711 3.63e-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: 3.63e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1618 IYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRvLQRALECLPskEHVDVIAKFAQLEFQLGDAER 1697
Cdd:COG3063     1 LYLKLGDLEEAEEYYEKALELDPDNADALNNLGLLLLEQGRYDEAIA-LEKALKLDP--NNAEALLNLAELLLELGDYDE 77

                          90
                  ....*....|....
gi 767962239 1698 AKAIFENTLSTYPK 1711
Cdd:COG3063    78 ALAYLERALELDPS 91
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 950-1348 5.87e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 53.73  E-value: 5.87e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  950 LSIGDMVTGTVKSIKPTHVVVTLEDGII-GCIHASHILDDVPEGTSPTtkLKVGKTVTARVIGGRDMKtfKYLpishprf 1028
Cdd:PRK06676   15 VEVGDVVTGEVLKVEDKQVFVNIEGYKVeGVIPISELSNDHIEDINDV--VKVGDELEVYVLKVEDGE--GNL------- 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1029 vrtipELSVRPSELEDGHTALNthsvspmekiKQYQAGQTVTCFLKKynVVKKWLEVEIApDIRGRIPLLLTSLSFKvlk 1108
Cdd:PRK06676   84 -----LLSKRRLEAEKAWDKLE----------EKFEEGEVVEVKVTE--VVKGGLVVDVE-GVRGFIPASLISTRFV--- 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1109 hPDKKFRVGQALRATVVGPDSSKTLLCLSltgpHK-----------------LEEGEVAMGRVVKVTPnegltvsfpFG- 1170
Cdd:PRK06676  143 -EDFSDFKGKTLEVKIIELDPEKNRVILS----RRavveeeraakkeellssLKEGDVVEGTVARLTD---------FGa 208

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1171 --KIGTVS-IFHMSD-SYS--ETPLEDFVPQKVVRCYILStAD---NVLTLSLRSsrTNPETKSKVEdpeinsiQDIKEG 1241
Cdd:PRK06676  209 fvDIGGVDgLVHISElSHErvEKPSEVVSVGQEVEVKVLS-IDwetERISLSLKD--TLPGPWEGVE-------EKLPEG 278

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1242 QLLRGYVGSIQPHGVFFRLGPSVVGLArysHVSQHSpskkalyNKH-------LPEGKLLTARVLRLNHQKNLVELSflp 1314
Cdd:PRK06676  279 DVIEGTVKRLTDFGAFVEVLPGVEGLV---HISQIS-------HKHiatpsevLEEGQEVKVKVLEVNEEEKRISLS--- 345

                         410       420       430
                  ....*....|....*....|....*....|....
gi 767962239 1315 gdtgKPDVLSASLEGQLTKQEERKTEAEErDQKG 1348
Cdd:PRK06676  346 ----IKALEEAPAEEEDRREEYRQYELPE-EETG 374
PRK08059 PRK08059
general stress protein 13; Validated
 641-715 8.62e-07

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 49.66  E-value: 8.62e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239  641 SEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
Cdd:PRK08059    3 SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1511-1700 9.62e-07

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 51.93  E-value: 9.62e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1511 EALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisfreeqeKLNVWVALLNLENMYG 1590
Cdd:COG0457    16 LAYRRLGRYEEAIEDYEKALELDPDDAEALYNLGLAYLRLGRYEEALADYEQALEL--------DPDDAEALNNLGLALQ 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1591 SQESLTK---VFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVL 1666
Cdd:COG0457    88 ALGRYEEaleDYDKALELDpDDAEALYNLGLALLELGRYDEAIEAYERALELDPDDADALYNLGIALEKLGRYEEALELL 167

                         170       180       190
                  ....*....|....*....|....*....|....
gi 767962239 1667 QRALECLPSKEHVDVIAKFAQLEFQLGDAERAKA 1700
Cdd:COG0457   168 EKLEAAALAALLAAALGEAALALAAAEVLLALLL 201
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 459-528 1.15e-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: 1.15e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  459 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPsKERMLLSFK 528
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK 69
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 366-438 1.17e-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: 1.17e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767962239  366 DIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTL 438
Cdd:cd04461    11 DLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 1234-1312 1.29e-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: 1.29e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239 1234 SIQDIKEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKalyNKHLPEGKLLTARVLRLNHQKNLVELSF 1312
Cdd:cd04461     8 NFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDP---SFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
102-173 1.40e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.60  E-value: 1.40e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767962239    102 KPGMLLTGTVSSLEDHGYLVDIGvDGTRAFLPLLKAQEYiRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 173
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLG-NGVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 370-439 1.57e-06

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


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 47.32  E-value: 1.57e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767962239  370 GAVVKGTVLTIKSYGMLVKV-GEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 439
Cdd:cd05708     3 GQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73
RNA14 COG5107
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ...
 1526-1786 2.05e-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: 2.05e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1526 FDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALK---TISFR-EEQEKLNvwvalLNLENMYGSQESLTKVFER 1601
Cdd:COG5107   291 HNQILDYFYYAEEVWFDYSEYLIGISDKQKALKTVERGIEmspSLTMFlSEYYELV-----NDEEAVYGCFDKCTQDLKR 365

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1602 AVQYNEplkvflhlADIYAKSE-KFQEAGELynrMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEcLPSKEHvD 1680
Cdd:COG5107   366 KYSMGE--------SESASKVDnNFEYSKEL---LLKRINKLTFVFCVHLNYVLRKRGLEAARKLFIKLRK-EGIVGH-H 432

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1681 VIAKFAQLEFQ-LGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVIHlSLAPKRMKFFFKRYLDY 1759
Cdd:COG5107   433 VYIYCAFIEYYaTGDRATAYNIFELGLLKFPDSTLYKEKYLLFLIRINDEENARALFETSVE-RLEKTQLKRIYDKMIEY 511

                         250       260
                  ....*....|....*....|....*..
gi 767962239 1760 EKQHGTEKDVQAVKAKALEYVEAKSSV 1786
Cdd:COG5107   512 ESMVGSLNNVYSLEERFRELVPQENLI 538
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 295-351 2.13e-06

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


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 46.60  E-value: 2.13e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767962239  295 KKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLS 351
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. ...
 646-715 2.34e-06

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


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 46.81  E-value: 2.34e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767962239  646 GMLLIGFVKSIKDYGVFI---QFPsGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
Cdd:cd04452     4 GELVVVTVKSIADMGAYVsllEYG-NIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK 75
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 99-441 3.09e-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: 51.20  E-value: 3.09e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   99 EALKPGMLLTGTVSSLEDHGYLVDIGvdGTRAFLPLlkAQEYIRQKNKGAKLkVGQYLNCIVEKV--KGNGGVVSlsvgH 176
Cdd:COG0539    98 EAFENGEPVEGKVKGVVKGGLIVDIG--GVRAFLPA--SQVDVRPVRDLDEY-VGKTLEFKIIKLdrKRNNVVVS----R 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  177 SEVSTAIATEQQSWNLNNLLPGLVVKAQVQKVTPFGLTLNFltfftGVVDFMhldpkkagtyfsnqavracilcvhprtr 256
Cdd:COG0539   169 RAVLEEEREEKREELLEKLEEGDVVEGTVKNITDFGAFVDL-----GGVDGL---------------------------- 215

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  257 vVHLSlrpiflqpgrpltrlscqnlgavlDdvpvqgffkkagatfrlkdgvLAYARLSHLSdsknvfnpEAFKPGNTHKC 336
Cdd:COG0539   216 -LHIS------------------------E---------------------ISWGRVKHPS--------EVLKVGDEVEV 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  337 RIIDYSQMDELALLSLRT------SIIEAQYlryhdiEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVppmHLADILM--- 407
Cdd:COG0539   242 KVLKIDREKERISLSLKQlqpdpwENIAEKY------PVGDVVKGKVTRLTDFGAFVELEPGVEGLV---HISEMSWtkr 312

                         330       340       350
                  ....*....|....*....|....*....|....*
gi 767962239  408 -KNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKT 441
Cdd:COG0539   313 vAHPSDVVKVGDEVEVKVLDIDPEERRISLSIKQL 347
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 371-535 4.94e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 50.57  E-value: 4.94e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  371 AVVKGTVLTIKSYGMLVKVgEQMRGLVPPMHLAdilmKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIESKLPVI 450
Cdd:PRK07400  120 ATVRSEVFATNRGGALVRI-EGLRGFIPGSHIS----TRKPKEELVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRL 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  451 tcyadaKPGLQTHGFIIRVKDYGCIVKFyNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKlS 530
Cdd:PRK07400  195 ------EVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTK-Q 266


                  ....*
gi 767962239  531 SDPEP 535
Cdd:PRK07400  267 LEPEP 271
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
295-353 5.63e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 45.67  E-value: 5.63e-06
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239    295 KKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSLR 353
Cdd:smart00316   14 TPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 643-713 6.32e-06

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


Pssm-ID: 240210 [Multi-domain]  Cd Length: 74  Bit Score: 45.47  E-value: 6.32e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767962239  643 IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTS---DHFVEGQTVAAKVTNVDEEKQRMLLS 713
Cdd:cd05705     1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSlynKYLPEGKLLTAKVLSVNSEKNLVELS 74
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 543-817 1.18e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 49.87  E-value: 1.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  543 SQKKGKAINIGQLVDVKVLEKTKDGLEVAVLPHNIRAFLPTSHLS-DHVANGPLLhhwLQAGDILH-RVLCLSQSEGRVL 620
Cdd:PRK06676    8 SLNSVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSnDHIEDINDV---VKVGDELEvYVLKVEDGEGNLL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  621 LCRKPALVStveggqdpKNFSEI----HPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDhFVeGQTV 696
Cdd:PRK06676   85 LSKRRLEAE--------KAWDKLeekfEEGEVVEVKVTEVVKGGLVVDV-EGVRGFIPASLISTRFVEDFSD-FK-GKTL 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  697 AAKVTNVDEEKQRMLLSLRlsdcglgdlAItsllllnqcLEElqgvrSLMSNRDSVLiQTLAEmtpGMFLDLVVQEVLED 776
Cdd:PRK06676  154 EVKIIELDPEKNRVILSRR---------AV---------VEE-----ERAAKKEELL-SSLKE---GDVVEGTVARLTDF 206

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 767962239  777 GSVVFSGGpVPDLV----LKASRYHRAGQEVESGQKKKVVILNVD 817
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 ...
 646-713 1.27e-05

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


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 44.59  E-value: 1.27e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767962239  646 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 713
Cdd:cd05707     1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 949-1305 1.80e-05

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 48.89  E-value: 1.80e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  949 TLSIGDMVTGTVKSIKPTHVVVTL---EDGIIgciHASHILDDvpegtSPTTKLKVGKTVTARVIGGRDmktfkylpish 1025
Cdd:COG0539    15 ELKEGDIVKGTVVSIDDDEVLVDIgykSEGII---PLSEFSDE-----PGELEVKVGDEVEVYVEKVED----------- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1026 pRFVRTIpeLSVRPSELEDGhtalnthsvspMEKIKQ-YQAGQTVTCFLKkyNVVKKWLEVEIApDIRGRIP-------- 1096
Cdd:COG0539    76 -GEGEIV--LSKKKADREKA-----------WEELEEaFENGEPVEGKVK--GVVKGGLIVDIG-GVRAFLPasqvdvrp 138

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1097 ------LLLTSLSFKVLKHPDKKFRVgqalratVVgpdSSKTLL----------CLSltgphKLEEGEVAMGRVVKVTpN 1160
Cdd:COG0539   139 vrdldeYVGKTLEFKIIKLDRKRNNV-------VV---SRRAVLeeereekreeLLE-----KLEEGDVVEGTVKNIT-D 202

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1161 EGLTVSFPfGKIGTVsifHMSD-SYS--ETPlEDFVpqKV---VRCYILS--TADNVLTLSLrssrtnpetKSKVEDPEI 1232
Cdd:COG0539   203 FGAFVDLG-GVDGLL---HISEiSWGrvKHP-SEVL--KVgdeVEVKVLKidREKERISLSL---------KQLQPDPWE 266

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767962239 1233 NSIQDIKEGQLLRGYVGSIQPHGVFFRLGPSVVGLArysHVSQHSPSKKalyNKH----LPEGKLLTARVLRLNHQK 1305
Cdd:COG0539   267 NIAEKYPVGDVVKGKVTRLTDFGAFVELEPGVEGLV---HISEMSWTKR---VAHpsdvVKVGDEVEVKVLDIDPEE 337
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1151-1214 1.91e-05

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


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 43.91  E-value: 1.91e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767962239 1151 MGRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILSTADNVLTLSL 1214
Cdd:cd00164     2 TGKVVSITKF-GVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISL 64
COG4700 COG4700
Uncharacterized conserved protein ECs_4300, contains TPR-like domain [Function unknown];
1600-1756 2.13e-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: 2.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1600 ERAVQYNEPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVwIKYGA----FLLRRSQAAASHrvLQRALECLPS 1675
Cdd:COG4700    80 EKALEFADTVQNRVRLADALLELGRYDEAIELYEEALTGIFADDPH-ILLGLaqalFELGRYAEALET--LEKLIAKNPD 156

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1676 KEHVDVIAKFAQ-LEfQLGDAERAKAIFENTLSTYPKRtDVWSVYIDMTIKHGSQKDVRDIFERVIHLSlapKRMKFFFK 1754
Cdd:COG4700   157 FKSSDAHLLYARaLE-ALGDLEAAEAELEALARRYSGP-EARYRYAKFLARQGRTAEAKELLEEILDEA---KHMPKHYR 231


                  ..
gi 767962239 1755 RY 1756
Cdd:COG4700   232 RL 233
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1064-1138 2.24e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 44.13  E-value: 2.24e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239   1064 QAGQTVTCFLKkyNVVKKWLEVEIAPDIRGRIPLllTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTLLCLSL 1138
Cdd:smart00316    1 EVGDVVEGTVT--EITPGGAFVDLGNGVEGLIPI--SELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 366-425 2.61e-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: 2.61e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767962239  366 DIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVppmH---LADILMKNPEKKYHIGDEVKCRVL 425
Cdd:COG1098     2 SIEVGDIVEGKVTGITPFGAFVELPEGTTGLV---HiseIADGYVKDINDYLKVGDEVKVKVL 61
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 641-715 4.49e-05

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 48.51  E-value: 4.49e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239  641 SEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDeEKQRMLLSLR 715
Cdd:PRK11824  617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRLSRK 690
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
551-624 4.96e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.98  E-value: 4.96e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239    551 NIGQLVDVKVLEKTKDGLEVAvLPHNIRAFLPTSHLSDHvaNGPLLHHWLQAGDILH-RVLCLSQSEGRVLLCRK 624
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVD-LGNGVEGLIPISELSDK--RVKDPEEVLKVGDEVKvKVLSVDEEKGRIILSLK 72
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 370-439 5.21e-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: 5.21e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  370 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 439
Cdd:cd05691     1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
197-263 5.42e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.98  E-value: 5.42e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767962239    197 PGLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKAG----TYFSNQAVRACILCVHPRTRVVHLSLR 263
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKdpeeVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 953-1010 5.51e-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: 5.51e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 767962239  953 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPegTSPTTKLKVGKTVTARVI 1010
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 ...
 1239-1314 5.78e-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: 5.78e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767962239 1239 KEGQLLRGYVGSIQPHGVFFRL-GPSVVGLArysHVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELSFLP 1314
Cdd:cd05708     1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLC---HKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKA 74
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1511-1638 5.86e-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: 5.86e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1511 EALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisFREEQEklnVWVALLNLENMYG 1590
Cdd:COG4783    12 QALLLAGDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALEL--DPDEPE---ARLNLGLALLKAG 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 767962239 1591 SQESLTKVFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKR 1638
Cdd:COG4783    87 DYDEALALLEKALKLDpEHPEAYLRLARAYRALGRPDEAIAALEKALEL 135
PTZ00121 PTZ00121
MAEBL; Provisional
 1319-1610 6.39e-05

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 48.21  E-value: 6.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1319 KPDVLSASLEgQLTKQEERKTEAEERDQKGEKKNQKRNEKKN----QKGQEEVempsKEKQQPQKPQAQKRGGRECRESG 1394
Cdd:PTZ00121 1379 KADAAKKKAE-EKKKADEAKKKAEEDKKKADELKKAAAAKKKadeaKKKAEEK----KKADEAKKKAEEAKKADEAKKKA 1453

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1395 SEQERVSKKPKKAGLSEEDDSLVDvyYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAwnvglDSLTPA-------- 1466
Cdd:PTZ00121 1454 EEAKKAEEAKKKAEEAKKADEAKK--KAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKA-----DEAKKAeeakkade 1526

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1467 LPPLAESSDSEEDEKPHQ---ATQIKKSKKERELEKQKAEKELSRIEEALMDPGRQPESADDFDRLVLSSPNSSILWLQY 1543
Cdd:PTZ00121 1527 AKKAEEAKKADEAKKAEEkkkADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKK 1606

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767962239 1544 MAFHlQATEIEKARAVAERALKtisfrEEQEKLNVWVALLNLENMYGSQESLTKVFERAVQYNEPLK 1610
Cdd:PTZ00121 1607 MKAE-EAKKAEEAKIKAEELKK-----AEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEA 1667
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 464-546 6.58e-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: 6.58e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  464 GFIIRVKDYGCIVKFYNNVQGLVpkH--ELSTEYIPDPERVFYTGQVVKVVVLNCEPSKeRMLLSFK-LSSDPEPKKEPA 540
Cdd:COG1098    11 GKVTGITPFGAFVELPEGTTGLV--HisEIADGYVKDINDYLKVGDEVKVKVLSIDEDG-KISLSIKqAEEKPKRPPRPR 87


                  ....*.
gi 767962239  541 GHSQKK 546
Cdd:COG1098    88 RNSRPK 93
CpoB COG1729
Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane ...
 1617-1711 9.68e-05

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: 9.68e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1617 DIYAKSEKFQEAGELYNRMLKRFRQEK---AVWIKYGAFLLRRSQAAASHRVLQRALECLP-SKEHVDVIAKFAQLEFQL 1692
Cdd:COG1729     1 KALLKAGDYDEAIAAFKAFLKRYPNSPlapDALYWLGEAYYALGDYDEAAEAFEKLLKRYPdSPKAPDALLKLGLSYLEL 80

                          90
                  ....*....|....*....
gi 767962239 1693 GDAERAKAIFENTLSTYPK 1711
Cdd:COG1729    81 GDYDKARATLEELIKKYPD 99
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 370-425 9.83e-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: 9.83e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767962239  370 GAVVKGTVLTIKSYGMLVKVGEQMRGLVppmHLADIL-----MKNPEKKYHIGDEVKCRVL 425
Cdd:cd05702     1 GDLVKAKVKSVKPTQLNVQLADNVHGRI---HVSEVFdewpdGKNPLSKFKIGQKIKARVI 58
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 369-434 1.00e-04

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


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 42.23  E-value: 1.00e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  369 PGAVVKGTVLTIKSYGMLVKVGeQMRGLVppmHLADIL---MKNPEKKYHIGDEVKCRVLLCDPEAKKL 434
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 ...
 952-1011 1.05e-04

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 42.27  E-value: 1.05e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   952 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1011
Cdd:pfam00575    3 KGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVE--DPDEVIKVGDEVKVKVLK 60
PRK08059 PRK08059
general stress protein 13; Validated
 469-546 1.06e-04

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 43.50  E-value: 1.06e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  469 VKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKLSSD-PEPKKEPAGHSQKK 546
Cdd:PRK08059   18 IQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEaPEAKRKKGKILIPN 96
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 643-718 1.07e-04

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


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 42.97  E-value: 1.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  643 IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVT-------------------STSDHFVEGQTVAAKVTNV 703
Cdd:cd05693     1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTErleeldeeseeeddeeelpDLEDLFSVGQLVRCKVVSL 80

                          90
                  ....*....|....*...
gi 767962239  704 DEE---KQRMLLSLRLSD 718
Cdd:cd05693    81 DKSksgKKRIELSLEPEL 98
Suf pfam05843
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ...
 1645-1787 1.18e-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: 46.21  E-value: 1.18e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1645 VWIKYGAFLlRRSQAAASHR-VLQRALEclpsKEHV--DVIAKFAQLEFQLG-DAERAKAIFENTLSTYPKRTDVWSVYI 1720
Cdd:pfam05843    3 VWIQYMRAM-RRAEGIKGARkVFKKARK----RPRLtyHVYVASALMEYYCSkDPAVAFKIFELGLKLFPEDEEFVLKYL 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767962239  1721 DMTIKHGSQKDVRDIFERVIHlSLAPKRM-KFFFKRYLDYEKQHGTEKDVQAVKAKALEYVEAKSSVL 1787
Cdd:pfam05843   78 DYLISLNDDNNARVLFERVLT-RLAQEKEaKPLWKKFISYESTFGDLASILKLEKRMAELFPEDPPLA 144
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 370-434 1.37e-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: 1.37e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  370 GAVVKGTVLTIKSYGMLVKVGEQMRGLVppmHLADI----LMKNPEKKYHIGDEVKCRVLLCDPEAKKL 434
Cdd:cd05690     1 GTVVSGKIKSITDFGIFVGLDGGIDGLV---HISDIswtqRVRHPSEIYKKGQEVEAVVLNIDVERERI 66
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 464-530 1.42e-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: 1.42e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767962239  464 GFIIRVKDYGCIVKFYN-NVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKLS 530
Cdd:cd05708     8 GTVRRVEDYGVFIDIDGtNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75
rpsA PRK13806
30S ribosomal protein S1; Provisional
 363-715 1.51e-04

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 46.26  E-value: 1.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  363 RYHDIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPmhlADILMKNPEKKYHIGDEVKCRVLLCDPEAKKL-------- 434
Cdd:PRK13806   28 RKTELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDR---AELLDADGELTVAVGDEVELYVVSVNGQEIRLskalsgqg 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  435 -MMTLKKTLiESKLPVITCYADAKPGlqthGFIIRV--KDYGCivkfynnvqglvPKHELSTEYIPDPERvfYTGQVVKV 511
Cdd:PRK13806  105 gAAMLEEAY-ENGVPVEGKVTGTCKG----GFNVEVlgRRAFC------------PVSQIDLRYVEDPES--YVGQTFQF 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  512 VVLNCEPSKERMLLSFKLSSDPEPKKEPAGHSQKkgkaINIGQLVDVKVLEKTKDGLEVAVLPhNIRAFLPTSHLSDHVA 591
Cdd:PRK13806  166 LITRVEENGRNIVVSRRALLEREQKEALEAFMET----VKEGDVVEGTVTRLAPFGAFVELAP-GVEGMVHISELSWSRV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  592 NGPllHHWLQAGDILH-RVLCLSQSEG----RVLLCRKPAlvstvegGQDPKNF--SEIHPGMLLIGFVKSIKDYGVFIQ 664
Cdd:PRK13806  241 QKA--DEAVSVGDTVRvKVLGIERAKKgkglRISLSIKQA-------GGDPWDTvgDRLKAGDKVTGKVVRLAPFGAFVE 311

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 767962239  665 FPSGLSGLAPKAIMS-DKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
Cdd:PRK13806  312 ILPGIEGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLR 363
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 953-1011 1.66e-04

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


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 41.49  E-value: 1.66e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  953 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1011
Cdd:cd05691     1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVE--DATERFKVGDEVEAKITN 57
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 370-432 1.70e-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: 1.70e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767962239  370 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAK 432
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGR 63
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 364-424 1.78e-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: 41.44  E-value: 1.78e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767962239  364 YHDIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLvppMHLADILMknpekKYHIGDEVKCRV 424
Cdd:cd04473    11 MEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGL---IHRSNLLR-----DYEVGDEVIVQV 63
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
950-1010 2.08e-04

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 42.77  E-value: 2.08e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239  950 LSIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHI----LDDVPEgtspttKLKVGKTVTARVI 1010
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 ...
 370-437 2.36e-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: 2.36e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767962239  370 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMT 437
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 ...
 1144-1205 2.61e-04

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


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 41.82  E-value: 2.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1144 LEEGEVAMGRVVKVTPNEgLTVSFPFGKIGTVSIFHMSDSYS-----------------ETP-LED-FVPQKVVRCYILS 1204
Cdd:cd05693     1 LSEGMLVLGQVKEITKLD-LVISLPNGLTGYVPITNISDAYTerleeldeeseeeddeeELPdLEDlFSVGQLVRCKVVS 79


                  .
gi 767962239 1205 T 1205
Cdd:cd05693    80 L 80
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 1523-1674 2.67e-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: 2.67e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1523 ADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTISFREEQEKLNVWVALLNLENMygsQESLtKVFERA 1602
Cdd:COG5010     5 EGFDRLPLYLLLLTKLRTLVEKYEAALAGANNTKEDELAAAGRDKLAKAFAIESPSDNLYNKLGDF---EESL-ALLEQA 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767962239 1603 VQYNEPL-KVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLP 1674
Cdd:COG5010    81 LQLDPNNpELYYNLALLYSRSGDKDEAKEYYEKALALSPDNPNAYSNLAALLLSLGQDDEAKAALQRALGTSP 153
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 651-715 2.87e-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: 2.87e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239  651 GFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
Cdd:cd05691     6 GKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 4-87 2.98e-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: 40.80  E-value: 2.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239    4 LGCVKEVNELE-LVISLPNGLQGFVQVTEICDAYTkklneqvtqEQPLKDllhlpelFSPGMLVRCVVSSlgitdRGKKS 82
Cdd:cd05704     8 LGMVTKVIPHSgLTVQLPFGKTGLVSIFHLSDSYT---------ENPLEG-------FKPGKIVRCCILS-----KKDGK 66


                  ....*
gi 767962239   83 VKLSL 87
Cdd:cd05704    67 YQLSL 71
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 464-514 3.19e-04

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


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 40.60  E-value: 3.19e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 767962239  464 GFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVL 514
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 ...
 464-526 3.30e-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: 3.30e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767962239  464 GFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 526
Cdd:cd05707     6 GFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 953-1011 3.69e-04

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


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 40.35  E-value: 3.69e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  953 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDvpEGTSPTTKLKVGKTVTARVIG 1011
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHK--RVKDVKDVLKEGDKVKVKVLS 57
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 103-173 3.74e-04

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


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 40.30  E-value: 3.74e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767962239  103 PGMLLTGTVSSLEDHGYLVDIG-VDGtraflpLLKAQE--YIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 173
Cdd:cd05688     1 EGDVVEGTVKSITDFGAFVDLGgVDG------LLHISDmsWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
952-1010 3.85e-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: 3.85e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  952 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVI 1010
Cdd:PRK00087  562 VGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRID--KPEDVLSEGEEVKAKIL 618
PTZ00121 PTZ00121
MAEBL; Provisional
 1319-1528 3.87e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 45.52  E-value: 3.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1319 KPDVLSASLEGQLTKQEERKTEAEERDQKGEKKNQKRNE--KKNQKGQEEVEMPSKEKQQPQKPQAQKRGGRECRESGSE 1396
Cdd:PTZ00121 1634 KVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEdkKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAE 1713

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1397 QERVSKKPKKAglSEEDDSLVDVYYREGKEE---AEETNVLPKEK----QTKPAEAPRLQLSSGFAWNV---GLDSLTPA 1466
Cdd:PTZ00121 1714 EKKKAEELKKA--EEENKIKAEEAKKEAEEDkkkAEEAKKDEEEKkkiaHLKKEEEKKAEEIRKEKEAVieeELDEEDEK 1791

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767962239 1467 LPPLAESsdSEEDEKPHQATQIKKSKKERELEKQKAEKELSRIEEALMDPGRQPESADDFDR 1528
Cdd:PTZ00121 1792 RRMEVDK--KIKDIFDNFANIIEGGKEGNLVINDSKEMEDSAIKEVADSKNMQLEEADAFEK 1851
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1-87 3.90e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 40.66  E-value: 3.90e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239      1 MRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQvtqeqplkdllhlpelFSPGMLVRCVVSSLgitDRGK 80
Cdd:smart00316    4 DVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEV----------------LKVGDEVKVKVLSV---DEEK 64


                    ....*..
gi 767962239     81 KSVKLSL 87
Cdd:smart00316   65 GRIILSL 71
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 643-715 4.02e-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: 40.31  E-value: 4.02e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767962239  643 IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
Cdd:cd05706     1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73
PRK08582 PRK08582
RNA-binding protein S1;
643-706 4.36e-04

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 42.33  E-value: 4.36e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767962239  643 IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEE 706
Cdd:PRK08582    3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDD 66
PTZ00121 PTZ00121
MAEBL; Provisional
 1333-1643 4.98e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 45.13  E-value: 4.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1333 KQEERKTEAEERDQKGEKKNQKRN--EKKNQKGQEEVEMPSKEKQQPQKPQAQKRGGRECRESGSEQERVSKKPKKAglS 1410
Cdd:PTZ00121 1323 KAEEAKKKADAAKKKAEEAKKAAEaaKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKK--A 1400

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1411 EEDDSLVDVYYR--EGKEEAEETNVLPKEK------QTKPAEAPRLQLSSGFAWNVglDSLTPALPPLAESSDSEE-DEK 1481
Cdd:PTZ00121 1401 EEDKKKADELKKaaAAKKKADEAKKKAEEKkkadeaKKKAEEAKKADEAKKKAEEA--KKAEEAKKKAEEAKKADEaKKK 1478

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1482 PHQATQIKKSKKERELEKQKAEkELSRIEEA--LMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAV 1559
Cdd:PTZ00121 1479 AEEAKKADEAKKKAEEAKKKAD-EAKKAAEAkkKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEEL 1557

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1560 --AERALKTISFREEQEKlnvwvallnlENMYGSQESLTKVFERAvQYNEPLKVFLHLADIYAKSEKFQEAGELYNRMLK 1637
Cdd:PTZ00121 1558 kkAEEKKKAEEAKKAEED----------KNMALRKAEEAKKAEEA-RIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELK 1626


                  ....*.
gi 767962239 1638 RFRQEK 1643
Cdd:PTZ00121 1627 KAEEEK 1632
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 459-525 5.64e-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: 5.64e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767962239  459 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLL 525
Cdd:cd05690     1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1077-1137 5.95e-04

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


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 39.67  E-value: 5.95e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767962239 1077 NVVKKWLEVEIAPDIRGRIPLllTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTLLCLS 1137
Cdd:cd00164     7 SITKFGVFVELEDGVEGLVHI--SELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 646-714 6.80e-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: 6.80e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  646 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSL 714
Cdd:cd05697     1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 370-434 6.85e-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: 39.52  E-value: 6.85e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239  370 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKL 434
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRI 65
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 87-224 7.06e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 44.10  E-value: 7.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   87 LNPKNVNRVLSAEA----------------LKPGMLLTGTVSSLEDHGYLVDIG-VDGtraflpLLKAQE--YIRQKNKG 147
Cdd:PRK06676  160 LDPEKNRVILSRRAvveeeraakkeellssLKEGDVVEGTVARLTDFGAFVDIGgVDG------LVHISElsHERVEKPS 233

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  148 AKLKVGQYLNCIVEKVKGNGGVVSLSVGhsevstaiATEQQSWNL--NNLLPGLVVKAQVQKVTPFGLtlnFLTFFTGV 224
Cdd:PRK06676  234 EVVSVGQEVEVKVLSIDWETERISLSLK--------DTLPGPWEGveEKLPEGDVIEGTVKRLTDFGA---FVEVLPGV 301
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
3-263 7.23e-04

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 44.55  E-value: 7.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239    3 ILGCVKEVNELELVISLpNGLQGFVQVTEICDAYTKKLNEQVTQEQPLKDLlhlpElFSPGMLVRCVVSslgitdrgKKS 82
Cdd:PRK00087  393 VKGKVKEVVKGGLLVDY-GGVRAFLPASHVELGYVEDLSEYKGQELEVKII----E-FNRKRRKKVVLS--------RKA 458

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239   83 VKLSLNPKNVNRVLsaEALKPGMLLTGTVSSLEDHGYLVDI-GVDGtraflpLLKAQE--YIRQKNKGAKLKVGQYLNCI 159
Cdd:PRK00087  459 ILEEEKEKKKEETW--NSLEEGDVVEGEVKRLTDFGAFVDIgGVDG------LLHVSEisWGRVEKPSDVLKVGDEIKVY 530

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  160 VEKVKGNGGVVSLSvghsevstaiateqqswnLNNLLP------------GLVVKAQVQKVTPFGLtlnFLTFFTGVVDF 227
Cdd:PRK00087  531 ILDIDKENKKLSLS------------------LKKLLPdpwenveekypvGSIVLGKVVRIAPFGA---FVELEPGVDGL 589

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 767962239  228 MHLD---------PKKAgtYFSNQAVRACILCVHPRTRVVHLSLR 263
Cdd:PRK00087  590 VHISqiswkridkPEDV--LSEGEEVKAKILEVDPEEKRIRLSIK 632
rpsA PRK13806
30S ribosomal protein S1; Provisional
 1085-1267 8.69e-04

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 43.94  E-value: 8.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1085 VEIAPDIRGRIPLllTSLSFKVLKHPDKKFRVGQALRATVVGPDSSK----TLLCLSL---------TGPHKLEEGEVAM 1151
Cdd:PRK13806  220 VELAPGVEGMVHI--SELSWSRVQKADEAVSVGDTVRVKVLGIERAKkgkgLRISLSIkqaggdpwdTVGDRLKAGDKVT 297

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1152 GRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFV-PQKVVRCYI--LSTADNVLTLSLRSSRTnpetkskve 1228
Cdd:PRK13806  298 GKVVRLAPF-GAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVaPGDAVAVKIkdIDPAKRRISLSLRDAEG--------- 367

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 767962239 1229 DPEINSIQDIKEGQLLRGYVGSIQPHGVFFRLGPSVVGL 1267
Cdd:PRK13806  368 DPWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGL 406
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 645-715 9.03e-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: 9.03e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767962239  645 PGMLLIGFV-KSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVtnVDEEKQRMLLSLR 715
Cdd:cd05704     3 EGAVTLGMVtKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCI--LSKKDGKYQLSLR 72
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 457-715 1.04e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 43.93  E-value: 1.04e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  457 KPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTeyipdPERvfyTGQVVKVVVLNCEPSKERMllsFKLSSDPEPK 536
Cdd:PRK12269  320 EPGSVRMGTVVQVNAGTVFVDIGGKSEGRVPVEEFEA-----PPK---AGDGVRVYVERVTPYGPEL---SKTKADRLGL 388

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  537 KEPAGHSQKKGKAINiGQLVDvkvLEKTKDGLEVAvLPHNIRAFLPTSHLSDHVANGPLLHHWLQAGDILHRVLCLSQSE 616
Cdd:PRK12269  389 KVKLRDAERDGTPVE-GRIVR---LTEKKSGFEVD-LGAGMMAFLPISQSDCQKVDAPESLIGLTSKFYIERISQSKQHR 463

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  617 GR--VLLCRKPALVSTVEGGQDpKNFSEIHPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQ 694
Cdd:PRK12269  464 GNdnIVINRRRYLEERARQARE-EFFNSVHIEDSVSGVVKSFTSFGAFIDL-GGFDGLLHVNDMSWGHVARPREFVKKGQ 541

                         250       260
                  ....*....|....*....|.
gi 767962239  695 TVAAKVTNVDEEKQRMLLSLR 715
Cdd:PRK12269  542 TIELKVIRLDQAEKRINLSLK 562
PTZ00121 PTZ00121
MAEBL; Provisional
 1330-1511 1.06e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 44.36  E-value: 1.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1330 QLTKQEE-RKTE----AEERDQKGEKKNQKRNEKKNQKGQEEVEMPSKEKQQPQKPQAQKRGGRECRESGSEQERVSKKP 1404
Cdd:PTZ00121 1556 ELKKAEEkKKAEeakkAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKV 1635

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1405 KKAGLSEEDdslvDVYYREGKEEAEETNVLPKEKQTKPAEAPRLQlssgfawnvgldsltpalpplAESSDSEEDEKPHQ 1484
Cdd:PTZ00121 1636 EQLKKKEAE----EKKKAEELKKAEEENKIKAAEEAKKAEEDKKK---------------------AEEAKKAEEDEKKA 1690

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 767962239 1485 ATQIKKS----------KKERELEKQKAEkELSRIEE 1511
Cdd:PTZ00121 1691 AEALKKEaeeakkaeelKKKEAEEKKKAE-ELKKAEE 1726
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
949-1311 1.13e-03

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 43.78  E-value: 1.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  949 TLSIGDMVTGTVKSIKPTHVVVTL---EDGIIGCIHASHilddvPEGTSPTTKLKVGKTVTARVIGGRDmktfkylpish 1025
Cdd:PRK00087  299 QIRRGDIVKGTVVSVNENEVFVDVgykSEGVIPLRELTL-----DEISSLKESVKVGDEIEVKVLKLED----------- 362

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1026 prfvrtipelsvrpselEDGHTALN---THSVSPMEKIKQ-YQAGQTVTCFLKKynVVKKWLEVEIApDIRGRIPLLLTS 1101
Cdd:PRK00087  363 -----------------EDGYVVLSkkeADREKAWKELEEaFENGEPVKGKVKE--VVKGGLLVDYG-GVRAFLPASHVE 422

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1102 LSFKvlkhPDKKFRVGQALRATVVGPD---------SSKTLLCLSLTGPHK-----LEEGEVAMGRVVKVTPNeGLtvsf 1167
Cdd:PRK00087  423 LGYV----EDLSEYKGQELEVKIIEFNrkrrkkvvlSRKAILEEEKEKKKEetwnsLEEGDVVEGEVKRLTDF-GA---- 493

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1168 pFGKIGTVS-IFHMSD---SYSETPLEDFVPQKVVRCYILSTADNVLTLSLrsSRtnpetKSKVEDPEINSIQDIKEGQL 1243
Cdd:PRK00087  494 -FVDIGGVDgLLHVSEiswGRVEKPSDVLKVGDEIKVYILDIDKENKKLSL--SL-----KKLLPDPWENVEEKYPVGSI 565

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767962239 1244 LRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQH---SPSKKalynkhLPEGKLLTARVLRLNHQKNLVELS 1311
Cdd:PRK00087  566 VLGKVVRIAPFGAFVELEPGVDGLVHISQISWKridKPEDV------LSEGEEVKAKILEVDPEEKRIRLS 630
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1416-1711 1.24e-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: 43.92  E-value: 1.24e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1416 LVDVYYREGKEEaEETNVLPKEKQTKPAE-APRLQLSSGFawnVGLDSLTPALPPLAESSDSEEDEKphQATQIKKSKke 1494
Cdd:TIGR02917  539 LAGLYLRTGNEE-EAVAWLEKAAELNPQEiEPALALAQYY---LGKGQLKKALAILNEAADAAPDSP--EAWLMLGRA-- 610

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1495 relekQKAEKELSRIEEAlmdpgrqpesaddFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALktisfreeQE 1574
Cdd:TIGR02917  611 -----QLAAGDLNKAVSS-------------FKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRAL--------EL 664

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1575 KLNVWVALL---NLENMYGSQESLTKVFeRAVQYNEPLKVFLH--LADIYAKSEKFQEAGELYNRMLKRFRQEKAVwIKY 1649
Cdd:TIGR02917  665 KPDNTEAQIglaQLLLAAKRTESAKKIA-KSLQKQHPKAALGFelEGDLYLRQKDYPAAIQAYRKALKRAPSSQNA-IKL 742

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 767962239  1650 GAFLLRRSQAAASHRVLQRALeclpsKEHV-DVIAKFAQLEFQLGDAERAKAI--FENTLSTYPK 1711
Cdd:TIGR02917  743 HRALLASGNTAEAVKTLEAWL-----KTHPnDAVLRTALAELYLAQKDYDKAIkhYQTVVKKAPD 802
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 1613-1743 1.32e-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: 1.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1613 LHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQL 1692
Cdd:COG5010    24 VEKYEAALAGANNTKEDELAAAGRDKLAKAFAIESPSDNLYNKLGDFEESLALLEQALQLDP--NNPELYYNLALLYSRS 101

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 767962239 1693 GDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVIHLS 1743
Cdd:COG5010   102 GDKDEAKEYYEKALALSPDNPNAYSNLAALLLSLGQDDEAKAALQRALGTS 152
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 5-86 1.33e-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: 1.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239    5 GCVKEVNELELVISLPNGLQGFVQVTEICDAYTKklneqvtqeqplkdllHLPELFSPGMLVRCVVSSLgitDRGKKSVK 84
Cdd:cd00164     3 GKVVSITKFGVFVELEDGVEGLVHISELSDKFVK----------------DPSEVFKVGDEVEVKVLEV---DPEKGRIS 63


                  ..
gi 767962239   85 LS 86
Cdd:cd00164    64 LS 65
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1512-1700 1.34e-03

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 42.30  E-value: 1.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1512 ALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisfreeqeKLNVWVALLNLENMYGS 1591
Cdd:COG0457    51 AYLRLGRYEEALADYEQALELDPDDAEALNNLGLALQALGRYEEALEDYDKALEL--------DPDDAEALYNLGLALLE 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1592 QESLTK---VFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNrmlKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQ 1667
Cdd:COG0457   123 LGRYDEaieAYERALELDpDDADALYNLGIALEKLGRYEEALELLE---KLEAAALAALLAAALGEAALALAAAEVLLAL 199

                         170       180       190
                  ....*....|....*....|....*....|...
gi 767962239 1668 RALECLPSKEHVDVIAKFAQLEFQLGDAERAKA 1700
Cdd:COG0457   200 LLALEQALRKKLAILTLAALAELLLLALALLLA 232
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 107-173 1.43e-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: 1.43e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767962239  107 LTGTVSSLEDHGYLVDIGvDGTRAFLPLLKAQEYiRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 173
Cdd:cd00164     1 VTGKVVSITKFGVFVELE-DGVEGLVHISELSDK-FVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 7-51 1.63e-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: 1.63e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 767962239    7 VKEVNELELVISLPNGLQGFVQVTEICDAYTkklneqvTQEQPLK 51
Cdd:cd05702     8 VKSVKPTQLNVQLADNVHGRIHVSEVFDEWP-------DGKNPLS 45
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 360-440 2.02e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 42.72  E-value: 2.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  360 QYLRYHDIepGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 439
Cdd:PRK07899  286 QFARTHAI--GQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLK 363


                  .
gi 767962239  440 K 440
Cdd:PRK07899  364 Q 364
PTZ00121 PTZ00121
MAEBL; Provisional
 1330-1575 2.24e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 43.21  E-value: 2.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1330 QLTKQEERKTEAEERDQKGEKK--NQKRNEKKNQKGQEEVEMPSKEKQQPQKPQAQKRGGRECR---ESGSEQERVSKKP 1404
Cdd:PTZ00121 1501 EAKKAAEAKKKADEAKKAEEAKkaDEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKkaeEAKKAEEDKNMAL 1580

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1405 KKAGLSEE-----DDSLVDVYYREGKEEAEETNVLPKEK----QTKPAEAPRLQLSSgfawnvgLDSLTPALPPLAESSD 1475
Cdd:PTZ00121 1581 RKAEEAKKaeearIEEVMKLYEEEKKMKAEEAKKAEEAKikaeELKKAEEEKKKVEQ-------LKKKEAEEKKKAEELK 1653

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1476 SEEDEKPHQATQIKKSKKE---RELEKQKAEKELSRIEEALMDPGRQPESADDFDRLVLSSPNssilwlqymafhlQATE 1552
Cdd:PTZ00121 1654 KAEEENKIKAAEEAKKAEEdkkKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKK-------------KAEE 1720

                         250       260
                  ....*....|....*....|...
gi 767962239 1553 IEKARAVAERALKTISFREEQEK 1575
Cdd:PTZ00121 1721 LKKAEEENKIKAEEAKKEAEEDK 1743
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
1547-1638 2.25e-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: 2.25e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1547 HLQATEIEKARAVAERALKTisfreeqeKLNVWVALLNLENMYGSQESltkvFERAVQYNEPLK-------VFLHLADIY 1619
Cdd:COG3063     2 YLKLGDLEEAEEYYEKALEL--------DPDNADALNNLGLLLLEQGR----YDEAIALEKALKldpnnaeALLNLAELL 69

                          90
                  ....*....|....*....
gi 767962239 1620 AKSEKFQEAGELYNRMLKR 1638
Cdd:COG3063    70 LELGDYDEALAYLERALEL 88
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 553-624 2.38e-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: 2.38e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767962239  553 GQLVDVKVLEKTKDGLEVAVlpHNIRAFLPTSHLSD-HVAN-GPLLHHWLQAgdilhRVLCLSQSEGRVLLCRK 624
Cdd:cd04465     1 GEIVEGKVTEKVKGGLIVDI--EGVRAFLPASQVDLrPVEDlDEYVGKELKF-----KIIEIDRERNNIVLSRR 67
PRK08582 PRK08582
RNA-binding protein S1;
367-425 3.03e-03

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 39.63  E-value: 3.03e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  367 IEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVL 425
Cdd:PRK08582    3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVL 61
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 459-525 3.06e-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: 3.06e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767962239  459 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLL 525
Cdd:cd05689     4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDwTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISL 71
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1666-1747 3.06e-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: 3.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1666 LQRALECLPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLA 1745
Cdd:COG4235     6 LRQALAANP--NDAEGWLLLGRAYLRLGRYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEELLERA--LALD 81


                  ..
gi 767962239 1746 PK 1747
Cdd:COG4235    82 PD 83
DUF612 pfam04747
Protein of unknown function, DUF612; This family includes several uncharacterized proteins ...
 1316-1516 3.32e-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: 3.32e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1316 DTGKPDVLSASLEGQLTKQEERKTEAEERDQKGEKKNQKRNEKKNQKGQEEVEMPSKEKQQPQKPQAQkrggRECRESGS 1395
Cdd:pfam04747   49 DQRKEAFASLELTEQPQQVEKVKKSEKKKAQKQIAKDHEAEQKVNAKKAAEKEARRAEAEAKKRAAQE----EEHKQWKA 124

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1396 EQERVSKKPKKaglseEDDSLVDVYYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAWNVGLD-SLTPALPPLAESS 1474
Cdd:pfam04747  125 EQERIQKEQEK-----KEADLKKLQAEKKKEKAVKAEKAEKAEKTKKASTPAPVEEEIVVKKVANDrSAAPAPEPKTPTN 199

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 767962239  1475 DSEEDEKPHQATQIKKSKKERELEKQKAEKELSRIEEALMDP 1516
Cdd:pfam04747  200 TPAEPAEQVQEITGKKNKKNKKKSESEATAAPASVEQVVEQP 241
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1489-1711 4.17e-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: 4.17e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1489 KKSKKERELEKQ--------KAEKELSRIEealMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVA 1560
Cdd:TIGR02917  480 DLAKAREAFEKAlsiepdffPAAANLARID---IQEGNPDDAIQRFEKVLTIDPKNLRAILALAGLYLRTGNEEEAVAWL 556

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1561 ERALKTISfREEQEKLNVWVALLNLENMygsQESLTKVFERAVQYNEPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFR 1640
Cdd:TIGR02917  557 EKAAELNP-QEIEPALALAQYYLGKGQL---KKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQP 632

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767962239  1641 QEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPK 1711
Cdd:TIGR02917  633 DSALALLLLADAYAVMKNYAKAITSLKRALELKP--DNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQHPK 701
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1527-1710 5.20e-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: 5.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1527 DRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisfreEQEKLNvwvALLNLENMYGSQESL---TKVFERAV 1603
Cdd:TIGR02917  455 KKLEKKQPDNASLHNLLGAIYLGKGDLAKAREAFEKALSI-----EPDFFP---AAANLARIDIQEGNPddaIQRFEKVL 526

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  1604 QYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLP-SKEHVDV 1681
Cdd:TIGR02917  527 TIDpKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAADAAPdSPEAWLM 606

                          170       180
                   ....*....|....*....|....*....
gi 767962239  1682 IAKfAQLefQLGDAERAKAIFENTLSTYP 1710
Cdd:TIGR02917  607 LGR-AQL--AAGDLNKAVSSFKKLLALQP 632
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1241-1311 5.23e-03

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


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 37.27  E-value: 5.23e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767962239 1241 GQLLRGYVGSIQPHGVFFRLGPSVVGLARyshVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1311
Cdd:cd05707     1 GDVVRGFVKNIANNGVFVTLGRGVDARVR---VSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 1494-1751 5.37e-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: 5.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1494 ERELEKQKAEKELSRIEEALMDPGRQPESADDFDRLVLSSPNSSILWLqYMAFHLQATE-IEKARAVAERALKtisfree 1572
Cdd:COG3914    69 AAAAALLLLAALLELAALLLQALGRYEEALALYRRALALNPDNAEALF-NLGNLLLALGrLEEALAALRRALA------- 140

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1573 qeklnvwvalLNLENmygsqesltkvferavqynepLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAF 1652
Cdd:COG3914   141 ----------LNPDF---------------------AEAYLNLGEALRRLGRLEEAIAALRRALELDPDNAEALNNLGNA 189

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1653 LLRRSQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQLGDAERAkAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDV 1732
Cdd:COG3914   190 LQDLGRLEEAIAAYRRALELDP--DNADAHSNLLFALRQACDWEVY-DRFEELLAALARGPSELSPFALLYLPDDDPAEL 266

                         250       260
                  ....*....|....*....|..
gi 767962239 1733 RDI---FERVIHLSLAPKRMKF 1751
Cdd:COG3914   267 LALaraWAQLVAAAAAPELPPP 288
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 577-713 5.84e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 40.94  E-value: 5.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239  577 IRAFLPTSHLSDHVANGPLLHHWLQAgdilhRVLCLSQSEGRVLLCRKPALVStveggqdpKNFSEIHPGMLLIGFVKSI 656
Cdd:PRK07400  141 LRGFIPGSHISTRKPKEELVGEELPL-----KFLEVDEERNRLVLSHRRALVE--------RKMNRLEVGEVVVGTVRGI 207

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 767962239  657 KDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 713
Cdd:PRK07400  208 KPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLS 263
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 1143-1214 6.34e-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: 6.34e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767962239 1143 KLEEGEVAMGRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILS--TADNVLTLSL 1214
Cdd:cd04461    11 DLKPGMVVHGYVRNITPY-GVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSvdEEKQRFLLSL 83
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1597-1684 6.66e-03

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


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 38.45  E-value: 6.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767962239 1597 KVFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPS 1675
Cdd:COG4235    38 AAYEKALRLDpDNADALLDLAEALLAAGDTEEAEELLERALALDPDNPEALYLLGLAAFQQGDYAEAIAAWQKLLALLPA 117


                  ....*....
gi 767962239 1676 KEHVDVIAK 1684
Cdd:COG4235   118 DAPARLLEA 126
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
649-715 7.32e-03

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 38.14  E-value: 7.32e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767962239  649 LIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 715
Cdd:PRK07252    7 LKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLR 73
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 458-526 8.68e-03

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


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 36.45  E-value: 8.68e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767962239  458 PGLQTHGFIIRVKDYGCIVKFyNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 526
Cdd:cd05688     1 EGDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 950-1010 8.93e-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: 8.93e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767962239  950 LSIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPegTSPTTKLKVGKTVTARVI 1010
Cdd:cd04461    12 LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFV--TDPSFGFKKGQSVTAKVT 70
 
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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