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Conserved domains on  [gi|54607128|ref|NP_035183|]
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protein RRP5 homolog [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 80-176 1.28e-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: 136.96  E-value: 1.28e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   80 LCEGMRILGCVKEVSELELVVSLPNGLQGFVQVTEVCDAYTQKLNEQVAQEE---PLEDLLRLPELFSPGMLVRCVVSSL 156
Cdd:cd05693    1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEeedDEEELPDLEDLFSVGQLVRCKVVSL 80

                         90       100
                 ....*....|....*....|
gi 54607128  157 DVTESGKKSVKLSVNPKRVN 176
Cdd:cd05693   81 DKSKSGKKRIELSLEPELVN 100
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 636-707 1.10e-35

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 cd05699:

Pssm-ID: 471952 [Multi-domain]  Cd Length: 72  Bit Score: 130.29  E-value: 1.10e-35
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54607128  636 GQLVDVKVLEKTKTGLEVAILPHNTPAFLPTPHLSDHAANGPLLHHWLQTGDTLHRVLCLSQSERHILLCRK 707
Cdd:cd05699    1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLSNYKGRIILTKK 72
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 715-797 1.38e-34

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: 127.70  E-value: 1.38e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  715 EGGQDPKSLSEIQPGMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRML 794
Cdd:cd04461    1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                 ...
gi 54607128  795 LSL 797
Cdd:cd04461   81 LSL 83
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1238-1309 1.51e-33

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: 124.39  E-value: 1.51e-33
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54607128 1238 LEEGEVAMGRVMKVVPNRGLTVSFPFGKIGKVSMFHLSDSYSEAPLEDFCPQKIVRCYILSTAHRVLALSLR 1309
Cdd:cd05704    1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDGKYQLSLR 72
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 542-611 2.27e-31

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: 117.71  E-value: 2.27e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  542 GLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLSFR 611
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 453-521 9.39e-30

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: 113.10  E-value: 9.39e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 54607128  453 GTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTL 521
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 926-993 6.65e-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 cd05701:

Pssm-ID: 471952  Cd Length: 69  Bit Score: 105.35  E-value: 6.65e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 54607128  926 SRHQGIVQHLEESFAVASLVETGHLVAFSLISHLNDTFHFDSEKLRVGQGVCLTLKTTEPGVTGLILA 993
Cdd:cd05701    2 SRHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNCLAGGPLLA 69
S1_Rrp5_repeat_hs4 cd05696
S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 365-435 7.49e-27

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: 105.04  E-value: 7.49e-27
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 54607128  365 GAVLDDVPVQGFFKNAGAIFRLKDGVLAYARVSHLSDSKKAFNAEAFKPGSTHKCRIIDYSQMDELALLSL 435
Cdd:cd05696    1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 183-263 3.12e-26

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: 103.48  E-value: 3.12e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  183 ALRPGMLLTGTVSSLEDHGYLVDIGVGGTRAFLSLKKAQEYirqknkgAKFKVGQYLTCVVEEVKSNGGVVSLSVEHSEV 262
Cdd:cd05694    1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73


                 .
gi 54607128  263 S 263
Cdd:cd05694   74 S 74
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1047-1116 1.27e-25

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: 101.51  E-value: 1.27e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1047 GDKVTGTIKAVKATHVVVTLADGFVGCIHASRILDDVPVGTSPTTTLKAGKKVTARVIGGRDVKTSKFLP 1116
Cdd:cd05702    1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 846-910 5.87e-25

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: 99.54  E-value: 5.87e-25
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607128  846 GMVLDAVVHEVLEDGSVVFSSDPVPDLVLRASRYHRAGQEVEPGQKKKVVVLHVDMLKLEVHVSL 910
Cdd:cd05700    1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1332-1405 2.55e-24

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 cd05705:

Pssm-ID: 471952 [Multi-domain]  Cd Length: 74  Bit Score: 97.85  E-value: 2.55e-24
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 54607128 1332 VKEGQLLRGYVKCVLPSSVIIGLGPSVLGLAKYSHVSECVPPEKELYNGCLPEGKLVTAKVLRVNPMKNLIELS 1405
Cdd:cd05705    1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1160-1234 3.52e-21

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: 88.78  E-value: 3.52e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607128 1160 GQTVTCFFKKYNVMKKWLEvdIGPDIRGRIPLLLTSLSFKVLKHPDKKFQVGQAIEATVVDPDVPRAFLCLSLIG 1234
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 ...
 284-344 5.31e-21

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: 88.10  E-value: 5.31e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607128  284 VKAQVQKVTQFGLQLNFLTFFKGLVDFMHLEPKK--MGSYSSNQTVKACILCVHPRTRVVRLS 344
Cdd:cd05695    4 VNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKssKSTYKEGQKVRARILYVDPSTKVVGLS 66
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1591-1851 1.48e-15

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: 79.00  E-value: 1.48e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1591 RQPESA-DDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfREEQEKLnvwvALLNLENMYGSQESLT 1669
Cdd:COG2956   22 GQPDKAiDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYLKAGLLD 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1670 K---VFERAVQYNEP-LKVFLHLADIYTKSEKYKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRALEC 1745
Cdd:COG2956   94 RaeeLLEKLLELDPDdAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1746 LPakEHVDVIVKFAQLEFQLGDVERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQTAVRDIFERVihLSLAPKRMKFF 1825
Cdd:COG2956  174 DP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA--LELDPSDDLLL 249

                        250       260
                 ....*....|....*....|....*.
gi 54607128 1826 FKRYLdYEKQHGTEKdVQAVKAKALE 1851
Cdd:COG2956  250 ALADL-LERKEGLEA-ALALLERQLR 273
 
Name Accession Description Interval E-value
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 80-176 1.28e-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: 136.96  E-value: 1.28e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   80 LCEGMRILGCVKEVSELELVVSLPNGLQGFVQVTEVCDAYTQKLNEQVAQEE---PLEDLLRLPELFSPGMLVRCVVSSL 156
Cdd:cd05693    1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEeedDEEELPDLEDLFSVGQLVRCKVVSL 80

                         90       100
                 ....*....|....*....|
gi 54607128  157 DVTESGKKSVKLSVNPKRVN 176
Cdd:cd05693   81 DKSKSGKKRIELSLEPELVN 100
S1_Rrp5_repeat_hs7 cd05699
S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 636-707 1.10e-35

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: 130.29  E-value: 1.10e-35
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54607128  636 GQLVDVKVLEKTKTGLEVAILPHNTPAFLPTPHLSDHAANGPLLHHWLQTGDTLHRVLCLSQSERHILLCRK 707
Cdd:cd05699    1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLSNYKGRIILTKK 72
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 715-797 1.38e-34

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: 127.70  E-value: 1.38e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  715 EGGQDPKSLSEIQPGMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRML 794
Cdd:cd04461    1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                 ...
gi 54607128  795 LSL 797
Cdd:cd04461   81 LSL 83
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1238-1309 1.51e-33

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: 124.39  E-value: 1.51e-33
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54607128 1238 LEEGEVAMGRVMKVVPNRGLTVSFPFGKIGKVSMFHLSDSYSEAPLEDFCPQKIVRCYILSTAHRVLALSLR 1309
Cdd:cd05704    1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDGKYQLSLR 72
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 542-611 2.27e-31

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: 117.71  E-value: 2.27e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  542 GLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLSFR 611
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 453-521 9.39e-30

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: 113.10  E-value: 9.39e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 54607128  453 GTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTL 521
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
S1_Rrp5_repeat_hs10 cd05701
S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 926-993 6.65e-27

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: 105.35  E-value: 6.65e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 54607128  926 SRHQGIVQHLEESFAVASLVETGHLVAFSLISHLNDTFHFDSEKLRVGQGVCLTLKTTEPGVTGLILA 993
Cdd:cd05701    2 SRHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNCLAGGPLLA 69
S1_Rrp5_repeat_hs4 cd05696
S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 365-435 7.49e-27

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: 105.04  E-value: 7.49e-27
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 54607128  365 GAVLDDVPVQGFFKNAGAIFRLKDGVLAYARVSHLSDSKKAFNAEAFKPGSTHKCRIIDYSQMDELALLSL 435
Cdd:cd05696    1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 183-263 3.12e-26

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: 103.48  E-value: 3.12e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  183 ALRPGMLLTGTVSSLEDHGYLVDIGVGGTRAFLSLKKAQEYirqknkgAKFKVGQYLTCVVEEVKSNGGVVSLSVEHSEV 262
Cdd:cd05694    1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73


                 .
gi 54607128  263 S 263
Cdd:cd05694   74 S 74
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1047-1116 1.27e-25

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: 101.51  E-value: 1.27e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1047 GDKVTGTIKAVKATHVVVTLADGFVGCIHASRILDDVPVGTSPTTTLKAGKKVTARVIGGRDVKTSKFLP 1116
Cdd:cd05702    1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 132-611 4.07e-25

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: 111.75  E-value: 4.07e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    132 PLEDLLRLPELFSPGMLVRCVvssLDVTESGKKSVKLSVNP--KRVNKVLSADALRPGMLLTGTVSSLEDHGYLVDIGvg 209
Cdd:TIGR00717   47 PKEEFLDAPLEIQVGDEVEVY---LDRVEDRFGETVLSREKaqRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIVDLN-- 121

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    210 GTRAFL-----SLKKAQEYIRQKNKGAKFkvgqyltCVVEEVKSNGGVVslsVEHSEVSSAFATEEQSWNLNNLLPGLLV 284
Cdd:TIGR00717  122 GVEAFLpgsqvDVKPIKDLDSLIGKTLKF-------KIIKLDQKRNNIV---VSRRAYLEEERSQAREELLENLKEGDVV 191

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    285 KAQVQKVTQFGLQLNFltffKGLVDFMHLE---------PKKMgsYSSNQTVKACILCVHPRTRVVRLSLRPIflhPGRP 355
Cdd:TIGR00717  192 KGVVKNITDFGAFVDL----GGVDGLLHITdmswkrvkhPSEY--VKVGQEVKVKVIKFDKEKGRISLSLKQL---GEDP 262

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    356 LTRISYQ-QLGAVLDDVPVQgfFKNAGAIFRLKDGVLAYARVSHLSDSKKAFN-AEAFKPGSTHKCRIIDYSQMDELALL 433
Cdd:TIGR00717  263 WEAIEKKfPVGDKITGRVTN--LTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHpSKVVKKGDEVEVMILDIDPERRRLSL 340

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    434 SLrKSIIAAPFLRYHDI-KIGTVVKGTVLAIKPFGILVKVGEQIKGLVpsmHLADIM----MKNPEKKYSPGDEVKCRVL 508
Cdd:TIGR00717  341 GL-KQCKANPWEQFEEKhPVGDRVTGKIKKITDFGAFVELEGGIDGLI---HLSDISwdkdGREADHLYKKGDEIEAVVL 416

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    509 LCDPEAKKLIMTLKKtLVTSKLSLITcyEGAKPGLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYT 588
Cdd:TIGR00717  417 AVDKEKKRISLGVKQ-LTENPWEKFA--AKYKVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKV 493

                          490       500
                   ....*....|....*....|...
gi 54607128    589 GQVVKVAVLSCEPSKERMLLSFR 611
Cdd:TIGR00717  494 GDEVEAKVVDIDKKNRKVSLSVK 516
S1_Rrp5_repeat_hs9 cd05700
S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 846-910 5.87e-25

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: 99.54  E-value: 5.87e-25
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607128  846 GMVLDAVVHEVLEDGSVVFSSDPVPDLVLRASRYHRAGQEVEPGQKKKVVVLHVDMLKLEVHVSL 910
Cdd:cd05700    1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1332-1405 2.55e-24

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: 97.85  E-value: 2.55e-24
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 54607128 1332 VKEGQLLRGYVKCVLPSSVIIGLGPSVLGLAKYSHVSECVPPEKELYNGCLPEGKLVTAKVLRVNPMKNLIELS 1405
Cdd:cd05705    1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1160-1234 3.52e-21

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: 88.78  E-value: 3.52e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607128 1160 GQTVTCFFKKYNVMKKWLEvdIGPDIRGRIPLLLTSLSFKVLKHPDKKFQVGQAIEATVVDPDVPRAFLCLSLIG 1234
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 ...
 284-344 5.31e-21

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: 88.10  E-value: 5.31e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607128  284 VKAQVQKVTQFGLQLNFLTFFKGLVDFMHLEPKK--MGSYSSNQTVKACILCVHPRTRVVRLS 344
Cdd:cd05695    4 VNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKssKSTYKEGQKVRARILYVDPSTKVVGLS 66
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 450-798 7.53e-20

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 96.00  E-value: 7.53e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   450 IKIGTVVKGTVLAIKPFGILVKVGeQIKGLVpsmHLADIMMK---NPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKTL- 525
Cdd:PRK06299  199 LEEGQVVEGVVKNITDYGAFVDLG-GVDGLL---HITDISWKrvnHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGe 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   526 -----VTSKLslitcyegaKPGLQTHGVIIRVKDYGCIVKFYNDVQGLVpkH--ELS-TQHIPDPETVFYTGQVVKVAVL 597
Cdd:PRK06299  275 dpweaIEKKY---------PVGSKVKGKVTNITDYGAFVELEEGIEGLV--HvsEMSwTKKNKHPSKVVSVGQEVEVMVL 343

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   598 SCEPSKERMLLSFRLLSDsrpkDPGVESSQKktgaVRIGQLVDVKVLEKTKTGLEVAI------LPHNTPAF--LPTPHL 669
Cdd:PRK06299  344 EIDEEKRRISLGLKQCKE----NPWEEFAEK----YPVGDVVEGKVKNITDFGAFVGLeggidgLVHLSDISwdKKGEEA 415

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   670 SDHaangpllhhwLQTGDTLH-RVLCLSQSERHILLCRKPALvstveggQDP--KSLSEIQPGMLLIGFVKCIKEYGVFV 746
Cdd:PRK06299  416 VEL----------YKKGDEVEaVVLKVDVEKERISLGIKQLE-------EDPfeEFAKKHKKGSIVTGTVTEVKDKGAFV 478

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 54607128   747 QFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK06299  479 ELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 450-611 6.35e-19

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: 90.49  E-value: 6.35e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  450 IKIGTVVKGTVLAIKPFGILVKVGEqIKGLVpsmHLADIM---MKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKTL- 525
Cdd:COG0539  187 LEEGDVVEGTVKNITDFGAFVDLGG-VDGLL---HISEISwgrVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQLQp 262

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  526 -----VTSKLslitcyegaKPGLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELS-TQHIPDPETVFYTGQVVKVAVLSC 599
Cdd:COG0539  263 dpwenIAEKY---------PVGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDI 333

                        170
                 ....*....|..
gi 54607128  600 EPSKERMLLSFR 611
Cdd:COG0539  334 DPEERRISLSIK 345
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
451-522 1.16e-16

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 76.10  E-value: 1.16e-16
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54607128     451 KIGTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLK 522
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1591-1851 1.48e-15

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: 79.00  E-value: 1.48e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1591 RQPESA-DDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfREEQEKLnvwvALLNLENMYGSQESLT 1669
Cdd:COG2956   22 GQPDKAiDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYLKAGLLD 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1670 K---VFERAVQYNEP-LKVFLHLADIYTKSEKYKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRALEC 1745
Cdd:COG2956   94 RaeeLLEKLLELDPDdAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1746 LPakEHVDVIVKFAQLEFQLGDVERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQTAVRDIFERVihLSLAPKRMKFF 1825
Cdd:COG2956  174 DP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA--LELDPSDDLLL 249

                        250       260
                 ....*....|....*....|....*.
gi 54607128 1826 FKRYLdYEKQHGTEKdVQAVKAKALE 1851
Cdd:COG2956  250 ALADL-LERKEGLEA-ALALLERQLR 273
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
727-798 1.90e-14

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 69.94  E-value: 1.90e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54607128     727 QPGMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
540-611 3.65e-13

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 66.09  E-value: 3.65e-13
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54607128     540 KPGLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLSFR 611
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 547-609 2.50e-09

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 55.37  E-value: 2.50e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607128    547 GVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLS 609
Cdd:pfam00575    9 GEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILS 71
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 451-518 5.68e-09

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 54.22  E-value: 5.68e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 54607128    451 KIGTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLI 518
Cdd:pfam00575    2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRII 69
PRK08059 PRK08059
general stress protein 13; Validated
 450-524 1.32e-08

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 55.05  E-value: 1.32e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607128   450 IKIGTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKT 524
Cdd:PRK08059    5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRAT 79
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
185-256 3.97e-07

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 49.14  E-value: 3.97e-07
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54607128     185 RPGMLLTGTVSSLEDHGYLVDIGvGGTRAFLSLKKAQEYiRQKNKGAKFKVGQYLTCVVEEVKSNGGVVSLS 256
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLG-NGVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1333-1406 1.43e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.60  E-value: 1.43e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 54607128    1333 KEGQLLRGYVKCVLPSSVIIGLGPSVLGLAKYSHVSECVPPEKELYngcLPEGKLVTAKVLRVNPMKNLIELSL 1406
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEV---LKVGDEVKVKVLSVDEEKGRIILSL 71
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 727-797 3.56e-06

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: 46.51  E-value: 3.56e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 54607128    727 QPGMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSL 797
Cdd:pfam00575    2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
378-436 4.68e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 46.06  E-value: 4.68e-06
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 54607128     378 KNAGAIFRLKDGVLAYARVSHLSDSKKAFNAEAFKPGSTHKCRIIDYSQMDELALLSLR 436
Cdd:smart00316   14 TPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1046-1105 9.96e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 44.90  E-value: 9.96e-06
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    1046 IGDKVTGTIKAVKATHVVVTLADGFVGCIHASRILDDvpVGTSPTTTLKAGKKVTARVIG 1105
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDK--RVKDPEEVLKVGDEVKVKVLS 59
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 728-798 1.13e-05

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 49.05  E-value: 1.13e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 54607128   728 PGMLLIGFVKCIKEYGVFV---QFPsGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK03987    8 EGELVVGTVKEVKDFGAFVtldEYP-GKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1158-1232 1.45e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 44.52  E-value: 1.45e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607128    1158 QAGQTVTCFFKkyNVMKKWLEVDIGPDIRGRIPLllTSLSFKVLKHPDKKFQVGQAIEATVVDPDVPRAFLCLSL 1232
Cdd:smart00316    1 EVGDVVEGTVT--EITPGGAFVDLGNGVEGLIPI--SELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 449-508 1.87e-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: 45.94  E-value: 1.87e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607128  449 DIKIGTVVKGTVLAIKPFGILVKVGEQIKGLVpsmH---LADIMMKNPEKKYSPGDEVKCRVL 508
Cdd:COG1098    2 SIEVGDIVEGKVTGITPFGAFVELPEGTTGLV---HiseIADGYVKDINDYLKVGDEVKVKVL 61
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
718-801 5.45e-05

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 48.10  E-value: 5.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  718 QDPKSLSEIQPGMLLIGFVKCIKEYGVFV-----QfpsglSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQR 792
Cdd:COG2183  631 EGVLKIEDLKPGMILEGTVTNVTDFGAFVdigvhQ-----DGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKR 705


                 ....*....
gi 54607128  793 MLLSLRLSD 801
Cdd:COG2183  706 ISLSMKLDD 714
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1239-1309 1.11e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.21  E-value: 1.11e-04
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607128    1239 EEGEVAMGRVMKVVPNrGLTVSFPFGKIGKVSMFHLSDSYSEAPLEDFCPQKIVRCYILS--TAHRVLALSLR 1309
Cdd:smart00316    1 EVGDVVEGTVTEITPG-GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSvdEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
82-169 4.75e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 40.28  E-value: 4.75e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128      82 EGMRILGCVKEVSELELVVSLPNGLQGFVQVTEVCDAYTQKLNEQvaqeepledllrlpelFSPGMLVRCVVSSLDVTes 161
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEV----------------LKVGDEVKVKVLSVDEE-- 63


                    ....*...
gi 54607128     162 gKKSVKLS 169
Cdd:smart00316   64 -KGRIILS 70
Suf pfam05843
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ...
 1718-1837 5.84e-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: 43.90  E-value: 5.84e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   1718 VWIKYGAFvLGRSQA-GASHRVLQRALEclpaKEHV--DVIVKFAQLEFQLG-DVERAKAIFENTLSTYPKRTDVWSVYI 1793
Cdd:pfam05843    3 VWIQYMRA-MRRAEGiKGARKVFKKARK----RPRLtyHVYVASALMEYYCSkDPAVAFKIFELGLKLFPEDEEFVLKYL 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 54607128   1794 DMTIKHGSQTAVRDIFERVIHlSLAPKRM-KFFFKRYLDYEKQHG 1837
Cdd:pfam05843   78 DYLISLNDDNNARVLFERVLT-RLAQEKEaKPLWKKFISYESTFG 121
PRK08059 PRK08059
general stress protein 13; Validated
 547-630 1.92e-03

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 40.03  E-value: 1.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   547 GVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLSFRLLSDSRPKDPGVESS 626
Cdd:PRK08059   13 GKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEAPEAKRKKGKI 92


                  ....
gi 54607128   627 QKKT 630
Cdd:PRK08059   93 LIPN 96
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1600-1783 2.98e-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: 42.76  E-value: 2.98e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   1600 DRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisfreEQEKLNvwvALLNLENMYGSQESL---TKVFERAV 1676
Cdd:TIGR02917  455 KKLEKKQPDNASLHNLLGAIYLGKGDLAKAREAFEKALSI-----EPDFFP---AAANLARIDIQEGNPddaIQRFEKVL 526

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   1677 QYN-EPLKVFLHLADIYTKSEKYKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRALecLPAKEHVDVI 1755
Cdd:TIGR02917  527 TIDpKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAA--DAAPDSPEAW 604

                          170       180
                   ....*....|....*....|....*...
gi 54607128   1756 VKFAQLEFQLGDVERAKAIFENTLSTYP 1783
Cdd:TIGR02917  605 LMLGRAQLAAGDLNKAVSSFKKLLALQP 632
 
Name Accession Description Interval E-value
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 80-176 1.28e-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: 136.96  E-value: 1.28e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   80 LCEGMRILGCVKEVSELELVVSLPNGLQGFVQVTEVCDAYTQKLNEQVAQEE---PLEDLLRLPELFSPGMLVRCVVSSL 156
Cdd:cd05693    1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEeedDEEELPDLEDLFSVGQLVRCKVVSL 80

                         90       100
                 ....*....|....*....|
gi 54607128  157 DVTESGKKSVKLSVNPKRVN 176
Cdd:cd05693   81 DKSKSGKKRIELSLEPELVN 100
S1_Rrp5_repeat_hs7 cd05699
S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 636-707 1.10e-35

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: 130.29  E-value: 1.10e-35
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54607128  636 GQLVDVKVLEKTKTGLEVAILPHNTPAFLPTPHLSDHAANGPLLHHWLQTGDTLHRVLCLSQSERHILLCRK 707
Cdd:cd05699    1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLSNYKGRIILTKK 72
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 715-797 1.38e-34

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: 127.70  E-value: 1.38e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  715 EGGQDPKSLSEIQPGMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRML 794
Cdd:cd04461    1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                 ...
gi 54607128  795 LSL 797
Cdd:cd04461   81 LSL 83
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1238-1309 1.51e-33

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: 124.39  E-value: 1.51e-33
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54607128 1238 LEEGEVAMGRVMKVVPNRGLTVSFPFGKIGKVSMFHLSDSYSEAPLEDFCPQKIVRCYILSTAHRVLALSLR 1309
Cdd:cd05704    1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDGKYQLSLR 72
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 542-611 2.27e-31

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: 117.71  E-value: 2.27e-31
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  542 GLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLSFR 611
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 453-521 9.39e-30

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: 113.10  E-value: 9.39e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 54607128  453 GTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTL 521
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
S1_Rrp5_repeat_hs10 cd05701
S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 926-993 6.65e-27

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: 105.35  E-value: 6.65e-27
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 54607128  926 SRHQGIVQHLEESFAVASLVETGHLVAFSLISHLNDTFHFDSEKLRVGQGVCLTLKTTEPGVTGLILA 993
Cdd:cd05701    2 SRHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNCLAGGPLLA 69
S1_Rrp5_repeat_hs4 cd05696
S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 365-435 7.49e-27

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: 105.04  E-value: 7.49e-27
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 54607128  365 GAVLDDVPVQGFFKNAGAIFRLKDGVLAYARVSHLSDSKKAFNAEAFKPGSTHKCRIIDYSQMDELALLSL 435
Cdd:cd05696    1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 183-263 3.12e-26

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: 103.48  E-value: 3.12e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  183 ALRPGMLLTGTVSSLEDHGYLVDIGVGGTRAFLSLKKAQEYirqknkgAKFKVGQYLTCVVEEVKSNGGVVSLSVEHSEV 262
Cdd:cd05694    1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73


                 .
gi 54607128  263 S 263
Cdd:cd05694   74 S 74
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1047-1116 1.27e-25

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: 101.51  E-value: 1.27e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1047 GDKVTGTIKAVKATHVVVTLADGFVGCIHASRILDDVPVGTSPTTTLKAGKKVTARVIGGRDVKTSKFLP 1116
Cdd:cd05702    1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 132-611 4.07e-25

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: 111.75  E-value: 4.07e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    132 PLEDLLRLPELFSPGMLVRCVvssLDVTESGKKSVKLSVNP--KRVNKVLSADALRPGMLLTGTVSSLEDHGYLVDIGvg 209
Cdd:TIGR00717   47 PKEEFLDAPLEIQVGDEVEVY---LDRVEDRFGETVLSREKaqRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIVDLN-- 121

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    210 GTRAFL-----SLKKAQEYIRQKNKGAKFkvgqyltCVVEEVKSNGGVVslsVEHSEVSSAFATEEQSWNLNNLLPGLLV 284
Cdd:TIGR00717  122 GVEAFLpgsqvDVKPIKDLDSLIGKTLKF-------KIIKLDQKRNNIV---VSRRAYLEEERSQAREELLENLKEGDVV 191

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    285 KAQVQKVTQFGLQLNFltffKGLVDFMHLE---------PKKMgsYSSNQTVKACILCVHPRTRVVRLSLRPIflhPGRP 355
Cdd:TIGR00717  192 KGVVKNITDFGAFVDL----GGVDGLLHITdmswkrvkhPSEY--VKVGQEVKVKVIKFDKEKGRISLSLKQL---GEDP 262

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    356 LTRISYQ-QLGAVLDDVPVQgfFKNAGAIFRLKDGVLAYARVSHLSDSKKAFN-AEAFKPGSTHKCRIIDYSQMDELALL 433
Cdd:TIGR00717  263 WEAIEKKfPVGDKITGRVTN--LTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHpSKVVKKGDEVEVMILDIDPERRRLSL 340

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    434 SLrKSIIAAPFLRYHDI-KIGTVVKGTVLAIKPFGILVKVGEQIKGLVpsmHLADIM----MKNPEKKYSPGDEVKCRVL 508
Cdd:TIGR00717  341 GL-KQCKANPWEQFEEKhPVGDRVTGKIKKITDFGAFVELEGGIDGLI---HLSDISwdkdGREADHLYKKGDEIEAVVL 416

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    509 LCDPEAKKLIMTLKKtLVTSKLSLITcyEGAKPGLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYT 588
Cdd:TIGR00717  417 AVDKEKKRISLGVKQ-LTENPWEKFA--AKYKVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKV 493

                          490       500
                   ....*....|....*....|...
gi 54607128    589 GQVVKVAVLSCEPSKERMLLSFR 611
Cdd:TIGR00717  494 GDEVEAKVVDIDKKNRKVSLSVK 516
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 351-798 4.69e-25

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: 111.75  E-value: 4.69e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    351 HPGRP-LTRISYQQ-------LGAVLDDVPVQG--FFKNAGAIFRLKDGVLAYARVSHlSDSKKAFNAEAFKpGSTHKCR 420
Cdd:TIGR00717   74 RFGETvLSREKAQRhelwiklEKAYEEGSIVEGkiVGKVKGGFIVDLNGVEAFLPGSQ-VDVKPIKDLDSLI-GKTLKFK 151

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    421 IIDYSQMDELALLSlRKSIIAAPFLRYHD-----IKIGTVVKGTVLAIKPFGILVKVGeQIKGLVPSMHLADIMMKNPEK 495
Cdd:TIGR00717  152 IIKLDQKRNNIVVS-RRAYLEEERSQAREellenLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPSE 229

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    496 KYSPGDEVKCRVLLCDPEAKKLIMTLKKTLVTSKLSLITCYegaKPGLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELS 575
Cdd:TIGR00717  230 YVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKF---PVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMS 306

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    576 -TQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLSFRLLSdSRPKDPGVESSQkktgavrIGQLVDVKVLEKTKTGLEVA 654
Cdd:TIGR00717  307 wVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCK-ANPWEQFEEKHP-------VGDRVTGKIKKITDFGAFVE 378

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    655 iLPHNTPAFLptpHLSDHA--ANGPLLHHWLQTGDTLHR-VLCLSQSERHILLCRKPALVSTVEggqdpKSLSEIQPGML 731
Cdd:TIGR00717  379 -LEGGIDGLI---HLSDISwdKDGREADHLYKKGDEIEAvVLAVDKEKKRISLGVKQLTENPWE-----KFAAKYKVGSV 449

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 54607128    732 LIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:TIGR00717  450 VKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
S1_Rrp5_repeat_hs9 cd05700
S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 846-910 5.87e-25

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: 99.54  E-value: 5.87e-25
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607128  846 GMVLDAVVHEVLEDGSVVFSSDPVPDLVLRASRYHRAGQEVEPGQKKKVVVLHVDMLKLEVHVSL 910
Cdd:cd05700    1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1332-1405 2.55e-24

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: 97.85  E-value: 2.55e-24
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 54607128 1332 VKEGQLLRGYVKCVLPSSVIIGLGPSVLGLAKYSHVSECVPPEKELYNGCLPEGKLVTAKVLRVNPMKNLIELS 1405
Cdd:cd05705    1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1160-1234 3.52e-21

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: 88.78  E-value: 3.52e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607128 1160 GQTVTCFFKKYNVMKKWLEvdIGPDIRGRIPLLLTSLSFKVLKHPDKKFQVGQAIEATVVDPDVPRAFLCLSLIG 1234
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 ...
 284-344 5.31e-21

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: 88.10  E-value: 5.31e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607128  284 VKAQVQKVTQFGLQLNFLTFFKGLVDFMHLEPKK--MGSYSSNQTVKACILCVHPRTRVVRLS 344
Cdd:cd05695    4 VNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKssKSTYKEGQKVRARILYVDPSTKVVGLS 66
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 172-671 1.15e-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: 1.15e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    172 PKRVNKVLSADALRPGMLLTGTVSSLEDHGYLVDIGvGGTRAFLSLkkaQEYIrqkNKGAKFKVGQYLTCVVEEVKSNGG 251
Cdd:TIGR00717    4 AQLLEESLKTEETRPGSIVKGTVVAINKDTVFVDVG-LKSEGRIPK---EEFL---DAPLEIQVGDEVEVYLDRVEDRFG 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    252 VVSLSVEHsevssafATEEQSWNLNNLLPG--LLVKAQVQKVTQFGlqlnFLTFFKGLVDFM---HLEPKKMGSYSS--N 324
Cdd:TIGR00717   77 ETVLSREK-------AQRHELWIKLEKAYEegSIVEGKIVGKVKGG----FIVDLNGVEAFLpgsQVDVKPIKDLDSliG 145

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    325 QTVKACILCVHPRTRVVRLSLRPIF--------------LHPGRPLtrisyqqLGAVLDDVPVqGFFKNAGAIfrlkDGV 390
Cdd:TIGR00717  146 KTLKFKIIKLDQKRNNIVVSRRAYLeeersqareellenLKEGDVV-------KGVVKNITDF-GAFVDLGGV----DGL 213

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    391 LAYARVSHLSDSKKAfnaEAFKPGSTHKCRIIDYSQMDELALLSLrKSIIAAPFLRYHD-IKIGTVVKGTVLAIKPFGIL 469
Cdd:TIGR00717  214 LHITDMSWKRVKHPS---EYVKVGQEVKVKVIKFDKEKGRISLSL-KQLGEDPWEAIEKkFPVGDKITGRVTNLTDYGVF 289

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    470 VKVGEQIKGLVPSMHLA-DIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKTlvtsKLSLITCYEGAKP-GLQTHG 547
Cdd:TIGR00717  290 VEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQC----KANPWEQFEEKHPvGDRVTG 365

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    548 VIIRVKDYGCIVKFYNDVQGLVPKHELS-TQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLSFRLLSDsrpkDPGVESS 626
Cdd:TIGR00717  366 KIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTE----NPWEKFA 441

                          490       500       510       520
                   ....*....|....*....|....*....|....*....|....*.
gi 54607128    627 QK-KTGAVrigqlVDVKVLEKTKTGLEVAiLPHNTPAFLPTPHLSD 671
Cdd:TIGR00717  442 AKyKVGSV-----VKGKVTEIKDFGAFVE-LPGGVEGLIRNSELSE 481
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 450-798 7.53e-20

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 96.00  E-value: 7.53e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   450 IKIGTVVKGTVLAIKPFGILVKVGeQIKGLVpsmHLADIMMK---NPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKTL- 525
Cdd:PRK06299  199 LEEGQVVEGVVKNITDYGAFVDLG-GVDGLL---HITDISWKrvnHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGe 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   526 -----VTSKLslitcyegaKPGLQTHGVIIRVKDYGCIVKFYNDVQGLVpkH--ELS-TQHIPDPETVFYTGQVVKVAVL 597
Cdd:PRK06299  275 dpweaIEKKY---------PVGSKVKGKVTNITDYGAFVELEEGIEGLV--HvsEMSwTKKNKHPSKVVSVGQEVEVMVL 343

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   598 SCEPSKERMLLSFRLLSDsrpkDPGVESSQKktgaVRIGQLVDVKVLEKTKTGLEVAI------LPHNTPAF--LPTPHL 669
Cdd:PRK06299  344 EIDEEKRRISLGLKQCKE----NPWEEFAEK----YPVGDVVEGKVKNITDFGAFVGLeggidgLVHLSDISwdKKGEEA 415

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   670 SDHaangpllhhwLQTGDTLH-RVLCLSQSERHILLCRKPALvstveggQDP--KSLSEIQPGMLLIGFVKCIKEYGVFV 746
Cdd:PRK06299  416 VEL----------YKKGDEVEaVVLKVDVEKERISLGIKQLE-------EDPfeEFAKKHKKGSIVTGTVTEVKDKGAFV 478

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|..
gi 54607128   747 QFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK06299  479 ELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 450-611 6.35e-19

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: 90.49  E-value: 6.35e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  450 IKIGTVVKGTVLAIKPFGILVKVGEqIKGLVpsmHLADIM---MKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKTL- 525
Cdd:COG0539  187 LEEGDVVEGTVKNITDFGAFVDLGG-VDGLL---HISEISwgrVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQLQp 262

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  526 -----VTSKLslitcyegaKPGLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELS-TQHIPDPETVFYTGQVVKVAVLSC 599
Cdd:COG0539  263 dpwenIAEKY---------PVGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDI 333

                        170
                 ....*....|..
gi 54607128  600 EPSKERMLLSFR 611
Cdd:COG0539  334 DPEERRISLSIK 345
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
413-611 1.02e-17

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 89.24  E-value: 1.02e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   413 PGSTHKCRIIDYSQMDELALLSLRKSIIAAPFLR-----YHDIKIGTVVKGTVLAIKPFGILVKVGeQIKGLVpsmHLAD 487
Cdd:PRK00087  433 KGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKkkeetWNSLEEGDVVEGEVKRLTDFGAFVDIG-GVDGLL---HVSE 508

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   488 I---MMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKTL------VTSKLslitcyegaKPGLQTHGVIIRVKDYGCI 558
Cdd:PRK00087  509 IswgRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLpdpwenVEEKY---------PVGSIVLGKVVRIAPFGAF 579

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 54607128   559 VKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLSFR 611
Cdd:PRK00087  580 VELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIK 632
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 540-798 3.18e-17

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 86.08  E-value: 3.18e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   540 KPGLQTHGVIIRVKDYGCIVKFYN-DVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLSFRLLSDSRP 618
Cdd:PRK06676   16 EVGDVVTGEVLKVEDKQVFVNIEGyKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKA 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   619 KDpgvessqKKTGAVRIGQLVDVKVLEKTKTGLEVAIlpHNTPAFLPTPHLSDH--AANGPLLhhwlqtGDTLH-RVLCL 695
Cdd:PRK06676   96 WD-------KLEEKFEEGEVVEVKVTEVVKGGLVVDV--EGVRGFIPASLISTRfvEDFSDFK------GKTLEvKIIEL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   696 SQSERHILLCRKpALVSTVEGGQDPKSLSEIQPGMLLIGFVKCIKEYGVFVQFpSGLSGLSPKTIMSDKFVTTPSEHFVE 775
Cdd:PRK06676  161 DPEKNRVILSRR-AVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELSHERVEKPSEVVSV 238

                         250       260
                  ....*....|....*....|...
gi 54607128   776 GQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK06676  239 GQEVEVKVLSIDWETERISLSLK 261
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
451-522 1.16e-16

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 76.10  E-value: 1.16e-16
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54607128     451 KIGTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLK 522
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 176-671 1.24e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 85.60  E-value: 1.24e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   176 NKVLSADALRPGMLLTGTVSSLEDHGYLVDIGvGGTRAFLSLKKaqeyIRQKNKGAKFKVGQYLTCVVEEVKSNGGVVSL 255
Cdd:PRK06299   20 EESLKESETREGSIVKGTVVAIDKDYVLVDVG-LKSEGRIPLEE----FKNEQGELEVKVGDEVEVYVERIEDGFGETVL 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   256 SVEHsevssafATEEQSWNL--NNLLPGLLVKAQVQKVTQFGL--QLNFLTFF--KGLVDfmhLEPKKMGSYSSNQTVKA 329
Cdd:PRK06299   95 SREK-------AKRLEAWDKleKAFENGEIVEGVINGKVKGGFtvDLNGVEAFlpGSQVD---VRPVRDTDPLEGKELEF 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   330 CILCVHPRTRVVRLSlRPIFLHPGRPLTRISY-QQL--GAVLDdvpvqGFFKNA---GAIFRLK--DGVL-----AYARV 396
Cdd:PRK06299  165 KVIKLDKKRNNIVVS-RRAVLEEERAEEREELlENLeeGQVVE-----GVVKNItdyGAFVDLGgvDGLLhitdiSWKRV 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   397 SHLSdskkafnaEAFKPGSTHKCRIIDYSQMDELALLSLrKSIIAAPFL----RYhdiKIGTVVKGTVLAIKPFGILVKV 472
Cdd:PRK06299  239 NHPS--------EVVNVGDEVKVKVLKFDKEKKRVSLGL-KQLGEDPWEaiekKY---PVGSKVKGKVTNITDYGAFVEL 306

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   473 GEQIKGLVpsmHLADI----MMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKTLVTSKLSLITCYegaKPGLQTHGV 548
Cdd:PRK06299  307 EEGIEGLV---HVSEMswtkKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKY---PVGDVVEGK 380

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   549 IIRVKDYGCIVKFYNDVQGLVPKHELS-TQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLSFRLLSDsrpkDPGVESSQ 627
Cdd:PRK06299  381 VKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEE----DPFEEFAK 456

                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....
gi 54607128   628 KktgaVRIGQLVDVKVLEKTKTGLEVAiLPHNTPAFLPTPHLSD 671
Cdd:PRK06299  457 K----HKKGSIVTGTVTEVKDKGAFVE-LEDGVEGLIRASELSR 495
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 407-615 2.11e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 83.39  E-value: 2.11e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   407 NAEAFKpGSTHKCRIIDYSQMDELALLSlRKSIIAAPFLRYHD-----IKIGTVVKGTVLAIKPFGILVKVGEqIKGLVP 481
Cdd:PRK06676  144 DFSDFK-GKTLEVKIIELDPEKNRVILS-RRAVVEEERAAKKEellssLKEGDVVEGTVARLTDFGAFVDIGG-VDGLVH 220

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   482 SMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKTL------VTSKLslitcyegaKPGLQTHGVIIRVKDY 555
Cdd:PRK06676  221 ISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLpgpwegVEEKL---------PEGDVIEGTVKRLTDF 291

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   556 GCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLSFRLLSD 615
Cdd:PRK06676  292 GAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEE 351
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 729-798 3.12e-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: 74.95  E-value: 3.12e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  729 GMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1591-1851 1.48e-15

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: 79.00  E-value: 1.48e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1591 RQPESA-DDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfREEQEKLnvwvALLNLENMYGSQESLT 1669
Cdd:COG2956   22 GQPDKAiDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYLKAGLLD 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1670 K---VFERAVQYNEP-LKVFLHLADIYTKSEKYKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRALEC 1745
Cdd:COG2956   94 RaeeLLEKLLELDPDdAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1746 LPakEHVDVIVKFAQLEFQLGDVERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQTAVRDIFERVihLSLAPKRMKFF 1825
Cdd:COG2956  174 DP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA--LELDPSDDLLL 249

                        250       260
                 ....*....|....*....|....*.
gi 54607128 1826 FKRYLdYEKQHGTEKdVQAVKAKALE 1851
Cdd:COG2956  250 ALADL-LERKEGLEA-ALALLERQLR 273
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
449-798 1.79e-15

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 82.30  E-value: 1.79e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   449 DIKIGTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKtlVTS 528
Cdd:PRK00087  299 QIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKE--ADR 376

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   529 KLSLITCYEGAKPGLQTHGVIIRVKDYGCIVKfYNDVQGLVPKHELSTQHIPDPETvfYTGQVVKVAVLSCEPSKERML- 607
Cdd:PRK00087  377 EKAWKELEEAFENGEPVKGKVKEVVKGGLLVD-YGGVRAFLPASHVELGYVEDLSE--YKGQELEVKIIEFNRKRRKKVv 453

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   608 LSFR-LLSDSRpkdpgvESSQKKTGAVR-IGQLVDVKVLEKTKTGLEVAIlpHNTPAFLPTPHLSDHAANGPLLHhwLQT 685
Cdd:PRK00087  454 LSRKaILEEEK------EKKKEETWNSLeEGDVVEGEVKRLTDFGAFVDI--GGVDGLLHVSEISWGRVEKPSDV--LKV 523

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   686 GDTLH-RVLCLSQSERHILLCRKPALvstveggQDP--KSLSEIQPGMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMS 762
Cdd:PRK00087  524 GDEIKvYILDIDKENKKLSLSLKKLL-------PDPweNVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQIS 596

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 54607128   763 DKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK00087  597 WKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIK 632
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 540-798 1.09e-14

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: 79.01  E-value: 1.09e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    540 KPGLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHElstqhIPDPETVFYTGQVVKVAVLSCEPSKERMLLSfrllsdsRPK 619
Cdd:TIGR00717   17 RPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEE-----FLDAPLEIQVGDEVEVYLDRVEDRFGETVLS-------REK 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    620 DPGVESSQKKTGAVRIGQLVDVKVLEKTKTGLEVAIlpHNTPAFLPTPHLSDHAANGPLLHhwlqTGDTLH-RVLCLSQS 698
Cdd:TIGR00717   85 AQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIVDL--NGVEAFLPGSQVDVKPIKDLDSL----IGKTLKfKIIKLDQK 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    699 ERHILLCRKPALVSTVEGGQDpKSLSEIQPGMLLIGFVKCIKEYGVFVQFpSGLSGLSPKTIMSDKFVTTPSEHFVEGQT 778
Cdd:TIGR00717  159 RNNIVVSRRAYLEEERSQARE-ELLENLKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVKHPSEYVKVGQE 236

                          250       260
                   ....*....|....*....|
gi 54607128    779 VVAKVTNVDESKQRMLLSLR 798
Cdd:TIGR00717  237 VKVKVIKFDKEKGRISLSLK 256
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
727-798 1.90e-14

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 69.94  E-value: 1.90e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54607128     727 QPGMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 540-798 1.27e-13

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: 74.31  E-value: 1.27e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  540 KPGLQTHGVIIRVKDYGCIVkfynDV----QGLVPKHELSTqhipDPETVFYT-GQVVKVAVLSCEPSKERMLLSFRLLS 614
Cdd:COG0539   17 KEGDIVKGTVVSIDDDEVLV----DIgyksEGIIPLSEFSD----EPGELEVKvGDEVEVYVEKVEDGEGEIVLSKKKAD 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  615 DSRPKDpGVESSQKKtgavriGQLVDVKVLEKTKTGLEVAIlpHNTPAFLPTPHLSDHAAN--GPLLhhwlqtGDTLH-R 691
Cdd:COG0539   89 REKAWE-ELEEAFEN------GEPVEGKVKGVVKGGLIVDI--GGVRAFLPASQVDVRPVRdlDEYV------GKTLEfK 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  692 VLCLSQSERHILLCRKPALVSTVEGGQDpKSLSEIQPGMLLIGFVKCIKEYGVFVQFPsGLSGLSPKTIMSDKFVTTPSE 771
Cdd:COG0539  154 IIKLDRKRNNVVVSRRAVLEEEREEKRE-ELLEKLEEGDVVEGTVKNITDFGAFVDLG-GVDGLLHISEISWGRVKHPSE 231

                        250       260
                 ....*....|....*....|....*..
gi 54607128  772 HFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:COG0539  232 VLKVGDEVEVKVLKIDREKERISLSLK 258
rpsA PRK13806
30S ribosomal protein S1; Provisional
 371-688 3.57e-13

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 74.38  E-value: 3.57e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   371 VPVQGffKNAGAI---FRLKdgVL---AYARVSHLsDSKKAFNAEAFKpGSTHKCRIIDYSQ------MDELALLSLRKS 438
Cdd:PRK13806  117 VPVEG--KVTGTCkggFNVE--VLgrrAFCPVSQI-DLRYVEDPESYV-GQTFQFLITRVEEngrnivVSRRALLEREQK 190

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   439 IIAAPFLRyhDIKIGTVVKGTVLAIKPFGILVKVGEQIKGLVpsmHLADI---MMKNPEKKYSPGDEVKCRVLLCDPEAK 515
Cdd:PRK13806  191 EALEAFME--TVKEGDVVEGTVTRLAPFGAFVELAPGVEGMV---HISELswsRVQKADEAVSVGDTVRVKVLGIERAKK 265

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   516 ----KLIMTLKKTL------VTSKLslitcyegaKPGLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELS-TQHIPDPET 584
Cdd:PRK13806  266 gkglRISLSIKQAGgdpwdtVGDRL---------KAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSwTRRVNKPED 336

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   585 VFYTGQVVKVAVLSCEPSKERMLLSFRllsdSRPKDPGVESSQKktgaVRIGQLVDVKVLEKTKTGLEVAILPHNTpAFL 664
Cdd:PRK13806  337 VVAPGDAVAVKIKDIDPAKRRISLSLR----DAEGDPWADVAER----FAPGTTVTGTVEKRAQFGLFVNLAPGVT-GLL 407

                         330       340
                  ....*....|....*....|....
gi 54607128   665 PTPHLSDhaANGPLLHHWLQTGDT 688
Cdd:PRK13806  408 PASVISR--AGKPATYEKLKPGDS 429
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
540-611 3.65e-13

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 66.09  E-value: 3.65e-13
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54607128     540 KPGLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLSFR 611
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 531-610 8.10e-13

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: 65.69  E-value: 8.10e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  531 SLITCYEGAKPGLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLSF 610
Cdd:cd04461    4 TLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 180-524 1.12e-12

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: 71.61  E-value: 1.12e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  180 SADALRPGMLLTGTVSSLEDHGYLVDIGvGGTRAFLSLkkaqEYIRQKNKGAKFKVGQYLTCVVEEVKSNGGVVSLSVEH 259
Cdd:COG0539   12 SLKELKEGDIVKGTVVSIDDDEVLVDIG-YKSEGIIPL----SEFSDEPGELEVKVGDEVEVYVEKVEDGEGEIVLSKKK 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  260 -------SEVSSAFATEEqswnlnnllpglLVKAQVQKVTQFGLQLNFltffKGLVDFM---HLEPKKMGSYSS--NQTV 327
Cdd:COG0539   87 adrekawEELEEAFENGE------------PVEGKVKGVVKGGLIVDI----GGVRAFLpasQVDVRPVRDLDEyvGKTL 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  328 KACILCVHPRTRVVRLSLRPIflhpgrpLTRISYQQLGAVLD-----DVpVQGFFKNA---GAIFRLkDGV--------L 391
Cdd:COG0539  151 EFKIIKLDRKRNNVVVSRRAV-------LEEEREEKREELLEkleegDV-VEGTVKNItdfGAFVDL-GGVdgllhiseI 221

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  392 AYARVSHLSdskkafnaEAFKPGSTHKCRIIDYSQMDELALLSLrKSIIAAPFL----RYhdiKIGTVVKGTVLAIKPFG 467
Cdd:COG0539  222 SWGRVKHPS--------EVLKVGDEVEVKVLKIDREKERISLSL-KQLQPDPWEniaeKY---PVGDVVKGKVTRLTDFG 289

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 54607128  468 ILVKVGEQIKGLVpsmHLADIMM----KNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKT 524
Cdd:COG0539  290 AFVELEPGVEGLV---HISEMSWtkrvAHPSDVVKVGDEVEVKVLDIDPEERRISLSIKQL 347
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 456-520 2.77e-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: 63.55  E-value: 2.77e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607128  456 VKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMT 520
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 732-796 7.30e-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: 62.40  E-value: 7.30e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607128  732 LIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLS 796
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 373-522 1.48e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 69.42  E-value: 1.48e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   373 VQGFFKNA---GAIFRLKDGVLAYARVSHLSDSKKAFNA-EAFKPGSTHKCRIIDYSQMDELALLSlRKSIIAAPFLRYH 448
Cdd:PRK06299  377 VEGKVKNItdfGAFVGLEGGIDGLVHLSDISWDKKGEEAvELYKKGDEVEAVVLKVDVEKERISLG-IKQLEEDPFEEFA 455

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607128   449 DI-KIGTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLK 522
Cdd:PRK06299  456 KKhKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
182-524 2.46e-11

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 68.82  E-value: 2.46e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   182 DALRPGMLLTGTVSSLEDHGYLVDIGvGGTRAFLSLKkaqEYIRQKNKGAK--FKVGQYLTCVVEEVKSNGGVVSLSVEH 259
Cdd:PRK00087  298 KQIRRGDIVKGTVVSVNENEVFVDVG-YKSEGVIPLR---ELTLDEISSLKesVKVGDEIEVKVLKLEDEDGYVVLSKKE 373

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   260 SEVSSAFATEEQSWNLNNLlpgllVKAQVQKVTQFGLQLN------FLTffKGLVDFMHLEPKkmgSYSSNQTVKACILC 333
Cdd:PRK00087  374 ADREKAWKELEEAFENGEP-----VKGKVKEVVKGGLLVDyggvraFLP--ASHVELGYVEDL---SEYKGQELEVKIIE 443

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   334 VHP-RTRVVRLSlRPIFLHPGRPLTRisyQQLGAVL--DDVpVQGFFK---NAGAIFRLK--DGVL-----AYARVSHLS 400
Cdd:PRK00087  444 FNRkRRKKVVLS-RKAILEEEKEKKK---EETWNSLeeGDV-VEGEVKrltDFGAFVDIGgvDGLLhvseiSWGRVEKPS 518

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   401 DskkafnaeAFKPGSTHKCRIIDYSQMDELALLSLRKsIIAAPF----LRYhdiKIGTVVKGTVLAIKPFGILVKVGEQI 476
Cdd:PRK00087  519 D--------VLKVGDEIKVYILDIDKENKKLSLSLKK-LLPDPWenveEKY---PVGSIVLGKVVRIAPFGAFVELEPGV 586

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*...
gi 54607128   477 KGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKT 524
Cdd:PRK00087  587 DGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEV 634
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1584-1782 5.48e-11

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: 65.52  E-value: 5.48e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1584 EALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfrEEQEKLNVWVALLNLENMYG 1663
Cdd:COG2956   84 QDYLKAGLLDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLK-----LGPENAHAYCELAELYLEQG 158

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1664 SQESLTKVFERAVQYN-EPLKVFLHLADIYTKSEKYKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRA 1742
Cdd:COG2956  159 DYDEAIEALEKALKLDpDCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA 238

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 54607128 1743 LECLPAkehVDVIVKFAQLEFQLGDVERAKAIFENTLSTY 1782
Cdd:COG2956  239 LELDPS---DDLLLALADLLERKEGLEAALALLERQLRRH 275
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 453-798 6.01e-11

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: 67.07  E-value: 6.01e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    453 GTVVKGTVLAIKPFGILVKVGEQIKGLVPsmhLADImmKNPEKKYSPGDEVkcRVLLCDPEAKKLIMTLKKTLVTSKLSL 532
Cdd:TIGR00717   19 GSIVKGTVVAINKDTVFVDVGLKSEGRIP---KEEF--LDAPLEIQVGDEV--EVYLDRVEDRFGETVLSREKAQRHELW 91

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    533 IT----CYEGAkpglQTHGVIIRVKDYGCIVKFyNDVQGLVPKHELSTQHIPDPETvfYTGQVVKVAVLSCEPSKERMLL 608
Cdd:TIGR00717   92 IKlekaYEEGS----IVEGKIVGKVKGGFIVDL-NGVEAFLPGSQVDVKPIKDLDS--LIGKTLKFKIIKLDQKRNNIVV 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    609 SFRLL---SDSRPKDPGVESSQ---KKTGAVR----IGQLVDVKVLEktktglevailphntpAFLPTPHLSDHAANGPl 678
Cdd:TIGR00717  165 SRRAYleeERSQAREELLENLKegdVVKGVVKnitdFGAFVDLGGVD----------------GLLHITDMSWKRVKHP- 227

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    679 lHHWLQTGDTLH-RVLCLSQSERHILLCRKpalvstvEGGQDP--KSLSEIQPGMLLIGFVKCIKEYGVFVQFPSGLSGL 755
Cdd:TIGR00717  228 -SEYVKVGQEVKvKVIKFDKEKGRISLSLK-------QLGEDPweAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGL 299

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....
gi 54607128    756 SPKTIMS-DKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:TIGR00717  300 VHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 449-798 7.67e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 66.05  E-value: 7.67e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   449 DIKIGTVVKGTVLAIKPFGILVKV-GEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKTLVT 527
Cdd:PRK06676   14 EVEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAE 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   528 SKLS-LITCYEGAKPglqthgVIIRVKDY---GCIVKFYNdVQGLVPKHELSTQHIPDPETvfYTGQVVKVAVLSCEPSK 603
Cdd:PRK06676   94 KAWDkLEEKFEEGEV------VEVKVTEVvkgGLVVDVEG-VRGFIPASLISTRFVEDFSD--FKGKTLEVKIIELDPEK 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   604 ERMLLSFRLLSDsrpkdpgvESSQKKTGAVR----IGQLVDVKVLEKTKTGLEVAI-----LPHNTpaflptpHLSDHAA 674
Cdd:PRK06676  165 NRVILSRRAVVE--------EERAAKKEELLsslkEGDVVEGTVARLTDFGAFVDIggvdgLVHIS-------ELSHERV 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   675 NGPllHHWLQTGDTLH-RVLCLSQSERHILLCRKPALVSTVEGGQDpkslsEIQPGMLLIGFVKCIKEYGVFVQFPSGLS 753
Cdd:PRK06676  230 EKP--SEVVSVGQEVEvKVLSIDWETERISLSLKDTLPGPWEGVEE-----KLPEGDVIEGTVKRLTDFGAFVEVLPGVE 302

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*
gi 54607128   754 GLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK06676  303 GLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIK 347
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 546-609 4.56e-10

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: 57.01  E-value: 4.56e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 54607128  546 HGVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLS 609
Cdd:cd00164    2 TGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 453-522 5.93e-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: 56.85  E-value: 5.93e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  453 GTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLK 522
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 449-798 1.21e-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: 1.21e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  449 DIKIGTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADimmKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKTL-VT 527
Cdd:COG0539   15 ELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSD---EPGELEVKVGDEVEVYVEKVEDGEGEIVLSKKKADrEK 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  528 SKLSLITCYEGAKPglqTHGVIIRVKDYGCIVKfYNDVQGLVPKHELSTQHIPDPETvfYTGQVVKVAVLSCEPSKERML 607
Cdd:COG0539   92 AWEELEEAFENGEP---VEGKVKGVVKGGLIVD-IGGVRAFLPASQVDVRPVRDLDE--YVGKTLEFKIIKLDRKRNNVV 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  608 LSFR-LLSDSRpkdpgveSSQKKT--GAVRIGQLVDVKVLEKTKTGlevailphntpAF---------LptpHLSDHAan 675
Cdd:COG0539  166 VSRRaVLEEER-------EEKREEllEKLEEGDVVEGTVKNITDFG-----------AFvdlggvdglL---HISEIS-- 222

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  676 gpllhhW---------LQTGDTLH-RVLCLSQSERHILLCRKpALvstvegGQDP-KSLSE-IQPGMLLIGFVKCIKEYG 743
Cdd:COG0539  223 ------WgrvkhpsevLKVGDEVEvKVLKIDREKERISLSLK-QL------QPDPwENIAEkYPVGDVVKGKVTRLTDFG 289

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 54607128  744 VFVQFPSGLSGLSPKTIMS-DKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:COG0539  290 AFVELEPGVEGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 547-797 1.34e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 62.87  E-value: 1.34e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   547 GVIIRVKDYGCIVkfynDV----QGLVPKHELSTqhiPDPETVFYTGQVVKVAVLSCEPSKERMLLSfrllsdsRPKDPG 622
Cdd:PRK06299   36 GTVVAIDKDYVLV----DVglksEGRIPLEEFKN---EQGELEVKVGDEVEVYVERIEDGFGETVLS-------REKAKR 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   623 VESSQKKTGAVRIGQLVDVKVLEKTKTGLEVAIlpHNTPAFLPTPHLSDHaangpllhhwlQTGDTLH--------RVLC 694
Cdd:PRK06299  102 LEAWDKLEKAFENGEIVEGVINGKVKGGFTVDL--NGVEAFLPGSQVDVR-----------PVRDTDPlegkelefKVIK 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   695 LSQSERHILLCRKpALVSTVEGGQDPKSLSEIQPGMLLIGFVKCIKEYGVFVQFpSGLSGLSPKTIMSDKFVTTPSEHFV 774
Cdd:PRK06299  169 LDKKRNNIVVSRR-AVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDL-GGVDGLLHITDISWKRVNHPSEVVN 246

                         250       260
                  ....*....|....*....|...
gi 54607128   775 EGQTVVAKVTNVDESKQRMLLSL 797
Cdd:PRK06299  247 VGDEVKVKVLKFDKEKKRVSLGL 269
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 377-677 1.80e-09

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 62.81  E-value: 1.80e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   377 FKNAGAIFRLK--DGVLayaRVSHLSDSKKAFNAEAFKPGSTHKCRIIDYSQMDELALLSLrKSIIAAPFLRYHD-IKIG 453
Cdd:PRK12269  504 FTSFGAFIDLGgfDGLL---HVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSL-KHFQPDPWLEFENkFGVN 579

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   454 TVVKGTVLAIKPFGILVKVGEQIKGLVpsmHLADI----MMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKTLVTSK 529
Cdd:PRK12269  580 DVVKGRVTKIADFGAFIELAEGIEGLA---HISEFswvkKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPW 656

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   530 LSLitcyEGAKP-GLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDP-ETVFYTGQVVKVAVLSCEPSKERML 607
Cdd:PRK12269  657 EEI----EARYPvGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPaDHELEVGKEIECMVIECDPQARRIR 732

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   608 LSFRLLSDSrpkdpgveSSQKKTGAVRIGQLVDVKVLEKTKTGLEVAIlPHNTPAFLPTPHLSDHAANGP 677
Cdd:PRK12269  733 LGVKQLSDN--------PWQVFANAYGVGSTVEGEVSSVTDFGIFVRV-PGGVEGLVRKQHLVENRDGDP 793
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 547-609 2.50e-09

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 55.37  E-value: 2.50e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607128    547 GVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLS 609
Cdd:pfam00575    9 GEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILS 71
rpsA PRK13806
30S ribosomal protein S1; Provisional
 381-609 2.80e-09

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 61.66  E-value: 2.80e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   381 GAIFRLKDGVLAYARVSHLSDSKKAFNAEAFKPGSTHKCRIIDYSQMDELALLSLRKSIIAA---PFLRYHD-IKIGTVV 456
Cdd:PRK13806  217 GAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAggdPWDTVGDrLKAGDKV 296

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   457 KGTVLAIKPFGILVKVGEQIKGLVpsmHLADI----MMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKTLVTSKLsl 532
Cdd:PRK13806  297 TGKVVRLAPFGAFVEILPGIEGLV---HVSEMswtrRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWA-- 371

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 54607128   533 iTCYEGAKPGLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLS 609
Cdd:PRK13806  372 -DVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLA 447
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1670-1784 5.16e-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: 56.35  E-value: 5.16e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1670 KVFERAVQYN-EPLKVFLHLADIYTKSEKYKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRALECLPa 1748
Cdd:COG4783   25 ALLEKALELDpDNPEAFALLGEILLQLGDLDEAIVLLHEALELDPDEPEARLNLGLALLKAGDYDEALALLEKALKLDP- 103

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 54607128 1749 kEHVDVIVKFAQLEFQLGDVERAKAIFENTLSTYPK 1784
Cdd:COG4783  104 -EHPEAYLRLARAYRALGRPDEAIAALEKALELDPD 138
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 451-518 5.68e-09

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 54.22  E-value: 5.68e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 54607128    451 KIGTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLI 518
Cdd:pfam00575    2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRII 69
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 729-798 6.83e-09

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: 53.83  E-value: 6.83e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  729 GMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKqRMLLSLR 798
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARG-RISLSIK 69
rpsA PRK13806
30S ribosomal protein S1; Provisional
 537-796 8.45e-09

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 60.12  E-value: 8.45e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   537 EGAKPGLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKE----RMLLSFRL 612
Cdd:PRK13806  198 ETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIKQ 277

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   613 LSDsrpkDPGVESSQKktgaVRIGQLVDVKVLEKTKTGLEVAILphntPAFLPTPHLSDHA----ANGPllHHWLQTGDT 688
Cdd:PRK13806  278 AGG----DPWDTVGDR----LKAGDKVTGKVVRLAPFGAFVEIL----PGIEGLVHVSEMSwtrrVNKP--EDVVAPGDA 343

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   689 LH-RVLCLSQSERHILLCRKPAlvstvEGgqDPKSLSEIQ--PGMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKF 765
Cdd:PRK13806  344 VAvKIKDIDPAKRRISLSLRDA-----EG--DPWADVAERfaPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAG 416

                         250       260       270
                  ....*....|....*....|....*....|.
gi 54607128   766 VTTPSEHFVEGQTVVAKVTNVDESKQRMLLS 796
Cdd:PRK13806  417 KPATYEKLKPGDSVTLVVEEIDTAKRKISLA 447
PRK08059 PRK08059
general stress protein 13; Validated
 450-524 1.32e-08

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 55.05  E-value: 1.32e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607128   450 IKIGTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKT 524
Cdd:PRK08059    5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRAT 79
rpsA PRK13806
30S ribosomal protein S1; Provisional
 446-798 1.80e-08

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 58.97  E-value: 1.80e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   446 RYHDIKIGTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADimmKNPEKKYSPGDEVKCRVL-LCDPEakkliMTLKKT 524
Cdd:PRK13806   28 RKTELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLD---ADGELTVAVGDEVELYVVsVNGQE-----IRLSKA 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   525 LvTSKLSLITCYEGAKPGLQTHGVIIRVkdygCIVKFYNDVQG---LVPKHELSTQHIPDPETvfYTGQVVKVAVLSCEP 601
Cdd:PRK13806  100 L-SGQGGAAMLEEAYENGVPVEGKVTGT----CKGGFNVEVLGrraFCPVSQIDLRYVEDPES--YVGQTFQFLITRVEE 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   602 SKERMLLSFRLLSDSRPKdpgvESSQKKTGAVRIGQLVDVKVLEKTKTGLEVAIlphnTPAFLPTPHLSDHAangpllhh 681
Cdd:PRK13806  173 NGRNIVVSRRALLEREQK----EALEAFMETVKEGDVVEGTVTRLAPFGAFVEL----APGVEGMVHISELS-------- 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   682 W---------LQTGDTLH-RVLCLSQSER----HILLCRKPAlvstvegGQDP-KSLSE-IQPGMLLIGFVKCIKEYGVF 745
Cdd:PRK13806  237 WsrvqkadeaVSVGDTVRvKVLGIERAKKgkglRISLSIKQA-------GGDPwDTVGDrLKAGDKVTGKVVRLAPFGAF 309

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 54607128   746 VQFPSGLSGLSPKTIMS-DKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK13806  310 VEILPGIEGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLR 363
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 729-800 3.27e-08

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: 52.33  E-value: 3.27e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607128  729 GMLLIGFVKCIKEYGVFVQF-PSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLRLS 800
Cdd:cd05708    3 GQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 45-346 3.34e-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: 58.21  E-value: 3.34e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128     45 KKSQKGPAKTKKLKIEKRKSIKSIK-------EKFEilslESLCEGMRILGCVKEVSELELVVSLPNGLQGFVQVTEVcd 117
Cdd:TIGR00717  232 KVGQEVKVKVIKFDKEKGRISLSLKqlgedpwEAIE----KKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEM-- 305

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    118 AYTQKLneqvaqEEPledllrlPELFSPGMLVRCVVSSLDvtesgKKSVKLSVNPKRV--NKVLSADALRP-GMLLTGTV 194
Cdd:TIGR00717  306 SWVKKN------SHP-------SKVVKKGDEVEVMILDID-----PERRRLSLGLKQCkaNPWEQFEEKHPvGDRVTGKI 367

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    195 SSLEDHGYLVDIGvGGTRAFLSLKKAQEYIRQKNKGAKFKVGQYLTCVVEEVKSNGGVVSLSVEHsevssafaTEEQSWN 274
Cdd:TIGR00717  368 KKITDFGAFVELE-GGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQ--------LTENPWE 438

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 54607128    275 LNNLL--PGLLVKAQVQKVTQFGLQLNFLTFFKGLVDFMHL----EPKKMGSYSSNQTVKACILCVHPRTRVVRLSLR 346
Cdd:TIGR00717  439 KFAAKykVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELsenrDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 177-611 3.64e-08

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 58.57  E-value: 3.64e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   177 KVLSADALRPGMLLTGTVSSLEDH--GYLVDIGvGGTRAFLSLKKAQeyiRQKNKGAKFKVGQYLTCVVEEV---KSNGG 251
Cdd:PRK12269  389 KVKLRDAERDGTPVEGRIVRLTEKksGFEVDLG-AGMMAFLPISQSD---CQKVDAPESLIGLTSKFYIERIsqsKQHRG 464

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   252 VVSLSVEHSEVSSAFATEEQSWNLNNLLPGLLVKAQVQKVTQFGLQLNfLTFFKGLvdfMHLEPKKMGSYS-------SN 324
Cdd:PRK12269  465 NDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFID-LGGFDGL---LHVNDMSWGHVArprefvkKG 540

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   325 QTVKACILCVHPRTRVVRLSLRPIflhpgRPLTRISYQQLGAVLDDVPVQ-GFFKNAGAIFRLKDGVLAYARVSHLSDSK 403
Cdd:PRK12269  541 QTIELKVIRLDQAEKRINLSLKHF-----QPDPWLEFENKFGVNDVVKGRvTKIADFGAFIELAEGIEGLAHISEFSWVK 615

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   404 KAFN-AEAFKPGSTHKCRIIDYSQMDELALLSLrKSIIAAPF----LRYhdiKIGTVVKGTVLAIKPFGILVKVGEQIKG 478
Cdd:PRK12269  616 KTSKpSDMVKIGDEVECMILGYDIQAGRVSLGL-KQVTANPWeeieARY---PVGARFTRRIVKVTNAGAFIEMEEGIDG 691

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   479 LVPSMHLADIMMKNP-EKKYSPGDEVKCRVLLCDPEAKKLIMTLKKtLVTSKLSLITCYEGAkpGLQTHGVIIRVKDYGC 557
Cdd:PRK12269  692 FLHVDDLSWVKRTRPaDHELEVGKEIECMVIECDPQARRIRLGVKQ-LSDNPWQVFANAYGV--GSTVEGEVSSVTDFGI 768

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 54607128   558 IVKFYNDVQGLVPKHELSTQHIPDPETV---FYTGQVVKVAVLSCEPSKERMLLSFR 611
Cdd:PRK12269  769 FVRVPGGVEGLVRKQHLVENRDGDPGEAlrkYAVGDRVKAVIVDMNVKDRKVAFSVR 825
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 444-523 1.83e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 55.82  E-value: 1.83e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   444 FLRYHdiKIGTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKK 523
Cdd:PRK07899  287 FARTH--AIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQ 364
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 451-522 2.29e-07

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: 50.02  E-value: 2.29e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607128  451 KIGTVVKGTVLAIKPFGILVKV-GEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLK 522
Cdd:cd05708    1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1672-1791 3.83e-07

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: 50.77  E-value: 3.83e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1672 FERAVQYN-EPLKVFLHLADIYTKSEKYKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRALECLPakE 1750
Cdd:COG4235    6 LRQALAANpNDAEGWLLLGRAYLRLGRYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEELLERALALDP--D 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 54607128 1751 HVDVIVKFAQLEFQLGDVERAKAIFENTLSTYPKRTDVWSV 1791
Cdd:COG4235   84 NPEALYLLGLAAFQQGDYAEAIAAWQKLLALLPADAPARLL 124
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
185-256 3.97e-07

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 49.14  E-value: 3.97e-07
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54607128     185 RPGMLLTGTVSSLEDHGYLVDIGvGGTRAFLSLKKAQEYiRQKNKGAKFKVGQYLTCVVEEVKSNGGVVSLS 256
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLG-NGVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 453-515 4.38e-07

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: 48.82  E-value: 4.38e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607128  453 GTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAK 515
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGR 63
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1680-1816 5.26e-07

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: 50.58  E-value: 5.26e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1680 EPLKVFLHLADIYTKSEKYKEAGELYNRMLKRFRQEKAVWIKYG--AFVLGRSQAGASHrvLQRALECLPakEHVDVIVK 1757
Cdd:COG4783    2 ACAEALYALAQALLLAGDYDEAEALLEKALELDPDNPEAFALLGeiLLQLGDLDEAIVL--LHEALELDP--DEPEARLN 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 54607128 1758 FAQLEFQLGDVERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQTAVRDIFERVIHLS 1816
Cdd:COG4783   78 LGLALLKAGDYDEALALLEKALKLDPEHPEAYLRLARAYRALGRPDEAIAALEKALELD 136
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 453-517 5.60e-07

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: 48.64  E-value: 5.60e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 54607128  453 GTVVKGTVLAIKPFGILVKVGEQIKGLVpsmHLADI----MMKNPEKKYSPGDEVKCRVLLCDPEAKKL 517
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLV---HISDIswtqRVRHPSEIYKKGQEVEAVVLNIDVERERI 66
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1333-1406 1.43e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.60  E-value: 1.43e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 54607128    1333 KEGQLLRGYVKCVLPSSVIIGLGPSVLGLAKYSHVSECVPPEKELYngcLPEGKLVTAKVLRVNPMKNLIELSL 1406
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEV---LKVGDEVKVKVLSVDEEKGRIILSL 71
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 729-796 1.76e-06

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: 47.23  E-value: 1.76e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 54607128  729 GMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLS 796
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 453-517 1.87e-06

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: 46.84  E-value: 1.87e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607128  453 GTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKL 517
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRI 65
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 728-796 3.24e-06

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: 46.47  E-value: 3.24e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 54607128  728 PGMLLIGFVKCIKEYGVFVQFpSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLS 796
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 729-797 3.47e-06

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: 46.08  E-value: 3.47e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 54607128  729 GMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSL 797
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 727-797 3.56e-06

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: 46.51  E-value: 3.56e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 54607128    727 QPGMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSL 797
Cdd:pfam00575    2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
RNA14 COG5107
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ...
 1599-1857 3.76e-06

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


Pssm-ID: 227438 [Multi-domain]  Cd Length: 660  Bit Score: 51.94  E-value: 3.76e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1599 FDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALK---TISFR-EEQEKLNvwvalLNLENMYGSQESLTKVFER 1674
Cdd:COG5107  291 HNQILDYFYYAEEVWFDYSEYLIGISDKQKALKTVERGIEmspSLTMFlSEYYELV-----NDEEAVYGCFDKCTQDLKR 365

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1675 AVQYNEplkvflhlADIYTKSE-KYKEAGELynrMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRALEcLPAKEHvD 1753
Cdd:COG5107  366 KYSMGE--------SESASKVDnNFEYSKEL---LLKRINKLTFVFCVHLNYVLRKRGLEAARKLFIKLRK-EGIVGH-H 432

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1754 VIVKFAQLEFQ-LGDVERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQTAVRDIFERVIHlSLAPKRMKFFFKRYLDY 1832
Cdd:COG5107  433 VYIYCAFIEYYaTGDRATAYNIFELGLLKFPDSTLYKEKYLLFLIRINDEENARALFETSVE-RLEKTQLKRIYDKMIEY 511

                        250       260
                 ....*....|....*....|....*
gi 54607128 1833 EKQHGTEKDVQAVKAKALEYVEAKS 1857
Cdd:COG5107  512 ESMVGSLNNVYSLEERFRELVPQEN 536
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 453-508 3.83e-06

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: 46.04  E-value: 3.83e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 54607128  453 GTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMM--KNPEKKYSPGDEVKCRVL 508
Cdd:cd05702    1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPdgKNPLSKFKIGQKIKARVI 58
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
378-436 4.68e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 46.06  E-value: 4.68e-06
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 54607128     378 KNAGAIFRLKDGVLAYARVSHLSDSKKAFNAEAFKPGSTHKCRIIDYSQMDELALLSLR 436
Cdd:smart00316   14 TPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 729-795 4.75e-06

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: 45.95  E-value: 4.75e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 54607128  729 GMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMS-DKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLL 795
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1688-1852 6.76e-06

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: 49.73  E-value: 6.76e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1688 LADIYTKSEKYKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRALEclPAKEHVDVIVKFAQLEFQLGD 1767
Cdd:COG2956   14 KGLNYLLNGQPDKAIDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE--RDPDRAEALLELAQDYLKAGL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1768 VERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQTAVRDIFERVIHLSlaPKRMKFFFKRYLDYEKQHGTEKDVQAVKa 1847
Cdd:COG2956   92 LDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLG--PENAHAYCELAELYLEQGDYDEAIEALE- 168


                 ....*
gi 54607128 1848 KALEY 1852
Cdd:COG2956  169 KALKL 173
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 378-434 6.84e-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: 45.45  E-value: 6.84e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 54607128  378 KNAGAIFRLKDGVLAYARVSHLSDSKKAFNAEAFKPGSTHKCRIIDYSQMDELALLS 434
Cdd:cd00164    9 TKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 80-155 9.63e-06

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


Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 45.04  E-value: 9.63e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 54607128   80 LCEGMRILGCVKEVSELE-LVVSLPNGLQGFVQVTEVCDAYTqklneqvaqEEPLEDllrlpelFSPGMLVRCVVSS 155
Cdd:cd05704    1 LEEGAVTLGMVTKVIPHSgLTVQLPFGKTGLVSIFHLSDSYT---------ENPLEG-------FKPGKIVRCCILS 61
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1046-1105 9.96e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 44.90  E-value: 9.96e-06
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    1046 IGDKVTGTIKAVKATHVVVTLADGFVGCIHASRILDDvpVGTSPTTTLKAGKKVTARVIG 1105
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDK--RVKDPEEVLKVGDEVKVKVLS 59
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 728-798 1.13e-05

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 49.05  E-value: 1.13e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 54607128   728 PGMLLIGFVKCIKEYGVFV---QFPsGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK03987    8 EGELVVGTVKEVKDFGAFVtldEYP-GKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1158-1232 1.45e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 44.52  E-value: 1.45e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607128    1158 QAGQTVTCFFKkyNVMKKWLEVDIGPDIRGRIPLllTSLSFKVLKHPDKKFQVGQAIEATVVDPDVPRAFLCLSL 1232
Cdd:smart00316    1 EVGDVVEGTVT--EITPGGAFVDLGNGVEGLIPI--SELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 542-609 1.54e-05

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: 44.58  E-value: 1.54e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 54607128  542 GLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPsKERMLLS 609
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLS 67
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 445-798 1.85e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 49.39  E-value: 1.85e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   445 LRYHDIKIGTVVKGTVLAIKPFGILVKVGEQIKGLVPsmhLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKT 524
Cdd:PRK06299   23 LKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIP---LEEFKNEQGELEVKVGDEVEVYVERIEDGFGETVLSREKA 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   525 LVTSK-LSLITCYEgakPGLQTHGVII-RVKDyGCIVkfynDVQGLV---PKHELSTQhiPDPETVFYTGQVVKVAVLSC 599
Cdd:PRK06299  100 KRLEAwDKLEKAFE---NGEIVEGVINgKVKG-GFTV----DLNGVEaflPGSQVDVR--PVRDTDPLEGKELEFKVIKL 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   600 EPSKERMLLSFR-LLSDSRpkdpgveSSQKKT--GAVRIGQLVDVKVLEKTKTGlevailphntpAF---------Lptp 667
Cdd:PRK06299  170 DKKRNNIVVSRRaVLEEER-------AEEREEllENLEEGQVVEGVVKNITDYG-----------AFvdlggvdglL--- 228

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   668 HLSDHAANGPllHH---WLQTGDTLH-RVLCLSQSERHILLCRKpALvstvegGQDP-KSLSE-IQPGMLLIGFVKCIKE 741
Cdd:PRK06299  229 HITDISWKRV--NHpseVVNVGDEVKvKVLKFDKEKKRVSLGLK-QL------GEDPwEAIEKkYPVGSKVKGKVTNITD 299

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 54607128   742 YGVFVQFPSGLSGLSPKTIMS-DKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK06299  300 YGAFVELEEGIEGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLK 357
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 449-508 1.87e-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: 45.94  E-value: 1.87e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607128  449 DIKIGTVVKGTVLAIKPFGILVKVGEQIKGLVpsmH---LADIMMKNPEKKYSPGDEVKCRVL 508
Cdd:COG1098    2 SIEVGDIVEGKVTGITPFGAFVELPEGTTGLV---HiseIADGYVKDINDYLKVGDEVKVKVL 61
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1584-1773 1.95e-05

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 48.08  E-value: 1.95e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1584 EALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisfreeqeKLNVWVALLNLENMYG 1663
Cdd:COG0457   16 LAYRRLGRYEEAIEDYEKALELDPDDAEALYNLGLAYLRLGRYEEALADYEQALEL--------DPDDAEALNNLGLALQ 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1664 SQESLTK---VFERAVQYN-EPLKVFLHLADIYTKSEKYKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVL 1739
Cdd:COG0457   88 ALGRYEEaleDYDKALELDpDDAEALYNLGLALLELGRYDEAIEAYERALELDPDDADALYNLGIALEKLGRYEEALELL 167

                        170       180       190
                 ....*....|....*....|....*....|....
gi 54607128 1740 QRALECLPAKEHVDVIVKFAQLEFQLGDVERAKA 1773
Cdd:COG0457  168 EKLEAAALAALLAAALGEAALALAAAEVLLALLL 201
PRK08059 PRK08059
general stress protein 13; Validated
 723-798 2.02e-05

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 45.81  E-value: 2.02e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 54607128   723 LSEIQPGMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK08059    2 MSQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 726-798 2.85e-05

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: 43.78  E-value: 2.85e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607128  726 IQPGMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:cd05706    1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 453-522 2.90e-05

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


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 43.80  E-value: 2.90e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  453 GTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLK 522
Cdd:cd05691    1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 449-521 3.15e-05

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: 44.12  E-value: 3.15e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607128  449 DIKIGTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTL 521
Cdd:cd04461   11 DLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1578-1711 3.69e-05

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: 47.42  E-value: 3.69e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1578 ELSRIEEALmdpgRQPESADD-FDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfrEEQEKLNVWVALL 1656
Cdd:COG2956  149 ELAELYLEQ----GDYDEAIEaLEKALKLDPDCARALLLLAELYLEQGDYEEAIAALERALE-----QDPDYLPALPRLA 219

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 54607128 1657 NLENMYGSQESLTKVFERAVQYNEPLKVFLHLADIYTKSEKYKEAGELYNRMLKR 1711
Cdd:COG2956  220 ELYEKLGDPEEALELLRKALELDPSDDLLLALADLLERKEGLEAALALLERQLRR 274
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
44-346 4.26e-05

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 48.40  E-value: 4.26e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128    44 RKKSQKGPAKTKKLKIEKRKSIKSIKEKFEilsleslcEGMRILGCVKEVSELELVVSLpNGLQGFVQVTEVCDAYTQKL 123
Cdd:PRK00087  359 KLEDEDGYVVLSKKEADREKAWKELEEAFE--------NGEPVKGKVKEVVKGGLLVDY-GGVRAFLPASHVELGYVEDL 429

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   124 NEQVAQEepLEdlLRLPElFSPGMLVRCVVSSLDVTESGKKsvklsvnpKRVNKVLsaDALRPGMLLTGTVSSLEDHGYL 203
Cdd:PRK00087  430 SEYKGQE--LE--VKIIE-FNRKRRKKVVLSRKAILEEEKE--------KKKEETW--NSLEEGDVVEGEVKRLTDFGAF 494

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   204 VDIgvGGTRAFLSL--------KKAQEYIrqknkgakfKVGQYLTCVVEEVKSNGGVVSLSVEhsevssafATEEQSWNL 275
Cdd:PRK00087  495 VDI--GGVDGLLHVseiswgrvEKPSDVL---------KVGDEIKVYILDIDKENKKLSLSLK--------KLLPDPWEN 555

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 54607128   276 NNLL--PGLLVKAQVQKVTQFGLQLNFLTFFKGLVDFMHLEPKKMGS----YSSNQTVKACILCVHPRTRVVRLSLR 346
Cdd:PRK00087  556 VEEKypVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKpedvLSEGEEVKAKILEVDPEEKRIRLSIK 632
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 452-517 4.95e-05

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


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 43.00  E-value: 4.95e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 54607128  452 IGTVVKGTVLAIKPFGILVKVGeQIKGLVpsmHLADIM---MKNPEKKYSPGDEVKCRVLLCDPEAKKL 517
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDLG-GVDGLL---HISDMSwgrVKHPSEVVNVGDEVEVKVLKIDKERKRI 65
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 525-798 5.13e-05

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 48.17  E-value: 5.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   525 LVTSKLSLITCYEGAKPGLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKE 604
Cdd:PRK12269  305 LVPRQLQERYSFEAPEPGSVRMGTVVQVNAGTVFVDIGGKSEGRVPVEEFEAPPKAGDGVRVYVERVTPYGPELSKTKAD 384

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   605 RMLLSFRLLSDSRPKDPgVESsqkktgavRIgqlvdVKVLEKtKTGLEVAiLPHNTPAFLPTPHLSDHAANGPLLHHWLQ 684
Cdd:PRK12269  385 RLGLKVKLRDAERDGTP-VEG--------RI-----VRLTEK-KSGFEVD-LGAGMMAFLPISQSDCQKVDAPESLIGLT 448

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   685 TGDTLHRVlclSQSERH-----ILLCRKPALVSTVEGGQDpKSLSEIQPGMLLIGFVKCIKEYGVFVQFpSGLSGLSPKT 759
Cdd:PRK12269  449 SKFYIERI---SQSKQHrgndnIVINRRRYLEERARQARE-EFFNSVHIEDSVSGVVKSFTSFGAFIDL-GGFDGLLHVN 523

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 54607128   760 IMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK12269  524 DMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLK 562
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
718-801 5.45e-05

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 48.10  E-value: 5.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  718 QDPKSLSEIQPGMLLIGFVKCIKEYGVFV-----QfpsglSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQR 792
Cdd:COG2183  631 EGVLKIEDLKPGMILEGTVTNVTDFGAFVdigvhQ-----DGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKR 705


                 ....*....
gi 54607128  793 MLLSLRLSD 801
Cdd:COG2183  706 ISLSMKLDD 714
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 456-613 7.55e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 47.10  E-value: 7.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   456 VKGTVLAIKPFGILVKVgEQIKGLVPSMHladIMMKNPeKKYSPGDEVKCRVLLCDPEAKKLIMTLKKTLVTSKLSLITC 535
Cdd:PRK07400  122 VRSEVFATNRGGALVRI-EGLRGFIPGSH---ISTRKP-KEELVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRLEV 196

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   536 YE---GAKPGLQTHGVIIrvkDYGcivkfynDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLSFRL 612
Cdd:PRK07400  197 GEvvvGTVRGIKPYGAFI---DIG-------GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQ 266


                  .
gi 54607128   613 L 613
Cdd:PRK07400  267 L 267
COG4700 COG4700
Uncharacterized conserved protein ECs_4300, contains TPR-like domain [Function unknown];
1673-1829 7.57e-05

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


Pssm-ID: 443735 [Multi-domain]  Cd Length: 249  Bit Score: 46.41  E-value: 7.57e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1673 ERAVQYNEPLKVFLHLADIYTKSEKYKEAGELYNRMLKRFRQEKAVwIKYGA----FVLGRSQAGASHrvLQRALECLPA 1748
Cdd:COG4700   80 EKALEFADTVQNRVRLADALLELGRYDEAIELYEEALTGIFADDPH-ILLGLaqalFELGRYAEALET--LEKLIAKNPD 156

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1749 KEHVDVIVKFAQ-LEfQLGDVERAKAIFENTLSTYPKRtDVWSVYIDMTIKHGSQTAVRDIFERVIHLSlapKRMKFFFK 1827
Cdd:COG4700  157 FKSSDAHLLYARaLE-ALGDLEAAEAELEALARRYSGP-EARYRYAKFLARQGRTAEAKELLEEILDEA---KHMPKHYR 231


                 ..
gi 54607128 1828 RY 1829
Cdd:COG4700  232 RL 233
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1584-1711 8.23e-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: 44.41  E-value: 8.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1584 EALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisFREEQEklnVWVALLNLENMYG 1663
Cdd:COG4783   12 QALLLAGDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALEL--DPDEPE---ARLNLGLALLKAG 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 54607128 1664 SQESLTKVFERAVQYN-EPLKVFLHLADIYTKSEKYKEAGELYNRMLKR 1711
Cdd:COG4783   87 DYDEALALLEKALKLDpEHPEAYLRLARAYRALGRPDEAIAALEKALEL 135
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 1335-1406 9.46e-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: 42.23  E-value: 9.46e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 54607128 1335 GQLLRGYVKCVLPSSVIIGLGPSVLGLAKYSHVSEC--VPPEKELYngclpEGKLVTAKVLRVNPMKNLIELSL 1406
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVrlKHPEKKFK-----PGLKVKCRVLSVEPERKRLVLTL 69
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 1328-1406 9.50e-05

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: 42.57  E-value: 9.50e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1328 SIEDVKEGQLLRGYVKCVLPSSVIIGLGPSVLGLAKYSHVS-ECVPPEKELYngclPEGKLVTAKVLRVNPMKNLIELSL 1406
Cdd:cd04461    8 NFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISdEFVTDPSFGF----KKGQSVTAKVTSVDEEKQRFLLSL 83
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 726-798 9.65e-05

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: 42.34  E-value: 9.65e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 54607128  726 IQPGMLLIGFV-KCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVtnVDESKQRMLLSLR 798
Cdd:cd05704    1 LEEGAVTLGMVtKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCI--LSKKDGKYQLSLR 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1239-1309 1.11e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.21  E-value: 1.11e-04
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607128    1239 EEGEVAMGRVMKVVPNrGLTVSFPFGKIGKVSMFHLSDSYSEAPLEDFCPQKIVRCYILS--TAHRVLALSLR 1309
Cdd:smart00316    1 EVGDVVEGTVTEITPG-GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSvdEEKGRIILSLK 72
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
1691-1784 1.24e-04

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


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 42.85  E-value: 1.24e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1691 IYTKSEKYKEAGELYNRMLKRFRQEKAVWIKYGAF--VLGR-SQAgashRVLQRALECLPakEHVDVIVKFAQLEFQLGD 1767
Cdd:COG3063    1 LYLKLGDLEEAEEYYEKALELDPDNADALNNLGLLllEQGRyDEA----IALEKALKLDP--NNAEALLNLAELLLELGD 74

                         90
                 ....*....|....*..
gi 54607128 1768 VERAKAIFENTLSTYPK 1784
Cdd:COG3063   75 YDEALAYLERALELDPS 91
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1171-1231 1.57e-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: 41.60  E-value: 1.57e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 54607128 1171 NVMKKWLEVDIGPDIRGRIPLllTSLSFKVLKHPDKKFQVGQAIEATVVDPDVPRAFLCLS 1231
Cdd:cd00164    7 SITKFGVFVELEDGVEGLVHI--SELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 726-801 1.81e-04

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


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 42.20  E-value: 1.81e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  726 IQPGMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEH-------------------FVEGQTVVAKVTNV 786
Cdd:cd05693    1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELdeeseeeddeeelpdledlFSVGQLVRCKVVSL 80

                         90
                 ....*....|....*...
gi 54607128  787 DES---KQRMLLSLRLSD 801
Cdd:cd05693   81 DKSksgKKRIELSLEPEL 98
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1179-1406 1.92e-04

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: 46.27  E-value: 1.92e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   1179 VDIGPDIRGRIPLLLTSLSFKVlKHPDKKFQVGQAIEATVVDPDVPRAFLCLSL----IGPYRLEE-----GEVAMGRVM 1249
Cdd:TIGR00717  290 VEIEEGIEGLVHVSEMSWVKKN-SHPSKVVKKGDEVEVMILDIDPERRRLSLGLkqckANPWEQFEekhpvGDRVTGKIK 368

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   1250 KVVpNRGLTVSFPFGKIGkvsMFHLSDSYSEAPLEDFCPQKIVRCYIlstAHRVLALSLRSSRTNRETKNRIEDPEINSI 1329
Cdd:TIGR00717  369 KIT-DFGAFVELEGGIDG---LIHLSDISWDKDGREADHLYKKGDEI---EAVVLAVDKEKKRISLGVKQLTENPWEKFA 441

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 54607128   1330 EDVKEGQLLRGYVKCVLPSSVIIGLGPSVLGLAKYSHVSECVPPEKELYngcLPEGKLVTAKVLRVNPMKNLIELSL 1406
Cdd:TIGR00717  442 AKYKVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDE---IKVGDEVEAKVVDIDKKNRKVSLSV 515
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 453-520 1.92e-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: 1.92e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 54607128  453 GTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMT 520
Cdd:cd05707    1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 541-609 1.98e-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: 41.08  E-value: 1.98e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 54607128  541 PGLQTHGVIIRVKDYGCIVKFyNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLS 609
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 450-529 2.63e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 45.64  E-value: 2.63e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   450 IKIGTVVKGTVLAIKPFGILVKVGEQIKGLVpsmHLADIMMK---NPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKKTLV 526
Cdd:PRK06676  275 LPEGDVIEGTVKRLTDFGAFVEVLPGVEGLV---HISQISHKhiaTPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEE 351


                  ...
gi 54607128   527 TSK 529
Cdd:PRK06676  352 APA 354
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 729-798 2.99e-04

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: 41.03  E-value: 2.99e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607128  729 GMLLIGFVKCIKEYGVFV---QFPsGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:cd04452    4 GELVVVTVKSIADMGAYVsllEYG-NIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK 75
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 90-122 3.36e-04

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


Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 40.65  E-value: 3.36e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 54607128   90 VKEVSELELVVSLPNGLQGFVQVTEVCDAYTQK 122
Cdd:cd05702    8 VKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDG 40
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 729-796 3.44e-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: 3.44e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 54607128  729 GMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLS 796
Cdd:cd05707    1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
S1_Rrp5_repeat_hs3 cd05695
S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 453-515 3.57e-04

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: 40.34  E-value: 3.57e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607128  453 GTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADImmKNPEKKYSPGDEVKCRVLLCDPEAK 515
Cdd:cd05695    1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPE--KSSKSTYKEGQKVRARILYVDPSTK 61
PRK05807 PRK05807
RNA-binding protein S1;
450-529 3.76e-04

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 42.43  E-value: 3.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   450 IKIGTVVKGTVLAIKPFGILVKVgEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVLLCDPEAkKLIMTLKKTLVTSK 529
Cdd:PRK05807    3 LKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNG-KISLSIKQAMKQKK 80
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
82-169 4.75e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 40.28  E-value: 4.75e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128      82 EGMRILGCVKEVSELELVVSLPNGLQGFVQVTEVCDAYTQKLNEQvaqeepledllrlpelFSPGMLVRCVVSSLDVTes 161
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEV----------------LKVGDEVKVKVLSVDEE-- 63


                    ....*...
gi 54607128     162 gKKSVKLS 169
Cdd:smart00316   64 -KGRIILS 70
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 190-256 5.25e-04

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


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 40.06  E-value: 5.25e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 54607128  190 LTGTVSSLEDHGYLVDIGvGGTRAFLSLKKAQEYiRQKNKGAKFKVGQYLTCVVEEVKSNGGVVSLS 256
Cdd:cd00164    1 VTGKVVSITKFGVFVELE-DGVEGLVHISELSDK-FVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
Suf pfam05843
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ...
 1718-1837 5.84e-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: 43.90  E-value: 5.84e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   1718 VWIKYGAFvLGRSQA-GASHRVLQRALEclpaKEHV--DVIVKFAQLEFQLG-DVERAKAIFENTLSTYPKRTDVWSVYI 1793
Cdd:pfam05843    3 VWIQYMRA-MRRAEGiKGARKVFKKARK----RPRLtyHVYVASALMEYYCSkDPAVAFKIFELGLKLFPEDEEFVLKYL 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 54607128   1794 DMTIKHGSQTAVRDIFERVIHlSLAPKRM-KFFFKRYLDYEKQHG 1837
Cdd:pfam05843   78 DYLISLNDDNNARVLFERVLT-RLAQEKEaKPLWKKFISYESTFG 121
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1238-1406 8.43e-04

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 44.17  E-value: 8.43e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  1238 LEEGEVAMGRVMKVVPNrGLtvsfpFGKIGKVSMF-HLSD---SYSEAPLEDFCPQKIVRCYILS--TAHRVLALSLrss 1311
Cdd:PRK00087  475 LEEGDVVEGEVKRLTDF-GA-----FVDIGGVDGLlHVSEiswGRVEKPSDVLKVGDEIKVYILDidKENKKLSLSL--- 545

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  1312 rtnretKNRIEDPEINSIEDVKEGQLLRGYVKCVLPSSVIIGLGPSVLGLAKYSHVSE--CVPPEKElyngcLPEGKLVT 1389
Cdd:PRK00087  546 ------KKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWkrIDKPEDV-----LSEGEEVK 614

                         170
                  ....*....|....*..
gi 54607128  1390 AKVLRVNPMKNLIELSL 1406
Cdd:PRK00087  615 AKILEVDPEEKRIRLSI 631
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 1691-1783 9.72e-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: 41.87  E-value: 9.72e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1691 IYTKSEKYKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRALECLPakEHVDVIVKFAQLEFQLGDVER 1770
Cdd:COG5010   63 LYNKLGDFEESLALLEQALQLDPNNPELYYNLALLYSRSGDKDEAKEYYEKALALSP--DNPNAYSNLAALLLSLGQDDE 140

                         90
                 ....*....|...
gi 54607128 1771 AKAIFENTLSTYP 1783
Cdd:COG5010  141 AKAALQRALGTSP 153
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 453-508 9.92e-04

S1_RPS1_repeat_ec1_hs1: 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 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240192 [Multi-domain]  Cd Length: 70  Bit Score: 39.43  E-value: 9.92e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 54607128  453 GTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVL 508
Cdd:cd05687    1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVL 56
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 542-608 1.01e-03

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


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 39.40  E-value: 1.01e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 54607128  542 GLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELS-TQHIPDPETVFYTGQVVKVAVLSCEPSKERMLL 608
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
CpoB COG1729
Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane ...
 1694-1784 1.02e-03

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: 40.75  E-value: 1.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1694 KSEKYKEAGELYNRMLKRFRQEKAV-----WIKYGAFVLGRSQAGASHrvLQRALECLPAKEHV-DVIVKFAQLEFQLGD 1767
Cdd:COG1729    5 KAGDYDEAIAAFKAFLKRYPNSPLApdalyWLGEAYYALGDYDEAAEA--FEKLLKRYPDSPKApDALLKLGLSYLELGD 82

                         90
                 ....*....|....*..
gi 54607128 1768 VERAKAIFENTLSTYPK 1784
Cdd:COG1729   83 YDKARATLEELIKKYPD 99
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 1043-1406 1.22e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 43.33  E-value: 1.22e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  1043 SLAIGDKVTGTIKAVKATHVVVTLADGFV-GCIHASRILDDVPVgtSPTTTLKAGKKVTARVIGGRDVKTSkflpishpr 1121
Cdd:PRK06676   14 EVEVGDVVTGEVLKVEDKQVFVNIEGYKVeGVIPISELSNDHIE--DINDVVKVGDELEVYVLKVEDGEGN--------- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  1122 fvltiLELSVRPSELKGSYSALNthsespvekiRQYQAGQTVTCFFKKynVMKKWLEVDIGpDIRGRIPLLLTSLSFKvl 1201
Cdd:PRK06676   83 -----LLLSKRRLEAEKAWDKLE----------EKFEEGEVVEVKVTE--VVKGGLVVDVE-GVRGFIPASLISTRFV-- 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  1202 khPDKKFQVGQAIEATVVDPDVPRAFLCLS---------------LIGpyRLEEGEVAMGRVMKVVpnrgltvsfPFG-- 1264
Cdd:PRK06676  143 --EDFSDFKGKTLEVKIIELDPEKNRVILSrravveeeraakkeeLLS--SLKEGDVVEGTVARLT---------DFGaf 209

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128  1265 -KIGKVS-MFHLSD-SYS--EAPLEDFCPQKIVRCYILST---AHRVlALSLrssrtnretKNRIEDPEINSIEDVKEGQ 1336
Cdd:PRK06676  210 vDIGGVDgLVHISElSHErvEKPSEVVSVGQEVEVKVLSIdweTERI-SLSL---------KDTLPGPWEGVEEKLPEGD 279

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 54607128  1337 LLRGYVKCVLPSSVIIGLGPSVLGLAkysHVSECV------PPEKelyngcLPEGKLVTAKVLRVNPMKNLIELSL 1406
Cdd:PRK06676  280 VIEGTVKRLTDFGAFVEVLPGVEGLV---HISQIShkhiatPSEV------LEEGQEVKVKVLEVNEEEKRISLSI 346
PRK08582 PRK08582
RNA-binding protein S1;
450-508 1.31e-03

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 40.79  E-value: 1.31e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 54607128   450 IKIGTVVKGTVLAIKPFGILVKVGEQIKGLVPSMHLADIMMKNPEKKYSPGDEVKCRVL 508
Cdd:PRK08582    3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVL 61
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
1620-1711 1.69e-03

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


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 39.38  E-value: 1.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1620 HLQATEIEKARAVAERALKTisfreeqeKLNVWVALLNLENMYGSQESltkvFERAVQYNEPLK-------VFLHLADIY 1692
Cdd:COG3063    2 YLKLGDLEEAEEYYEKALEL--------DPDNADALNNLGLLLLEQGR----YDEAIALEKALKldpnnaeALLNLAELL 69

                         90
                 ....*....|....*....
gi 54607128 1693 TKSEKYKEAGELYNRMLKR 1711
Cdd:COG3063   70 LELGDYDEALAYLERALEL 88
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1179-1406 1.80e-03

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: 43.18  E-value: 1.80e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   1179 VDIGpDIRGRIPLllTSLSFKVLKHPDKKFQVGQAIEATVVDPDVPRAFLCLSLI----GPY-----RLEEGEVAMGRVM 1249
Cdd:TIGR00717  205 VDLG-GVDGLLHI--TDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKqlgeDPWeaiekKFPVGDKITGRVT 281

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   1250 KVVPnRGLTVSFPFGKIGKVSMFHLS-DSYSEAPLEDFCPQKIVRCYILS--TAHRVLALSLRSSRTNretknriedPEI 1326
Cdd:TIGR00717  282 NLTD-YGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDidPERRRLSLGLKQCKAN---------PWE 351

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   1327 NSIEDVKEGQLLRGYVKCVLPSSVIIGLGPSVLGLAKYSHVSECVP--PEKELYNGclpeGKLVTAKVLRVNPMKNLIEL 1404
Cdd:TIGR00717  352 QFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDgrEADHLYKK----GDEIEAVVLAVDKEKKRISL 427


                   ..
gi 54607128   1405 SL 1406
Cdd:TIGR00717  428 GV 429
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 540-796 1.84e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 42.48  E-value: 1.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   540 KPGLQTHGVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLSFRLLSDSRPK 619
Cdd:PRK07400   30 KPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRIEYMRAW 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   620 DPgVESSQKKTGAVRigqlvdVKVLEKTKTGLEVAIlpHNTPAFLPTPHLSDHAANGPLLHHWLQTgdtlhRVLCLSQSE 699
Cdd:PRK07400  110 ER-VRQLQKEDATVR------SEVFATNRGGALVRI--EGLRGFIPGSHISTRKPKEELVGEELPL-----KFLEVDEER 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   700 RHILLCRKPALVStveggqdpKSLSEIQPGMLLIGFVKCIKEYGVFVQFpSGLSGLSPKTIMSDKFVTTPSEHFVEGQTV 779
Cdd:PRK07400  176 NRLVLSHRRALVE--------RKMNRLEVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEM 246

                         250
                  ....*....|....*..
gi 54607128   780 VAKVTNVDESKQRMLLS 796
Cdd:PRK07400  247 KVMIIDLDAERGRISLS 263
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1684-1855 1.85e-03

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 41.92  E-value: 1.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1684 VFLHLADIYTKSEKYKEAGELYNRMLKRFRQEKAVWIKYGA--FVLGRSQAGASHrvLQRALECLPakEHVDVIVKFAQL 1761
Cdd:COG0457   10 AYNNLGLAYRRLGRYEEAIEDYEKALELDPDDAEALYNLGLayLRLGRYEEALAD--YEQALELDP--DDAEALNNLGLA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1762 EFQLGDVERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQTAVRDIFERVihLSLAPKRMKFFFKRYLDYEKQHGTEKD 1841
Cdd:COG0457   86 LQALGRYEEALEDYDKALELDPDDAEALYNLGLALLELGRYDEAIEAYERA--LELDPDDADALYNLGIALEKLGRYEEA 163

                        170
                 ....*....|....
gi 54607128 1842 VQAVKAKALEYVEA 1855
Cdd:COG0457  164 LELLEKLEAAALAA 177
PRK08059 PRK08059
general stress protein 13; Validated
 547-630 1.92e-03

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 40.03  E-value: 1.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   547 GVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLSFRLLSDSRPKDPGVESS 626
Cdd:PRK08059   13 GKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEAPEAKRKKGKI 92


                  ....
gi 54607128   627 QKKT 630
Cdd:PRK08059   93 LIPN 96
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 547-611 2.52e-03

S1_RPS1_repeat_ec1_hs1: 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 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240192 [Multi-domain]  Cd Length: 70  Bit Score: 38.28  E-value: 2.52e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607128  547 GVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLSCEPSKERMLLSFR 611
Cdd:cd05687    6 GTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1600-1783 2.98e-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: 42.76  E-value: 2.98e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   1600 DRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisfreEQEKLNvwvALLNLENMYGSQESL---TKVFERAV 1676
Cdd:TIGR02917  455 KKLEKKQPDNASLHNLLGAIYLGKGDLAKAREAFEKALSI-----EPDFFP---AAANLARIDIQEGNPddaIQRFEKVL 526

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   1677 QYN-EPLKVFLHLADIYTKSEKYKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRALecLPAKEHVDVI 1755
Cdd:TIGR02917  527 TIDpKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAA--DAAPDSPEAW 604

                          170       180
                   ....*....|....*....|....*...
gi 54607128   1756 VKFAQLEFQLGDVERAKAIFENTLSTYP 1783
Cdd:TIGR02917  605 LMLGRAQLAAGDLNKAVSSFKKLLALQP 632
PRK08582 PRK08582
RNA-binding protein S1;
726-788 3.16e-03

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 39.63  E-value: 3.16e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607128   726 IQPGMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDE 788
Cdd:PRK08582    3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED 65
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 724-798 3.33e-03

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 42.34  E-value: 3.33e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607128   724 SEIQPGMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDEsKQRMLLSLR 798
Cdd:PRK11824  617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDK-RGRIRLSRK 690
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 547-598 3.42e-03

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: 37.91  E-value: 3.42e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 54607128  547 GVIIRVKDYGCIVKFYNDVQGLVPKHELSTQHIPDPETVFYTGQVVKVAVLS 598
Cdd:cd04472    6 GKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIE 57
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 726-796 3.44e-03

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: 38.15  E-value: 3.44e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 54607128  726 IQPGMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPS---EHFVEGQTVVAKVTNVDESKQRMLLS 796
Cdd:cd05705    1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSlynKYLPEGKLLTAKVLSVNSEKNLVELS 74
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1047-1105 4.37e-03

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: 37.64  E-value: 4.37e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54607128 1047 GDKVTGTIKAVKATHVVVTLADGFVGCIHASRI----LDDVPvgtsptTTLKAGKKVTARVIG 1105
Cdd:cd05691    1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELsrdrVEDAT------ERFKVGDEVEAKITN 57
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1739-1820 4.64e-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: 39.22  E-value: 4.64e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1739 LQRALECLPakEHVDVIVKFAQLEFQLGDVERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQTAVRDIFERVihLSLA 1818
Cdd:COG4235    6 LRQALAANP--NDAEGWLLLGRAYLRLGRYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEELLERA--LALD 81


                 ..
gi 54607128 1819 PK 1820
Cdd:COG4235   82 PD 83
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 284-344 4.80e-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: 37.36  E-value: 4.80e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54607128  284 VKAQVQKVTQFGLQLNFLTFFKGLVDFMHLEPKKMGS----YSSNQTVKACILCVHPRTRVVRLS 344
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDpsevFKVGDEVEVKVLEVDPEKGRISLS 65
rpsA PRK13806
30S ribosomal protein S1; Provisional
 639-800 5.03e-03

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 41.63  E-value: 5.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   639 VDVKVLEKTKTGLEVAILPHNtpAFLPTPHLSDHAANGPLLHhwlqTGDTLH-RVLCLSQSERHILLCRKpALVSTVEGG 717
Cdd:PRK13806  119 VEGKVTGTCKGGFNVEVLGRR--AFCPVSQIDLRYVEDPESY----VGQTFQfLITRVEENGRNIVVSRR-ALLEREQKE 191

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128   718 QDPKSLSEIQPGMLLIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSL 797
Cdd:PRK13806  192 ALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRI 271


                  ...
gi 54607128   798 RLS 800
Cdd:PRK13806  272 SLS 274
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1338-1405 5.90e-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: 36.97  E-value: 5.90e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 54607128 1338 LRGYVKCVLPSSVIIGLGPSVLGLAKYSHVSECVPPEKELYngcLPEGKLVTAKVLRVNPMKNLIELS 1405
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEV---FKVGDEVEVKVLEVDPEKGRISLS 65
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1238-1314 7.39e-03

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: 37.58  E-value: 7.39e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54607128 1238 LEEGEVAMGRVmKVVPNRGLTVSFPFGKIGKVSMFHLSDSYSEA------------------PLED-FCPQKIVRCYILS 1298
Cdd:cd05693    1 LSEGMLVLGQV-KEITKLDLVISLPNGLTGYVPITNISDAYTERleeldeeseeeddeeelpDLEDlFSVGQLVRCKVVS 79

                         90       100
                 ....*....|....*....|.
gi 54607128 1299 T-----AHRVLALSLRSSRTN 1314
Cdd:cd05693   80 LdksksGKKRIELSLEPELVN 100
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 476-523 7.64e-03

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: 36.78  E-value: 7.64e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 54607128  476 IKGLVPSMHLAD--IMMKNPEKKYSPGDEVKCRVLLCDPEAKKLIMTLKK 523
Cdd:cd05703   24 VKGRIPLLDLSDdvSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
732-798 8.98e-03

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 38.14  E-value: 8.98e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 54607128   732 LIGFVKCIKEYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK07252    7 LKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLR 73
 
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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