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Conserved domains on  [gi|158186708|ref|NP_001101074|]
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protein RRP5 homolog [Rattus norvegicus]

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 2.98e-38

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: 138.50  E-value: 2.98e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   80 LCEGMRILGCVKEVNELELVVSLPNGLQGFVQVTEICDAYTQKLNEQVAQEE---PLEDLLRLPELFSPGMLVRCVVSSL 156
Cdd:cd05693     1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEeedDEEELPDLEDLFSVGQLVRCKVVSL 80

                          90       100
                  ....*....|....*....|
gi 158186708  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 3.42e-38

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


:

Pssm-ID: 240204 [Multi-domain]  Cd Length: 72  Bit Score: 137.60  E-value: 3.42e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 158186708  636 GQLVDVKVLEKTKNGLEVAILPHNIPAFLPTPHLSDHVANGPLLHHWLQTGDTLHRVLCLSQSEKHILLCRK 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 6.23e-36

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: 131.56  E-value: 6.23e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  715 EGGQDPKSLSEIQPGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRML 794
Cdd:cd04461     1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                  ...
gi 158186708  795 LSL 797
Cdd:cd04461    81 LSL 83
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 542-611 3.06e-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: 3.06e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  542 GLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLSFK 611
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1232-1303 3.27e-30

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: 114.76  E-value: 3.27e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 158186708 1232 LEEGDVAMGRVLKVLPNKGLTVSFPFGRIGKVSVFHLSDSYSEEPLTDFCPQKIVRCYILSTAHRMLALSLR 1303
Cdd:cd05704     1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDGKYQLSLR 72
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 7.65e-29

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: 110.79  E-value: 7.65e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 158186708  453 GTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTL 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 ...
 925-993 1.84e-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: 106.89  E-value: 1.84e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 158186708  925 NSRHQGIVQHLEESFAVASLVETGHLVAFSLISHLNDTFHFDSEKLRVGQGVCLTLKTTEPGVTGLILA 993
Cdd:cd05701     1 DSRHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNCLAGGPLLA 69
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1041-1110 1.71e-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: 101.13  E-value: 1.71e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1041 GDKVTGTIKSVKATHAVVTLDDGFIGCIHVSRILDDVPEGVSPTTTLKAGKKVTARVIGGRDVKTSKFLP 1110
Cdd:cd05702     1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 183-263 2.29e-25

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: 100.79  E-value: 2.29e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  183 ALRPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLSLQKAQEYirqknkgAKFKVGQYLTCVVEELKSNGGVVSLSVEHSQV 262
Cdd:cd05694     1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73


                  .
gi 158186708  263 S 263
Cdd:cd05694    74 S 74
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 846-910 4.06e-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 cd05700:

Pssm-ID: 471952  Cd Length: 65  Bit Score: 97.23  E-value: 4.06e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708  846 GMVLDAMVQEVLENGSVVFGGGPVPDLILRASRYHRAGQELEPGQKKKVVVLHVDALKLEVHVSL 910
Cdd:cd05700     1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65
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 2.97e-23

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: 94.64  E-value: 2.97e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 158186708  365 GTVLDDASVEGFFEKAGAIFRLRDGVLAYARLSHLSDSKKAFSAEAFKLGSTHRCRIIDYSQMDELALLSL 435
Cdd:cd05696     1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1154-1228 5.50e-23

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: 94.18  E-value: 5.50e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708 1154 GQTVTCFLKKYNVMKKWLEvdIEPDIRGRIPLLLTSLSFKVLKHPDKKFQIGQAIKATVVGPDIPRAFLCLSLIG 1228
Cdd:cd05703     1 GQEVTGFVNNVSKEFVWLT--ISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
S1_Rrp5_repeat_hs3 cd05695
S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 281-344 2.80e-22

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: 91.95  E-value: 2.80e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 158186708  281 GLVVRAQVQKVTQFGLQLNFLTFFTGLVDFMHLEPKK--MGSYSSKQTVKACILCVHPRTRVVRLS 344
Cdd:cd05695     1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKssKSTYKEGQKVRARILYVDPSTKVVGLS 66
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1326-1399 3.43e-22

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: 92.07  E-value: 3.43e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 158186708 1326 IQAGQLLRGYVKSILPSSVVIGLGPSVMGLVKHSHVSQCVSREKELYDKCLPEGKLVTARVLCVNPKKNLIELS 1399
Cdd:cd05705     1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1604-1864 7.82e-16

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: 79.77  E-value: 7.82e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1604 RQPESA-DDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfREEQEKLnvwvALLNLENMYGSQESLA 1682
Cdd:COG2956    22 GQPDKAiDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYLKAGLLD 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1683 K---VFERAVQYNEP-LKVFLHLADIYTKSEKFKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRALEC 1758
Cdd:COG2956    94 RaeeLLEKLLELDPDdAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1759 LPtkEHVDVIVKFAQLEFQLGDVERAKAIFENTLTTYPKRTDVWSVYIDMTIKHGSQKEVRDIFERVihLSLAPKRMKFF 1838
Cdd:COG2956   174 DP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA--LELDPSDDLLL 249

                         250       260
                  ....*....|....*....|....*.
gi 158186708 1839 FKRYLdYEKQHGTEKdVQAVKAKALE 1864
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 2.98e-38

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: 138.50  E-value: 2.98e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   80 LCEGMRILGCVKEVNELELVVSLPNGLQGFVQVTEICDAYTQKLNEQVAQEE---PLEDLLRLPELFSPGMLVRCVVSSL 156
Cdd:cd05693     1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEeedDEEELPDLEDLFSVGQLVRCKVVSL 80

                          90       100
                  ....*....|....*....|
gi 158186708  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 3.42e-38

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


Pssm-ID: 240204 [Multi-domain]  Cd Length: 72  Bit Score: 137.60  E-value: 3.42e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 158186708  636 GQLVDVKVLEKTKNGLEVAILPHNIPAFLPTPHLSDHVANGPLLHHWLQTGDTLHRVLCLSQSEKHILLCRK 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 6.23e-36

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: 131.56  E-value: 6.23e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  715 EGGQDPKSLSEIQPGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRML 794
Cdd:cd04461     1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                  ...
gi 158186708  795 LSL 797
Cdd:cd04461    81 LSL 83
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 542-611 3.06e-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: 3.06e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  542 GLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLSFK 611
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1232-1303 3.27e-30

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: 114.76  E-value: 3.27e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 158186708 1232 LEEGDVAMGRVLKVLPNKGLTVSFPFGRIGKVSVFHLSDSYSEEPLTDFCPQKIVRCYILSTAHRMLALSLR 1303
Cdd:cd05704     1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDGKYQLSLR 72
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 7.65e-29

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: 110.79  E-value: 7.65e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 158186708  453 GTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTL 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 ...
 925-993 1.84e-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: 106.89  E-value: 1.84e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 158186708  925 NSRHQGIVQHLEESFAVASLVETGHLVAFSLISHLNDTFHFDSEKLRVGQGVCLTLKTTEPGVTGLILA 993
Cdd:cd05701     1 DSRHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNCLAGGPLLA 69
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 351-798 3.19e-26

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: 115.22  E-value: 3.19e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   351 HPGRP-LTRISYQQ-------LGTVLDDASVEGFFE---KAGAIFRLrDGVLAYARLSHlSDSKKAFSAEAFkLGSTHRC 419
Cdd:TIGR00717   74 RFGETvLSREKAQRhelwiklEKAYEEGSIVEGKIVgkvKGGFIVDL-NGVEAFLPGSQ-VDVKPIKDLDSL-IGKTLKF 150

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   420 RIIDYSQMDELALLSlRKSIIAAPFLRYQD-----IKTGTIVKGKVLALKPFGMLVKVGeQMRGLVPSMHLADIMMKNPE 494
Cdd:TIGR00717  151 KIIKLDQKRNNIVVS-RRAYLEEERSQAREellenLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPS 228

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   495 KKFNTGDEVKCRVLLCDPEAKKLIMTLKKTlvtSKLPAITCYEDAKPGLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHEL 574
Cdd:TIGR00717  229 EYVKVGQEVKVKVIKFDKEKGRISLSLKQL---GEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEM 305

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   575 S-AQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLSFKLLSgSEPKDESVknskkkgSTVNTGQLVDVKVLEKTKNGLEV 653
Cdd:TIGR00717  306 SwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCK-ANPWEQFE-------EKHPVGDRVTGKIKKITDFGAFV 377

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   654 AiLPHNIPAFLptpHLSD--HVANGPLLHHWLQTGDTLHR-VLCLSQSEKHILLCRKPALVSTVEggqdpKSLSEIQPGM 730
Cdd:TIGR00717  378 E-LEGGIDGLI---HLSDisWDKDGREADHLYKKGDEIEAvVLAVDKEKKRISLGVKQLTENPWE-----KFAAKYKVGS 448

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 158186708   731 LLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:TIGR00717  449 VVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1041-1110 1.71e-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: 101.13  E-value: 1.71e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1041 GDKVTGTIKSVKATHAVVTLDDGFIGCIHVSRILDDVPEGVSPTTTLKAGKKVTARVIGGRDVKTSKFLP 1110
Cdd:cd05702     1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 183-263 2.29e-25

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: 100.79  E-value: 2.29e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  183 ALRPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLSLQKAQEYirqknkgAKFKVGQYLTCVVEELKSNGGVVSLSVEHSQV 262
Cdd:cd05694     1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73


                  .
gi 158186708  263 S 263
Cdd:cd05694    74 S 74
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 4.06e-24

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: 97.23  E-value: 4.06e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708  846 GMVLDAMVQEVLENGSVVFGGGPVPDLILRASRYHRAGQELEPGQKKKVVVLHVDALKLEVHVSL 910
Cdd:cd05700     1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65
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 2.97e-23

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: 94.64  E-value: 2.97e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 158186708  365 GTVLDDASVEGFFEKAGAIFRLRDGVLAYARLSHLSDSKKAFSAEAFKLGSTHRCRIIDYSQMDELALLSL 435
Cdd:cd05696     1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1154-1228 5.50e-23

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: 94.18  E-value: 5.50e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708 1154 GQTVTCFLKKYNVMKKWLEvdIEPDIRGRIPLLLTSLSFKVLKHPDKKFQIGQAIKATVVGPDIPRAFLCLSLIG 1228
Cdd:cd05703     1 GQEVTGFVNNVSKEFVWLT--ISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
S1_Rrp5_repeat_hs3 cd05695
S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 281-344 2.80e-22

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: 91.95  E-value: 2.80e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 158186708  281 GLVVRAQVQKVTQFGLQLNFLTFFTGLVDFMHLEPKK--MGSYSSKQTVKACILCVHPRTRVVRLS 344
Cdd:cd05695     1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKssKSTYKEGQKVRARILYVDPSTKVVGLS 66
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1326-1399 3.43e-22

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: 92.07  E-value: 3.43e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 158186708 1326 IQAGQLLRGYVKSILPSSVVIGLGPSVMGLVKHSHVSQCVSREKELYDKCLPEGKLVTARVLCVNPKKNLIELS 1399
Cdd:cd05705     1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
445-798 2.46e-19

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 94.63  E-value: 2.46e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  445 LRYQDIKTGTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLKKt 524
Cdd:PRK00087  295 ELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKE- 373

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  525 lVTSKLpAITCYEDAKPGLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERvfYTGQVVKVAVLNCEPSKE 604
Cdd:PRK00087  374 -ADREK-AWKELEEAFENGEPVKGKVKEVVKGGLLVDYGGVRAFLPASHVELGYVEDLSE--YKGQELEVKIIEFNRKRR 449

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  605 RML-LSFKLLSgsepKDESVKNSKKKGSTVNTGQLVDVKVLEKTKNGLEVAIlpHNIPAFLPTPHLSDHVANGPLLHhwL 683
Cdd:PRK00087  450 KKVvLSRKAIL----EEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDI--GGVDGLLHVSEISWGRVEKPSDV--L 521

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  684 QTGDTLH-RVLCLSQSEKHILLCRKPALvstveggQDP--KSLSEIQPGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTI 760
Cdd:PRK00087  522 KVGDEIKvYILDIDKENKKLSLSLKKLL-------PDPweNVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQ 594

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 158186708  761 MSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK00087  595 ISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIK 632
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 540-798 3.52e-18

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 88.18  E-value: 3.52e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  540 KPGLQTHGVIIRVKDYGCLVkfynDV----QGLVPKHELSAQHIPDPERVfytGQVVKVAVLNCEPSKERMLLSFKLLSG 615
Cdd:COG0539    17 KEGDIVKGTVVSIDDDEVLV----DIgyksEGIIPLSEFSDEPGELEVKV---GDEVEVYVEKVEDGEGEIVLSKKKADR 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  616 SEPKDEsVKNSKKKGSTVntgqlvDVKVLEKTKNGLEVAIlpHNIPAFLPTPHLSDH-VAN-GPLLhhwlqtGDTLH-RV 692
Cdd:COG0539    90 EKAWEE-LEEAFENGEPV------EGKVKGVVKGGLIVDI--GGVRAFLPASQVDVRpVRDlDEYV------GKTLEfKI 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  693 LCLSQSEKHILLCRKPALVSTVEGGQDpKSLSEIQPGMLLIGFVKSIKDYGVFVQFPsGLSGLSPKTIMSDKFVTTPSEH 772
Cdd:COG0539   155 IKLDRKRNNVVVSRRAVLEEEREEKRE-ELLEKLEEGDVVEGTVKNITDFGAFVDLG-GVDGLLHISEISWGRVKHPSEV 232

                         250       260
                  ....*....|....*....|....*.
gi 158186708  773 FVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:COG0539   233 LKVGDEVEVKVLKIDREKERISLSLK 258
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1604-1864 7.82e-16

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: 79.77  E-value: 7.82e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1604 RQPESA-DDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfREEQEKLnvwvALLNLENMYGSQESLA 1682
Cdd:COG2956    22 GQPDKAiDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYLKAGLLD 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1683 K---VFERAVQYNEP-LKVFLHLADIYTKSEKFKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRALEC 1758
Cdd:COG2956    94 RaeeLLEKLLELDPDdAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1759 LPtkEHVDVIVKFAQLEFQLGDVERAKAIFENTLTTYPKRTDVWSVYIDMTIKHGSQKEVRDIFERVihLSLAPKRMKFF 1838
Cdd:COG2956   174 DP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA--LELDPSDDLLL 249

                         250       260
                  ....*....|....*....|....*.
gi 158186708 1839 FKRYLdYEKQHGTEKdVQAVKAKALE 1864
Cdd:COG2956   250 ALADL-LERKEGLEA-ALALLERQLR 273
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
727-798 1.62e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 72.64  E-value: 1.62e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 158186708    727 QPGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
453-522 8.77e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 70.71  E-value: 8.77e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708    453 GTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLK 522
Cdd:smart00316    3 GDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
540-611 7.21e-13

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 65.32  E-value: 7.21e-13
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 158186708    540 KPGLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLSFK 611
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
PRK08059 PRK08059
general stress protein 13; Validated
 450-524 3.16e-10

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 59.68  E-value: 3.16e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708  450 IKTGTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLKKT 524
Cdd:PRK08059    5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRAT 79
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 547-609 3.36e-10

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 57.68  E-value: 3.36e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 158186708   547 GVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLS 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 ...
 727-797 1.78e-07

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 49.98  E-value: 1.78e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 158186708   727 QPGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSL 797
Cdd:pfam00575    2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 451-518 3.10e-07

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 49.21  E-value: 3.10e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 158186708   451 KTGTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLI 518
Cdd:pfam00575    2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRII 69
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1040-1099 4.20e-07

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 49.14  E-value: 4.20e-07
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   1040 IGDKVTGTIKSVKATHAVVTLDDGFIGCIHVSRILDDVPEgvSPTTTLKAGKKVTARVIG 1099
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVK--DPEEVLKVGDEVKVKVLS 59
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 728-798 6.51e-07

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 52.90  E-value: 6.51e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 158186708  728 PGMLLIGFVKSIKDYGVFV---QFPsGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK03987    8 EGELVVGTVKEVKDFGAFVtldEYP-GKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1327-1400 1.04e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.98  E-value: 1.04e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 158186708   1327 QAGQLLRGYVKSILPSSVVIGLGPSVMGLVKHSHVSQcvSREKELYDKcLPEGKLVTARVLCVNPKKNLIELSL 1400
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSD--KRVKDPEEV-LKVGDEVKVKVLSVDEEKGRIILSL 71
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
185-256 1.37e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.60  E-value: 1.37e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 158186708    185 RPGMLLTGTVSSLEDHGYLVDIGvDGTRAFLSLQKAQEYiRQKNKGAKFKVGQYLTCVVEELKSNGGVVSLS 256
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLG-NGVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
718-801 1.72e-06

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 53.11  E-value: 1.72e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  718 QDPKSLSEIQPGMLLIGFVKSIKDYGVFV-----QfpsglSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQR 792
Cdd:COG2183   631 EGVLKIEDLKPGMILEGTVTNVTDFGAFVdigvhQ-----DGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKR 705


                  ....*....
gi 158186708  793 MLLSLRLSD 801
Cdd:COG2183   706 ISLSMKLDD 714
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1152-1226 1.59e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 44.52  E-value: 1.59e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708   1152 QAGQTVTCFLKkyNVMKKWLEVDIEPDIRGRIPLllTSLSFKVLKHPDKKFQIGQAIKATVVGPDIPRAFLCLSL 1226
Cdd:smart00316    1 EVGDVVEGTVT--EITPGGAFVDLGNGVEGLIPI--SELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 449-508 4.03e-05

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 45.17  E-value: 4.03e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 158186708  449 DIKTGTIVKGKVLALKPFGMLVKVGEQMRGLVpsmH---LADIMMKNPEKKFNTGDEVKCRVL 508
Cdd:COG1098     2 SIEVGDIVEGKVTGITPFGAFVELPEGTTGLV---HiseIADGYVKDINDYLKVGDEVKVKVL 61
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
1040-1098 7.91e-05

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 43.92  E-value: 7.91e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 158186708 1040 IGDKVTGTIKSVKATHAVVTLDDGFIGCIHVSRI----LDDVPEgvspttTLKAGKKVTARVI 1098
Cdd:PRK07252    3 IGDKLKGTITGIKPYGAFVALENGTTGLIHISEIktgfIDNIHQ------LLKVGEEVLVQVV 59
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
373-436 8.51e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.59  E-value: 8.51e-05
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 158186708    373 VEGF---FEKAGAIFRLRDGVLAYARLSHLSDSKKAFSAEAFKLGSTHRCRIIDYSQMDELALLSLR 436
Cdd:smart00316    6 VEGTvteITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
82-169 1.12e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.21  E-value: 1.12e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708     82 EGMRILGCVKEVNELELVVSLPNGLQGFVQVTEICDAYTQKLNEQvaqeepledllrlpelFSPGMLVRCVVSSLDVTes 161
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEV----------------LKVGDEVKVKVLSVDEE-- 63


                    ....*...
gi 158186708    162 gKKSVKLS 169
Cdd:smart00316   64 -KGRIILS 70
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1233-1292 1.34e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 41.82  E-value: 1.34e-04
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   1233 EEGDVAMGRVLKVLPnKGLTVSFPFGRIGKVSVFHLSDSYSEEPLTDFCPQKIVRCYILS 1292
Cdd:smart00316    1 EVGDVVEGTVTEITP-GGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLS 59
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
280-346 1.03e-03

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 39.51  E-value: 1.03e-03
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 158186708    280 PGLVVRAQVQKVTQFGLQLNFLTFFTGLVDFMHLEPKKMGSYSSK----QTVKACILCVHPRTRVVRLSLR 346
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVlkvgDEVKVKVLSVDEEKGRIILSLK 72
Suf pfam05843
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ...
 1731-1850 3.07e-03

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: 41.59  E-value: 3.07e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  1731 VWIKYGAFvLGRSQA-GASHRVLQRALEclptKEHV--DVIVKFAQLEFQLG-DVERAKAIFENTLTTYPKRTDVWSVYI 1806
Cdd:pfam05843    3 VWIQYMRA-MRRAEGiKGARKVFKKARK----RPRLtyHVYVASALMEYYCSkDPAVAFKIFELGLKLFPEDEEFVLKYL 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 158186708  1807 DMTIKHGSQKEVRDIFERVIHlSLAPKRM-KFFFKRYLDYEKQHG 1850
Cdd:pfam05843   78 DYLISLNDDNNARVLFERVLT-RLAQEKEaKPLWKKFISYESTFG 121
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1587-1797 3.68e-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: 42.38  E-value: 3.68e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  1587 KAEKELSRIEealMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtiSFREEQEKlnvwv 1666
Cdd:TIGR02917  500 PAAANLARID---IQEGNPDDAIQRFEKVLTIDPKNLRAILALAGLYLRTGNEEEAVAWLEKAAE--LNPQEIEP----- 569

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  1667 aLLNLENMYGSQESLAKVFERAVQY--NEPLKV--FLHLADIYTKSEKFKEAGELYNRMLKRFRQEKAVWIKYGAFVLGR 1742
Cdd:TIGR02917  570 -ALALAQYYLGKGQLKKALAILNEAadAAPDSPeaWLMLGRAQLAAGDLNKAVSSFKKLLALQPDSALALLLLADAYAVM 648

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 158186708  1743 SQAGASHRVLQRALECLPtkEHVDVIVKFAQLEFQLGDVERAKAIFENTLTTYPK 1797
Cdd:TIGR02917  649 KNYAKAITSLKRALELKP--DNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQHPK 701
PRK08059 PRK08059
general stress protein 13; Validated
 547-632 5.17e-03

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 38.87  E-value: 5.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  547 GVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLSFKLLS-GSEPKDESVKN 625
Cdd:PRK08059   13 GKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEeAPEAKRKKGKI 92


                  ....*..
gi 158186708  626 SKKKGST 632
Cdd:PRK08059   93 LIPNPSE 99
 
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 2.98e-38

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: 138.50  E-value: 2.98e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   80 LCEGMRILGCVKEVNELELVVSLPNGLQGFVQVTEICDAYTQKLNEQVAQEE---PLEDLLRLPELFSPGMLVRCVVSSL 156
Cdd:cd05693     1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEeedDEEELPDLEDLFSVGQLVRCKVVSL 80

                          90       100
                  ....*....|....*....|
gi 158186708  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 3.42e-38

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


Pssm-ID: 240204 [Multi-domain]  Cd Length: 72  Bit Score: 137.60  E-value: 3.42e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 158186708  636 GQLVDVKVLEKTKNGLEVAILPHNIPAFLPTPHLSDHVANGPLLHHWLQTGDTLHRVLCLSQSEKHILLCRK 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 6.23e-36

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: 131.56  E-value: 6.23e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  715 EGGQDPKSLSEIQPGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRML 794
Cdd:cd04461     1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                  ...
gi 158186708  795 LSL 797
Cdd:cd04461    81 LSL 83
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 542-611 3.06e-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: 3.06e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  542 GLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLSFK 611
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1232-1303 3.27e-30

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: 114.76  E-value: 3.27e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 158186708 1232 LEEGDVAMGRVLKVLPNKGLTVSFPFGRIGKVSVFHLSDSYSEEPLTDFCPQKIVRCYILSTAHRMLALSLR 1303
Cdd:cd05704     1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDGKYQLSLR 72
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 7.65e-29

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: 110.79  E-value: 7.65e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 158186708  453 GTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTL 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 ...
 925-993 1.84e-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: 106.89  E-value: 1.84e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 158186708  925 NSRHQGIVQHLEESFAVASLVETGHLVAFSLISHLNDTFHFDSEKLRVGQGVCLTLKTTEPGVTGLILA 993
Cdd:cd05701     1 DSRHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNCLAGGPLLA 69
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 351-798 3.19e-26

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: 115.22  E-value: 3.19e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   351 HPGRP-LTRISYQQ-------LGTVLDDASVEGFFE---KAGAIFRLrDGVLAYARLSHlSDSKKAFSAEAFkLGSTHRC 419
Cdd:TIGR00717   74 RFGETvLSREKAQRhelwiklEKAYEEGSIVEGKIVgkvKGGFIVDL-NGVEAFLPGSQ-VDVKPIKDLDSL-IGKTLKF 150

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   420 RIIDYSQMDELALLSlRKSIIAAPFLRYQD-----IKTGTIVKGKVLALKPFGMLVKVGeQMRGLVPSMHLADIMMKNPE 494
Cdd:TIGR00717  151 KIIKLDQKRNNIVVS-RRAYLEEERSQAREellenLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPS 228

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   495 KKFNTGDEVKCRVLLCDPEAKKLIMTLKKTlvtSKLPAITCYEDAKPGLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHEL 574
Cdd:TIGR00717  229 EYVKVGQEVKVKVIKFDKEKGRISLSLKQL---GEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEM 305

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   575 S-AQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLSFKLLSgSEPKDESVknskkkgSTVNTGQLVDVKVLEKTKNGLEV 653
Cdd:TIGR00717  306 SwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCK-ANPWEQFE-------EKHPVGDRVTGKIKKITDFGAFV 377

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   654 AiLPHNIPAFLptpHLSD--HVANGPLLHHWLQTGDTLHR-VLCLSQSEKHILLCRKPALVSTVEggqdpKSLSEIQPGM 730
Cdd:TIGR00717  378 E-LEGGIDGLI---HLSDisWDKDGREADHLYKKGDEIEAvVLAVDKEKKRISLGVKQLTENPWE-----KFAAKYKVGS 448

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 158186708   731 LLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:TIGR00717  449 VVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1041-1110 1.71e-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: 101.13  E-value: 1.71e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1041 GDKVTGTIKSVKATHAVVTLDDGFIGCIHVSRILDDVPEGVSPTTTLKAGKKVTARVIGGRDVKTSKFLP 1110
Cdd:cd05702     1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 183-263 2.29e-25

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: 100.79  E-value: 2.29e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  183 ALRPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLSLQKAQEYirqknkgAKFKVGQYLTCVVEELKSNGGVVSLSVEHSQV 262
Cdd:cd05694     1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73


                  .
gi 158186708  263 S 263
Cdd:cd05694    74 S 74
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 4.06e-24

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: 97.23  E-value: 4.06e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708  846 GMVLDAMVQEVLENGSVVFGGGPVPDLILRASRYHRAGQELEPGQKKKVVVLHVDALKLEVHVSL 910
Cdd:cd05700     1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65
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 2.97e-23

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: 94.64  E-value: 2.97e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 158186708  365 GTVLDDASVEGFFEKAGAIFRLRDGVLAYARLSHLSDSKKAFSAEAFKLGSTHRCRIIDYSQMDELALLSL 435
Cdd:cd05696     1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1154-1228 5.50e-23

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: 94.18  E-value: 5.50e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708 1154 GQTVTCFLKKYNVMKKWLEvdIEPDIRGRIPLLLTSLSFKVLKHPDKKFQIGQAIKATVVGPDIPRAFLCLSLIG 1228
Cdd:cd05703     1 GQEVTGFVNNVSKEFVWLT--ISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 172-671 2.37e-22

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: 103.28  E-value: 2.37e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   172 PKRVNKVLSAEALRPGMLLTGTVSSLEDHGYLVDIGVDgTRAFLSLQKAqeyirqKNKGAKFKVGQYLTCVVEELKSNGG 251
Cdd:TIGR00717    4 AQLLEESLKTEETRPGSIVKGTVVAINKDTVFVDVGLK-SEGRIPKEEF------LDAPLEIQVGDEVEVYLDRVEDRFG 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   252 VVSLSVEHSQVSSAFATEEQSWNLNNLLPGLVVRaqvqKVTQfglqlNFLTFFTGLVDFM---HLEPKKMGSYSSKQ--T 326
Cdd:TIGR00717   77 ETVLSREKAQRHELWIKLEKAYEEGSIVEGKIVG----KVKG-----GFIVDLNGVEAFLpgsQVDVKPIKDLDSLIgkT 147

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   327 VKACILCVHPRTRVVRLSLRPIF--------------LHPGRPLTRI--SYQQLGTVLDDASVEGFFEKAGaifrlrdgv 390
Cdd:TIGR00717  148 LKFKIIKLDQKRNNIVVSRRAYLeeersqareellenLKEGDVVKGVvkNITDFGAFVDLGGVDGLLHITD--------- 218

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   391 LAYARLSHLSdskkafsaEAFKLGSTHRCRIIDYSQMDELALLSLrKSIIAAPFLRYQD-IKTGTIVKGKVLALKPFGML 469
Cdd:TIGR00717  219 MSWKRVKHPS--------EYVKVGQEVKVKVIKFDKEKGRISLSL-KQLGEDPWEAIEKkFPVGDKITGRVTNLTDYGVF 289

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   470 VKVGEQMRGLVPSMHLA-DIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLKKTlvtsKLPAITCYEDAKP-GLQTHG 547
Cdd:TIGR00717  290 VEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQC----KANPWEQFEEKHPvGDRVTG 365

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   548 VIIRVKDYGCLVKFYNDVQGLVPKHELS-AQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLSFKLLSGSePKDEsVKNS 626
Cdd:TIGR00717  366 KIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTEN-PWEK-FAAK 443

                          490       500       510       520
                   ....*....|....*....|....*....|....*....|....*
gi 158186708   627 KKKGSTVNTgqlvdvKVLEKTKNGLEVAiLPHNIPAFLPTPHLSD 671
Cdd:TIGR00717  444 YKVGSVVKG------KVTEIKDFGAFVE-LPGGVEGLIRNSELSE 481
S1_Rrp5_repeat_hs3 cd05695
S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 281-344 2.80e-22

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: 91.95  E-value: 2.80e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 158186708  281 GLVVRAQVQKVTQFGLQLNFLTFFTGLVDFMHLEPKK--MGSYSSKQTVKACILCVHPRTRVVRLS 344
Cdd:cd05695     1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKssKSTYKEGQKVRARILYVDPSTKVVGLS 66
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1326-1399 3.43e-22

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: 92.07  E-value: 3.43e-22
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 158186708 1326 IQAGQLLRGYVKSILPSSVVIGLGPSVMGLVKHSHVSQCVSREKELYDKCLPEGKLVTARVLCVNPKKNLIELS 1399
Cdd:cd05705     1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 182-522 9.87e-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: 95.19  E-value: 9.87e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   182 EALRPGMLLTGTVSSLEDHGYLVDIGvdGTRAFLSLQKAQeYIRQKNKGAKFKVGQYLTCVVEELKSNGGVVSLSVEHsq 261
Cdd:TIGR00717  183 ENLKEGDVVKGVVKNITDFGAFVDLG--GVDGLLHITDMS-WKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQ-- 257

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   262 vssafaTEEQSWN--LNNLLPGLVVRAQVQKVTQFGLqlnFLTFFTGLVDFMHLE----------PKKMgsYSSKQTVKA 329
Cdd:TIGR00717  258 ------LGEDPWEaiEKKFPVGDKITGRVTNLTDYGV---FVEIEEGIEGLVHVSemswvkknshPSKV--VKKGDEVEV 326

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   330 CILCVHPRTRVVRLSLRPIflhPGRPLTRI-SYQQLGTVLDD--ASVEGFfekaGAIFRLRDGVLAYARLSHLS-DSKKA 405
Cdd:TIGR00717  327 MILDIDPERRRLSLGLKQC---KANPWEQFeEKHPVGDRVTGkiKKITDF----GAFVELEGGIDGLIHLSDISwDKDGR 399

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   406 FSAEAFKLGSTHRCRIIDYSQMDELALLSLrKSIIAAPFLRYQDI-KTGTIVKGKVLALKPFGMLVKVGEQMRGLVPSMH 484
Cdd:TIGR00717  400 EADHLYKKGDEIEAVVLAVDKEKKRISLGV-KQLTENPWEKFAAKyKVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSE 478

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 158186708   485 LADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLK 522
Cdd:TIGR00717  479 LSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
445-798 2.46e-19

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 94.63  E-value: 2.46e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  445 LRYQDIKTGTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLKKt 524
Cdd:PRK00087  295 ELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKE- 373

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  525 lVTSKLpAITCYEDAKPGLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERvfYTGQVVKVAVLNCEPSKE 604
Cdd:PRK00087  374 -ADREK-AWKELEEAFENGEPVKGKVKEVVKGGLLVDYGGVRAFLPASHVELGYVEDLSE--YKGQELEVKIIEFNRKRR 449

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  605 RML-LSFKLLSgsepKDESVKNSKKKGSTVNTGQLVDVKVLEKTKNGLEVAIlpHNIPAFLPTPHLSDHVANGPLLHhwL 683
Cdd:PRK00087  450 KKVvLSRKAIL----EEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDI--GGVDGLLHVSEISWGRVEKPSDV--L 521

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  684 QTGDTLH-RVLCLSQSEKHILLCRKPALvstveggQDP--KSLSEIQPGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTI 760
Cdd:PRK00087  522 KVGDEIKvYILDIDKENKKLSLSLKKLL-------PDPweNVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQ 594

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 158186708  761 MSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK00087  595 ISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIK 632
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 450-798 2.52e-19

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 94.08  E-value: 2.52e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  450 IKTGTIVKGKVLALKPFGMLVKVGeQMRGLVpsmHLADIMMK---NPEKKFNTGDEVKCRVLLCDPEAKKLIMTLKKTL- 525
Cdd:PRK06299  199 LEEGQVVEGVVKNITDYGAFVDLG-GVDGLL---HITDISWKrvnHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGe 274

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  526 -----VTSKLPaitcyedakPGLQTHGVIIRVKDYGCLVKFYNDVQGLVpkH--ELS-AQHIPDPERVFYTGQVVKVAVL 597
Cdd:PRK06299  275 dpweaIEKKYP---------VGSKVKGKVTNITDYGAFVELEEGIEGLV--HvsEMSwTKKNKHPSKVVSVGQEVEVMVL 343

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  598 NCEPSKERMLLSFKLLsgsEPKD-ESVKNSKKKGSTVnTGqlvdvKVLEKTKNGLEVAiLPHNIPAFLptpHLSD--HVA 674
Cdd:PRK06299  344 EIDEEKRRISLGLKQC---KENPwEEFAEKYPVGDVV-EG-----KVKNITDFGAFVG-LEGGIDGLV---HLSDisWDK 410

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  675 NG--PLLHhwLQTGDTLH-RVLCLSQSEKHILLCRKPALvstveggQDP--KSLSEIQPGMLLIGFVKSIKDYGVFVQFP 749
Cdd:PRK06299  411 KGeeAVEL--YKKGDEVEaVVLKVDVEKERISLGIKQLE-------EDPfeEFAKKHKKGSIVTGTVTEVKDKGAFVELE 481

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 158186708  750 SGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK06299  482 DGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 565-798 2.62e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 89.16  E-value: 2.62e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  565 VQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLSFKLLSGSEPKDESVKNSKKkgstvntGQLVDVKVL 644
Cdd:PRK06676   42 VEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDKLEEKFEE-------GEVVEVKVT 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  645 EKTKNGLEVAIlpHNIPAFLPTPHLSDH-VANGPLLhhwlqTGDTLH-RVLCLSQSEKHILLCRKpALVSTVEGGQDPKS 722
Cdd:PRK06676  115 EVVKGGLVVDV--EGVRGFIPASLISTRfVEDFSDF-----KGKTLEvKIIELDPEKNRVILSRR-AVVEEERAAKKEEL 186

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 158186708  723 LSEIQPGMLLIGFVKSIKDYGVFVQFpSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK06676  187 LSSLKEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLK 261
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 540-798 3.52e-18

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 88.18  E-value: 3.52e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  540 KPGLQTHGVIIRVKDYGCLVkfynDV----QGLVPKHELSAQHIPDPERVfytGQVVKVAVLNCEPSKERMLLSFKLLSG 615
Cdd:COG0539    17 KEGDIVKGTVVSIDDDEVLV----DIgyksEGIIPLSEFSDEPGELEVKV---GDEVEVYVEKVEDGEGEIVLSKKKADR 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  616 SEPKDEsVKNSKKKGSTVntgqlvDVKVLEKTKNGLEVAIlpHNIPAFLPTPHLSDH-VAN-GPLLhhwlqtGDTLH-RV 692
Cdd:COG0539    90 EKAWEE-LEEAFENGEPV------EGKVKGVVKGGLIVDI--GGVRAFLPASQVDVRpVRDlDEYV------GKTLEfKI 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  693 LCLSQSEKHILLCRKPALVSTVEGGQDpKSLSEIQPGMLLIGFVKSIKDYGVFVQFPsGLSGLSPKTIMSDKFVTTPSEH 772
Cdd:COG0539   155 IKLDRKRNNVVVSRRAVLEEEREEKRE-ELLEKLEEGDVVEGTVKNITDFGAFVDLG-GVDGLLHISEISWGRVKHPSEV 232

                         250       260
                  ....*....|....*....|....*.
gi 158186708  773 FVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:COG0539   233 LKVGDEVEVKVLKIDREKERISLSLK 258
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 450-611 1.40e-17

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: 86.25  E-value: 1.40e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  450 IKTGTIVKGKVLALKPFGMLVKVGEqMRGLVpsmHLADIM---MKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLKKTLV 526
Cdd:COG0539   187 LEEGDVVEGTVKNITDFGAFVDLGG-VDGLL---HISEISwgrVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQLQP 262

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  527 TsklPAITCYEDAKPGLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELSA-QHIPDPERVFYTGQVVKVAVLNCEPSKER 605
Cdd:COG0539   263 D---PWENIAEKYPVGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEMSWtKRVAHPSDVVKVGDEVEVKVLDIDPEERR 339


                  ....*.
gi 158186708  606 MLLSFK 611
Cdd:COG0539   340 ISLSIK 345
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
413-611 4.19e-17

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 87.31  E-value: 4.19e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  413 LGSTHRCRIIDYSQMDELALLSLRKSIIAAPFLRYQD-----IKTGTIVKGKVLALKPFGMLVKVGeQMRGLVpsmHLAD 487
Cdd:PRK00087  433 KGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEetwnsLEEGDVVEGEVKRLTDFGAFVDIG-GVDGLL---HVSE 508

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  488 I---MMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLKKTLvtsKLPAITCYEDAKPGLQTHGVIIRVKDYGCLVKFYND 564
Cdd:PRK00087  509 IswgRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLL---PDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPG 585

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 158186708  565 VQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLSFK 611
Cdd:PRK00087  586 VDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIK 632
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 451-638 6.76e-17

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 86.37  E-value: 6.76e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  451 KTGTIVKGKVLALKPFGMLVKVGEQMRGLVpsmHLADI----MMKNPEKKFNTGDEVKCRVLLCDPEAKKLimTL-KKTL 525
Cdd:PRK06299  372 PVGDVVEGKVKNITDFGAFVGLEGGIDGLV---HLSDIswdkKGEEAVELYKKGDEVEAVVLKVDVEKERI--SLgIKQL 446

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  526 VTSKLPAITcyEDAKPGLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKER 605
Cdd:PRK06299  447 EEDPFEEFA--KKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRR 524

                         170       180       190
                  ....*....|....*....|....*....|...
gi 158186708  606 MLLSFKLLSGSEPKDESVKNSKKKGSTVNTGQL 638
Cdd:PRK06299  525 ISLSIKALDEAEEKEAIAEYNSASDSKTTLGDL 557
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 450-641 7.00e-17

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 84.93  E-value: 7.00e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  450 IKTGTIVKGKVLALKPFGMLVKVGEqMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLKKTLVTsk 529
Cdd:PRK06676  190 LKEGDVVEGTVARLTDFGAFVDIGG-VDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPG-- 266

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  530 lPAITCYEDAKPGLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLS 609
Cdd:PRK06676  267 -PWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLS 345

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 158186708  610 FKLL---SGSEPKDESVKNSKKKGSTVNTGQLVDV 641
Cdd:PRK06676  346 IKALeeaPAEEEDRREEYRQYELPEEETGFSLGDL 380
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 176-671 7.97e-17

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 86.37  E-value: 7.97e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  176 NKVLSAEALRPGMLLTGTVSSLEDHGYLVDIG--VDGtraFLSLqkaqEYIRQKNKGAKFKVGQYLTCVVEELKSNGGVV 253
Cdd:PRK06299   20 EESLKESETREGSIVKGTVVAIDKDYVLVDVGlkSEG---RIPL----EEFKNEQGELEVKVGDEVEVYVERIEDGFGET 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  254 SLSVEHsqvssafATEEQSWN-LNNLL-PGLVVRAQVQKVTQFGL--QLNFLTFF--TGLVD------FMHLEPKKMgsy 321
Cdd:PRK06299   93 VLSREK-------AKRLEAWDkLEKAFeNGEIVEGVINGKVKGGFtvDLNGVEAFlpGSQVDvrpvrdTDPLEGKEL--- 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  322 sskqtvKACILCVHPRTRVVRLSLRPIF--------------LHPGRPLTrisyqqlGTV--LDDAsveGFFEKAGAIfr 385
Cdd:PRK06299  163 ------EFKVIKLDKKRNNIVVSRRAVLeeeraeereellenLEEGQVVE-------GVVknITDY---GAFVDLGGV-- 224

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  386 lrDGVL-----AYARLSHLSdskkafsaEAFKLGSTHRCRIIDYSQMDELALLSLrKSIIAAPFL----RYqdiKTGTIV 456
Cdd:PRK06299  225 --DGLLhitdiSWKRVNHPS--------EVVNVGDEVKVKVLKFDKEKKRVSLGL-KQLGEDPWEaiekKY---PVGSKV 290

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  457 KGKVLALKPFGMLVKVGEQMRGLVpsmHLADI----MMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLKKTL------V 526
Cdd:PRK06299  291 KGKVTNITDYGAFVELEEGIEGLV---HVSEMswtkKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKenpweeF 367

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  527 TSKLPaitcyedakPGLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELSAQH-IPDPERVFYTGQVVKVAVLNCEPSKER 605
Cdd:PRK06299  368 AEKYP---------VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKkGEEAVELYKKGDEVEAVVLKVDVEKER 438

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 158186708  606 MLLSFKLLSGSePKDESVKNSKKkgstvntGQLVDVKVLEKTKNGLEVAiLPHNIPAFLPTPHLSD 671
Cdd:PRK06299  439 ISLGIKQLEED-PFEEFAKKHKK-------GSIVTGTVTEVKDKGAFVE-LEDGVEGLIRASELSR 495
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1604-1864 7.82e-16

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: 79.77  E-value: 7.82e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1604 RQPESA-DDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfREEQEKLnvwvALLNLENMYGSQESLA 1682
Cdd:COG2956    22 GQPDKAiDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYLKAGLLD 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1683 K---VFERAVQYNEP-LKVFLHLADIYTKSEKFKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRALEC 1758
Cdd:COG2956    94 RaeeLLEKLLELDPDdAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1759 LPtkEHVDVIVKFAQLEFQLGDVERAKAIFENTLTTYPKRTDVWSVYIDMTIKHGSQKEVRDIFERVihLSLAPKRMKFF 1838
Cdd:COG2956   174 DP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA--LELDPSDDLLL 249

                         250       260
                  ....*....|....*....|....*.
gi 158186708 1839 FKRYLdYEKQHGTEKdVQAVKAKALE 1864
Cdd:COG2956   250 ALADL-LERKEGLEA-ALALLERQLR 273
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 8.26e-16

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


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 73.41  E-value: 8.26e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  729 GMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
727-798 1.62e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 72.64  E-value: 1.62e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 158186708    727 QPGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
453-522 8.77e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 70.71  E-value: 8.77e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708    453 GTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLK 522
Cdd:smart00316    3 GDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 537-1099 5.98e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 77.13  E-value: 5.98e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  537 EDAKPGLQTHGVIIRVKDYGCLVkfynDV----QGLVPKHELSAqhiPDPERVFYTGQVVKVAVLNCEPSKERMLLSFKL 612
Cdd:PRK06299   26 SETREGSIVKGTVVAIDKDYVLV----DVglksEGRIPLEEFKN---EQGELEVKVGDEVEVYVERIEDGFGETVLSREK 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  613 LSgsepKDESVKNSKKKGstvNTGQLVDVKVLEKTKNGLEVAIlpHNIPAFLPtphlSDHVANGPllhhwlqTGDTLH-- 690
Cdd:PRK06299   99 AK----RLEAWDKLEKAF---ENGEIVEGVINGKVKGGFTVDL--NGVEAFLP----GSQVDVRP-------VRDTDPle 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  691 ------RVLCLSQSEKHILLCRKpALVSTVEGGQDPKSLSEIQPGMLLIGFVKSIKDYGVFVQFpSGLSGLSPKTIMSDK 764
Cdd:PRK06299  159 gkelefKVIKLDKKRNNIVVSRR-AVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDL-GGVDGLLHITDISWK 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  765 FVTTPSEHFVEGQTVVAKVTNVDESKQRMLLslrlsdcslgdsastsflllcqcleelqGIRSLMSN----------QDS 834
Cdd:PRK06299  237 RVNHPSEVVNVGDEVKVKVLKFDKEKKRVSL----------------------------GLKQLGEDpweaiekkypVGS 288

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  835 VLIQTLADMTP-GMVLDamvqevLENGsvvfgggpVPDLI-----------LRASRYHRAGQELEpgqkkkVVVLHVDAL 902
Cdd:PRK06299  289 KVKGKVTNITDyGAFVE------LEEG--------IEGLVhvsemswtkknKHPSKVVSVGQEVE------VMVLEIDEE 348

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  903 KLEVHVSLHQDLVN---RKARKLRKNSRHQGivqhleesfAVASLVETGHLVAFS-----LIsHLNDTFHFD-----SEK 969
Cdd:PRK06299  349 KRRISLGLKQCKENpweEFAEKYPVGDVVEG---------KVKNITDFGAFVGLEggidgLV-HLSDISWDKkgeeaVEL 418

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  970 LRVGQgvcltlkttepGVTGLILAVEgPASKRIRM--------PAQRDSETVDdkgeeeeeeeeedltvrskkshslaIG 1041
Cdd:PRK06299  419 YKKGD-----------EVEAVVLKVD-VEKERISLgikqleedPFEEFAKKHK-------------------------KG 461

                         570       580       590       600       610
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 158186708 1042 DKVTGTIKSVKATHAVVTLDDGFIGCIHVSRILDDvpEGVSPTTTLKAGKKVTARVIG 1099
Cdd:PRK06299  462 SIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRD--RVEDATEVLKVGDEVEAKVIN 517
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 732-796 1.48e-13

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


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 67.02  E-value: 1.48e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708  732 LIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLS 796
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 522-610 5.75e-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: 66.07  E-value: 5.75e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  522 KKTLVTSklpaitcYEDAKPGLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEP 601
Cdd:cd04461     2 EGTLPTN-------FSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDE 74


                  ....*....
gi 158186708  602 SKERMLLSF 610
Cdd:cd04461    75 EKQRFLLSL 83
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 448-798 6.12e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 72.60  E-value: 6.12e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  448 QDIKTGTIVKGKVLALKPFGMLVKV-GEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLKKtlv 526
Cdd:PRK06676   13 KEVEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRR--- 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  527 tskLPAITCYEDAKPGLQTHGVI-IRVKDY--GCLVKFYNDVQGLVPKHELSAQHIPDPERvfYTGQVVKVAVLNCEPSK 603
Cdd:PRK06676   90 ---LEAEKAWDKLEEKFEEGEVVeVKVTEVvkGGLVVDVEGVRGFIPASLISTRFVEDFSD--FKGKTLEVKIIELDPEK 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  604 ERMLLSFKLLsgsepkDESVKNSKKKG--STVNTGQLVDVKVLEKTKNGLEVAIlpHNIPAFLPTPHLS-DHVANgplLH 680
Cdd:PRK06676  165 NRVILSRRAV------VEEERAAKKEEllSSLKEGDVVEGTVARLTDFGAFVDI--GGVDGLVHISELShERVEK---PS 233

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  681 HWLQTGDTLH-RVLCLSQSEKHILLCRKPALVSTVEGGQDpkslsEIQPGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKT 759
Cdd:PRK06676  234 EVVSVGQEVEvKVLSIDWETERISLSLKDTLPGPWEGVEE-----KLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHIS 308

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 158186708  760 IMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK06676  309 QISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIK 347
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
540-611 7.21e-13

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 65.32  E-value: 7.21e-13
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 158186708    540 KPGLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLSFK 611
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 456-520 1.67e-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: 63.94  E-value: 1.67e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708  456 VKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMT 520
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
rpsA PRK13806
30S ribosomal protein S1; Provisional
 364-631 7.35e-12

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 70.14  E-value: 7.35e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  364 LGTVLDDASVEGFFEKA---GAIFRLRDGVLAYARLSHLSDSKKAFSAEAFKLGSTHRCRIIDYSQMDELALLSLRKSII 440
Cdd:PRK13806  197 METVKEGDVVEGTVTRLapfGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIK 276

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  441 AAPFLRYQDI----KTGTIVKGKVLALKPFGMLVKVGEQMRGLVpsmHLADI----MMKNPEKKFNTGDEVKCRVLLCDP 512
Cdd:PRK13806  277 QAGGDPWDTVgdrlKAGDKVTGKVVRLAPFGAFVEILPGIEGLV---HVSEMswtrRVNKPEDVVAPGDAVAVKIKDIDP 353

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  513 EAKKLIMTLKKTLVTsklPAITCYEDAKPGLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERVFYTGQVV 592
Cdd:PRK13806  354 AKRRISLSLRDAEGD---PWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSV 430

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 158186708  593 KVAVLNCEPSKERMLLSFKLLSGSEPKDESVKNSKKKGS 631
Cdd:PRK13806  431 TLVVEEIDTAKRKISLAPAGAAGSGADDDDWKQFAPKKS 469
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 432-798 3.10e-11

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: 66.99  E-value: 3.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  432 LLSLRKSIIAAPFLRYQDI-KTGTIVKGKVLALKPFGMLVKVGEqMRGLVPSMHLADimmkNPEKKFNT--GDEVKCRVL 508
Cdd:COG0539    81 VLSKKKADREKAWEELEEAfENGEPVEGKVKGVVKGGLIVDIGG-VRAFLPASQVDV----RPVRDLDEyvGKTLEFKII 155

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  509 LCDPEAKKLIM-----------TLKKTLVtSKLpaitcyedaKPGLQTHGVIIRVKDYGCLVkfynD---VQGLVPKHEL 574
Cdd:COG0539   156 KLDRKRNNVVVsrravleeereEKREELL-EKL---------EEGDVVEGTVKNITDFGAFV----DlggVDGLLHISEI 221

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  575 SAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLSFKllsgsepkdesvknskkkgstvntgQLvdvkvlektkngleva 654
Cdd:COG0539   222 SWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLK-------------------------QL---------------- 260

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  655 ilphnipafLPTPhlsdhvangpllhhWLQtgdtlhrvlclsQSEKHillcrkpalvstveggqdpkslseiQPGMLLIG 734
Cdd:COG0539   261 ---------QPDP--------------WEN------------IAEKY-------------------------PVGDVVKG 280

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708  735 FVKSIKDYGVFVQFPSGLSGLSPKTIMS-DKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:COG0539   281 KVTRLTDFGAFVELEPGVEGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1597-1795 1.88e-10

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: 63.59  E-value: 1.88e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1597 EALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfrEEQEKLNVWVALLNLENMYG 1676
Cdd:COG2956    84 QDYLKAGLLDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLK-----LGPENAHAYCELAELYLEQG 158

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1677 SQESLAKVFERAVQYN-EPLKVFLHLADIYTKSEKFKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRA 1755
Cdd:COG2956   159 DYDEAIEALEKALKLDpDCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA 238

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 158186708 1756 LECLPTkehVDVIVKFAQLEFQLGDVERAKAIFENTLTTY 1795
Cdd:COG2956   239 LELDPS---DDLLLALADLLERKEGLEAALALLERQLRRH 275
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
57-524 2.56e-10

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 65.35  E-value: 2.56e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   57 LKIEKRKSNKSMKEKFEILSLESLCE-----GMRILGCVKEVNELELVVSLPNGLQGFVQVTEICDaytqklneqvaqee 131
Cdd:PRK00087  272 IKKMSELDNMEEVEENEQLEYMNELEkqirrGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTL-------------- 337

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  132 plEDLLRLPELFSPGMLVRCVVSSLDvTESGKksVKLSVnpKRVNKVLS----AEALRPGMLLTGTVSSLEDHGYLVDIG 207
Cdd:PRK00087  338 --DEISSLKESVKVGDEIEVKVLKLE-DEDGY--VVLSK--KEADREKAwkelEEAFENGEPVKGKVKEVVKGGLLVDYG 410

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  208 vdGTRAFL-SLQKAQEYIRQKNKGakfkVGQYLTCVVEELKSNG-GVVSLSVEHSQVSSAFATEEQSWNlnNLLPGLVVR 285
Cdd:PRK00087  411 --GVRAFLpASHVELGYVEDLSEY----KGQELEVKIIEFNRKRrKKVVLSRKAILEEEKEKKKEETWN--SLEEGDVVE 482

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  286 AQVQKVTQFGLqlnfltfftgLVDfmhlepkkmgsysskqtvkacilcvhprtrvvrlslrpiflhpgrpltrisyqqLG 365
Cdd:PRK00087  483 GEVKRLTDFGA----------FVD------------------------------------------------------IG 498

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  366 TVlddasvEGFfekagaifrLRDGVLAYARLSHLSDskkafsaeAFKLGSTHRCRIIDYSQMDELALLSLRKsIIAAPF- 444
Cdd:PRK00087  499 GV------DGL---------LHVSEISWGRVEKPSD--------VLKVGDEIKVYILDIDKENKKLSLSLKK-LLPDPWe 554

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  445 ---LRYqdiKTGTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTL 521
Cdd:PRK00087  555 nveEKY---PVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSI 631


                  ...
gi 158186708  522 KKT 524
Cdd:PRK00087  632 KEV 634
PRK08059 PRK08059
general stress protein 13; Validated
 450-524 3.16e-10

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 59.68  E-value: 3.16e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708  450 IKTGTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLKKT 524
Cdd:PRK08059    5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRAT 79
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 547-609 3.36e-10

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 57.68  E-value: 3.36e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 158186708   547 GVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLS 609
Cdd:pfam00575    9 GEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILS 71
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 729-798 4.12e-10

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


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 57.30  E-value: 4.12e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  729 GMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKqRMLLSLR 798
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARG-RISLSIK 69
rpsA PRK13806
30S ribosomal protein S1; Provisional
 537-796 4.19e-10

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 64.36  E-value: 4.19e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  537 EDAKPGLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKE----RMLLSFKL 612
Cdd:PRK13806  198 ETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIKQ 277

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  613 LSGsEPKDESvknskkkGSTVNTGQLVDVKVLEKTKNGLEVAILPhNIPAFLptpHLSD--HV--ANGPllHHWLQTGDT 688
Cdd:PRK13806  278 AGG-DPWDTV-------GDRLKAGDKVTGKVVRLAPFGAFVEILP-GIEGLV---HVSEmsWTrrVNKP--EDVVAPGDA 343

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  689 LH-RVLCLSQSEKHILLCRKPAlvstvEGgqDPKSLSEIQ--PGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKF 765
Cdd:PRK13806  344 VAvKIKDIDPAKRRISLSLRDA-----EG--DPWADVAERfaPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAG 416

                         250       260       270
                  ....*....|....*....|....*....|.
gi 158186708  766 VTTPSEHFVEGQTVVAKVTNVDESKQRMLLS 796
Cdd:PRK13806  417 KPATYEKLKPGDSVTLVVEEIDTAKRKISLA 447
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 180-524 5.12e-10

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: 63.14  E-value: 5.12e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  180 SAEALRPGMLLTGTVSSLEDHGYLVDIG--VDGtraFLSLqkaqEYIRQKNKGAKFKVGQYLTCVVEELKSNGGVVSLSV 257
Cdd:COG0539    12 SLKELKEGDIVKGTVVSIDDDEVLVDIGykSEG---IIPL----SEFSDEPGELEVKVGDEVEVYVEKVEDGEGEIVLSK 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  258 EHsqvssafATEEQSWN-----LNNllpGLVVRAQVQKVTQFGLQLNFLtfftGLVDFM---HLEPKKMGSYSS--KQTV 327
Cdd:COG0539    85 KK-------ADREKAWEeleeaFEN---GEPVEGKVKGVVKGGLIVDIG----GVRAFLpasQVDVRPVRDLDEyvGKTL 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  328 KACILCVHPRTRVVRLSLRPIF--------------LHPGRPLTrisyqqlGTVlddASVEGFfekaGAIFRLrDGV--- 390
Cdd:COG0539   151 EFKIIKLDRKRNNVVVSRRAVLeeereekreellekLEEGDVVE-------GTV---KNITDF----GAFVDL-GGVdgl 215

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  391 -----LAYARLSHLSdskkafsaEAFKLGSTHRCRIIDYSQMDELALLSLrKSIIAAPFLRY-QDIKTGTIVKGKVLALK 464
Cdd:COG0539   216 lhiseISWGRVKHPS--------EVLKVGDEVEVKVLKIDREKERISLSL-KQLQPDPWENIaEKYPVGDVVKGKVTRLT 286

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 158186708  465 PFGMLVKVGEQMRGLVpsmHLADIMM----KNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLKKT 524
Cdd:COG0539   287 DFGAFVELEPGVEGLV---HISEMSWtkrvAHPSDVVKVGDEVEVKVLDIDPEERRISLSIKQL 347
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 546-609 7.20e-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: 56.62  E-value: 7.20e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 158186708  546 HGVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLS 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 9.64e-10

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


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 56.47  E-value: 9.64e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  453 GTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLK 522
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 168-522 1.31e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 62.87  E-value: 1.31e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  168 LSVNPKRVNKVLS----------------AEALRPGMLLTGTVSSLEDHGYLVDI-GVDG----TRafLSlqkaqeYIRQ 226
Cdd:PRK06299  167 IKLDKKRNNIVVSrravleeeraeereelLENLEEGQVVEGVVKNITDYGAFVDLgGVDGllhiTD--IS------WKRV 238

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  227 KNKGAKFKVGQYLTCVVEELKSNGGVVSLSVEhsqvssafATEEQSW-NLNNLLP-GLVVRAQVQKVTQFGLqlnFLTFF 304
Cdd:PRK06299  239 NHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLK--------QLGEDPWeAIEKKYPvGSKVKGKVTNITDYGA---FVELE 307

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  305 TGLVDFMH----------LEPKKMGSYSskQTVKACILCVHPRTRVVRLSLRPifLHPgRPLTRIS--YQqLGTVlddas 372
Cdd:PRK06299  308 EGIEGLVHvsemswtkknKHPSKVVSVG--QEVEVMVLEIDEEKRRISLGLKQ--CKE-NPWEEFAekYP-VGDV----- 376

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  373 VEG-------FfekaGAIFRLRDGVLAYARLSHLSDSKKAFSA-EAFKLGSTHRCRIIDYSQMDELALLSlRKSIIAAPF 444
Cdd:PRK06299  377 VEGkvknitdF----GAFVGLEGGIDGLVHLSDISWDKKGEEAvELYKKGDEVEAVVLKVDVEKERISLG-IKQLEEDPF 451

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 158186708  445 LRYQDI-KTGTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLK 522
Cdd:PRK06299  452 EEFAKKhKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 45-346 1.76e-09

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 62.44  E-value: 1.76e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708    45 KKSQKGPAKTKKLKIEKRKSNKSMK-------EKFEilslESLCEGMRILGCVKEVNELELVVSLPNGLQGFVQVTEIcd 117
Cdd:TIGR00717  232 KVGQEVKVKVIKFDKEKGRISLSLKqlgedpwEAIE----KKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEM-- 305

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   118 AYTQKLneqvaqEEPledllrlPELFSPGMLVRCVVSSLDvtesgKKSVKLSVNPKRV--NKVLSAEALRP-GMLLTGTV 194
Cdd:TIGR00717  306 SWVKKN------SHP-------SKVVKKGDEVEVMILDID-----PERRRLSLGLKQCkaNPWEQFEEKHPvGDRVTGKI 367

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   195 SSLEDHGYLVDIGvDGTRAFLSLQKAQEYIRQKNKGAKFKVGQYLTCVVEELKSNGGVVSLSVEHsqvssafaTEEQSWN 274
Cdd:TIGR00717  368 KKITDFGAFVELE-GGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQ--------LTENPWE 438

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 158186708   275 -LNNLLP-GLVVRAQVQKVTQFGLQLNFLTFFTGLVDFMHL----EPKKMGSYSSKQTVKACILCVHPRTRVVRLSLR 346
Cdd:TIGR00717  439 kFAAKYKvGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELsenrDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 729-800 4.44e-09

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: 54.64  E-value: 4.44e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 158186708  729 GMLLIGFVKSIKDYGVFVQF-PSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLRLS 800
Cdd:cd05708     3 GQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 450-798 4.78e-09

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 60.90  E-value: 4.78e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   450 IKTGTIVKGKVLALKPFGMLVKVGEQMRGLVPsmhLADImmKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLKK-TLVTS 528
Cdd:TIGR00717   16 TRPGSIVKGTVVAINKDTVFVDVGLKSEGRIP---KEEF--LDAPLEIQVGDEVEVYLDRVEDRFGETVLSREKaQRHEL 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   529 KLPAITCYEDAKPglqTHGVIIRVKDYGCLVKFyNDVQGLVPKHELSAQHIPDPERvfYTGQVVKVAVLNCEPSKERMLL 608
Cdd:TIGR00717   91 WIKLEKAYEEGSI---VEGKIVGKVKGGFIVDL-NGVEAFLPGSQVDVKPIKDLDS--LIGKTLKFKIIKLDQKRNNIVV 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   609 SFKLL---SGSEPKDESVknskkkgSTVNTGQLVDVKVLEKTKNGleVAILPHNIPAFLPTPHLS-DHVANgPllHHWLQ 684
Cdd:TIGR00717  165 SRRAYleeERSQAREELL-------ENLKEGDVVKGVVKNITDFG--AFVDLGGVDGLLHITDMSwKRVKH-P--SEYVK 232

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   685 TGDTLH-RVLCLSQSEKHILLCRKpalvstvEGGQDP--KSLSEIQPGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIM 761
Cdd:TIGR00717  233 VGQEVKvKVIKFDKEKGRISLSLK-------QLGEDPweAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEM 305

                          330       340       350
                   ....*....|....*....|....*....|....*...
gi 158186708   762 S-DKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:TIGR00717  306 SwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1659-1797 1.47e-08

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: 55.20  E-value: 1.47e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1659 QEKLNVWVALLNLENMYGSQESLAKVFERAVQYN-EPLKVFLHLADIYTKSEKFKEAGELYNRMLKRFRQEKAVWIKYGA 1737
Cdd:COG4783     1 AACAEALYALAQALLLAGDYDEAEALLEKALELDpDNPEAFALLGEILLQLGDLDEAIVLLHEALELDPDEPEARLNLGL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1738 FVLGRSQAGASHRVLQRALECLPtkEHVDVIVKFAQLEFQLGDVERAKAIFENTLTTYPK 1797
Cdd:COG4783    81 ALLKAGDYDEALALLEKALKLDP--EHPEAYLRLARAYRALGRPDEAIAALEKALELDPD 138
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 177-621 2.29e-08

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 59.34  E-value: 2.29e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  177 KVLSAEALRPGMLLTGTVSSLEDH--GYLVDIGVdGTRAFLSLQKAQeyiRQKNKGAKFKVGQYLTCVVEEL---KSNGG 251
Cdd:PRK12269  389 KVKLRDAERDGTPVEGRIVRLTEKksGFEVDLGA-GMMAFLPISQSD---CQKVDAPESLIGLTSKFYIERIsqsKQHRG 464

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  252 VVSLSVEHSQVSSAFATEEQSWNLNNLLPGLVVRAQVQKVTQFGLQLNfLTFFTGLvdfMHLEPKKMGSYS-------SK 324
Cdd:PRK12269  465 NDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFID-LGGFDGL---LHVNDMSWGHVArprefvkKG 540

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  325 QTVKACILCVHPRTRVVRLSLRPIflhpgRPLTRISYQQLGTVLDdaSVEGFFEKA---GAIFRLRDGVLAYARLSHLSD 401
Cdd:PRK12269  541 QTIELKVIRLDQAEKRINLSLKHF-----QPDPWLEFENKFGVND--VVKGRVTKIadfGAFIELAEGIEGLAHISEFSW 613

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  402 SKKAFS-AEAFKLGSTHRCRIIDYSQMDELALLSLrKSIIAAPF----LRYqdiKTGTIVKGKVLALKPFGMLVKVGEQM 476
Cdd:PRK12269  614 VKKTSKpSDMVKIGDEVECMILGYDIQAGRVSLGL-KQVTANPWeeieARY---PVGARFTRRIVKVTNAGAFIEMEEGI 689

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  477 RGLVPSMHLADIMMKNP-EKKFNTGDEVKCRVLLCDPEAKKLIMTLKKtlvTSKLPAITCYEDAKPGLQTHGVIIRVKDY 555
Cdd:PRK12269  690 DGFLHVDDLSWVKRTRPaDHELEVGKEIECMVIECDPQARRIRLGVKQ---LSDNPWQVFANAYGVGSTVEGEVSSVTDF 766

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 158186708  556 GCLVKFYNDVQGLVPKHELSAQHIPDPE---RVFYTGQVVKVAVLNCEPSKERMLLSFKLLSGSEPKDE 621
Cdd:PRK12269  767 GIFVRVPGGVEGLVRKQHLVENRDGDPGealRKYAVGDRVKAVIVDMNVKDRKVAFSVRDYQRKVQRDE 835
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 388-652 3.16e-08

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 58.96  E-value: 3.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  388 DGVLayaRLSHLSDSKKAFSAEAFKLGSTHRCRIIDYSQMDELALLSLrKSIIAAPFLRYQD-IKTGTIVKGKVLALKPF 466
Cdd:PRK12269  517 DGLL---HVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSL-KHFQPDPWLEFENkFGVNDVVKGRVTKIADF 592

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  467 GMLVKVGEQMRGLVpsmHLADI----MMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLKKtlVTSKlPAITCYEDAKPG 542
Cdd:PRK12269  593 GAFIELAEGIEGLA---HISEFswvkKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQ--VTAN-PWEEIEARYPVG 666

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  543 LQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDP-ERVFYTGQVVKVAVLNCEPSKERMLLSFKLLSGSEPkdE 621
Cdd:PRK12269  667 ARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPaDHELEVGKEIECMVIECDPQARRIRLGVKQLSDNPW--Q 744

                         250       260       270
                  ....*....|....*....|....*....|...
gi 158186708  622 SVKNSKKKGSTV--NTGQLVDVKVLEKTKNGLE 652
Cdd:PRK12269  745 VFANAYGVGSTVegEVSSVTDFGIFVRVPGGVE 777
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 728-796 4.34e-08

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: 51.48  E-value: 4.34e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 158186708  728 PGMLLIGFVKSIKDYGVFVQFpSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLS 796
Cdd:cd05688     1 EGDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 729-796 4.68e-08

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: 51.46  E-value: 4.68e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 158186708  729 GMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLS 796
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 729-795 1.02e-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: 50.57  E-value: 1.02e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 158186708  729 GMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMS-DKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLL 795
Cdd:cd05690     1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 727-797 1.78e-07

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 49.98  E-value: 1.78e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 158186708   727 QPGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSL 797
Cdd:pfam00575    2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1693-1829 1.91e-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: 52.12  E-value: 1.91e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1693 EPLKVFLHLADIYTKSEKFKEAGELYNRMLKRFRQEKAVWIKYG--AFVLGRSQAGASHrvLQRALECLPtkEHVDVIVK 1770
Cdd:COG4783     2 ACAEALYALAQALLLAGDYDEAEALLEKALELDPDNPEAFALLGeiLLQLGDLDEAIVL--LHEALELDP--DEPEARLN 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 158186708 1771 FAQLEFQLGDVERAKAIFENTLTTYPKRTDVWSVYIDMTIKHGSQKEVRDIFERVIHLS 1829
Cdd:COG4783    78 LGLALLKAGDYDEALALLEKALKLDPEHPEAYLRLARAYRALGRPDEAIAALEKALELD 136
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 451-518 3.10e-07

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 49.21  E-value: 3.10e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 158186708   451 KTGTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLI 518
Cdd:pfam00575    2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRII 69
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1040-1099 4.20e-07

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 49.14  E-value: 4.20e-07
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   1040 IGDKVTGTIKSVKATHAVVTLDDGFIGCIHVSRILDDVPEgvSPTTTLKAGKKVTARVIG 1099
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVK--DPEEVLKVGDEVKVKVLS 59
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1681-1804 5.63e-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: 50.39  E-value: 5.63e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1681 LAKVFERAVQYN-EPLKVFLHLADIYTKSEKFKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRALECL 1759
Cdd:COG4235     2 AIARLRQALAANpNDAEGWLLLGRAYLRLGRYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEELLERALALD 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 158186708 1760 PtkEHVDVIVKFAQLEFQLGDVERAKAIFENTLTTYPKRTDVWSV 1804
Cdd:COG4235    82 P--DNPEALYLLGLAAFQQGDYAEAIAAWQKLLALLPADAPARLL 124
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 728-798 6.51e-07

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 52.90  E-value: 6.51e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 158186708  728 PGMLLIGFVKSIKDYGVFV---QFPsGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK03987    8 EGELVVGTVKEVKDFGAFVtldEYP-GKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1185-1400 9.82e-07

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 53.58  E-value: 9.82e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  1185 LLLTSLSFKVLKHPDKKFQIGQAIKATVVGPDIPRAFLCLSLI----GPY-----KLEEGDVAMGRVLKVLPnKGLTVSF 1255
Cdd:TIGR00717  214 LHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKqlgeDPWeaiekKFPVGDKITGRVTNLTD-YGVFVEI 292

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  1256 PFGRIGKVSVFHLS-DSYSEEPLTDFCPQKIVRCYILS--TAHRMLALSLRSSRTNketkskiedPEVNSIEDIQAGQLL 1332
Cdd:TIGR00717  293 EEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDidPERRRLSLGLKQCKAN---------PWEQFEEKHPVGDRV 363

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 158186708  1333 RGYVKSILPSSVVIGLGPSVMGLVKHSHVSQcvSREKELYDKCLPEGKLVTARVLCVNPKKNLIELSL 1400
Cdd:TIGR00717  364 TGKIKKITDFGAFVELEGGIDGLIHLSDISW--DKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGV 429
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
18-346 1.01e-06

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 53.80  E-value: 1.01e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   18 KSEKSSQPVVEQDNLFDISTE-EGSVKRKKSQKGPAKTKKLKIEKRKSNKSMKEKFEilsleslcEGMRILGCVKEVNEL 96
Cdd:PRK00087  332 LRELTLDEISSLKESVKVGDEiEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFE--------NGEPVKGKVKEVVKG 403

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   97 ELVVSLpNGLQGFVQVTEICDAYTQKLNEQVAQEepLEdlLRLPElFSPGMLVRCVVSSLDVTESGKKsvklsvnpKRVN 176
Cdd:PRK00087  404 GLLVDY-GGVRAFLPASHVELGYVEDLSEYKGQE--LE--VKIIE-FNRKRRKKVVLSRKAILEEEKE--------KKKE 469

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  177 KVLsaEALRPGMLLTGTVSSLEDHGYLVDI-GVDGtraflsLQKAQE--YIRQKNKGAKFKVGQYLTCVVEELKSNGGVV 253
Cdd:PRK00087  470 ETW--NSLEEGDVVEGEVKRLTDFGAFVDIgGVDG------LLHVSEisWGRVEKPSDVLKVGDEIKVYILDIDKENKKL 541

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  254 SLSVEhsqvssafATEEQSW-NLNNLLP-GLVVRAQVQKVTQFGLQLNFLTFFTGLVDFMHLEPKKMGS----YSSKQTV 327
Cdd:PRK00087  542 SLSLK--------KLLPDPWeNVEEKYPvGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKpedvLSEGEEV 613

                         330
                  ....*....|....*....
gi 158186708  328 KACILCVHPRTRVVRLSLR 346
Cdd:PRK00087  614 KAKILEVDPEEKRIRLSIK 632
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1327-1400 1.04e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.98  E-value: 1.04e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 158186708   1327 QAGQLLRGYVKSILPSSVVIGLGPSVMGLVKHSHVSQcvSREKELYDKcLPEGKLVTARVLCVNPKKNLIELSL 1400
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSD--KRVKDPEEV-LKVGDEVKVKVLSVDEEKGRIILSL 71
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 1.13e-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: 47.62  E-value: 1.13e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 158186708  729 GMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSL 797
Cdd:cd05697     1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
185-256 1.37e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.60  E-value: 1.37e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 158186708    185 RPGMLLTGTVSSLEDHGYLVDIGvDGTRAFLSLQKAQEYiRQKNKGAKFKVGQYLTCVVEELKSNGGVVSLS 256
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLG-NGVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 453-523 1.51e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 53.12  E-value: 1.51e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 158186708  453 GTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLKK 523
Cdd:PRK07899  294 GQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQ 364
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 445-798 1.51e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 53.24  E-value: 1.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  445 LRYQDIKTGTIVKGKVLALKPFGMLVKVGEQMRGLVPsmhLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLKKT 524
Cdd:PRK06299   23 LKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIP---LEEFKNEQGELEVKVGDEVEVYVERIEDGFGETVLSREKA 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  525 LVTSKLPAItcYEDAKPGLQTHGVII-RVKdyGCLVKFYNDVQGLVPKHELSAQHIPDPErvFYTGQVVKVAVLNCEPSK 603
Cdd:PRK06299  100 KRLEAWDKL--EKAFENGEIVEGVINgKVK--GGFTVDLNGVEAFLPGSQVDVRPVRDTD--PLEGKELEFKVIKLDKKR 173

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  604 ERMLLSFKLL---SGSEPKDESVKNSKKkgstvntGQLVDVKVLEKTKNGlevailphnipAFlptphlsdhVANGP--- 677
Cdd:PRK06299  174 NNIVVSRRAVleeERAEEREELLENLEE-------GQVVEGVVKNITDYG-----------AF---------VDLGGvdg 226

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  678 LLHH----W---------LQTGDTLH-RVLCLSQSEKHILLCRKpALvstvegGQDP-KSLSE-IQPGMLLIGFVKSIKD 741
Cdd:PRK06299  227 LLHItdisWkrvnhpsevVNVGDEVKvKVLKFDKEKKRVSLGLK-QL------GEDPwEAIEKkYPVGSKVKGKVTNITD 299

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 158186708  742 YGVFVQFPSGLSGLSPKTIMS-DKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK06299  300 YGAFVELEEGIEGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLK 357
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
718-801 1.72e-06

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 53.11  E-value: 1.72e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  718 QDPKSLSEIQPGMLLIGFVKSIKDYGVFV-----QfpsglSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQR 792
Cdd:COG2183   631 EGVLKIEDLKPGMILEGTVTNVTDFGAFVdigvhQ-----DGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKR 705


                  ....*....
gi 158186708  793 MLLSLRLSD 801
Cdd:COG2183   706 ISLSMKLDD 714
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 525-798 1.76e-06

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 53.18  E-value: 1.76e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  525 LVTSKLPAITCYEDAKPGLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELSAQ-HIPDPERVFytgqVVKVAVLNCEPSK 603
Cdd:PRK12269  305 LVPRQLQERYSFEAPEPGSVRMGTVVQVNAGTVFVDIGGKSEGRVPVEEFEAPpKAGDGVRVY----VERVTPYGPELSK 380

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  604 ---ERMLLSFKLlsgsepkdesvKNSKKKGSTVNtGQLVDvkvLEKTKNGLEVAiLPHNIPAFLPTPHLSDHVANGPLLH 680
Cdd:PRK12269  381 tkaDRLGLKVKL-----------RDAERDGTPVE-GRIVR---LTEKKSGFEVD-LGAGMMAFLPISQSDCQKVDAPESL 444

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  681 HWLQTGDTLHRVlclSQSEKH-----ILLCRKPALVSTVEGGQDpKSLSEIQPGMLLIGFVKSIKDYGVFVQFpSGLSGL 755
Cdd:PRK12269  445 IGLTSKFYIERI---SQSKQHrgndnIVINRRRYLEERARQARE-EFFNSVHIEDSVSGVVKSFTSFGAFIDL-GGFDGL 519

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 158186708  756 SPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK12269  520 LHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLK 562
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 456-628 1.86e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 52.11  E-value: 1.86e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  456 VKGKVLALKPFGMLVKVgEQMRGLVPSMHladIMMKNPEKKFnTGDEVKCRVLLCDPEAKKLIMTLKKTLVTSKLPaitc 535
Cdd:PRK07400  122 VRSEVFATNRGGALVRI-EGLRGFIPGSH---ISTRKPKEEL-VGEELPLKFLEVDEERNRLVLSHRRALVERKMN---- 192

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  536 yedakpGLQTHGVIIR----VKDYGCLVKFyNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLSFK 611
Cdd:PRK07400  193 ------RLEVGEVVVGtvrgIKPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTK 265

                         170
                  ....*....|....*..
gi 158186708  612 LLSgSEPKDeSVKNSKK 628
Cdd:PRK07400  266 QLE-PEPGD-MLKDPQK 280
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1667-1824 2.77e-06

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 50.78  E-value: 2.77e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1667 ALLNLENMYGSQESLAK---VFERAVQYN-EPLKVFLHLADIYTKSEKFKEAGELYNRMLKRFRQEKAVWIKYGA--FVL 1740
Cdd:COG0457    10 AYNNLGLAYRRLGRYEEaieDYEKALELDpDDAEALYNLGLAYLRLGRYEEALADYEQALELDPDDAEALNNLGLalQAL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1741 GRSQAGASHrvLQRALECLPtkEHVDVIVKFAQLEFQLGDVERAKAIFENTLTTYPKRTDVWSVYIDMTIKHGSQKEVRD 1820
Cdd:COG0457    90 GRYEEALED--YDKALELDP--DDAEALYNLGLALLELGRYDEAIEAYERALELDPDDADALYNLGIALEKLGRYEEALE 165


                  ....
gi 158186708 1821 IFER 1824
Cdd:COG0457   166 LLEK 169
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 556-798 3.05e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 51.97  E-value: 3.05e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  556 GCLVKFYND---------VQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLSfKLLSGSEPKDESVKNS 626
Cdd:PRK07899   41 GTVVKVDRDevlldigykTEGVIPSRELSIKHDVDPNEVVEVGDEVEALVLQKEDKEGRLILS-KKRAQYERAWGTIEKI 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  627 KKKGSTVnTGqlvdvKVLEKTKNGLevaILPHNIPAFLPTP--------HLSDHVangpllhhwlqtGDTLH-RVLCLSQ 697
Cdd:PRK07899  120 KEKDGVV-TG-----TVIEVVKGGL---ILDIGLRGFLPASlvemrrvrDLQPYI------------GQEIEaKIIELDK 178

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  698 SEKHILLCRKPALVSTveggqdpKS------LSEIQPGMLLIGFVKSIKDYGVFVQFpSGLSGLSPKTIMSDKFVTTPSE 771
Cdd:PRK07899  179 NRNNVVLSRRAWLEQT-------QSevrsefLNQLQKGQVRKGVVSSIVNFGAFVDL-GGVDGLVHVSELSWKHIDHPSE 250

                         250       260
                  ....*....|....*....|....*..
gi 158186708  772 HFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK07899  251 VVEVGQEVTVEVLDVDMDRERVSLSLK 277
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 451-522 3.24e-06

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


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 46.55  E-value: 3.24e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 158186708  451 KTGTIVKGKVLALKPFGMLVKV-GEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLK 522
Cdd:cd05708     1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 453-515 3.59e-06

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


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 46.12  E-value: 3.59e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 158186708  453 GTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAK 515
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGR 63
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 80-155 3.71e-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: 46.19  E-value: 3.71e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 158186708   80 LCEGMRILGCVKEVNELE-LVVSLPNGLQGFVQVTEICDAYTqklneqvaqEEPLEDllrlpelFSPGMLVRCVVSS 155
Cdd:cd05704     1 LEEGAVTLGMVTKVIPHSgLTVQLPFGKTGLVSIFHLSDSYT---------ENPLEG-------FKPGKIVRCCILS 61
PRK08059 PRK08059
general stress protein 13; Validated
 723-798 3.75e-06

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 47.73  E-value: 3.75e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 158186708  723 LSEIQPGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 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 5.32e-06

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: 45.71  E-value: 5.32e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 158186708  726 IQPGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:cd05706     1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1037-1400 5.74e-06

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: 51.27  E-value: 5.74e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  1037 SLAIGDKVTGTIKSVKATHAVVTLDdGFIGCIHVSRILDDVPegVSPTTTLKAGKKVTARVIggRDVKTSKFLpishprf 1116
Cdd:TIGR00717  184 NLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRV--KHPSEYVKVGQEVKVKVI--KFDKEKGRI------- 251

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  1117 vltilELSVRpsELKGDyralnthsvsPMEKI-RQYQAGQTVTCflKKYNVMKKWLEVDIEPDIRGRIPLLLTSLSFKVl 1195
Cdd:TIGR00717  252 -----SLSLK--QLGED----------PWEAIeKKFPVGDKITG--RVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKN- 311

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  1196 KHPDKKFQIGQAIKATVVGPDIPRAFLCLSL----IGPY-KLEE----GDVAMGRVLKvLPNKGLTVSFPFGRIGkvsVF 1266
Cdd:TIGR00717  312 SHPSKVVKKGDEVEVMILDIDPERRRLSLGLkqckANPWeQFEEkhpvGDRVTGKIKK-ITDFGAFVELEGGIDG---LI 387

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  1267 HLSDSYSEEPLTDFCPQKIVRCYIlstAHRMLALSLRSSRTNKETKSKIEDPEVNSIEDIQAGQLLRGYVKSILPSSVVI 1346
Cdd:TIGR00717  388 HLSDISWDKDGREADHLYKKGDEI---EAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKDFGAFV 464

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....
gi 158186708  1347 GLGPSVMGLVKHSHVSQCVSREKELYdkcLPEGKLVTARVLCVNPKKNLIELSL 1400
Cdd:TIGR00717  465 ELPGGVEGLIRNSELSENRDEDKTDE---IKVGDEVEAKVVDIDKKNRKVSLSV 515
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 542-611 5.80e-06

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


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 45.74  E-value: 5.80e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  542 GLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPsKERMLLSFK 611
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK 69
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 453-522 6.27e-06

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: 45.72  E-value: 6.27e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  453 GTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTLK 522
Cdd:cd05691     1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1701-1865 7.32e-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: 7.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1701 LADIYTKSEKFKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRALEclPTKEHVDVIVKFAQLEFQLGD 1780
Cdd:COG2956    14 KGLNYLLNGQPDKAIDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE--RDPDRAEALLELAQDYLKAGL 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1781 VERAKAIFENTLTTYPKRTDVWSVYIDMTIKHGSQKEVRDIFERVIHLSlaPKRMKFFFKRYLDYEKQHGTEKDVQAVKa 1860
Cdd:COG2956    92 LDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLG--PENAHAYCELAELYLEQGDYDEAIEALE- 168


                  ....*
gi 158186708 1861 KALEY 1865
Cdd:COG2956   169 KALKL 173
RNA14 COG5107
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ...
 1612-1870 7.43e-06

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


Pssm-ID: 227438 [Multi-domain]  Cd Length: 660  Bit Score: 50.79  E-value: 7.43e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1612 FDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALK---TISFR-EEQEKLNvwvalLNLENMYGSQESLAKVFER 1687
Cdd:COG5107   291 HNQILDYFYYAEEVWFDYSEYLIGISDKQKALKTVERGIEmspSLTMFlSEYYELV-----NDEEAVYGCFDKCTQDLKR 365

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1688 AVQYNEplkvflhlADIYTKSE-KFKEAGELynrMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRALEcLPTKEHvD 1766
Cdd:COG5107   366 KYSMGE--------SESASKVDnNFEYSKEL---LLKRINKLTFVFCVHLNYVLRKRGLEAARKLFIKLRK-EGIVGH-H 432

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1767 VIVKFAQLEFQ-LGDVERAKAIFENTLTTYPKRTDVWSVYIDMTIKHGSQKEVRDIFERVIHlSLAPKRMKFFFKRYLDY 1845
Cdd:COG5107   433 VYIYCAFIEYYaTGDRATAYNIFELGLLKFPDSTLYKEKYLLFLIRINDEENARALFETSVE-RLEKTQLKRIYDKMIEY 511

                         250       260
                  ....*....|....*....|....*
gi 158186708 1846 EKQHGTEKDVQAVKAKALEYVEAKS 1870
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 9.05e-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: 45.27  E-value: 9.05e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 158186708  453 GTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMM--KNPEKKFNTGDEVKCRVL 508
Cdd:cd05702     1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPdgKNPLSKFKIGQKIKARVI 58
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 1322-1400 9.51e-06

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


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 45.66  E-value: 9.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1322 SIEDIQAGQLLRGYVKSILPSSVVIGLGPSVMGLVKHSHVS-QCVSREKELYDKclpeGKLVTARVLCVNPKKNLIELSL 1400
Cdd:cd04461     8 NFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISdEFVTDPSFGFKK----GQSVTAKVTSVDEEKQRFLLSL 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 1.22e-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: 44.65  E-value: 1.22e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 158186708  726 IQPGMLLIGFV-KSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVtnVDESKQRMLLSLR 798
Cdd:cd05704     1 LEEGAVTLGMVtKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCI--LSKKDGKYQLSLR 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1152-1226 1.59e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 44.52  E-value: 1.59e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708   1152 QAGQTVTCFLKkyNVMKKWLEVDIEPDIRGRIPLllTSLSFKVLKHPDKKFQIGQAIKATVVGPDIPRAFLCLSL 1226
Cdd:smart00316    1 EVGDVVEGTVT--EITPGGAFVDLGNGVEGLIPI--SELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 729-798 1.69e-05

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: 44.50  E-value: 1.69e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 158186708  729 GMLLIGFVKSIKDYGVFV---QFPsGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:cd04452     4 GELVVVTVKSIADMGAYVsllEYG-NIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK 75
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 729-796 2.57e-05

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


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 43.82  E-value: 2.57e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 158186708  729 GMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLS 796
Cdd:cd05707     1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1591-1724 3.28e-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: 47.80  E-value: 3.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1591 ELSRIEEALmdpgRQPESADD-FDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfrEEQEKLNVWVALL 1669
Cdd:COG2956   149 ELAELYLEQ----GDYDEAIEaLEKALKLDPDCARALLLLAELYLEQGDYEEAIAALERALE-----QDPDYLPALPRLA 219

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 158186708 1670 NLENMYGSQESLAKVFERAVQYNEPLKVFLHLADIYTKSEKFKEAGELYNRMLKR 1724
Cdd:COG2956   220 ELYEKLGDPEEALELLRKALELDPSDDLLLALADLLERKEGLEAALALLERQLRR 274
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 453-517 3.54e-05

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: 43.64  E-value: 3.54e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 158186708  453 GTIVKGKVLALKPFGMLVKVGEQMRGLVpsmHLADI----MMKNPEKKFNTGDEVKCRVLLCDPEAKKL 517
Cdd:cd05690     1 GTVVSGKIKSITDFGIFVGLDGGIDGLV---HISDIswtqRVRHPSEIYKKGQEVEAVVLNIDVERERI 66
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 449-508 4.03e-05

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 45.17  E-value: 4.03e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 158186708  449 DIKTGTIVKGKVLALKPFGMLVKVGEQMRGLVpsmH---LADIMMKNPEKKFNTGDEVKCRVL 508
Cdd:COG1098     2 SIEVGDIVEGKVTGITPFGAFVELPEGTTGLV---HiseIADGYVKDINDYLKVGDEVKVKVL 61
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 56-346 4.09e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 47.95  E-value: 4.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   56 KLKIEKRKSNKSMKEKFEilsleslcEGMRILGCVKEVNELELVVSLpNGLQGFVQVTEICDAYTQKLNEQVAQEepLEd 135
Cdd:PRK06676   87 KRRLEAEKAWDKLEEKFE--------EGEVVEVKVTEVVKGGLVVDV-EGVRGFIPASLISTRFVEDFSDFKGKT--LE- 154

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  136 lLRLPELFSPGMlvRCVVSSLDVTESGKKSVKLSVnpkrvnkvlsAEALRPGMLLTGTVSSLEDHGYLVDIG-VDGtraf 214
Cdd:PRK06676  155 -VKIIELDPEKN--RVILSRRAVVEEERAAKKEEL----------LSSLKEGDVVEGTVARLTDFGAFVDIGgVDG---- 217

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  215 lsLQKAQE--YIRQKNKGAKFKVGQYLTCVVEELKSNGGVVSLSVEhsqvssafATEEQSWNL--NNLLPGLVVRAQVQK 290
Cdd:PRK06676  218 --LVHISElsHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLK--------DTLPGPWEGveEKLPEGDVIEGTVKR 287

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 158186708  291 VTQFGLqlnFLTFFT---GLVDFMHLEPKKMGSYSSK----QTVKACILCVHPRTRVVRLSLR 346
Cdd:PRK06676  288 LTDFGA---FVEVLPgveGLVHISQISHKHIATPSEVleegQEVKVKVLEVNEEEKRISLSIK 347
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1332-1399 4.32e-05

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


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 43.14  E-value: 4.32e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 158186708 1332 LRGYVKSILPSSVVIGLGPSVMGLVkhsHVSQCVSREKELYDKCLPEGKLVTARVLCVNPKKNLIELS 1399
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLV---HISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1597-1757 4.61e-05

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 46.92  E-value: 4.61e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1597 EALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisfreeqeKLNVWVALLNLENMYG 1676
Cdd:COG0457    16 LAYRRLGRYEEAIEDYEKALELDPDDAEALYNLGLAYLRLGRYEEALADYEQALEL--------DPDDAEALNNLGLALQ 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1677 SQESLAK---VFERAVQYN-EPLKVFLHLADIYTKSEKFKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVL 1752
Cdd:COG0457    88 ALGRYEEaleDYDKALELDpDDAEALYNLGLALLELGRYDEAIEAYERALELDPDDADALYNLGIALEKLGRYEEALELL 167


                  ....*
gi 158186708 1753 QRALE 1757
Cdd:COG0457   168 EKLEA 172
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1597-1724 4.80e-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: 45.18  E-value: 4.80e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1597 EALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisFREEQEklnVWVALLNLENMYG 1676
Cdd:COG4783    12 QALLLAGDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALEL--DPDEPE---ARLNLGLALLKAG 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 158186708 1677 SQESLAKVFERAVQYN-EPLKVFLHLADIYTKSEKFKEAGELYNRMLKR 1724
Cdd:COG4783    87 DYDEALALLEKALKLDpEHPEAYLRLARAYRALGRPDEAIAALEKALEL 135
COG4700 COG4700
Uncharacterized conserved protein ECs_4300, contains TPR-like domain [Function unknown];
1686-1842 4.99e-05

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


Pssm-ID: 443735 [Multi-domain]  Cd Length: 249  Bit Score: 46.80  E-value: 4.99e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1686 ERAVQYNEPLKVFLHLADIYTKSEKFKEAGELYNRMLKRFRQEKAVwIKYGA----FVLGRSQAGASHrvLQRALECLPT 1761
Cdd:COG4700    80 EKALEFADTVQNRVRLADALLELGRYDEAIELYEEALTGIFADDPH-ILLGLaqalFELGRYAEALET--LEKLIAKNPD 156

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1762 KEHVDVIVKFAQ-LEfQLGDVERAKAIFENTLTTYPKRtDVWSVYIDMTIKHGSQKEVRDIFERVIHLSlapKRMKFFFK 1840
Cdd:COG4700   157 FKSSDAHLLYARaLE-ALGDLEAAEAELEALARRYSGP-EARYRYAKFLARQGRTAEAKELLEEILDEA---KHMPKHYR 231


                  ..
gi 158186708 1841 RY 1842
Cdd:COG4700   232 RL 233
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 541-609 6.13e-05

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


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 42.62  E-value: 6.13e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 158186708  541 PGLQTHGVIIRVKDYGCLVKFyNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLS 609
Cdd:cd05688     1 EGDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
1040-1098 7.91e-05

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 43.92  E-value: 7.91e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 158186708 1040 IGDKVTGTIKSVKATHAVVTLDDGFIGCIHVSRI----LDDVPEgvspttTLKAGKKVTARVI 1098
Cdd:PRK07252    3 IGDKLKGTITGIKPYGAFVALENGTTGLIHISEIktgfIDNIHQ------LLKVGEEVLVQVV 59
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
373-436 8.51e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.59  E-value: 8.51e-05
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 158186708    373 VEGF---FEKAGAIFRLRDGVLAYARLSHLSDSKKAFSAEAFKLGSTHRCRIIDYSQMDELALLSLR 436
Cdd:smart00316    6 VEGTvteITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA PRK13806
30S ribosomal protein S1; Provisional
 77-347 8.54e-05

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 47.41  E-value: 8.54e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   77 LESLCEGMRILGCVKEVNELELVVSLPNGLQGFVQVTEICDAYTQKLNEQVaqeepledllrlpelfSPGMLVRCVVSSL 156
Cdd:PRK13806  197 METVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAV----------------SVGDTVRVKVLGI 260

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  157 DVTESGKKsVKLSVNPKRV-----NKVlsAEALRPGMLLTGTVSSLEDHGYLVDI--GVDGtraflsLQKAQE--YIRQK 227
Cdd:PRK13806  261 ERAKKGKG-LRISLSIKQAggdpwDTV--GDRLKAGDKVTGKVVRLAPFGAFVEIlpGIEG------LVHVSEmsWTRRV 331

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  228 NK-GAKFKVGQYLTCVVEELKSNGGVVSLSVEHSQVSSAFATEEQswnlnnLLPGLVVRAQVQKVTQFGLQLNFLTFFTG 306
Cdd:PRK13806  332 NKpEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAER------FAPGTTVTGTVEKRAQFGLFVNLAPGVTG 405

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 158186708  307 L----VDFMHLEPKKMGSYSSKQTVKACILCVHPRTRvvRLSLRP 347
Cdd:PRK13806  406 LlpasVISRAGKPATYEKLKPGDSVTLVVEEIDTAKR--KISLAP 448
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 9.12e-05

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


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 43.36  E-value: 9.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  726 IQPGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEH-------------------FVEGQTVVAKVTNV 786
Cdd:cd05693     1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELdeeseeeddeeelpdledlFSVGQLVRCKVVSL 80

                          90
                  ....*....|....*...
gi 158186708  787 DES---KQRMLLSLRLSD 801
Cdd:cd05693    81 DKSksgKKRIELSLEPEL 98
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 724-798 9.90e-05

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 47.35  E-value: 9.90e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708  724 SEIQPGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDEsKQRMLLSLR 798
Cdd:PRK11824  617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDK-RGRIRLSRK 690
rpsA PRK13806
30S ribosomal protein S1; Provisional
 449-798 9.96e-05

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 47.03  E-value: 9.96e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  449 DIKTGTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADimmKNPEKKFNTGDEVKCRVL-LCDPEakkliMTLKKTLvT 527
Cdd:PRK13806   31 ELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLD---ADGELTVAVGDEVELYVVsVNGQE-----IRLSKAL-S 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  528 SKLPAITCYEDAKPGLQTHGVIIRVkdygCLVKFYNDVQG---LVPKHELSAQHIPDPERvfYTGQVVKVAVLNCEPSKE 604
Cdd:PRK13806  102 GQGGAAMLEEAYENGVPVEGKVTGT----CKGGFNVEVLGrraFCPVSQIDLRYVEDPES--YVGQTFQFLITRVEENGR 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  605 RMLLSFKLLSGSEPKDESVKNSKkkgsTVNTGQLVDVKVLEKTKNG--LEVAilphniPAFLPTPHLSD----HVANGpl 678
Cdd:PRK13806  176 NIVVSRRALLEREQKEALEAFME----TVKEGDVVEGTVTRLAPFGafVELA------PGVEGMVHISElswsRVQKA-- 243

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  679 lHHWLQTGDTLH-RVLCLSQSEK----HILLCRKPAlvstvegGQDP-KSLSE-IQPGMLLIGFVKSIKDYGVFVQFPSG 751
Cdd:PRK13806  244 -DEAVSVGDTVRvKVLGIERAKKgkglRISLSIKQA-------GGDPwDTVGDrLKAGDKVTGKVVRLAPFGAFVEILPG 315

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*...
gi 158186708  752 LSGLSPKTIMS-DKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK13806  316 IEGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLR 363
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 1.03e-04

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


Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 42.19  E-value: 1.03e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 158186708   90 VKEVNELELVVSLPNGLQGFVQVTEICDAYTQK 122
Cdd:cd05702     8 VKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDG 40
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
82-169 1.12e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.21  E-value: 1.12e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708     82 EGMRILGCVKEVNELELVVSLPNGLQGFVQVTEICDAYTQKLNEQvaqeepledllrlpelFSPGMLVRCVVSSLDVTes 161
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEV----------------LKVGDEVKVKVLSVDEE-- 63


                    ....*...
gi 158186708    162 gKKSVKLS 169
Cdd:smart00316   64 -KGRIILS 70
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 1329-1400 1.17e-04

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


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 41.84  E-value: 1.17e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 158186708 1329 GQLLRGYVKSILPSSVVIGLGPSVMGLVKHSHVS--QCVSREKELYdkclpEGKLVTARVLCVNPKKNLIELSL 1400
Cdd:cd05697     1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLAdvRLKHPEKKFK-----PGLKVKCRVLSVEPERKRLVLTL 69
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1233-1292 1.34e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 41.82  E-value: 1.34e-04
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   1233 EEGDVAMGRVLKVLPnKGLTVSFPFGRIGKVSVFHLSDSYSEEPLTDFCPQKIVRCYILS 1292
Cdd:smart00316    1 EVGDVVEGTVTEITP-GGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLS 59
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 726-796 1.70e-04

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: 41.61  E-value: 1.70e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 158186708  726 IQPGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPS---EHFVEGQTVVAKVTNVDESKQRMLLS 796
Cdd:cd05705     1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSlynKYLPEGKLLTAKVLSVNSEKNLVELS 74
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 453-517 1.76e-04

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


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 41.45  E-value: 1.76e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708  453 GTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKL 517
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRI 65
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 542-608 1.77e-04

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


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 41.33  E-value: 1.77e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 158186708  542 GLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELS-AQHIPDPERVFYTGQVVKVAVLNCEPSKERMLL 608
Cdd:cd05690     1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 621-976 1.85e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 46.02  E-value: 1.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  621 ESVKNSKKKGSTVNTGQLVDVKVLEKTKNGLEVAILPHNIPAFLPTPHLS-DHVANGPLLhhwLQTGDTLH-RVLCLSQS 698
Cdd:PRK06676    3 EEFEESLNSVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSnDHIEDINDV---VKVGDELEvYVLKVEDG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  699 EKHILLCRKPALVStveggqdpKSLSEIQ----PGMLLIGFVKSIKDYGVFVQFpSGLSGLSPKTIMSDKFVTTPSEhFV 774
Cdd:PRK06676   80 EGNLLLSKRRLEAE--------KAWDKLEekfeEGEVVEVKVTEVVKGGLVVDV-EGVRGFIPASLISTRFVEDFSD-FK 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  775 eGQTVVAKVTNVDESKQRMLLSLRlsdcslgdsastsflllcqcleelQGIRSLMSNQDSVLIQTLAdmtPGMVLDAMVQ 854
Cdd:PRK06676  150 -GKTLEVKIIELDPEKNRVILSRR------------------------AVVEEERAAKKEELLSSLK---EGDVVEGTVA 201

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  855 EVLENGSVV-FGG--GPVPDLILRASRYHRAGQELEPGQKKKVVVLHVDALKLEVHVSLHQDLVN---RKARKLRKNSRH 928
Cdd:PRK06676  202 RLTDFGAFVdIGGvdGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGpweGVEEKLPEGDVI 281

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 158186708  929 QGIVQHLeESFA----VASLVETghLVAFSLISHLndtfHFD--SEKLRVGQGV 976
Cdd:PRK06676  282 EGTVKRL-TDFGafveVLPGVEG--LVHISQISHK----HIAtpSEVLEEGQEV 328
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 1173-1399 2.02e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 46.31  E-value: 2.02e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1173 VDIEPDIRGripLLLTS-LSF-KVLKHPDKKFQIGQAIKATVVGPDIPRAFLCLSL----IGPY-----KLEEGDVAMGR 1241
Cdd:PRK06299  304 VELEEGIEG---LVHVSeMSWtKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLkqckENPWeefaeKYPVGDVVEGK 380

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1242 VlKVLPNKGLTVSFPFGRIGKVsvfHLSD-SYS---EEPLTDFCPQKIVRCYILS--TAHRMLALSLrssrtnketKSKI 1315
Cdd:PRK06299  381 V-KNITDFGAFVGLEGGIDGLV---HLSDiSWDkkgEEAVELYKKGDEVEAVVLKvdVEKERISLGI---------KQLE 447

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1316 EDPEVNSIEDIQAGQLLRGYVKSILPSSVVIGLGPSVMGLVKHSHVSQcvSREKELYDKcLPEGKLVTARVLCVNPKKNL 1395
Cdd:PRK06299  448 EDPFEEFAKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSR--DRVEDATEV-LKVGDEVEAKVINIDRKNRR 524


                  ....
gi 158186708 1396 IELS 1399
Cdd:PRK06299  525 ISLS 528
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 378-434 2.43e-04

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


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 40.83  E-value: 2.43e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 158186708  378 EKAGAIFRLRDGVLAYARLSHLSDSKKAFSAEAFKLGSTHRCRIIDYSQMDELALLS 434
Cdd:cd00164     9 TKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1165-1225 2.96e-04

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


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 40.83  E-value: 2.96e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 158186708 1165 NVMKKWLEVDIEPDIRGRIPLllTSLSFKVLKHPDKKFQIGQAIKATVVGPDIPRAFLCLS 1225
Cdd:cd00164     7 SITKFGVFVELEDGVEGLVHI--SELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
1633-1724 3.08e-04

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


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 41.69  E-value: 3.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1633 HLQATEIEKARAVAERALKTisfreeqeKLNVWVALLNLENMYGSQESL--AKVFERAVQYN-EPLKVFLHLADIYTKSE 1709
Cdd:COG3063     2 YLKLGDLEEAEEYYEKALEL--------DPDNADALNNLGLLLLEQGRYdeAIALEKALKLDpNNAEALLNLAELLLELG 73

                          90
                  ....*....|....*
gi 158186708 1710 KFKEAGELYNRMLKR 1724
Cdd:COG3063    74 DYDEALAYLERALEL 88
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 547-611 4.84e-04

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


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 40.39  E-value: 4.84e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 158186708  547 GVIIRVKDYGCLVKFYN-DVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLSFK 611
Cdd:cd05708     8 GTVRRVEDYGVFIDIDGtNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 190-256 4.98e-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: 4.98e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 158186708  190 LTGTVSSLEDHGYLVDIGvDGTRAFLSL-QKAQEYIRQKNKgaKFKVGQYLTCVVEELKSNGGVVSLS 256
Cdd:cd00164     1 VTGKVVSITKFGVFVELE-DGVEGLVHIsELSDKFVKDPSE--VFKVGDEVEVKVLEVDPEKGRISLS 65
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
1704-1797 5.06e-04

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


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 40.92  E-value: 5.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1704 IYTKSEKFKEAGELYNRMLKRFRQEKAVWIKYGAF--VLGR-SQAgashRVLQRALECLPtkEHVDVIVKFAQLEFQLGD 1780
Cdd:COG3063     1 LYLKLGDLEEAEEYYEKALELDPDNADALNNLGLLllEQGRyDEA----IALEKALKLDP--NNAEALLNLAELLLELGD 74

                          90
                  ....*....|....*..
gi 158186708 1781 VERAKAIFENTLTTYPK 1797
Cdd:COG3063    75 YDEALAYLERALELDPS 91
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1044-1099 6.31e-04

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


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 39.67  E-value: 6.31e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 158186708 1044 VTGTIKSVKATHAVVTLDDGFIGCIHVSRILDDVPEgvSPTTTLKAGKKVTARVIG 1099
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVK--DPSEVFKVGDEVEVKVLE 54
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 447-521 7.06e-04

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: 40.26  E-value: 7.06e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708  447 YQDIKTGTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAKKLIMTL 521
Cdd:cd04461     9 FSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 453-517 7.80e-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: 39.53  E-value: 7.80e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 158186708  453 GTIVKGKVLALKPFGMLVKVGeQMRGLVpsmHLADIM---MKNPEKKFNTGDEVKCRVLLCDPEAKKL 517
Cdd:cd05688     2 GDVVEGTVKSITDFGAFVDLG-GVDGLL---HISDMSwgrVKHPSEVVNVGDEVEVKVLKIDKERKRI 65
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 1033-1400 8.04e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 44.10  E-value: 8.04e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1033 KKSHSLAIGDKVTGTIKSVKATHAVVTLDD-GFIGCIHVSRILDDVPEgvSPTTTLKAGKKVTARVIGGRDVKTSkflpi 1111
Cdd:PRK06676   10 NSVKEVEVGDVVTGEVLKVEDKQVFVNIEGyKVEGVIPISELSNDHIE--DINDVVKVGDELEVYVLKVEDGEGN----- 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1112 shprfvltiLELSVRpselKGDYRALNTHsvspMEKirQYQAGQTVTCFLKKynVMKKWLEVDIEpDIRGRIPLLLTSLS 1191
Cdd:PRK06676   83 ---------LLLSKR----RLEAEKAWDK----LEE--KFEEGEVVEVKVTE--VVKGGLVVDVE-GVRGFIPASLISTR 140

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1192 FKvlkhPDKKFQIGQAIKATVVGPDIPRAFLCLS---------------LIGpyKLEEGDVAMGRVLKvLPNKGLTVSfp 1256
Cdd:PRK06676  141 FV----EDFSDFKGKTLEVKIIELDPEKNRVILSrravveeeraakkeeLLS--SLKEGDVVEGTVAR-LTDFGAFVD-- 211

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1257 fgrIGKVS-VFHLSD-SYS--EEPLTDFCPQKIVRCYILST---AHRmLALSLrssrtnKETKskiEDPEVNSIEDIQAG 1329
Cdd:PRK06676  212 ---IGGVDgLVHISElSHErvEKPSEVVSVGQEVEVKVLSIdweTER-ISLSL------KDTL---PGPWEGVEEKLPEG 278

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 158186708 1330 QLLRGYVKSILPSSVVIGLGPSVMGLVkhsHVSQCVSREKELYDKCLPEGKLVTARVLCVNPKKNLIELSL 1400
Cdd:PRK06676  279 DVIEGTVKRLTDFGAFVEVLPGVEGLV---HISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSI 346
PRK08582 PRK08582
RNA-binding protein S1;
726-788 9.66e-04

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 41.17  E-value: 9.66e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 158186708  726 IQPGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDE 788
Cdd:PRK08582    3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED 65
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1752-1833 1.03e-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: 41.14  E-value: 1.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1752 LQRALECLPtkEHVDVIVKFAQLEFQLGDVERAKAIFENTLTTYPKRTDVWSVYIDMTIKHGSQKEVRDIFERVihLSLA 1831
Cdd:COG4235     6 LRQALAANP--NDAEGWLLLGRAYLRLGRYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEELLERA--LALD 81


                  ..
gi 158186708 1832 PK 1833
Cdd:COG4235    82 PD 83
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
280-346 1.03e-03

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 39.51  E-value: 1.03e-03
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 158186708    280 PGLVVRAQVQKVTQFGLQLNFLTFFTGLVDFMHLEPKKMGSYSSK----QTVKACILCVHPRTRVVRLSLR 346
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVlkvgDEVKVKVLSVDEEKGRIILSLK 72
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 734-798 1.45e-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: 39.18  E-value: 1.45e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708  734 GFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:cd05691     6 GKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 1704-1796 1.70e-03

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


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 41.10  E-value: 1.70e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1704 IYTKSEKFKEAGELYNRMLKRFRQEKAVWIKYGAFVLGRSQAGASHRVLQRALECLPtkEHVDVIVKFAQLEFQLGDVER 1783
Cdd:COG5010    63 LYNKLGDFEESLALLEQALQLDPNNPELYYNLALLYSRSGDKDEAKEYYEKALALSP--DNPNAYSNLAALLLSLGQDDE 140

                          90
                  ....*....|...
gi 158186708 1784 AKAIFENTLTTYP 1796
Cdd:COG5010   141 AKAALQRALGTSP 153
PRK08582 PRK08582
RNA-binding protein S1;
450-508 2.02e-03

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 40.40  E-value: 2.02e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 158186708  450 IKTGTIVKGKVLALKPFGMLVKVGEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVL 508
Cdd:PRK08582    3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVL 61
rpsA PRK13806
30S ribosomal protein S1; Provisional
 634-800 2.05e-03

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 42.79  E-value: 2.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  634 NTGQLVDVKVLEKTKNGLEVAILPHNipAFLPTPHLSDHVANGPLLHhwlqTGDTLH-RVLCLSQSEKHILLCRKpALVS 712
Cdd:PRK13806  114 ENGVPVEGKVTGTCKGGFNVEVLGRR--AFCPVSQIDLRYVEDPESY----VGQTFQfLITRVEENGRNIVVSRR-ALLE 186

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  713 TVEGGQDPKSLSEIQPGMLLIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQR 792
Cdd:PRK13806  187 REQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKG 266


                  ....*...
gi 158186708  793 MLLSLRLS 800
Cdd:PRK13806  267 KGLRISLS 274
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 540-796 2.16e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 42.48  E-value: 2.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  540 KPGLQTHGVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLSFKLLSGSEPK 619
Cdd:PRK07400   30 KPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRIEYMRAW 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  620 dESVKNSKKKGSTVNTgqlvdvKVLEKTKNGLEVAIlpHNIPAFLPTPHLSDHVANGPLLHHWLQTgdtlhRVLCLSQSE 699
Cdd:PRK07400  110 -ERVRQLQKEDATVRS------EVFATNRGGALVRI--EGLRGFIPGSHISTRKPKEELVGEELPL-----KFLEVDEER 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  700 KHILLCRKPALVStveggqdpKSLSEIQPGMLLIGFVKSIKDYGVFVQFpSGLSGLSPKTIMSDKFVTTPSEHFVEGQTV 779
Cdd:PRK07400  176 NRLVLSHRRALVE--------RKMNRLEVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEM 246

                         250
                  ....*....|....*..
gi 158186708  780 VAKVTNVDESKQRMLLS 796
Cdd:PRK07400  247 KVMIIDLDAERGRISLS 263
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1041-1099 2.16e-03

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: 38.42  E-value: 2.16e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 158186708 1041 GDKVTGTIKSVKATHAVVTLDDGFIGCIHVSRILDDVPEgvSPTTTLKAGKKVTARVIG 1099
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVK--DVKDVLKEGDKVKVKVLS 57
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1041-1099 2.26e-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: 38.41  E-value: 2.26e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 158186708 1041 GDKVTGTIKSVKATHAVVTLDDGFIGCIHVSRILDDVPEGVspTTTLKAGKKVTARVIG 1099
Cdd:cd05691     1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDA--TERFKVGDEVEAKITN 57
CpoB COG1729
Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane ...
 1707-1797 2.88e-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: 39.20  E-value: 2.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1707 KSEKFKEAGELYNRMLKRFRQEKAV-----WIKYGAFVLGRSQAGASHrvLQRALECLPTKEHV-DVIVKFAQLEFQLGD 1780
Cdd:COG1729     5 KAGDYDEAIAAFKAFLKRYPNSPLApdalyWLGEAYYALGDYDEAAEA--FEKLLKRYPDSPKApDALLKLGLSYLELGD 82

                          90
                  ....*....|....*..
gi 158186708 1781 VERAKAIFENTLTTYPK 1797
Cdd:COG1729    83 YDKARATLEELIKKYPD 99
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 86-346 3.01e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 42.39  E-value: 3.01e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   86 ILGCVKEVNELELVVSLPNGLQGFVQVTEIcdAYTQKLNEQvaqeeplEDLLRLpelfspGMLVRCVVSSLDVtESGKks 165
Cdd:PRK12269  582 VKGRVTKIADFGAFIELAEGIEGLAHISEF--SWVKKTSKP-------SDMVKI------GDEVECMILGYDI-QAGR-- 643

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  166 VKLSVNPKRVNKVLSAEALRP-GMLLTGTVSSLEDHGYLVDI--GVDGtraFLSLQKAQEYIRQKNKGAKFKVGQYLTCV 242
Cdd:PRK12269  644 VSLGLKQVTANPWEEIEARYPvGARFTRRIVKVTNAGAFIEMeeGIDG---FLHVDDLSWVKRTRPADHELEVGKEIECM 720

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  243 VEELKSNGGVVSLSVEhsQVSsafateEQSWNL--NNLLPGLVVRAQVQKVTQFGLQLNFLTFFTGLVDFMHLEPKKMG- 319
Cdd:PRK12269  721 VIECDPQARRIRLGVK--QLS------DNPWQVfaNAYGVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGd 792

                         250       260       270
                  ....*....|....*....|....*....|...
gi 158186708  320 ------SYSSKQTVKACILCVHPRTRVVRLSLR 346
Cdd:PRK12269  793 pgealrKYAVGDRVKAVIVDMNVKDRKVAFSVR 825
Suf pfam05843
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ...
 1731-1850 3.07e-03

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: 41.59  E-value: 3.07e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  1731 VWIKYGAFvLGRSQA-GASHRVLQRALEclptKEHV--DVIVKFAQLEFQLG-DVERAKAIFENTLTTYPKRTDVWSVYI 1806
Cdd:pfam05843    3 VWIQYMRA-MRRAEGiKGARKVFKKARK----RPRLtyHVYVASALMEYYCSkDPAVAFKIFELGLKLFPEDEEFVLKYL 77

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 158186708  1807 DMTIKHGSQKEVRDIFERVIHlSLAPKRM-KFFFKRYLDYEKQHG 1850
Cdd:pfam05843   78 DYLISLNDDNNARVLFERVLT-RLAQEKEaKPLWKKFISYESTFG 121
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 547-597 3.25e-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: 3.25e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 158186708  547 GVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVL 597
Cdd:cd04472     6 GKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVI 56
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1232-1308 3.32e-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: 38.74  E-value: 3.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1232 LEEGDVAMGRVLKVLPnKGLTVSFPFGRIGKVSVFHLSDSYSE------------------EPLTD-FCPQKIVRCYILS 1292
Cdd:cd05693     1 LSEGMLVLGQVKEITK-LDLVISLPNGLTGYVPITNISDAYTErleeldeeseeeddeeelPDLEDlFSVGQLVRCKVVS 79

                          90       100
                  ....*....|....*....|.
gi 158186708 1293 T-----AHRMLALSLRSSRTN 1308
Cdd:cd05693    80 LdksksGKKRIELSLEPELVN 100
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1231-1400 3.52e-03

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 42.24  E-value: 3.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1231 KLEEGDVAMGRVlkvlpnKGLTvsfPFG---RIGKVSVF-HLSD-SYS-----EEPLTDfcpQKIVRCYILS--TAHRML 1298
Cdd:PRK00087  474 SLEEGDVVEGEV------KRLT---DFGafvDIGGVDGLlHVSEiSWGrvekpSDVLKV---GDEIKVYILDidKENKKL 541

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708 1299 ALSLrssrtnketKSKIEDPEVNSIEDIQAGQLLRGYVKSILPSSVVIGLGPSVMGLVKHSHVSqcvSREKELYDKCLPE 1378
Cdd:PRK00087  542 SLSL---------KKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQIS---WKRIDKPEDVLSE 609

                         170       180
                  ....*....|....*....|..
gi 158186708 1379 GKLVTARVLCVNPKKNLIELSL 1400
Cdd:PRK00087  610 GEEVKAKILEVDPEEKRIRLSI 631
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1587-1797 3.68e-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: 42.38  E-value: 3.68e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  1587 KAEKELSRIEealMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtiSFREEQEKlnvwv 1666
Cdd:TIGR02917  500 PAAANLARID---IQEGNPDDAIQRFEKVLTIDPKNLRAILALAGLYLRTGNEEEAVAWLEKAAE--LNPQEIEP----- 569

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  1667 aLLNLENMYGSQESLAKVFERAVQY--NEPLKV--FLHLADIYTKSEKFKEAGELYNRMLKRFRQEKAVWIKYGAFVLGR 1742
Cdd:TIGR02917  570 -ALALAQYYLGKGQLKKALAILNEAadAAPDSPeaWLMLGRAQLAAGDLNKAVSSFKKLLALQPDSALALLLLADAYAVM 648

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 158186708  1743 SQAGASHRVLQRALECLPtkEHVDVIVKFAQLEFQLGDVERAKAIFENTLTTYPK 1797
Cdd:TIGR02917  649 KNYAKAITSLKRALELKP--DNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQHPK 701
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1329-1399 3.89e-03

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


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 37.66  E-value: 3.89e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 158186708 1329 GQLLRGYVKSILPSSVVIGLGPSVMGLVKHSHVSQCVSREkelYDKCLPEGKLVTARVLCVNPKKNLIELS 1399
Cdd:cd05707     1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKD---WKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
PRK08059 PRK08059
general stress protein 13; Validated
 547-632 5.17e-03

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 38.87  E-value: 5.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  547 GVIIRVKDYGCLVKFYNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLSFKLLS-GSEPKDESVKN 625
Cdd:PRK08059   13 GKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEeAPEAKRKKGKI 92


                  ....*..
gi 158186708  626 SKKKGST 632
Cdd:PRK08059   93 LIPNPSE 99
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
732-798 5.59e-03

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 38.53  E-value: 5.59e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 158186708  732 LIGFVKSIKDYGVFVQFPSGLSGLSPKTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRMLLSLR 798
Cdd:PRK07252    7 LKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLR 73
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 88-169 5.77e-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: 5.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708   88 GCVKEVNELELVVSLPNGLQGFVQVTEICDAYTQKLNeqvaqeepledllrlpELFSPGMLVRCVVSSLDVtesGKKSVK 167
Cdd:cd00164     3 GKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPS----------------EVFKVGDEVEVKVLEVDP---EKGRIS 63


                  ..
gi 158186708  168 LS 169
Cdd:cd00164    64 LS 65
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 547-611 6.10e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 41.18  E-value: 6.10e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708  547 GVIIRVKDYGCLVKFyNDVQGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLSFK 611
Cdd:PRK07899  214 GVVSSIVNFGAFVDL-GGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLK 277
PRK05807 PRK05807
RNA-binding protein S1;
450-529 6.62e-03

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 38.96  E-value: 6.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 158186708  450 IKTGTIVKGKVLALKPFGMLVKVgEQMRGLVPSMHLADIMMKNPEKKFNTGDEVKCRVLLCDPEAkKLIMTLKKTLVTSK 529
Cdd:PRK05807    3 LKAGSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNG-KISLSIKQAMKQKK 80
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 542-609 6.97e-03

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: 36.83  E-value: 6.97e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 158186708  542 GLQTHGVIIRVKDYGCLVkfynDV----QGLVPKHELSAQHIPDPERVFYTGQVVKVAVLNCEPSKERMLLS 609
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFV----DIgvkqDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 734-801 7.30e-03

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 37.22  E-value: 7.30e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 158186708  734 GFVKSIKDYGVFVQFP------SGLSGLSpkTIMSDKFVTTPSEHFVEGQTVVAKVTNVDESKQRmlLSLRLSD 801
Cdd:cd05684     6 GKVTSIMDFGCFVQLEglkgrkEGLVHIS--QLSFEGRVANPSDVVKRGQKVKVKVISIQNGKIS--LSMKDVD 75
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1329-1400 9.46e-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: 9.46e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 158186708 1329 GQLLRGYVKSILPSSVVIGLGPSVMGLVKHSHVSQCVSREKELyDKCLPEGKLVTARVLCVNPKKNLIELSL 1400
Cdd:cd05703     1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHP-EKKFPIGQALKAKVVGVDKEHKLLRLSA 71
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 284-344 9.72e-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: 36.59  E-value: 9.72e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 158186708  284 VRAQVQKVTQFGLQLNFLTFFTGLVDFMHLEPKKMGSYSSK----QTVKACILCVHPRTRVVRLS 344
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVfkvgDEVEVKVLEVDPEKGRISLS 65
 
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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