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Conserved domains on  [gi|17552198|ref|NP_498398|]
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S1 motif domain-containing protein [Caenorhabditis elegans]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1469-1621 1.71e-12

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: 69.76  E-value: 1.71e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1469 EKSEEDHSRLVRSDPNSAINWIEYMSHFIEKSDLAAARKTAEEALgAINPTESDellkiwtAYLNMEVAY---GDAATVQ 1545
Cdd:COG2956  127 EKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKAL-KLDPDCAR-------ALLLLAELYleqGDYEEAI 198

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17552198 1546 KVFERACK-NANAYTVHKTLSKIYQKFEKNAEATQILEQMVKkfRANQLEVWTLLAEHLMTQNDQKAARELLPRALK 1621
Cdd:COG2956  199 AALERALEqDPDYLPALPRLAELYEKLGDPEEALELLRKALE--LDPSDDLLLALADLLERKEGLEAALALLERQLR 273
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
427-500 1.02e-09

Ribosomal protein S1-like RNA-binding domain;


:

Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 56.46  E-value: 1.02e-09
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17552198     427 KCGDVLDARVHHVAKSGVYFMVCNFVKAFAPLSMLSDKPLPaqKMKNIYKVGTEVKCRVWQICDERKNLIVTCR 500
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVK--DPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 702-777 4.11e-09

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 cd04461:

Pssm-ID: 471952 [Multi-domain]  Cd Length: 83  Bit Score: 54.90  E-value: 4.11e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17552198  702 KLPKKIDELKVGKVIVGIVgQVITNVGVFVELVGG-SGLVGKV-LERKNAKNTSELLEVGQVIVGTIESIDTTKKSFL 777
Cdd:cd04461    4 TLPTNFSDLKPGMVVHGYV-RNITPYGVFVEFLGGlTGLAPKSyISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1564-1690 7.09e-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: 53.27  E-value: 7.09e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1564 LSKIYQKFEKNAEATQILEQMVKKFRANqLEVWTLLAEHLMTQNDQKAARELLPRALKSAPKaqqHVQLISKFAQLEFKH 1643
Cdd:COG4783   10 LAQALLLAGDYDEAEALLEKALELDPDN-PEAFALLGEILLQLGDLDEAIVLLHEALELDPD---EPEARLNLGLALLKA 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 17552198 1644 GDAERGRTLLEGLVTAHPKKTDLWLVYAEAVLKHLGIEHARKVLERA 1690
Cdd:COG4783   86 GDYDEALALLEKALKLDPEHPEAYLRLARAYRALGRPDEAIAALEKA 132
rpsA super family cl36730
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 166-530 1.97e-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]


The actual alignment was detected with superfamily member TIGR00717:

Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 52.43  E-value: 1.97e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198    166 GLVLHTAVVSIEEKGAILDVGLdQITGFIEKSQFPAA--GLKEGMPLIVRVLSSTSR----VVKVTSFVEQDNLnmtscE 239
Cdd:TIGR00717   19 GSIVKGTVVAINKDTVFVDVGL-KSEGRIPKEEFLDAplEIQVGDEVEVYLDRVEDRfgetVLSREKAQRHELW-----I 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198    240 KLqLNHLMPGTILECEPTGdAVTAGVIVNIgNGLKGILPRRNLPPRLRENPEKL-GKAIRA-IVMFCQQNSKILVlnAHP 317
Cdd:TIGR00717   93 KL-EKAYEEGSIVEGKIVG-KVKGGFIVDL-NGVEAFLPGSQVDVKPIKDLDSLiGKTLKFkIIKLDQKRNNIVV--SRR 167

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198    318 DIVAASRIEKR-TSFEGISIGDKVKCTVIDvlptksmvyfalpaIDGKKSLVTAVSSRGLLEKPD-------QVSTEYEV 389
Cdd:TIGR00717  168 AYLEEERSQAReELLENLKEGDVVKGVVKN--------------ITDFGAFVDLGGVDGLLHITDmswkrvkHPSEYVKV 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198    390 GTEKLCRVTGFRYADRSITISTRKDILNQKITKYQDAKCGDVLDARVHHVAKSGVYFMVCNFVKAFAPLSMLS--DKPlp 467
Cdd:TIGR00717  234 GQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwvKKN-- 311

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17552198    468 aQKMKNIYKVGTEVKCRVWQICDERKNLivtcresILGLKSPSVNSVQELE----IGVTVPCVIRKV 530
Cdd:TIGR00717  312 -SHPSKVVKKGDEVEVMILDIDPERRRL-------SLGLKQCKANPWEQFEekhpVGDRVTGKIKKI 370
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1288-1351 2.48e-05

Ribosomal protein S1-like RNA-binding domain;


:

Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.75  E-value: 2.48e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17552198    1288 KEGDQYDGIVENASKGSLFIELGPGVSGRIPVNE-------ENQDLLEIGtnSVIRVTVVKV--AKNEITLKL 1351
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISElsdkrvkDPEEVLKVG--DEVKVKVLSVdeEKGRIILSL 71
rpsA super family cl35465
30S ribosomal protein S1; Reviewed
 1101-1193 6.14e-04

30S ribosomal protein S1; Reviewed


The actual alignment was detected with superfamily member PRK06299:

Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 44.38  E-value: 6.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198  1101 YKSNYKIGDVVKCfganTMTEKQE--LKVEVNPVWTGTISRENLSDDLKVTAADggivdlALKKGEMREAKITAVDRKNM 1178
Cdd:PRK06299  454 FAKKHKKGSIVTG----TVTEVKDkgAFVELEDGVEGLIRASELSRDRVEDATE------VLKVGDEVEAKVINIDRKNR 523

                          90
                  ....*....|....*...
gi 17552198  1179 SLKLT---LDTAEEAFEI 1193
Cdd:PRK06299  524 RISLSikaLDEAEEKEAI 541
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
77-149 4.83e-03

Ribosomal protein S1-like RNA-binding domain;


:

Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 37.20  E-value: 4.83e-03
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17552198      77 GVVSEVFDDGVLLHTAGTHTVKIHASEVSKKFTElfneekiEIKNAFQLGQMVPFRVISKKQgnDKGKVKGTC 149
Cdd:smart00316    8 GTVTEITPGGAFVDLGNGVEGLIPISELSDKRVK-------DPEEVLKVGDEVKVKVLSVDE--EKGRIILSL 71
 
Name Accession Description Interval E-value
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1469-1621 1.71e-12

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: 69.76  E-value: 1.71e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1469 EKSEEDHSRLVRSDPNSAINWIEYMSHFIEKSDLAAARKTAEEALgAINPTESDellkiwtAYLNMEVAY---GDAATVQ 1545
Cdd:COG2956  127 EKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKAL-KLDPDCAR-------ALLLLAELYleqGDYEEAI 198

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17552198 1546 KVFERACK-NANAYTVHKTLSKIYQKFEKNAEATQILEQMVKkfRANQLEVWTLLAEHLMTQNDQKAARELLPRALK 1621
Cdd:COG2956  199 AALERALEqDPDYLPALPRLAELYEKLGDPEEALELLRKALE--LDPSDDLLLALADLLERKEGLEAALALLERQLR 273
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
427-500 1.02e-09

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 56.46  E-value: 1.02e-09
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17552198     427 KCGDVLDARVHHVAKSGVYFMVCNFVKAFAPLSMLSDKPLPaqKMKNIYKVGTEVKCRVWQICDERKNLIVTCR 500
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVK--DPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 702-777 4.11e-09

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: 54.90  E-value: 4.11e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17552198  702 KLPKKIDELKVGKVIVGIVgQVITNVGVFVELVGG-SGLVGKV-LERKNAKNTSELLEVGQVIVGTIESIDTTKKSFL 777
Cdd:cd04461    4 TLPTNFSDLKPGMVVHGYV-RNITPYGVFVEFLGGlTGLAPKSyISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1564-1690 7.09e-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: 53.27  E-value: 7.09e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1564 LSKIYQKFEKNAEATQILEQMVKKFRANqLEVWTLLAEHLMTQNDQKAARELLPRALKSAPKaqqHVQLISKFAQLEFKH 1643
Cdd:COG4783   10 LAQALLLAGDYDEAEALLEKALELDPDN-PEAFALLGEILLQLGDLDEAIVLLHEALELDPD---EPEARLNLGLALLKA 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 17552198 1644 GDAERGRTLLEGLVTAHPKKTDLWLVYAEAVLKHLGIEHARKVLERA 1690
Cdd:COG4783   86 GDYDEALALLEKALKLDPEHPEAYLRLARAYRALGRPDEAIAALEKA 132
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 166-530 1.97e-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: 52.43  E-value: 1.97e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198    166 GLVLHTAVVSIEEKGAILDVGLdQITGFIEKSQFPAA--GLKEGMPLIVRVLSSTSR----VVKVTSFVEQDNLnmtscE 239
Cdd:TIGR00717   19 GSIVKGTVVAINKDTVFVDVGL-KSEGRIPKEEFLDAplEIQVGDEVEVYLDRVEDRfgetVLSREKAQRHELW-----I 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198    240 KLqLNHLMPGTILECEPTGdAVTAGVIVNIgNGLKGILPRRNLPPRLRENPEKL-GKAIRA-IVMFCQQNSKILVlnAHP 317
Cdd:TIGR00717   93 KL-EKAYEEGSIVEGKIVG-KVKGGFIVDL-NGVEAFLPGSQVDVKPIKDLDSLiGKTLKFkIIKLDQKRNNIVV--SRR 167

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198    318 DIVAASRIEKR-TSFEGISIGDKVKCTVIDvlptksmvyfalpaIDGKKSLVTAVSSRGLLEKPD-------QVSTEYEV 389
Cdd:TIGR00717  168 AYLEEERSQAReELLENLKEGDVVKGVVKN--------------ITDFGAFVDLGGVDGLLHITDmswkrvkHPSEYVKV 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198    390 GTEKLCRVTGFRYADRSITISTRKDILNQKITKYQDAKCGDVLDARVHHVAKSGVYFMVCNFVKAFAPLSMLS--DKPlp 467
Cdd:TIGR00717  234 GQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwvKKN-- 311

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17552198    468 aQKMKNIYKVGTEVKCRVWQICDERKNLivtcresILGLKSPSVNSVQELE----IGVTVPCVIRKV 530
Cdd:TIGR00717  312 -SHPSKVVKKGDEVEVMILDIDPERRRL-------SLGLKQCKANPWEQFEekhpVGDRVTGKIKKI 370
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1288-1351 2.48e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.75  E-value: 2.48e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17552198    1288 KEGDQYDGIVENASKGSLFIELGPGVSGRIPVNE-------ENQDLLEIGtnSVIRVTVVKV--AKNEITLKL 1351
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISElsdkrvkDPEEVLKVG--DEVKVKVLSVdeEKGRIILSL 71
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 163-232 4.43e-05

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: 43.39  E-value: 4.43e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17552198  163 LAAGLVLHTAVVSIEEKGAILDVGLDQITGFIEKSQFP-AAGLKEGMPLIVRVLS-STSRVVKVTSFVEQDN 232
Cdd:cd05694    2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGnFSKLKVGQLLLCVVEKvKDDGRVVSLSADPSKV 73
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1539-1692 2.40e-04

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: 46.23  E-value: 2.40e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198   1539 GDAATVQKVFERAcknANAYTV-HKT---------LSKIYQKFEKNAEATQILEQMVKKfRANQLEVWTLLAEHLMTQND 1608
Cdd:TIGR02917  710 GDLYLRQKDYPAA---IQAYRKaLKRapssqnaikLHRALLASGNTAEAVKTLEAWLKT-HPNDAVLRTALAELYLAQKD 785

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198   1609 -QKAARELL-------------------------PRALKSAPKA-----QQHvQLISKFAQLEFKHGDAERGRTLLEGLV 1657
Cdd:TIGR02917  786 yDKAIKHYQtvvkkapdnavvlnnlawlylelkdPRALEYAERAlklapNIP-AILDTLGWLLVEKGEADRALPLLRKAV 864

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 17552198   1658 TAHPKKTDLWLVYAEAVLKHLGIEHARKVLERACN 1692
Cdd:TIGR02917  865 NIAPEAAAIRYHLALALLATGRKAEARKELDKLLN 899
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 1101-1193 6.14e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 44.38  E-value: 6.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198  1101 YKSNYKIGDVVKCfganTMTEKQE--LKVEVNPVWTGTISRENLSDDLKVTAADggivdlALKKGEMREAKITAVDRKNM 1178
Cdd:PRK06299  454 FAKKHKKGSIVTG----TVTEVKDkgAFVELEDGVEGLIRASELSRDRVEDATE------VLKVGDEVEAKVINIDRKNR 523

                          90
                  ....*....|....*...
gi 17552198  1179 SLKLT---LDTAEEAFEI 1193
Cdd:PRK06299  524 RISLSikaLDEAEEKEAI 541
TPR_19 pfam14559
Tetratricopeptide repeat;
1572-1635 6.32e-04

Tetratricopeptide repeat;


Pssm-ID: 434038 [Multi-domain]  Cd Length: 65  Bit Score: 39.49  E-value: 6.32e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17552198   1572 EKNAEATQILEQMVKKFRANQlEVWTLLAEHLMTQNDQKAARELLPRALKSAPKAQQHVQLISK 1635
Cdd:pfam14559    2 GDYAEALELLEQALAEDPDNA-EARLGLAEALLALGRLDEAEALLAALPAADPDDPRYAALLAK 64
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
711-775 1.76e-03

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 38.74  E-value: 1.76e-03
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17552198     711 KVGKVIVGIVgQVITNVGVFVELvgGSGLVGKV----LERKNAKNTSELLEVGQVIVGTIESIDTTKKS 775
Cdd:smart00316    1 EVGDVVEGTV-TEITPGGAFVDL--GNGVEGLIpiseLSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGR 66
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 707-828 2.64e-03

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: 41.95  E-value: 2.64e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198  707 IDELKVGKVIVGIVgQVITNVGVFVELVGGSGLV-------GKVlerknaKNTSELLEVGQVIVGTIESIDTTK------ 773
Cdd:COG0539  184 LEKLEEGDVVEGTV-KNITDFGAFVDLGGVDGLLhiseiswGRV------KHPSEVLKVGDEVEVKVLKIDREKerisls 256

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 17552198  774 -KSFLIDPctdletgelmlkkyalpllesiveevkWLAEQSNYPIpGSKVNGKVTK 828
Cdd:COG0539  257 lKQLQPDP---------------------------WENIAEKYPV-GDVVKGKVTR 284
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 429-498 3.52e-03

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: 37.60  E-value: 3.52e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17552198  429 GDVLDARVHHVAKSGVYFMVCNFVKAFAPLSMLSDKPL--PAQKmkniYKVGTEVKCRVWQICDERKNLIVT 498
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLkhPEKK----FKPGLKVKCRVLSVEPERKRLVLT 68
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 707-839 4.01e-03

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 41.64  E-value: 4.01e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198    707 IDELKVGKVIVGIVGQvITNVGVFVELVGGSGLVGKV-LERKNAKNTSELLEVGQVIVGTIESIDTTKKsFLIdpctdle 785
Cdd:TIGR00717  182 LENLKEGDVVKGVVKN-ITDFGAFVDLGGVDGLLHITdMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKG-RIS------- 252

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 17552198    786 tgeLMLKKyalpllesiVEEVKWLAEQSNYPiPGSKVNGKVTKELDDLTLVEFE 839
Cdd:TIGR00717  253 ---LSLKQ---------LGEDPWEAIEKKFP-VGDKITGRVTNLTDYGVFVEIE 293
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
77-149 4.83e-03

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 37.20  E-value: 4.83e-03
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17552198      77 GVVSEVFDDGVLLHTAGTHTVKIHASEVSKKFTElfneekiEIKNAFQLGQMVPFRVISKKQgnDKGKVKGTC 149
Cdd:smart00316    8 GTVTEITPGGAFVDLGNGVEGLIPISELSDKRVK-------DPEEVLKVGDEVKVKVLSVDE--EKGRIILSL 71
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1560-1743 5.64e-03

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


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 41.61  E-value: 5.64e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198   1560 VHKTLSKIYQKFEKNAEATQILEQMVKKFRANqLEVWTLLAEHLMTQNDQKAARELLPRALKSAPKaqqHVQLISKFAQL 1639
Cdd:TIGR02917  467 LHNLLGAIYLGKGDLAKAREAFEKALSIEPDF-FPAAANLARIDIQEGNPDDAIQRFEKVLTIDPK---NLRAILALAGL 542

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198   1640 EFKHGDAERGRTLLEGLVTAHPKKTDLWLVYAEAVLKHLGIEHARKVLERACN-----------LGfSIHKM-------R 1701
Cdd:TIGR02917  543 YLRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAADaapdspeawlmLG-RAQLAagdlnkaV 621

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 17552198   1702 PLYKKWLEMESKHGDA----AAVELVK---AKAEKFLQAVADnvLEEDN 1743
Cdd:TIGR02917  622 SSFKKLLALQPDSALAllllADAYAVMknyAKAITSLKRALE--LKPDN 668
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
249-313 8.55e-03

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 36.81  E-value: 8.55e-03
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17552198     249 GTILECEPtgdavtAGVIVNIGNGLKGILPRRNLPPRLRENPE---KLGKAIRAIVMFCQQNSKILVL 313
Cdd:smart00316    8 GTVTEITP------GGAFVDLGNGVEGLIPISELSDKRVKDPEevlKVGDEVKVKVLSVDEEKGRIIL 69
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
705-839 8.92e-03

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 40.70  E-value: 8.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198   705 KKIDELKVGKVIVGIVGQvITNVGVFVELVGGSGLV-------GKVlerknaKNTSELLEVGQVIVGTIESIDTTKKSFL 777
Cdd:PRK00087  470 ETWNSLEEGDVVEGEVKR-LTDFGAFVDIGGVDGLLhvseiswGRV------EKPSDVLKVGDEIKVYILDIDKENKKLS 542

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17552198   778 idpctdletgeLMLKKyalpLLESIVEEVKwlaeqSNYPIpGSKVNGKVTKELDDLTLVEFE 839
Cdd:PRK00087  543 -----------LSLKK----LLPDPWENVE-----EKYPV-GSIVLGKVVRIAPFGAFVELE 583
 
Name Accession Description Interval E-value
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1469-1621 1.71e-12

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: 69.76  E-value: 1.71e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1469 EKSEEDHSRLVRSDPNSAINWIEYMSHFIEKSDLAAARKTAEEALgAINPTESDellkiwtAYLNMEVAY---GDAATVQ 1545
Cdd:COG2956  127 EKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKAL-KLDPDCAR-------ALLLLAELYleqGDYEEAI 198

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17552198 1546 KVFERACK-NANAYTVHKTLSKIYQKFEKNAEATQILEQMVKkfRANQLEVWTLLAEHLMTQNDQKAARELLPRALK 1621
Cdd:COG2956  199 AALERALEqDPDYLPALPRLAELYEKLGDPEEALELLRKALE--LDPSDDLLLALADLLERKEGLEAALALLERQLR 273
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1486-1741 2.35e-11

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


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 66.29  E-value: 2.35e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1486 AINWIEYMSHFIEKSDLAAARKTAEEALgAINPTESDellkiwtAYLNMEVAY---GDAATVQKVFERACK-NANAYTVH 1561
Cdd:COG2956    8 ALGWYFKGLNYLLNGQPDKAIDLLEEAL-ELDPETVE-------AHLALGNLYrrrGEYDRAIRIHQKLLErDPDRAEAL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1562 KTLSKIYQKFEKNAEATQILEQMVKKfRANQLEVWTLLAEHLMTQNDQKAARELLPRALKSAPK-AQQHVQLiskfAQLE 1640
Cdd:COG2956   80 LELAQDYLKAGLLDRAEELLEKLLEL-DPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPEnAHAYCEL----AELY 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1641 FKHGDAERGRTLLEGLVTAHPKKTDLWLVYAEAVLKH----LGIEHARKVLERACNLGFSIHKMRPLYKK---------W 1707
Cdd:COG2956  155 LEQGDYDEAIEALEKALKLDPDCARALLLLAELYLEQgdyeEAIAALERALEQDPDYLPALPRLAELYEKlgdpeealeL 234

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 17552198 1708 LE--MESKHGDAAAVELVKAKAEKFLQAVADNVLEE 1741
Cdd:COG2956  235 LRkaLELDPSDDLLLALADLLERKEGLEAALALLER 270
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
427-500 1.02e-09

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 56.46  E-value: 1.02e-09
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17552198     427 KCGDVLDARVHHVAKSGVYFMVCNFVKAFAPLSMLSDKPLPaqKMKNIYKVGTEVKCRVWQICDERKNLIVTCR 500
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVK--DPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 702-777 4.11e-09

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: 54.90  E-value: 4.11e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17552198  702 KLPKKIDELKVGKVIVGIVgQVITNVGVFVELVGG-SGLVGKV-LERKNAKNTSELLEVGQVIVGTIESIDTTKKSFL 777
Cdd:cd04461    4 TLPTNFSDLKPGMVVHGYV-RNITPYGVFVEFLGGlTGLAPKSyISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1564-1690 7.09e-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: 53.27  E-value: 7.09e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1564 LSKIYQKFEKNAEATQILEQMVKKFRANqLEVWTLLAEHLMTQNDQKAARELLPRALKSAPKaqqHVQLISKFAQLEFKH 1643
Cdd:COG4783   10 LAQALLLAGDYDEAEALLEKALELDPDN-PEAFALLGEILLQLGDLDEAIVLLHEALELDPD---EPEARLNLGLALLKA 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 17552198 1644 GDAERGRTLLEGLVTAHPKKTDLWLVYAEAVLKHLGIEHARKVLERA 1690
Cdd:COG4783   86 GDYDEALALLEKALKLDPEHPEAYLRLARAYRALGRPDEAIAALEKA 132
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1541-1669 2.95e-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: 51.16  E-value: 2.95e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1541 AATVQKVFERACKNANAYTVhktLSKIYQKFEKNAEATQILEQMVKkFRANQLEVWTLLAEHLMTQNDQKAARELLPRAL 1620
Cdd:COG4235    3 IARLRQALAANPNDAEGWLL---LGRAYLRLGRYDEALAAYEKALR-LDPDNADALLDLAEALLAAGDTEEAEELLERAL 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 17552198 1621 KSAPkaqQHVQLISKFAQLEFKHGDAERGRTLLEGLVTAHPKKTDLWLV 1669
Cdd:COG4235   79 ALDP---DNPEALYLLGLAAFQQGDYAEAIAAWQKLLALLPADAPARLL 124
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1576-1690 1.18e-06

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: 49.23  E-value: 1.18e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1576 EATQILEQMVKKfRANQLEVWTLLAEHLMTQNDQKAARELLPRALKSAPKaqqHVQLISKFAQLEFKHGDAERGRTLLEG 1655
Cdd:COG4235    1 EAIARLRQALAA-NPNDAEGWLLLGRAYLRLGRYDEALAAYEKALRLDPD---NADALLDLAEALLAAGDTEEAEELLER 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 17552198 1656 LVTAHPKKTDLWLVYAEAvLKHLG-----IEHARKVLERA 1690
Cdd:COG4235   77 ALALDPDNPEALYLLGLA-AFQQGdyaeaIAAWQKLLALL 115
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 166-530 1.97e-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: 52.43  E-value: 1.97e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198    166 GLVLHTAVVSIEEKGAILDVGLdQITGFIEKSQFPAA--GLKEGMPLIVRVLSSTSR----VVKVTSFVEQDNLnmtscE 239
Cdd:TIGR00717   19 GSIVKGTVVAINKDTVFVDVGL-KSEGRIPKEEFLDAplEIQVGDEVEVYLDRVEDRfgetVLSREKAQRHELW-----I 92

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198    240 KLqLNHLMPGTILECEPTGdAVTAGVIVNIgNGLKGILPRRNLPPRLRENPEKL-GKAIRA-IVMFCQQNSKILVlnAHP 317
Cdd:TIGR00717   93 KL-EKAYEEGSIVEGKIVG-KVKGGFIVDL-NGVEAFLPGSQVDVKPIKDLDSLiGKTLKFkIIKLDQKRNNIVV--SRR 167

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198    318 DIVAASRIEKR-TSFEGISIGDKVKCTVIDvlptksmvyfalpaIDGKKSLVTAVSSRGLLEKPD-------QVSTEYEV 389
Cdd:TIGR00717  168 AYLEEERSQAReELLENLKEGDVVKGVVKN--------------ITDFGAFVDLGGVDGLLHITDmswkrvkHPSEYVKV 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198    390 GTEKLCRVTGFRYADRSITISTRKDILNQKITKYQDAKCGDVLDARVHHVAKSGVYFMVCNFVKAFAPLSMLS--DKPlp 467
Cdd:TIGR00717  234 GQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwvKKN-- 311

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17552198    468 aQKMKNIYKVGTEVKCRVWQICDERKNLivtcresILGLKSPSVNSVQELE----IGVTVPCVIRKV 530
Cdd:TIGR00717  312 -SHPSKVVKKGDEVEVMILDIDPERRRL-------SLGLKQCKANPWEQFEekhpVGDRVTGKIKKI 370
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1590-1690 3.33e-06

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: 48.26  E-value: 3.33e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1590 ANQLEVWTLLAEHLMTQNDQKAARELLPRALKSAPkaqQHVQLISKFAQLEFKHGDAERGRTLLEGLVTAHPKKTDLWLV 1669
Cdd:COG4783    1 AACAEALYALAQALLLAGDYDEAEALLEKALELDP---DNPEAFALLGEILLQLGDLDEAIVLLHEALELDPDEPEARLN 77

                         90       100
                 ....*....|....*....|..
gi 17552198 1670 YAEAvLKHLG-IEHARKVLERA 1690
Cdd:COG4783   78 LGLA-LLKAGdYDEALALLEKA 98
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1288-1351 2.48e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.75  E-value: 2.48e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17552198    1288 KEGDQYDGIVENASKGSLFIELGPGVSGRIPVNE-------ENQDLLEIGtnSVIRVTVVKV--AKNEITLKL 1351
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISElsdkrvkDPEEVLKVG--DEVKVKVLSVdeEKGRIILSL 71
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 163-232 4.43e-05

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: 43.39  E-value: 4.43e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17552198  163 LAAGLVLHTAVVSIEEKGAILDVGLDQITGFIEKSQFP-AAGLKEGMPLIVRVLS-STSRVVKVTSFVEQDN 232
Cdd:cd05694    2 LVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGnFSKLKVGQLLLCVVEKvKDDGRVVSLSADPSKV 73
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 1501-1626 1.02e-04

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


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 44.57  E-value: 1.02e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1501 DLAAARKTAEEALGAINPTESDELLKIWTAYLNMEVAY---GDAATVQKVFERACK-NANAYTVHKTLSKIYQKFEKNAE 1576
Cdd:COG5010   27 YEAALAGANNTKEDELAAAGRDKLAKAFAIESPSDNLYnklGDFEESLALLEQALQlDPNNPELYYNLALLYSRSGDKDE 106

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 17552198 1577 ATQILEQMVKKFRANQlEVWTLLAEHLMTQNDQKAARELLPRALKSAPKA 1626
Cdd:COG5010  107 AKEYYEKALALSPDNP-NAYSNLAALLLSLGQDDEAKAALQRALGTSPLK 155
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1539-1692 2.40e-04

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: 46.23  E-value: 2.40e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198   1539 GDAATVQKVFERAcknANAYTV-HKT---------LSKIYQKFEKNAEATQILEQMVKKfRANQLEVWTLLAEHLMTQND 1608
Cdd:TIGR02917  710 GDLYLRQKDYPAA---IQAYRKaLKRapssqnaikLHRALLASGNTAEAVKTLEAWLKT-HPNDAVLRTALAELYLAQKD 785

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198   1609 -QKAARELL-------------------------PRALKSAPKA-----QQHvQLISKFAQLEFKHGDAERGRTLLEGLV 1657
Cdd:TIGR02917  786 yDKAIKHYQtvvkkapdnavvlnnlawlylelkdPRALEYAERAlklapNIP-AILDTLGWLLVEKGEADRALPLLRKAV 864

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 17552198   1658 TAHPKKTDLWLVYAEAVLKHLGIEHARKVLERACN 1692
Cdd:TIGR02917  865 NIAPEAAAIRYHLALALLATGRKAEARKELDKLLN 899
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1469-1587 4.14e-04

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: 42.49  E-value: 4.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1469 EKSEEDHSRLVRSDPNSAINWIEYMSHFIEKSDLAAARKTAEEALgAINPTESDellkiwtAYLNMEVAY---GDAATVQ 1545
Cdd:COG4783   21 DEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLHEAL-ELDPDEPE-------ARLNLGLALlkaGDYDEAL 92

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 17552198 1546 KVFERACK-NANAYTVHKTLSKIYQKFEKNAEATQILEQMVKK 1587
Cdd:COG4783   93 ALLEKALKlDPEHPEAYLRLARAYRALGRPDEAIAALEKALEL 135
RNA14 COG5107
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ...
 1475-1732 4.50e-04

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


Pssm-ID: 227438 [Multi-domain]  Cd Length: 660  Bit Score: 45.01  E-value: 4.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1475 HSRLVRSDPNSAINWIEYMSHFIEKSDLAAARKTAEEAlgaiNPTESDELLKIWTAY-LNMevaygDAATVQKVFERaCK 1553
Cdd:COG5107  291 HNQILDYFYYAEEVWFDYSEYLIGISDKQKALKTVERG----IEMSPSLTMFLSEYYeLVN-----DEEAVYGCFDK-CT 360

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1554 NANAYTVHKTLSKIYQKFEKNAEATQilEQMVKkfRANQLE-VWTLLAEHLMTQNDQKAARELLPRALKsAPKAQQHVQL 1632
Cdd:COG5107  361 QDLKRKYSMGESESASKVDNNFEYSK--ELLLK--RINKLTfVFCVHLNYVLRKRGLEAARKLFIKLRK-EGIVGHHVYI 435

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1633 ISKFaqLEFK-HGDAERGRTLLEGLVTAHPKKTdlwlVYAEAVLKHL----GIEHARKVLERACNlGFSIHKMRPLYKKW 1707
Cdd:COG5107  436 YCAF--IEYYaTGDRATAYNIFELGLLKFPDST----LYKEKYLLFLirinDEENARALFETSVE-RLEKTQLKRIYDKM 508

                        250       260
                 ....*....|....*....|....*.
gi 17552198 1708 LEMESKHGD-AAAVELVKAKAEKFLQ 1732
Cdd:COG5107  509 IEYESMVGSlNNVYSLEERFRELVPQ 534
HemYx COG3898
Uncharacterized protein HemY, contains HemY_N domain and TPR repeats (unrelated to HemY-type ...
 1501-1674 5.25e-04

Uncharacterized protein HemY, contains HemY_N domain and TPR repeats (unrelated to HemY-type protoporphyrinogen oxidase) [Function unknown];


Pssm-ID: 443105 [Multi-domain]  Cd Length: 468  Bit Score: 44.50  E-value: 5.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1501 DLAAARKTAEEALgAINPTesdeLLKIWTAYLNMEVAYGDAATVQKVFERACKnanaytvHKTLSKIYQKFEKNAEATQi 1580
Cdd:COG3898  167 DTEAALALAEEAL-ALAPK----LPWAQDALLELQAAAGDWDGALATLDAALK-------AGLLDKDVARRRRAVLLTA- 233

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1581 leqmvkkfRANQLEvwtllaehlmtQNDQKAARELLPRALKSAPkaqqhvqlisKF-------AQLEFKHGDAERGRTLL 1653
Cdd:COG3898  234 --------RARELE-----------EGDPDEARELAIEALKLAP----------DLvpaavlaARLLIAQGKLRKAAKVL 284

                        170       180
                 ....*....|....*....|...
gi 17552198 1654 EGL--VTAHPkktDLWLVYAEAV 1674
Cdd:COG3898  285 EKAwrAQPHP---DLAAAYAELR 304
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 1101-1193 6.14e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 44.38  E-value: 6.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198  1101 YKSNYKIGDVVKCfganTMTEKQE--LKVEVNPVWTGTISRENLSDDLKVTAADggivdlALKKGEMREAKITAVDRKNM 1178
Cdd:PRK06299  454 FAKKHKKGSIVTG----TVTEVKDkgAFVELEDGVEGLIRASELSRDRVEDATE------VLKVGDEVEAKVINIDRKNR 523

                          90
                  ....*....|....*...
gi 17552198  1179 SLKLT---LDTAEEAFEI 1193
Cdd:PRK06299  524 RISLSikaLDEAEEKEAI 541
TPR_19 pfam14559
Tetratricopeptide repeat;
1572-1635 6.32e-04

Tetratricopeptide repeat;


Pssm-ID: 434038 [Multi-domain]  Cd Length: 65  Bit Score: 39.49  E-value: 6.32e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17552198   1572 EKNAEATQILEQMVKKFRANQlEVWTLLAEHLMTQNDQKAARELLPRALKSAPKAQQHVQLISK 1635
Cdd:pfam14559    2 GDYAEALELLEQALAEDPDNA-EARLGLAEALLALGRLDEAEALLAALPAADPDDPRYAALLAK 64
COG4700 COG4700
Uncharacterized conserved protein ECs_4300, contains TPR-like domain [Function unknown];
1599-1720 7.10e-04

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


Pssm-ID: 443735 [Multi-domain]  Cd Length: 249  Bit Score: 43.33  E-value: 7.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1599 LAEHLMTQNDQKAARELLPRALKSApkAQQHVQLISKFAQLEFKHGDAERGRTLLEGLVTAHP--KKTDLWLVYAEAvLK 1676
Cdd:COG4700   95 LADALLELGRYDEAIELYEEALTGI--FADDPHILLGLAQALFELGRYAEALETLEKLIAKNPdfKSSDAHLLYARA-LE 171

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 17552198 1677 HLG-IEHARKVLERAcNLGFSIHKMRPLYKKWLEMESKHGDAAAV 1720
Cdd:COG4700  172 ALGdLEAAEAELEAL-ARRYSGPEARYRYAKFLARQGRTAEAKEL 215
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1501-1625 8.99e-04

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: 41.33  E-value: 8.99e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1501 DLAAARKTAEEALgAINPTESDellkIWTAYLNMEVAYGDAATVQKVFERACK-NANAYTVHKTLSKIYQKFEKNAEATQ 1579
Cdd:COG4783   19 DYDEAEALLEKAL-ELDPDNPE----AFALLGEILLQLGDLDEAIVLLHEALElDPDEPEARLNLGLALLKAGDYDEALA 93

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 17552198 1580 ILEQMVKKfRANQLEVWTLLAEHLMTQNDQKAARELLPRALKSAPK 1625
Cdd:COG4783   94 LLEKALKL-DPEHPEAYLRLARAYRALGRPDEAIAALEKALELDPD 138
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1499-1690 1.29e-03

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


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 43.53  E-value: 1.29e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198   1499 KSDLAAARKTAEEALgAINPTESDELLKIwtAYLNMevAYGDAATVQKVFERAC----KNANAytvHKTLSKIYQKFEKN 1574
Cdd:TIGR02917  138 LGQLELAQKSYEQAL-AIDPRSLYAKLGL--AQLAL--AENRFDEARALIDEVLtadpGNVDA---LLLKGDLLLSLGNI 209

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198   1575 AEATQILEQMVK-KFRANQLEVwtLLAEHLMTQNDQKAARELLPRALKSAPKAQQHVQLIskfAQLEFKHGDAERGRTLL 1653
Cdd:TIGR02917  210 ELALAAYRKAIAlRPNNIAVLL--ALATILIEAGEFEEAEKHADALLKKAPNSPLAHYLK---ALVDFQKKNYEDARETL 284

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 17552198   1654 EGLVTAHPKKTDLwLVYAEAVLKHLG-IEHARKVLERA 1690
Cdd:TIGR02917  285 QDALKSAPEYLPA-LLLAGASEYQLGnLEQAYQYLNQI 321
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1504-1639 1.61e-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: 40.37  E-value: 1.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1504 AARKTAEEALgAINPTESDELLKIWTAYLNMEvAYGDAAtvqKVFERACK----NANAYTvhkTLSKIYQKFEKNAEATQ 1579
Cdd:COG4235    1 EAIARLRQAL-AANPNDAEGWLLLGRAYLRLG-RYDEAL---AAYEKALRldpdNADALL---DLAEALLAAGDTEEAEE 72

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1580 ILEQMVKKfRANQLEVWTLLAEHLMTQNDQKAARELLPRALKSAPKAQQHVQLISKFAQL 1639
Cdd:COG4235   73 LLERALAL-DPDNPEALYLLGLAAFQQGDYAEAIAAWQKLLALLPADAPARLLEASIAEA 131
CpoB COG1729
Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane ...
 1573-1662 1.69e-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: 39.97  E-value: 1.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1573 KNAEATQILEQMVKKFRANQL--EVWTLLAEHLMTQNDQKAARELLPRALKSAPKAQQHVQLISKFAQLEFKHGDAERGR 1650
Cdd:COG1729    8 DYDEAIAAFKAFLKRYPNSPLapDALYWLGEAYYALGDYDEAAEAFEKLLKRYPDSPKAPDALLKLGLSYLELGDYDKAR 87

                         90
                 ....*....|..
gi 17552198 1651 TLLEGLVTAHPK 1662
Cdd:COG1729   88 ATLEELIKKYPD 99
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
711-775 1.76e-03

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 38.74  E-value: 1.76e-03
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17552198     711 KVGKVIVGIVgQVITNVGVFVELvgGSGLVGKV----LERKNAKNTSELLEVGQVIVGTIESIDTTKKS 775
Cdd:smart00316    1 EVGDVVEGTV-TEITPGGAFVDL--GNGVEGLIpiseLSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGR 66
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
1530-1628 2.03e-03

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


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 39.00  E-value: 2.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1530 AYLNMevayGDAATVQKVFERACK-NANAYTVHKTLSKIYQKFEKNAEATQIleQMVKKFRANQLEVWTLLAEHLMTQND 1608
Cdd:COG3063    1 LYLKL----GDLEEAEEYYEKALElDPDNADALNNLGLLLLEQGRYDEAIAL--EKALKLDPNNAEALLNLAELLLELGD 74

                         90       100
                 ....*....|....*....|
gi 17552198 1609 QKAARELLPRALKSAPKAQQ 1628
Cdd:COG3063   75 YDEALAYLERALELDPSALR 94
HemYx COG3071
Uncharacterized protein HemY, contains HemY_N domain and TPR repeats (unrelated to ...
 1594-1693 2.05e-03

Uncharacterized protein HemY, contains HemY_N domain and TPR repeats (unrelated to protoporphyrinogen oxidase HemY) [Function unknown];


Pssm-ID: 442305 [Multi-domain]  Cd Length: 323  Bit Score: 42.20  E-value: 2.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1594 EVWTLLAEHLMTQNDQKAARELLPRALksapKAQQHVQLISKFAQLEFkhGDAERGRTLLEGLVTAHPKKTDLWLVYAEA 1673
Cdd:COG3071  194 ELAAAYARALIALGDHDEAERLLREAL----KRQWDPRLVRLYGRLQG--GDPAKQLKRAEKWLKKHPNDPDLLLALGRL 267

                         90       100
                 ....*....|....*....|
gi 17552198 1674 VLKHLGIEHARKVLERACNL 1693
Cdd:COG3071  268 CLRNQLWGKAREYLEAALAL 287
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1553-1711 2.14e-03

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


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 41.92  E-value: 2.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1553 KNANAYTvhkTLSKIYQKFEKNAEATQILEQMVKKFRaNQLEVWTLLAEHLMTQNDQKAARELLPRALKSAPK-AQQHVQ 1631
Cdd:COG0457    6 DDAEAYN---NLGLAYRRLGRYEEAIEDYEKALELDP-DDAEALYNLGLAYLRLGRYEEALADYEQALELDPDdAEALNN 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1632 LiskfAQLEFKHGDAERGRTLLEGLVTAHPKKTDLWLVYAEAvLKHLG-----IEHARKVLERACNLGFSIHKMRPLYKK 1706
Cdd:COG0457   82 L----GLALQALGRYEEALEDYDKALELDPDDAEALYNLGLA-LLELGrydeaIEAYERALELDPDDADALYNLGIALEK 156


                 ....*
gi 17552198 1707 WLEME 1711
Cdd:COG0457  157 LGRYE 161
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 707-828 2.64e-03

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: 41.95  E-value: 2.64e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198  707 IDELKVGKVIVGIVgQVITNVGVFVELVGGSGLV-------GKVlerknaKNTSELLEVGQVIVGTIESIDTTK------ 773
Cdd:COG0539  184 LEKLEEGDVVEGTV-KNITDFGAFVDLGGVDGLLhiseiswGRV------KHPSEVLKVGDEVEVKVLKIDREKerisls 256

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 17552198  774 -KSFLIDPctdletgelmlkkyalpllesiveevkWLAEQSNYPIpGSKVNGKVTK 828
Cdd:COG0539  257 lKQLQPDP---------------------------WENIAEKYPV-GDVVKGKVTR 284
COG4700 COG4700
Uncharacterized conserved protein ECs_4300, contains TPR-like domain [Function unknown];
1477-1630 3.36e-03

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


Pssm-ID: 443735 [Multi-domain]  Cd Length: 249  Bit Score: 41.02  E-value: 3.36e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1477 RLVRSDpnSAINWIEYMSHFIEKSDLAAARKTAEEALGAINPTESDELLKIWTAYLNMevayGDAATVQKVFERACKNAN 1556
Cdd:COG4700   82 ALEFAD--TVQNRVRLADALLELGRYDEAIELYEEALTGIFADDPHILLGLAQALFEL----GRYAEALETLEKLIAKNP 155

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17552198 1557 AYT---VHKTLSKIYQKFEKNAEATQILEQMVKkfRANQLEVWTLLAEHLMTQNDQKAARELLPRALKSAPKAQQHV 1630
Cdd:COG4700  156 DFKssdAHLLYARALEALGDLEAAEAELEALAR--RYSGPEARYRYAKFLARQGRTAEAKELLEEILDEAKHMPKHY 230
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 429-498 3.52e-03

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: 37.60  E-value: 3.52e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17552198  429 GDVLDARVHHVAKSGVYFMVCNFVKAFAPLSMLSDKPL--PAQKmkniYKVGTEVKCRVWQICDERKNLIVT 498
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLkhPEKK----FKPGLKVKCRVLSVEPERKRLVLT 68
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 707-839 4.01e-03

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 41.64  E-value: 4.01e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198    707 IDELKVGKVIVGIVGQvITNVGVFVELVGGSGLVGKV-LERKNAKNTSELLEVGQVIVGTIESIDTTKKsFLIdpctdle 785
Cdd:TIGR00717  182 LENLKEGDVVKGVVKN-ITDFGAFVDLGGVDGLLHITdMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKG-RIS------- 252

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 17552198    786 tgeLMLKKyalpllesiVEEVKWLAEQSNYPiPGSKVNGKVTKELDDLTLVEFE 839
Cdd:TIGR00717  253 ---LSLKQ---------LGEDPWEAIEKKFP-VGDKITGRVTNLTDYGVFVEIE 293
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
77-149 4.83e-03

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 37.20  E-value: 4.83e-03
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17552198      77 GVVSEVFDDGVLLHTAGTHTVKIHASEVSKKFTElfneekiEIKNAFQLGQMVPFRVISKKQgnDKGKVKGTC 149
Cdd:smart00316    8 GTVTEITPGGAFVDLGNGVEGLIPISELSDKRVK-------DPEEVLKVGDEVKVKVLSVDE--EKGRIILSL 71
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1560-1743 5.64e-03

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


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 41.61  E-value: 5.64e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198   1560 VHKTLSKIYQKFEKNAEATQILEQMVKKFRANqLEVWTLLAEHLMTQNDQKAARELLPRALKSAPKaqqHVQLISKFAQL 1639
Cdd:TIGR02917  467 LHNLLGAIYLGKGDLAKAREAFEKALSIEPDF-FPAAANLARIDIQEGNPDDAIQRFEKVLTIDPK---NLRAILALAGL 542

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198   1640 EFKHGDAERGRTLLEGLVTAHPKKTDLWLVYAEAVLKHLGIEHARKVLERACN-----------LGfSIHKM-------R 1701
Cdd:TIGR02917  543 YLRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAADaapdspeawlmLG-RAQLAagdlnkaV 621

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*....
gi 17552198   1702 PLYKKWLEMESKHGDA----AAVELVK---AKAEKFLQAVADnvLEEDN 1743
Cdd:TIGR02917  622 SSFKKLLALQPDSALAllllADAYAVMknyAKAITSLKRALE--LKPDN 668
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1569-1690 6.73e-03

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


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 41.22  E-value: 6.73e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198   1569 QKFEKnaeATQILEQMVKKFRANQLeVWTLLAEHLMTQNDQKAARELLPRALKSAPkaqQHVQLISKFAQLEFKHGDAER 1648
Cdd:TIGR02917  445 GQFDK---ALAAAKKLEKKQPDNAS-LHNLLGAIYLGKGDLAKAREAFEKALSIEP---DFFPAAANLARIDIQEGNPDD 517

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 17552198   1649 GRTLLEGLVTAHPKKTDLWLVYAEAVLKHLGIEHARKVLERA 1690
Cdd:TIGR02917  518 AIQRFEKVLTIDPKNLRAILALAGLYLRTGNEEEAVAWLEKA 559
HemYx COG3071
Uncharacterized protein HemY, contains HemY_N domain and TPR repeats (unrelated to ...
 1473-1625 7.35e-03

Uncharacterized protein HemY, contains HemY_N domain and TPR repeats (unrelated to protoporphyrinogen oxidase HemY) [Function unknown];


Pssm-ID: 442305 [Multi-domain]  Cd Length: 323  Bit Score: 40.66  E-value: 7.35e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198 1473 EDHSRLVRSDPNSAInwiEYMSHFIEKSDLAAARKTAEEALGAinpTESDELLKIWTaylnmEVAYGDAATVQKVFERAC 1552
Cdd:COG3071  183 KALPRAERRDPELAA---AYARALIALGDHDEAERLLREALKR---QWDPRLVRLYG-----RLQGGDPAKQLKRAEKWL 251

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17552198 1553 K-NANAYTVHKTLSKIYQKFEKNAEATQILEQMVKkfRANQLEVWTLLAEHLMTQNDQKAARELLPRALKSAPK 1625
Cdd:COG3071  252 KkHPNDPDLLLALGRLCLRNQLWGKAREYLEAALA--LRPSAEAYAELARLLEQLGDPEEAAEHYRKALALALG 323
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
249-313 8.55e-03

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 36.81  E-value: 8.55e-03
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17552198     249 GTILECEPtgdavtAGVIVNIGNGLKGILPRRNLPPRLRENPE---KLGKAIRAIVMFCQQNSKILVL 313
Cdd:smart00316    8 GTVTEITP------GGAFVDLGNGVEGLIPISELSDKRVKDPEevlKVGDEVKVKVLSVDEEKGRIIL 69
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
705-839 8.92e-03

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 40.70  E-value: 8.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17552198   705 KKIDELKVGKVIVGIVGQvITNVGVFVELVGGSGLV-------GKVlerknaKNTSELLEVGQVIVGTIESIDTTKKSFL 777
Cdd:PRK00087  470 ETWNSLEEGDVVEGEVKR-LTDFGAFVDIGGVDGLLhvseiswGRV------EKPSDVLKVGDEIKVYILDIDKENKKLS 542

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17552198   778 idpctdletgeLMLKKyalpLLESIVEEVKwlaeqSNYPIpGSKVNGKVTKELDDLTLVEFE 839
Cdd:PRK00087  543 -----------LSLKK----LLPDPWENVE-----EKYPV-GSIVLGKVVRIAPFGAFVELE 583
 
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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