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Conserved domains on  [gi|1094089819|ref|WP_071080847|]
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MULTISPECIES: hypothetical protein [Klebsiella]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK13719 super family cl28301
conjugal transfer transcriptional regulator TraJ; Provisional
 1-229 3.13e-06

conjugal transfer transcriptional regulator TraJ; Provisional


The actual alignment was detected with superfamily member PRK13719:

Pssm-ID: 237479  Cd Length: 217  Bit Score: 46.65  E-value: 3.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1094089819   1 MCAMDRSSHDGLSQSvrDVISCVKSLYHNSPVSVCIRNERHEPIYFNDSFqqLFSFFKAESEKKIFQAGFVDLEYVLSQF 80
Cdd:PRK13719    1 MYPMDRRERATIRQI--DLPESLTAFIDDYSYPACIRNESGKFIFYNTLF--LKEFLGQLQSKEWWFSLPIDTATLLSRA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1094089819  81 EFDCIALGQGCVLCKDFKCGDYNFQVRMESLLIPGeRSYVLWQinlLINLPLKGRLRVVKGEPcEDNNYDNVISSIpdkN 160
Cdd:PRK13719   77 ELDAMSEPSGMNIIEDVFINNKLWDVIIESFIYGG-VVFFLWR---FFCAASNVISSIIRGLS-TNLEAKNKVTKY---Q 148

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1094089819 161 LESLSFFILGFSYRESAYYIGLPASTVRKRVERardvIVEFF--ASFEHFKAYLFKTKKIFFFLDYCSNII 229
Cdd:PRK13719  149 NDVFILYSFGFSHEYIAQLLNITVGSSKNKISE----ILKFFgiSSRDELLIILHTSEMIFYLYKKVFEII 215
 
Name Accession Description Interval E-value
PRK13719 PRK13719
conjugal transfer transcriptional regulator TraJ; Provisional
 1-229 3.13e-06

conjugal transfer transcriptional regulator TraJ; Provisional


Pssm-ID: 237479  Cd Length: 217  Bit Score: 46.65  E-value: 3.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1094089819   1 MCAMDRSSHDGLSQSvrDVISCVKSLYHNSPVSVCIRNERHEPIYFNDSFqqLFSFFKAESEKKIFQAGFVDLEYVLSQF 80
Cdd:PRK13719    1 MYPMDRRERATIRQI--DLPESLTAFIDDYSYPACIRNESGKFIFYNTLF--LKEFLGQLQSKEWWFSLPIDTATLLSRA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1094089819  81 EFDCIALGQGCVLCKDFKCGDYNFQVRMESLLIPGeRSYVLWQinlLINLPLKGRLRVVKGEPcEDNNYDNVISSIpdkN 160
Cdd:PRK13719   77 ELDAMSEPSGMNIIEDVFINNKLWDVIIESFIYGG-VVFFLWR---FFCAASNVISSIIRGLS-TNLEAKNKVTKY---Q 148

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1094089819 161 LESLSFFILGFSYRESAYYIGLPASTVRKRVERardvIVEFF--ASFEHFKAYLFKTKKIFFFLDYCSNII 229
Cdd:PRK13719  149 NDVFILYSFGFSHEYIAQLLNITVGSSKNKISE----ILKFFgiSSRDELLIILHTSEMIFYLYKKVFEII 215
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 167-198 5.94e-03

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 34.00  E-value: 5.94e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1094089819 167 FILGFSYRESAYYIGLPASTVRKRVERARDVI 198
Cdd:cd06171    23 FGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
 
Name Accession Description Interval E-value
PRK13719 PRK13719
conjugal transfer transcriptional regulator TraJ; Provisional
 1-229 3.13e-06

conjugal transfer transcriptional regulator TraJ; Provisional


Pssm-ID: 237479  Cd Length: 217  Bit Score: 46.65  E-value: 3.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1094089819   1 MCAMDRSSHDGLSQSvrDVISCVKSLYHNSPVSVCIRNERHEPIYFNDSFqqLFSFFKAESEKKIFQAGFVDLEYVLSQF 80
Cdd:PRK13719    1 MYPMDRRERATIRQI--DLPESLTAFIDDYSYPACIRNESGKFIFYNTLF--LKEFLGQLQSKEWWFSLPIDTATLLSRA 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1094089819  81 EFDCIALGQGCVLCKDFKCGDYNFQVRMESLLIPGeRSYVLWQinlLINLPLKGRLRVVKGEPcEDNNYDNVISSIpdkN 160
Cdd:PRK13719   77 ELDAMSEPSGMNIIEDVFINNKLWDVIIESFIYGG-VVFFLWR---FFCAASNVISSIIRGLS-TNLEAKNKVTKY---Q 148

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1094089819 161 LESLSFFILGFSYRESAYYIGLPASTVRKRVERardvIVEFF--ASFEHFKAYLFKTKKIFFFLDYCSNII 229
Cdd:PRK13719  149 NDVFILYSFGFSHEYIAQLLNITVGSSKNKISE----ILKFFgiSSRDELLIILHTSEMIFYLYKKVFEII 215
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 168-207 1.43e-03

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 38.48  E-value: 1.43e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1094089819 168 ILGFSYRESAYYIGLPASTVRKRVERARDVIVeffASFEH 207
Cdd:PRK09649  144 LLGLSYADAAAVCGCPVGTIRSRVARARDALL---ADAEP 180
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 167-195 2.06e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 37.64  E-value: 2.06e-03
                          10        20
                  ....*....|....*....|....*....
gi 1094089819 167 FILGFSYRESAYYIGLPASTVRKRVERAR 195
Cdd:PRK11924  138 YVEGLSYREIAEILGVPVGTVKSRLRRAR 166
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 167-198 5.94e-03

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 34.00  E-value: 5.94e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1094089819 167 FILGFSYRESAYYIGLPASTVRKRVERARDVI 198
Cdd:cd06171    23 FGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 152-200 6.18e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 36.41  E-value: 6.18e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1094089819 152 VISSIPDKNLESLSFF-ILGFSYRESAYYIGLPASTVRKRVERARDVIVE 200
Cdd:PRK12535  130 LIDALPPERREALILTqVLGYTYEEAAKIADVRVGTIRSRVARARADLIA 179
 
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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