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Conserved domains on  [gi|1172246593|ref|WP_080635939|]
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sigma-70 family RNA polymerase sigma factor [Rhizobium acaciae]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK07037 super family cl32185
extracytoplasmic-function sigma-70 factor; Validated
 16-165 5.95e-34

extracytoplasmic-function sigma-70 factor; Validated


The actual alignment was detected with superfamily member PRK07037:

Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 119.02  E-value: 5.95e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  16 AMIENKDKLLKTIESVVKSKSYSEDIFQDGVIKAYGV-KTDDIRCPIGYAFRMVYNLALDESRRRRQKMNNHRSIDQIQE 94
Cdd:PRK07037    3 VFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEApNQDAVKQPVAYLFRIVRNLAIDHYRRQALENKYHGDEEDGLD 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1172246593  95 ITAPVPTVLDQLVAAETLRNVLASLEALPKRTNDAFIRHRLNGVPQKDIAAELGVSRTLVNFMIKAAEEHC 165
Cdd:PRK07037   83 VPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHC 153
 
Name Accession Description Interval E-value
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 16-165 5.95e-34

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 119.02  E-value: 5.95e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  16 AMIENKDKLLKTIESVVKSKSYSEDIFQDGVIKAYGV-KTDDIRCPIGYAFRMVYNLALDESRRRRQKMNNHRSIDQIQE 94
Cdd:PRK07037    3 VFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEApNQDAVKQPVAYLFRIVRNLAIDHYRRQALENKYHGDEEDGLD 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1172246593  95 ITAPVPTVLDQLVAAETLRNVLASLEALPKRTNDAFIRHRLNGVPQKDIAAELGVSRTLVNFMIKAAEEHC 165
Cdd:PRK07037   83 VPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHC 153
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 19-165 6.97e-21

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 85.09  E-value: 6.97e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  19 ENKDKLLKTIESVVKSKSYSEDIFQDGVIKAYGV--KTDDIRCPIGYAFRMVYNLALDESRRRRQkmnNHRSIDQIQEIT 96
Cdd:TIGR02937   9 RYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEAldRFDPEGSFKAWLFRIARNLILDYLRRKRR---LRRELDLLEELL 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1172246593  97 APVPTVLDQLVAAETLRNVLASLEALPKRTNDAFIRHRLNGVPQKDIAAELGVSRTLVNFMIKAAEEHC 165
Cdd:TIGR02937  86 DSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 22-151 5.46e-17

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 75.42  E-value: 5.46e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  22 DKLLKTIESVVKSKSYSEDIFQDGVIKAYGV--KTDDIRCPIGYAFRMVYNLALDesRRRRQKMNNHRSIDQIQEITAPV 99
Cdd:COG1595    28 PRLYRYARRLLGDRADAEDLVQETFLRLWRKldSFRGRGSFRAWLYRIARNLAID--HLRKRRRRRELLDELAEELPDEA 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1172246593 100 PTVLDQLVAAETLRNVLASLEALPKRTNDAFIRHRLNGVPQKDIAAELGVSR 151
Cdd:COG1595   106 ADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISE 157
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 112-165 1.07e-07

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 47.07  E-value: 1.07e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1172246593 112 LRNVLASLEALPKRTNDAFIRHRLNGVPQKDIAAELGVSRTLVNFMIKAAEEHC 165
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
 
Name Accession Description Interval E-value
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 16-165 5.95e-34

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 119.02  E-value: 5.95e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  16 AMIENKDKLLKTIESVVKSKSYSEDIFQDGVIKAYGV-KTDDIRCPIGYAFRMVYNLALDESRRRRQKMNNHRSIDQIQE 94
Cdd:PRK07037    3 VFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEApNQDAVKQPVAYLFRIVRNLAIDHYRRQALENKYHGDEEDGLD 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1172246593  95 ITAPVPTVLDQLVAAETLRNVLASLEALPKRTNDAFIRHRLNGVPQKDIAAELGVSRTLVNFMIKAAEEHC 165
Cdd:PRK07037   83 VPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHC 153
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 19-165 6.97e-21

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 85.09  E-value: 6.97e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  19 ENKDKLLKTIESVVKSKSYSEDIFQDGVIKAYGV--KTDDIRCPIGYAFRMVYNLALDESRRRRQkmnNHRSIDQIQEIT 96
Cdd:TIGR02937   9 RYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEAldRFDPEGSFKAWLFRIARNLILDYLRRKRR---LRRELDLLEELL 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1172246593  97 APVPTVLDQLVAAETLRNVLASLEALPKRTNDAFIRHRLNGVPQKDIAAELGVSRTLVNFMIKAAEEHC 165
Cdd:TIGR02937  86 DSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 22-151 5.46e-17

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 75.42  E-value: 5.46e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  22 DKLLKTIESVVKSKSYSEDIFQDGVIKAYGV--KTDDIRCPIGYAFRMVYNLALDesRRRRQKMNNHRSIDQIQEITAPV 99
Cdd:COG1595    28 PRLYRYARRLLGDRADAEDLVQETFLRLWRKldSFRGRGSFRAWLYRIARNLAID--HLRKRRRRRELLDELAEELPDEA 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1172246593 100 PTVLDQLVAAETLRNVLASLEALPKRTNDAFIRHRLNGVPQKDIAAELGVSR 151
Cdd:COG1595   106 ADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISE 157
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 112-165 1.07e-07

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 47.07  E-value: 1.07e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1172246593 112 LRNVLASLEALPKRTNDAFIRHRLNGVPQKDIAAELGVSRTLVNFMIKAAEEHC 165
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 57-171 3.90e-07

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 48.23  E-value: 3.90e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  57 IRCPIGYAFRMVYNLALDESRRR--RQKMNNHrSIDQIQEITAPVPTVLDQLvaAETLRNVLASLEALPKRTNDAFIRHR 134
Cdd:PRK12527   42 IEHPRAFLYRTALNLVVDRHRRHrvRQAEPLE-VLDEEERLHSPSPQTRLDL--GQRLALLQRALAELPPACRDSFLLRK 118

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1172246593 135 LNGVPQKDIAAELGVSRTLVNFMIKAAEEHCHLAIAE 171
Cdd:PRK12527  119 LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQ 155
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 32-178 1.51e-06

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 46.73  E-value: 1.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  32 VKSKSYSEDIFQDGVIKAYGVKT-DDIRCPIGYAFRMVYNLALDESRRRRQKMNNHRSIDQIQEITAPVPTVLDQLVaaE 110
Cdd:PRK09651   31 LQSAFDADDIAQDTFLRVMVSETlSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYLEMLALMPEGGAPSPEERESQL--E 108

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1172246593 111 TLRNVLASLEALPKRTNDAFIRHRLNGVPQKDIAAELGVSRTLVNFMIKAAEEHCHLaiaepaFRHDH 178
Cdd:PRK09651  109 TLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLL------FRLEY 170
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 31-150 6.22e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 45.27  E-value: 6.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  31 VVKSKSYSEDIFQDGVIKAYGVKTD----DIRcPIGYAFRMVYNLALDESRRRRQKmnnHRSIDQIQEITAPVPTVLDQL 106
Cdd:PRK12524   46 VLGDRAEAEDVTQEAMLRLWRIAPDwrqgEAR-VSTWLYRVVCNLCTDRLRRRRRA---SVDLDDAPEPADAAPGAEEAL 121

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1172246593 107 VAAETLRNVLASLEALPKRTNDAFIRHRLNGVPQKDIAAELGVS 150
Cdd:PRK12524  122 IEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIG 165
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 22-150 8.28e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 44.58  E-value: 8.28e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  22 DKLLKTIESVVKSKSYSEDIFQDGVIKAY--GVKTDDIRCPIGYAFRMVYNLALDESRRRRqkmnnHRSIDQIQEITAPV 99
Cdd:PRK11924   24 PDLLRYARRQLGDRALAEDAVQEAFLRAWrkADLFNGKGSARTWLLTIARNVCYDLLRRRR-----REKAVLSDDALEPE 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1172246593 100 -----PTVLDQLVAAETLRNVLASLEALPKRTNDAFIRHRLNGVPQKDIAAELGVS 150
Cdd:PRK11924   99 faetaETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVP 154
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 38-165 9.55e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 44.54  E-value: 9.55e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  38 SEDIFQDGVIKAYGVKTDDIRCPIGYAFRMVYNLALdeSRRRRQKMNNH--RSIDQIQEITAPVPTvlDQLVAAETLRNV 115
Cdd:PRK12529   46 AHDIFLRILASRDGGQREAIRQPRAYLARIANCVLV--SWRRRQSLELAwlEALATLPEPLHPSPE--QQSVILETLHEI 121

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1172246593 116 LASLEALPKRTNDAFIRHRLNGVPQKDIAAELGVSRTLVNFMIKAAEEHC 165
Cdd:PRK12529  122 DALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYVTC 171
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 39-181 1.71e-05

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 44.53  E-value: 1.71e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  39 EDIFQDGVIKAYGVKTDDIRCPIGYAFRMVYNLALDE---SRRRRQKMNNhrsidqiQEITAPVPTVLDQ----LVAAET 111
Cdd:PRK09636   32 EDIVQEAWLRWNNADRAQIRDPRAWLTRVVTRLCLDRlrsARHRRETYVG-------PWLPEPVVEELDDpleaVVAAED 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1172246593 112 LRnvLASLEALPKRTND---AFIRHRLNGVPQKDIAAELGVS----RTLvnfmikAAEEHCHLAIAEPAFR-HDHAHR 181
Cdd:PRK09636  105 LS--LALMLALERLSPLeraAFLLHDVFGVPFDEIASTLGRSpaacRQL------ASRARKHVRAARPRFPvSDEEGA 174
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 23-149 1.90e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 43.66  E-value: 1.90e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  23 KLLKTIESVVKSKSYSEDIFQDGVIKAYGvKTDDIRC----PIGYAFRMVYNLALDESRRRRQKMNNhrsIDQIQEITAP 98
Cdd:PRK12514   31 KLFGICLRVLKDRSEAEEALQDVYVKIWT-KADRFAVsglsPMTWLITIARNHAIDRLRARKAVAVD---IDEAHDLADP 106

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1172246593  99 VPTVLDQLVAAETLRNVLASLEALPKRTNDAFIRHRLNGVPQKDIAAELGV 149
Cdd:PRK12514  107 SPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDV 157
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 19-172 2.18e-05

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 43.30  E-value: 2.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  19 ENKDKLLKTIESVVKSKSYSEDIFQDGVIKAYGV-KTDDIRCPIGYAFRMVYNLALDESRRRRQKMNNHRSIDQIQEITA 97
Cdd:PRK12523   18 DHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGRpELPTPREPRAFLAAVAKGLMFDHFRRAALEQAYLAELALVPEAEQ 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1172246593  98 PVPTvlDQLVAAETLRNVLASLEALPKRTNDAFIRHRLNGVPQKDIAAELGVSRTLVNFMIKAAEEHCHLAI-AEP 172
Cdd:PRK12523   98 PSPE--EQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALyGEP 171
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 65-149 1.92e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 40.47  E-value: 1.92e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  65 FRMVYNLALDESRRR-RQKMNNHRSIDQIQEITAPVPTVLDQLVAAETLRNVLASLeALPKRtnDAFIRHRLNGVPQKDI 143
Cdd:PRK12518   66 YRITWNVATDARRQFaQRPSRIQDDSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTL-SLEHR--AVLVLHDLEDLPQKEI 142


                  ....*.
gi 1172246593 144 AAELGV 149
Cdd:PRK12518  143 AEILNI 148
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 66-150 3.69e-04

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 40.02  E-value: 3.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  66 RMVYNLALDESRRRRqkmnnHRSIDQIQEITAPVPTVLDQLVAAETLRNVLASLEALPKRTNDAFIRHRLNGVPQKDIAA 145
Cdd:PRK05602   78 RVVLNLCYDRLRRRR-----EVPVEDAPDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAA 152


                  ....*
gi 1172246593 146 ELGVS 150
Cdd:PRK05602  153 VMDIS 157
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 57-171 5.61e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 39.16  E-value: 5.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  57 IRCPIGYAFRMVYNLALDESRRRRQKMNNHRSIDQIQEITAPVPTVLDQLVaaETLRNVLASLEALPKRTNDAFIRHRLN 136
Cdd:PRK12525   56 IREPRALLTTIARRLMYEGWRRQDLERAYLQSLAEAPEAVQPSPEEQWMVI--ETLLAIDRLLDGLSGKARAAFLMSQLE 133

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1172246593 137 GVPQKDIAAELGVSRTLVNFMIKAAEEHCHLAIAE 171
Cdd:PRK12525  134 GLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGFQE 168
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 79-169 2.92e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 37.13  E-value: 2.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  79 RRQKMNN--HRSIDQIQEITAPVPTvlDQLVAAETLRNVLASLEALPKRTNDAFIRHRLNGVPQKDIAAELGVSRTLVNF 156
Cdd:PRK12528   71 RRQDLERayLEALAQLPERVAPSEE--ERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKR 148

                          90
                  ....*....|...
gi 1172246593 157 MIKAAEEHCHLAI 169
Cdd:PRK12528  149 YLNKAAMRCYFAL 161
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 21-123 4.07e-03

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 36.98  E-value: 4.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1172246593  21 KDKLLKTIESVVKSKSYSEDIFQDGVIKAY-GVKTDDIRCPIG-YAFRMVYNLALDESRRRR------QKMNNHRSIDQI 92
Cdd:PRK09641   28 KDKIYQLCYRMLGNRHEAEDAAQEAFIRAYvNIDSYDINRKFStWLYRIATNLTIDRLRKRKpdyyldAEVAGTEGLTMY 107

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1172246593  93 QEITAPVPTVLDQLVAAETLRNVLASLEALP 123
Cdd:PRK09641  108 SQLAADDALPEEQVVSLELQETIQEAILQLP 138
 
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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