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Conserved domains on  [gi|1382135606|ref|WP_108004906|]
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sigma-70 family RNA polymerase sigma factor [Mycoplana dimorpha]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK12536 super family cl36141
RNA polymerase sigma factor; Provisional
 6-180 2.62e-45

RNA polymerase sigma factor; Provisional


The actual alignment was detected with superfamily member PRK12536:

Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 147.50  E-value: 2.62e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606   6 SEDTLKRLMMLSLDGDEAAYRRLLGALRHLLVGYYSRRIgAATRADMEDLVQETLMALHARRMTYDLRRSFTAWFFSIAR 85
Cdd:PRK12536    4 AEARLRALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRL-PQLPDEVEDLVQEILLAVHNARHTYRADQPLTAWVHAIAR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  86 YKLVDHHRGRGGRAMMETELEDDLE--GGFREEALTARMDVERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAV 163
Cdd:PRK12536   83 YKLMDFLRSRARREALHDPLDDESElfATSDDEAAEARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAV 162

                         170
                  ....*....|....*..
gi 1382135606 164 KVSIHRAIKALGEKLRG 180
Cdd:PRK12536  163 KVGIHRGLKALAAKIRG 179
 
Name Accession Description Interval E-value
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 6-180 2.62e-45

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 147.50  E-value: 2.62e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606   6 SEDTLKRLMMLSLDGDEAAYRRLLGALRHLLVGYYSRRIgAATRADMEDLVQETLMALHARRMTYDLRRSFTAWFFSIAR 85
Cdd:PRK12536    4 AEARLRALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRL-PQLPDEVEDLVQEILLAVHNARHTYRADQPLTAWVHAIAR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  86 YKLVDHHRGRGGRAMMETELEDDLE--GGFREEALTARMDVERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAV 163
Cdd:PRK12536   83 YKLMDFLRSRARREALHDPLDDESElfATSDDEAAEARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAV 162

                         170
                  ....*....|....*..
gi 1382135606 164 KVSIHRAIKALGEKLRG 180
Cdd:PRK12536  163 KVGIHRGLKALAAKIRG 179
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 11-180 2.01e-27

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: 101.61  E-value: 2.01e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  11 KRLMMLSLDGDEAAYRRLLGALRHLLVGYYSRRIGaaTRADMEDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVD 90
Cdd:COG1595     5 EELLERLRAGDEAAFEELYERYRPRLYRYARRLLG--DRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAID 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  91 HHRGRGGRAMMETELEDDLEGGFRE-----EALTARMDVERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKV 165
Cdd:COG1595    83 HLRKRRRRRELLDELAEELPDEAADpeealEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKS 162

                         170
                  ....*....|....*
gi 1382135606 166 SIHRAIKALGEKLRG 180
Cdd:COG1595   163 RLSRARKKLREALEE 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 22-178 3.69e-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: 84.71  E-value: 3.69e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  22 EAAYRRLLGALRHLLVGYYSRRigaatrADMEDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVDHHR----GRGG 97
Cdd:TIGR02937   4 EELYERYLPLVYRYARRYLGDD------ADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRrkrrLRRE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  98 RAMMETELEDDLEGGFREEALTARMDVERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIKALGEK 177
Cdd:TIGR02937  78 LDLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157


                  .
gi 1382135606 178 L 178
Cdd:TIGR02937 158 L 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 25-98 1.69e-07

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 46.43  E-value: 1.69e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1382135606  25 YRRLLGALRHLLVGYYSRRigaatrADMEDLVQETLMALHARRMTYDLRR--SFTAWFFSIARYKLVDHHRGRGGR 98
Cdd:pfam04542   2 VERYLPLVYSLARRYLGDG------ADAEDLVQEGFLGLWRAIERFDPERgvSFSTWLYTIIRNAIIDYLRKQRRT 71
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 123-174 5.45e-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: 33.62  E-value: 5.45e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1382135606 123 DVERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIKAL 174
Cdd:cd06171     3 RLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
 
Name Accession Description Interval E-value
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 6-180 2.62e-45

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 147.50  E-value: 2.62e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606   6 SEDTLKRLMMLSLDGDEAAYRRLLGALRHLLVGYYSRRIgAATRADMEDLVQETLMALHARRMTYDLRRSFTAWFFSIAR 85
Cdd:PRK12536    4 AEARLRALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRL-PQLPDEVEDLVQEILLAVHNARHTYRADQPLTAWVHAIAR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  86 YKLVDHHRGRGGRAMMETELEDDLE--GGFREEALTARMDVERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAV 163
Cdd:PRK12536   83 YKLMDFLRSRARREALHDPLDDESElfATSDDEAAEARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAV 162

                         170
                  ....*....|....*..
gi 1382135606 164 KVSIHRAIKALGEKLRG 180
Cdd:PRK12536  163 KVGIHRGLKALAAKIRG 179
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
7-174 5.92e-45

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 146.41  E-value: 5.92e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606   7 EDTLKRLMMLSLDGDEAAYRRLLGALRHLLVGYYSRRIGAATRA--DMEDLVQETLMALHARRMTYDLRRSFTAWFFSIA 84
Cdd:PRK12539    5 ENELKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGaeEAEDLVQEALMAIHTRRHTYDPEQPLTPWVYAIA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  85 RYKLVDH-HRGRGGRAMMETELEDDLEGGFREEALTARMDVERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAV 163
Cdd:PRK12539   85 RYKLIDHlRRTRASLADVPIDDADELVAHDDHAAVESTLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAV 164

                         170
                  ....*....|.
gi 1382135606 164 KVSIHRAIKAL 174
Cdd:PRK12539  165 KVSVHRGLKAL 175
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 7-179 9.76e-38

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 128.28  E-value: 9.76e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606   7 EDTLKRLMMLSLDGDEAAYRRLLGALRHLLVGYYSRRIGAATRA--DMEDLVQETLMALHARRMTYDLRRSFTAWFFSIA 84
Cdd:PRK12512    6 EDEWTDLMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPadQAEDIVQEILLAVHLKRHTWDPGAPFAPWLFAIA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  85 RYKLVDHHRGRGGRAMMETE-LEDDLEGGFREEALTARmDVERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAV 163
Cdd:PRK12512   86 RNKLIDALRRRGRRVFVDIDdFAETLPAEPATETLPAG-DVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAV 164

                         170
                  ....*....|....*.
gi 1382135606 164 KVSIHRAIKALGEKLR 179
Cdd:PRK12512  165 RVALHRGLAALAAKFR 180
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 11-180 2.01e-27

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: 101.61  E-value: 2.01e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  11 KRLMMLSLDGDEAAYRRLLGALRHLLVGYYSRRIGaaTRADMEDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVD 90
Cdd:COG1595     5 EELLERLRAGDEAAFEELYERYRPRLYRYARRLLG--DRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAID 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  91 HHRGRGGRAMMETELEDDLEGGFRE-----EALTARMDVERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKV 165
Cdd:COG1595    83 HLRKRRRRRELLDELAEELPDEAADpeealEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKS 162

                         170
                  ....*....|....*
gi 1382135606 166 SIHRAIKALGEKLRG 180
Cdd:COG1595   163 RLSRARKKLREALEE 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 22-178 3.69e-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: 84.71  E-value: 3.69e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  22 EAAYRRLLGALRHLLVGYYSRRigaatrADMEDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVDHHR----GRGG 97
Cdd:TIGR02937   4 EELYERYLPLVYRYARRYLGDD------ADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRrkrrLRRE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  98 RAMMETELEDDLEGGFREEALTARMDVERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIKALGEK 177
Cdd:TIGR02937  78 LDLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157


                  .
gi 1382135606 178 L 178
Cdd:TIGR02937 158 L 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 49-178 7.87e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 66.15  E-value: 7.87e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  49 RADMEDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVDHHRGRGGRAMMETELEDDLEGGFREEALTARMDV---- 124
Cdd:PRK11924   37 RALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKAVLSDDALEPEFAETAETPEAALLAkddl 116

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1382135606 125 ---ERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIKALGEKL 178
Cdd:PRK11924  117 ariDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECL 173
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 33-180 2.61e-13

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 64.62  E-value: 2.61e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  33 RHLLVGYYSRRIGAAtrADMEDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVDHHRGRGgramMETELEDDL--E 110
Cdd:PRK09637   11 KAQLKAFLHSRVSNE--ADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKN----RSEELPDDLlfE 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1382135606 111 GGFREEALTARMD--VERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIKALGEKLRG 180
Cdd:PRK09637   85 DEEREENAKKELApcLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
1-174 2.97e-13

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 64.61  E-value: 2.97e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606   1 MTTAHSEDTLKRLMMLSLDGDEAAYRRLLGALRHLLVGYYSRRIGAATR--ADMEDLVQETLMALHARRMTY-DLRRSFT 77
Cdd:PRK09648    2 AAMTDTGEELDALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERpgLSADDVAQEVCLAVITALPRYrDQGRPFL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  78 AWFFSIARYKLVDHHRGRG-GRAMMETELED--DLEGGFREEALTA--RMDVERLLGALPKAQQDLIRQVRLEGQSIALA 152
Cdd:PRK09648   82 AFVYGIAAHKVADAHRAAGrDKAVPTEEVPErpSDDAGPEERALRSesSNRMRELLDTLPEKQREILILRVVVGLSAEET 161

                         170       180
                  ....*....|....*....|..
gi 1382135606 153 ADRTGLSESAVKVSIHRAIKAL 174
Cdd:PRK09648  162 AEAVGSTPGAVRVAQHRALARL 183
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 7-178 3.04e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 62.01  E-value: 3.04e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606   7 EDTLKRLMMLSLDGDEAAYRRLLGALRHLLVGYYSRRIGAATRAdmEDLVQETLMALHARRMTYDLRRSFTAWFFSIARY 86
Cdd:PRK12513   10 AASDEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALA--EDIFQETWLRVIRARAQYQPRARFRTWLYQIARN 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  87 KLVDHHRGRGGRAMMETELEDDLEGGFR-----EEALTARMDVERL---LGALPKAQQDLIrQVRLEGQ-SIALAADRTG 157
Cdd:PRK12513   88 LLIDHWRRHGARQAPSLDADEQLHALADdgaapEQQLSLFRDRRRLqaaLETLPDEQREVF-LLREHGDlELEEIAELTG 166

                         170       180
                  ....*....|....*....|.
gi 1382135606 158 LSESAVKVSIHRAIKALGEKL 178
Cdd:PRK12513  167 VPEETVKSRLRYALQKLRELL 187
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 2-174 5.02e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 58.53  E-value: 5.02e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606   2 TTAHSEDTLKRLMMLSLDGDEAAYRRLLGALRHLLVGYYSRRIgaATRADMEDLVQETLMALHARRMTYDLRRSF-TAWF 80
Cdd:PRK12534    4 IPGHDDDETGRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMI--PQRAEAEEVLQDVFTLIWHKAGQFDPSRARgLTWL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  81 FSIARYKLVDHHRGRGGR----AMMET-EL-EDDLEGGFREEALTARMDVERLLGALPKAQQDLIRQVRLEGQSIALAAD 154
Cdd:PRK12534   82 AMIARNKAIDHLRANAPQrrnvALDDAgELrAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAA 161

                         170       180
                  ....*....|....*....|
gi 1382135606 155 RTGLSESAVKVSIHRAIKAL 174
Cdd:PRK12534  162 RTDTPIGTVKSWIRRGLAKL 181
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 13-179 8.99e-11

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 58.00  E-value: 8.99e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  13 LMMLSLDGDEAA----YRRLLGALRHLlvgyySRRIGAATrADMEDLVQETLMALHARRMTYDLRR-SFTAWFFSIARYK 87
Cdd:PRK13919   13 LLALVARGEEEAlralFRRYAGAFLAL-----ARRMGLDG-AAAEDVVQEVFIRVWKKAKEFDPRRgSARAWLLALAHHA 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  88 LVDHHRGRGGR--AMMETELED---DLEG-GFREEALTARMDVERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSES 161
Cdd:PRK13919   87 AVDHVRRRAARpqPLEPDEREPeafDLPGpGLDEEGHLDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLG 166

                         170
                  ....*....|....*...
gi 1382135606 162 AVKVSIHRAIKALGEKLR 179
Cdd:PRK13919  167 TLKTRARRALSRLKEVLR 184
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 47-174 6.94e-10

RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).


Pssm-ID: 274379 [Multi-domain]  Cd Length: 159  Bit Score: 55.02  E-value: 6.94e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  47 ATRADMEDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVDHHRGRG-GRAMMETELEDDLEGGFREEA---LTARM 122
Cdd:TIGR02989  23 ADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLGrDRLVFDDDLLEALAAEAEPTEaerLSDDR 102

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1382135606 123 D-VERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIKAL 174
Cdd:TIGR02989 103 QaLEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSL 155
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 19-180 1.13e-09

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 54.81  E-value: 1.13e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  19 DGDEAAYRRLLGALRHLLVGYYSRRIgaATRADMEDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVDHHRGRGGR 98
Cdd:PRK09652    6 RGDRAAFALLVRRYQPRVKRLLSRLT--RDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQGRR 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  99 ---AMMETELEDDLEGGFR--------EEALTARMD--VERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKV 165
Cdd:PRK09652   84 ppaSDVDAEEAEDFDLADAlrdistpeNELLSAELEqrVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRS 163

                         170
                  ....*....|....*
gi 1382135606 166 SIHRAIKALGEKLRG 180
Cdd:PRK09652  164 RIFRAREALRAKLQP 178
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 17-179 1.02e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 52.27  E-value: 1.02e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  17 SLDGDEAAYRRLLGALRHLLvGYYSRRIGAATRADmeDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVDHHRGRG 96
Cdd:PRK12516    5 SVEGTPPFKRELLAALPSLR-AFAVSLIGRHDRAD--DLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  97 grammeTELEDDlEGGFREEALTAR--------MDVERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIH 168
Cdd:PRK12516   82 ------REVQDT-DGMFTEQLAVHPsqygtldlQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVN 154

                         170
                  ....*....|.
gi 1382135606 169 RAIKALGEKLR 179
Cdd:PRK12516  155 RARQRLQEILQ 165
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
36-174 1.69e-08

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 51.62  E-value: 1.69e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  36 LVGYYSRRIGAATRAdmEDLVQETLM-ALHARRMTYDLRRSFTAWFFSIARYKLVDHHRGRGGR---AMMETELEDDLEG 111
Cdd:PRK09645   22 LWRYALRLTGDRARA--EDVVQETLLrAWQHPEVLADTGRSARAWLFTVARNLVIDERRSARARpveGGDDVLGVPEQSA 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1382135606 112 GFREEALTARMDVERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIKAL 174
Cdd:PRK09645  100 PDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRAL 162
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 25-98 1.69e-07

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 46.43  E-value: 1.69e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1382135606  25 YRRLLGALRHLLVGYYSRRigaatrADMEDLVQETLMALHARRMTYDLRR--SFTAWFFSIARYKLVDHHRGRGGR 98
Cdd:pfam04542   2 VERYLPLVYSLARRYLGDG------ADAEDLVQEGFLGLWRAIERFDPERgvSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 6-182 7.32e-07

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 47.24  E-value: 7.32e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606   6 SEDTLKRLMMLSLDGDEAAYRRLLGALRHLLVGYYSRRIGaaTRADMEDLVQETLMALHARRMTYDLRRSFTAWFFSIAR 85
Cdd:PRK09640    9 NDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLG--NDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITY 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  86 YKLVDHHRG-RGGRAMMETELEDDLEGGFREEA--LTARMDVERLLGALPKAQQD--LIRQV-RLEGQSIalaADRTGLS 159
Cdd:PRK09640   87 NECITQYRKeRRKRRLMDALSLDPLEEASEEKApkPEERGGLDRWLVHVNPIDREilVLRFVaELEFQEI---ADIMHMG 163

                         170       180
                  ....*....|....*....|...
gi 1382135606 160 ESAVKVSIHRAIKALGEKLRGGT 182
Cdd:PRK09640  164 LSATKMRYKRALDKLREKFAGLA 186
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 53-181 1.85e-06

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 45.71  E-value: 1.85e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  53 EDLVQETLMALHarRMTYDLRRSFTAWFFSIARYKLVDH------HRGRGGRAMMETELEDDL---EGGFREEaltARMD 123
Cdd:PRK09639   31 EDLAQEVFLRLY--RSDFKGIENEKGWLIKSARNVAYNYlrsekrRRARILGEFQWQEVDNEPspeEIWIRKE---EITK 105

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1382135606 124 VERLLGALPKAQQDLIrQVRLEGQSIALAADRTGLSESAVKVSIHRAIKALG---EKLRGG 181
Cdd:PRK09639  106 VQEVLAKMTERDRTVL-LLRFSGYSYKEIAEALGIKESSVGTTLARAKKKFRkiyEQMEEE 165
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 50-108 1.90e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 46.08  E-value: 1.90e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1382135606  50 ADMEDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVDHHRGRgGRAMMETELEDD 108
Cdd:PRK12532   31 DLAEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQI-GRQRKVFTLLDD 88
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 53-179 1.92e-06

RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot:


Pssm-ID: 274361 [Multi-domain]  Cd Length: 154  Bit Score: 45.52  E-value: 1.92e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  53 EDLVQETLMALHARRMTYDlRRSFTAWFFSIARYKLVDHHRGRGGRAMMETEL------------EDDLEGGFREEALTA 120
Cdd:TIGR02950  23 EDLLQETFLKAYIHLHSFK-DSSIKPWLFRIARNAFIDWYRKDKKIQTIDDDAigdleqhpvespEHHLLIKIEQEEITH 101

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1382135606 121 RMDverllgALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIKALGEKLR 179
Cdd:TIGR02950 102 HLS------RLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLLE 154
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 121-174 3.66e-06

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: 42.44  E-value: 3.66e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1382135606 121 RMDVERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIKAL 174
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sig70_famx1 TIGR02943
RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of ...
 49-112 5.55e-06

RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.


Pssm-ID: 274359 [Multi-domain]  Cd Length: 188  Bit Score: 44.76  E-value: 5.55e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1382135606  49 RADMEDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVDHHRgRGGRAMMETELEDDLEGG 112
Cdd:TIGR02943  26 RDLAEDAVQETLLAALSHRDSFAGRSALKTWLFAILKNKIIDALR-AKGREVKVSDLDDELDDE 88
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
12-99 8.68e-06

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 44.93  E-value: 8.68e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  12 RLMMLSLDGDEAAYRRLLGALRHLLVGYYSRRIGAATraDMEDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVDH 91
Cdd:PRK08241    8 ALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVH--DAEDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNVCLDA 85


                  ....*...
gi 1382135606  92 HRGRGGRA 99
Cdd:PRK08241   86 LEGRARRP 93
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 1-179 2.81e-05

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 42.77  E-value: 2.81e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606   1 MTTAHSEDTLKRLMMLSLDGDEAAYRRLLGalRHLLVGYYSRRIGAATRADMEDLVQETLMALHARRMTYDLRRSFTAWF 80
Cdd:PRK09643    5 PAVGFGERSDAELLAAHVAGDRYAFGELFR--RHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  81 FSIARYKLVDhhRGRGGRAMMETELEDDLEGGFREEALTARMD----VERLLGALPKAQQDLIRQVRLEGQSIALAADRT 156
Cdd:PRK09643   83 HRIVVNACLD--RLRRAKARPTVPLDDVYPVAQLERDPTARVEtalaVQRALMRLPVEQRAALVAVDMQGYSVADAARML 160

                         170       180
                  ....*....|....*....|...
gi 1382135606 157 GLSESAVKVSIHRAIKALGEKLR 179
Cdd:PRK09643  161 GVAEGTVKSRCARGRARLAELLG 183
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 53-181 3.25e-05

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 42.43  E-value: 3.25e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  53 EDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVDHHRGRGGRAMMETEledDLEGGFR------EEALTARMDVER 126
Cdd:PRK09415   44 EDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSWHNKKVIVTE---DIFTYMEsqkesvEEEVIQNAEDER 120

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1382135606 127 LLGA---LPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIKALGEKLRGG 181
Cdd:PRK09415  121 LASAvmsLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEEE 178
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 45-178 1.42e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 40.72  E-value: 1.42e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  45 GAATRADmeDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVDHHRGRggrammETELEDDlEGGF-----REEALT 119
Cdd:PRK12540   27 GNGDRAD--DLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRSDYRKR------RREVEDA-DGSYaktlkSQPGQN 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1382135606 120 ARMDVERL---LGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIKALGEKL 178
Cdd:PRK12540   98 AHLEFEEFraaLDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALL 159
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 7-179 1.87e-04

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 40.45  E-value: 1.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606   7 EDTLKRLMMLSLDGDEAAYRRLLGALRHLLVGYYSRRIGaaTRADMEDLVQETLMALHARRMTYDLRRSFTAWFFSIARY 86
Cdd:PRK09641    2 DLLIKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLG--NRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  87 KLVDHHRGR-----------GGRAM-METELEDDLEGGFRE-EALTARMDVERLLGALPKAQQDLIRQVRLEGQSIALAA 153
Cdd:PRK09641   80 LTIDRLRKRkpdyyldaevaGTEGLtMYSQLAADDALPEEQvVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEIS 159

                         170       180
                  ....*....|....*....|....*.
gi 1382135606 154 DRTGLSESAVKVSIHRAIKALGEKLR 179
Cdd:PRK09641  160 EILDLPVGTVKTRIHRGREALRKQLR 185
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 54-179 2.18e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 40.30  E-value: 2.18e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  54 DLVQETLMALHARRMTYDLRRS-FTAWFFSIARYKLVDHHRGRGGRAMM--------ETELEDDLEGGFREEALTARMDV 124
Cdd:PRK12531   56 EMVQETMSTVWQKAHLFDGQKSaLSTWIYTIIRNLCFDLLRKQKGKDLHihaddiwpSDYYPPDLVDHYSPEQDMLKEQV 135

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1382135606 125 ERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIkalgEKLR 179
Cdd:PRK12531  136 MKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAV----EKLR 186
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 19-180 2.85e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 39.71  E-value: 2.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  19 DGDEAAYRRLLGalRHLLVGYY--SRRIGAATRAdmEDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVDHHRGRg 96
Cdd:PRK12515   18 QGDRTAMQTLYG--RHHVRVYRfgLRLVRDEQTA--EDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSALRRR- 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  97 gramMETELEDDLEGGFREEALTARMDVER---------LLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSI 167
Cdd:PRK12515   93 ----KHEEIDDEAAAAIEDGADTPEVALQKsdtsaalraCLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRM 168

                         170
                  ....*....|...
gi 1382135606 168 HRAIKALGEKLRG 180
Cdd:PRK12515  169 FYARKKLAELLKA 181
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 1-174 3.16e-04

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 39.64  E-value: 3.16e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606   1 MTTAHSEDTLKRLMMLSLDGDEAAYRRLLGALRH---LLVGYYSRrIGAAtradmEDLVQETLMALHARRMTYDLRRSFT 77
Cdd:PRK09649    2 TATASDDEAVTALALSAAKGNGRALEAFIKATQQdvwRFVAYLSD-VGSA-----DDLTQETFLRAIGAIPRFSARSSAR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  78 AWFFSIARYKLVDH--HRGRGGRAMMETELEDDLEGGFREEALTARMDVERLLGALPKAQQDLIRQVRLEGQSIALAADR 155
Cdd:PRK09649   76 TWLLAIARHVVADHirHVRSRPRTTRGARPEHLIDGDRHARGFEDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAV 155

                         170
                  ....*....|....*....
gi 1382135606 156 TGLSESAVKVSIHRAIKAL 174
Cdd:PRK09649  156 CGCPVGTIRSRVARARDAL 174
PRK12545 PRK12545
RNA polymerase factor sigma-70;
21-111 3.21e-04

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 39.94  E-value: 3.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  21 DEAAYrrlLGALRHLLVGYYSRRIGAATRAdmEDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVDHHRGRgGRAM 100
Cdd:PRK12545    9 DDPAY---LAQLRHDLLRFARLQLRDADAA--EDAVQEALAAAWSQAGRFAGQSAHKTWVFGILRNKLIDTLRAR-QRTV 82

                          90
                  ....*....|.
gi 1382135606 101 METELEDDLEG 111
Cdd:PRK12545   83 NLSALDAELDG 93
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 53-179 4.99e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 38.70  E-value: 4.99e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  53 EDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVDHHRGRGgrammeTELEDDlEGGFRE--------EALTARMDV 124
Cdd:PRK12547   34 EDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKRG------REVQDS-DGVFTArvavhpaqYGSLDLQDF 106

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1382135606 125 ERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIKALGEKLR 179
Cdd:PRK12547  107 KKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLK 161
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 54-179 5.94e-04

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 38.41  E-value: 5.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  54 DLVQETLMALHARrmtYDlRRSFTAW---FFSIARYKLVDHHRGRGGRAMMETEL------EDDLEGGFREEALTARMDV 124
Cdd:PRK09047    9 DIVQDAMIKLAEK---YG-DRPAAEWpplFQRILQNRIHDWFRRQKVRNTWVSLFssfsddDDDDDFDPLETLDSADEGA 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1382135606 125 ----------------ERLLGALPKAQQD--LIRQvrLEGQSIALAADRTGLSESAVKVSIHRAIKALGEKLR 179
Cdd:PRK09047   85 espadkleraqvlqliEEAIQKLPARQREafLLRY--WEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALE 155
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 28-174 1.65e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 37.46  E-value: 1.65e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  28 LLGALRHllvgyYSRrigAATR--ADMEDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVDHHRGRGGRAMMETEL 105
Cdd:PRK12511   13 QLVPLRR-----YAR---SLTRdsAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVEARRADEL 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1382135606 106 ED--DLEGGFREEALTARMDVERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIKAL 174
Cdd:PRK12511   85 AVlaDASLPAAQEHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAAL 155
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 22-172 1.74e-03

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 37.52  E-value: 1.74e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  22 EAAYRRLLGAL----RHLLVGYYSRRIGAATRAdmEDLVQETLMALHARRmTYDLRRSFTAWFFSIARYKLVDHHRgrgg 97
Cdd:PRK12523    5 QSPHSELVGALyrdhRGWLLAWLRRNVACRQRA--EDLSQDTFVRLLGRP-ELPTPREPRAFLAAVAKGLMFDHFR---- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  98 RAMMETELEDDL------EGGFREEALTARMD---VERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIH 168
Cdd:PRK12523   78 RAALEQAYLAELalvpeaEQPSPEEQHLILEDlkaIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLA 157


                  ....
gi 1382135606 169 RAIK 172
Cdd:PRK12523  158 QGLR 161
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 53-108 2.17e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 37.05  E-value: 2.17e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1382135606  53 EDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVDHHRGRgGRAMMETELEDD 108
Cdd:PRK12530   35 EDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIRYR-KRFVNESELIEE 89
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 36-172 2.33e-03

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 37.06  E-value: 2.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  36 LVGYYSRRIGaaTRADMEDLVQETLMALHARRMTYDLRRSfTAWFFSIARYKLVDHHRGRGGRAMMETELEDDLEGGFrE 115
Cdd:PRK12527    8 LVRFLSARLG--NRQAAEDVAHDAYLRVLERSSSAQIEHP-RAFLYRTALNLVVDRHRRHRVRQAEPLEVLDEEERLH-S 83

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1382135606 116 EALTARMDVERLLGALPKAQQDLIRQVR-------LEGQSIALAADRTGLSESAVKVSIHRAIK 172
Cdd:PRK12527   84 PSPQTRLDLGQRLALLQRALAELPPACRdsfllrkLEGLSHQQIAEHLGISRSLVEKHIVNAMK 147
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 33-172 2.50e-03

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 36.97  E-value: 2.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  33 RHLLVGYYSRRIGAATRAdmEDLVQETLMALHARRMTYDLRRSFtAWFFSIARYKLVDHHRGRGGRAMMETELEDDL--- 109
Cdd:PRK07037    8 RSMLVKIAARIVGCRSRA--EDVVQDAFVKLVEAPNQDAVKQPV-AYLFRIVRNLAIDHYRRQALENKYHGDEEDGLdvp 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1382135606 110 -EGGFREEALTARMDVERL---LGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIK 172
Cdd:PRK07037   85 sPEASPEAALINRDTLRHVadaLSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALV 151
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 13-178 2.51e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 37.25  E-value: 2.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  13 LMMLSLDGDEAAYRRLLGALRHLLvgYYSRRIGAATRADMEDLVQETLMALHARRMTYDLRRSFTAWFFSIARYKLVDHH 92
Cdd:PRK11922   20 LVARVLAGDEAAFEALMRRHNRRL--YRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRL 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  93 RGRGGRAMMETELEDDLEGGFREEALTARMD--------------VERLLGALPkaqqDLIRQV----RLEGQSIALAAD 154
Cdd:PRK11922   98 RRRRRLVNLAEMVMASTIAGGERTPLADPAEdperaaarreiralLERAIDALP----DAFRAVfvlrVVEELSVEETAQ 173

                         170       180
                  ....*....|....*....|....
gi 1382135606 155 RTGLSESAVKVSIHRAIKALGEKL 178
Cdd:PRK11922  174 ALGLPEETVKTRLHRARRLLRESL 197
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 53-179 2.72e-03

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 36.78  E-value: 2.72e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  53 EDLVQETLMALHARRMTYDLRRsFTAWFFSIARYKLVDHHRGRGGRAMMETELEDDLEGGFREEALTARMDVERLLG--- 129
Cdd:PRK09644   29 EDLLQETFYRAYIYLEDYDNQK-VKPWLFKVAYHTFIDFVRKEKKVSFVGTDEIEAIQAESTEEYVVAKNSYEKLIQiih 107

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1382135606 130 ALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIKALGEKLR 179
Cdd:PRK09644  108 TLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 53-174 3.82e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 36.45  E-value: 3.82e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  53 EDLVQETL--MALHarrMTYDLRRSFTAWFFSIARYKLVDHHRGRGGRAMMETELEDDLEGGFREEALTARMDVERLL-- 128
Cdd:PRK12541   33 EDLMQETFyrMLVH---IDYYKGEEIRPWLFTIAYNAFIDWYRKEKKYKTTTIEEFHLPNVPSTEHEYFIKHEIASWLds 109

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1382135606 129 -GALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIKAL 174
Cdd:PRK12541  110 lSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKET 156
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 20-176 4.78e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 36.29  E-value: 4.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  20 GDEAAYRRLLGALRHLLVGYySRRIgAATRADMEDLVQETLMALHARRMTYDLRR-SFTAWFFSIARYKLVDHHRGRGGR 98
Cdd:PRK12537   20 GDRRALQALYQQESARLLGV-ARRI-VRDRALAEDIVHDAFIKIWTGAASFDPARgSARGWIYSVTRHLALNVLRDTRRE 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  99 AMMETELEDDLEGG------FREEALTARmdVERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIK 172
Cdd:PRK12537   98 VVLDDDAEETAQTLheiiddFDLWANSGK--IHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLK 175


                  ....
gi 1382135606 173 ALGE 176
Cdd:PRK12537  176 ALRE 179
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 123-174 5.45e-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: 33.62  E-value: 5.45e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1382135606 123 DVERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVSIHRAIKAL 174
Cdd:cd06171     3 RLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 13-178 5.49e-03

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 36.17  E-value: 5.49e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  13 LMMLSLDGDEAAYRRLLGalRHL--LVGYYSRRIGAATRAdmEDLVQETLMAL--HARRMTYDLRRsFTAWFFSIARYKL 88
Cdd:PRK05602   10 LLARVAAGDPAAFRVLVA--RKLprLLALATRMLGDPAEA--EDVAQETFLRIwkQAPSWRPGEAR-FDTWLHRVVLNLC 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382135606  89 VDHHRGRGGRAMMET-ELEDDLEGG-FREEALTARMDVERLLGALPKAQQDLIRQVRLEGQSIALAADRTGLSESAVKVS 166
Cdd:PRK05602   85 YDRLRRRREVPVEDApDVPDPAPGPdAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESL 164

                         170
                  ....*....|..
gi 1382135606 167 IHRAIKALGEKL 178
Cdd:PRK05602  165 LARGRRALRAQL 176
 
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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