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Conserved domains on  [gi|1903802017|dbj|GGR81417|]
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hypothetical protein GCM10010205_07690 [Streptomyces nojiriensis]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 11496226)

sigma-70 family RNA polymerase sigma factor is an initiation factor that promotes the attachment of RNA polymerase to specific initiation sites and is then released; similar to Streptomyces griseus ECF sigma factor AdsA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sig70_famx2 TIGR02952
RNA polymerase sigma-70 factor, TIGR02952 family; This group of sigma factors are members of ...
 96-265 7.33e-94

RNA polymerase sigma-70 factor, TIGR02952 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. This family is found in a limited number of Gram-positive bacterial lineages.


:

Pssm-ID: 131997 [Multi-domain]  Cd Length: 170  Bit Score: 273.99  E-value: 7.33e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  96 LVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRDFGAWLVTIARNLVADHFK 175
Cdd:TIGR02952   1 LLERAQDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKNSFEAWLFTIARNVVNDYFR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 176 SSRFRLEVTTGEMLDANEVERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQY 255
Cdd:TIGR02952  81 GSKRHPLFSLDVFKELLSNEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQF 160

                         170
                  ....*....|
gi 1903802017 256 RAVRTLARLL 265
Cdd:TIGR02952 161 RAIKKLARQM 170
 
Name Accession Description Interval E-value
Sig70_famx2 TIGR02952
RNA polymerase sigma-70 factor, TIGR02952 family; This group of sigma factors are members of ...
 96-265 7.33e-94

RNA polymerase sigma-70 factor, TIGR02952 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. This family is found in a limited number of Gram-positive bacterial lineages.


Pssm-ID: 131997 [Multi-domain]  Cd Length: 170  Bit Score: 273.99  E-value: 7.33e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  96 LVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRDFGAWLVTIARNLVADHFK 175
Cdd:TIGR02952   1 LLERAQDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKNSFEAWLFTIARNVVNDYFR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 176 SSRFRLEVTTGEMLDANEVERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQY 255
Cdd:TIGR02952  81 GSKRHPLFSLDVFKELLSNEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQF 160

                         170
                  ....*....|
gi 1903802017 256 RAVRTLARLL 265
Cdd:TIGR02952 161 RAIKKLARQM 170
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 95-270 1.94e-49

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: 161.32  E-value: 1.94e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  95 DLVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRdFGAWLVTIARNLVADHF 174
Cdd:COG1595     6 ELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGS-FRAWLYRIARNLAIDHL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 175 KSSRFRLEVTTGEMLDANEVERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQ 254
Cdd:COG1595    85 RKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRL 164

                         170
                  ....*....|....*.
gi 1903802017 255 YRAVRTLARLLPEDAR 270
Cdd:COG1595   165 SRARKKLREALEEEGA 180
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 106-265 1.58e-29

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 109.27  E-value: 1.58e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 106 EAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRistfTWQGR-DFGAWLVTIARNLVADHFKSSRfRLEVT 184
Cdd:PRK09639    3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS----DFKGIeNEKGWLIKSARNVAYNYLRSEK-RRRAR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 185 TGEMLDANEVER--SPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFlQGLSVAETARVMGKNEGAIKTLQYRAVRTLA 262
Cdd:PRK09639   78 ILGEFQWQEVDNepSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAKKKFR 156


                  ...
gi 1903802017 263 RLL 265
Cdd:PRK09639  157 KIY 159
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 111-180 3.41e-16

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: 71.08  E-value: 3.41e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1903802017 111 LYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTF-TWQGRDFGAWLVTIARNLVADHFKSSRFR 180
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFdPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 208-261 1.40e-10

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: 55.57  E-value: 1.40e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1903802017 208 NAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTL 261
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
 
Name Accession Description Interval E-value
Sig70_famx2 TIGR02952
RNA polymerase sigma-70 factor, TIGR02952 family; This group of sigma factors are members of ...
 96-265 7.33e-94

RNA polymerase sigma-70 factor, TIGR02952 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. This family is found in a limited number of Gram-positive bacterial lineages.


Pssm-ID: 131997 [Multi-domain]  Cd Length: 170  Bit Score: 273.99  E-value: 7.33e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  96 LVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRDFGAWLVTIARNLVADHFK 175
Cdd:TIGR02952   1 LLERAQDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKNSFEAWLFTIARNVVNDYFR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 176 SSRFRLEVTTGEMLDANEVERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQY 255
Cdd:TIGR02952  81 GSKRHPLFSLDVFKELLSNEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQF 160

                         170
                  ....*....|
gi 1903802017 256 RAVRTLARLL 265
Cdd:TIGR02952 161 RAIKKLARQM 170
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 95-270 1.94e-49

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: 161.32  E-value: 1.94e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  95 DLVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRdFGAWLVTIARNLVADHF 174
Cdd:COG1595     6 ELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGS-FRAWLYRIARNLAIDHL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 175 KSSRFRLEVTTGEMLDANEVERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQ 254
Cdd:COG1595    85 RKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRL 164

                         170
                  ....*....|....*.
gi 1903802017 255 YRAVRTLARLLPEDAR 270
Cdd:COG1595   165 SRARKKLREALEEEGA 180
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 106-265 4.58e-40

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: 136.32  E-value: 4.58e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 106 EAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRdFGAWLVTIARNLVADHFKSSRfRLEVTT 185
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGS-FKAWLFRIARNLILDYLRRKR-RLRREL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 186 GEMLDANEVERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTLARLL 265
Cdd:TIGR02937  79 DLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 106-265 1.58e-29

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 109.27  E-value: 1.58e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 106 EAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRistfTWQGR-DFGAWLVTIARNLVADHFKSSRfRLEVT 184
Cdd:PRK09639    3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS----DFKGIeNEKGWLIKSARNVAYNYLRSEK-RRRAR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 185 TGEMLDANEVER--SPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFlQGLSVAETARVMGKNEGAIKTLQYRAVRTLA 262
Cdd:PRK09639   78 ILGEFQWQEVDNepSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAKKKFR 156


                  ...
gi 1903802017 263 RLL 265
Cdd:PRK09639  157 KIY 159
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
104-267 2.30e-26

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 101.31  E-value: 2.30e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 104 EAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRDFGAWLVTIARNLVADHFKSSRFRLEV 183
Cdd:PRK09645    7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRSARAWLFTVARNLVIDERRSARARPVE 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 184 TTGEMLDANevERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTLAR 263
Cdd:PRK09645   87 GGDDVLGVP--EQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALRL 164


                  ....
gi 1903802017 264 LLPE 267
Cdd:PRK09645  165 ALQE 168
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 94-264 3.08e-26

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 101.20  E-value: 3.08e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  94 MDLVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTwQGRDFGAWLVTIARNLVADH 173
Cdd:PRK11924    1 GQLMPVDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN-GKGSARTWLLTIARNVCYDL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 174 FKSSRFRLEVTTGEML--DANEVERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIK 251
Cdd:PRK11924   80 LRRRRREKAVLSDDALepEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVK 159

                         170
                  ....*....|...
gi 1903802017 252 TLQYRAvRTLARL 264
Cdd:PRK11924  160 SRLRRA-RQLLRE 171
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 97-265 1.01e-24

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 97.18  E-value: 1.01e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  97 VERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFtwQGR-DFGAWLVTIARNLVADHFK 175
Cdd:PRK09652    1 VERVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSF--RGGaAFYTWLYRIARNTAINYLR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 176 SSRFRL--------EVTTGEMLDANEVERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNE 247
Cdd:PRK09652   79 KQGRRPpasdvdaeEAEDFDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPI 158

                         170
                  ....*....|....*...
gi 1903802017 248 GAIKTLQYRAVRTLARLL 265
Cdd:PRK09652  159 GTVRSRIFRAREALRAKL 176
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 86-267 2.42e-21

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 88.59  E-value: 2.42e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  86 ADSDQARMMdlveRAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRriSTFTWQGR-DFGAWLVT 164
Cdd:PRK12513   10 AASDEALML----RYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIR--ARAQYQPRaRFRTWLYQ 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 165 IARNLVADHFKSSRFR----LEVTTGEMLDANEvERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETA 240
Cdd:PRK12513   84 IARNLLIDHWRRHGARqapsLDADEQLHALADD-GAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIA 162

                         170       180
                  ....*....|....*....|....*..
gi 1903802017 241 RVMGKNEGAIKTLQYRAVRTLARLLPE 267
Cdd:PRK12513  163 ELTGVPEETVKSRLRYALQKLRELLAE 189
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
83-265 4.53e-21

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 87.72  E-value: 4.53e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  83 RPTADSDQARMMDLVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKA----TAEDLTSETFLRALRRISTFTWQGRDF 158
Cdd:PRK09648    1 SAAMTDTGEELDALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVErpglSADDVAQEVCLAVITALPRYRDQGRPF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 159 GAWLVTIARNLVADHFKSSRFRLEVTTGEMLDANEVERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAE 238
Cdd:PRK09648   81 LAFVYGIAAHKVADAHRAAGRDKAVPTEEVPERPSDDAGPEERALRSESSNRMRELLDTLPEKQREILILRVVVGLSAEE 160

                         170       180
                  ....*....|....*....|....*..
gi 1903802017 239 TARVMGKNEGAIKTLQYRAVRTLARLL 265
Cdd:PRK09648  161 TAEAVGSTPGAVRVAQHRALARLRAEI 187
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 112-265 4.57e-21

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: 86.74  E-value: 4.57e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 112 YDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFtwQGRDFGAWLVTIARNLVADHFKSSRfRLEVTTGEMLDA 191
Cdd:TIGR02950   1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSF--KDSSIKPWLFRIARNAFIDWYRKDK-KIQTIDDDAIGD 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1903802017 192 NEVE--RSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTLARLL 265
Cdd:TIGR02950  78 LEQHpvESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 106-261 1.31e-20

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 85.69  E-value: 1.31e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 106 EAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRAlrristftWQGRD-------FGAWLVTIARNLVADHFKSSR 178
Cdd:TIGR02985   1 EAFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKL--------WENREtleisesIKAYLFTIVKNRCLNYLRHKQ 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 179 FRLEVTTgEMLDANEVERS---PEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQY 255
Cdd:TIGR02985  73 VEEKYQE-ELAEIEERELSeadPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHIT 151


                  ....*.
gi 1903802017 256 RAVRTL 261
Cdd:TIGR02985 152 KALKFL 157
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 111-267 2.22e-20

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 85.57  E-value: 2.22e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 111 LYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFtwQGR-DFGAWLVTIARNLVADHFKSSRFRLEVTTGEML 189
Cdd:PRK09415   21 IMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTY--KGKsSLKTWLYRIAINHCKDYLKSWHNKKVIVTEDIF 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1903802017 190 DANEVE-RSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTLARLLPE 267
Cdd:PRK09415   99 TYMESQkESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 89-261 3.09e-19

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 82.38  E-value: 3.09e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  89 DQARMMDLVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFtwQGR-DFGAWLVTIAR 167
Cdd:PRK09638    1 MQMDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSF--QGRsKFSTWLISIAS 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 168 NLVADHF---KSSRFRLEVTTGEMLDANEVERSpedsvLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMG 244
Cdd:PRK09638   79 RLYKDHLrkqKREKLRLQRAKEETLRKEKWEAA-----IKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLN 153

                         170
                  ....*....|....*..
gi 1903802017 245 KNEGAIKTLQYRAVRTL 261
Cdd:PRK09638  154 IPEGTVKSRVHHGIKQL 170
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 106-263 3.26e-19

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: 81.98  E-value: 3.26e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 106 EAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTwQGRDFGAWLVTIARNLVADHFKSSRFRLEVTT 185
Cdd:TIGR02989   1 KAFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFD-PGTNFVAWARGIARNKVLNYRRKLGRDRLVFD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 186 GEMLDAneVERSPEDSVLESLSN--AALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTLAR 263
Cdd:TIGR02989  80 DDLLEA--LAAEAEPTEAERLSDdrQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSLRE 157
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 96-256 7.95e-19

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 81.67  E-value: 7.95e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  96 LVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQgRDFGAWLVTIARNLVADHFK 175
Cdd:PRK09641    8 LIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDIN-RKFSTWLYRIATNLTIDRLR 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 176 SSR--FRL--EVTTGEMLD-----ANEvERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKN 246
Cdd:PRK09641   87 KRKpdYYLdaEVAGTEGLTmysqlAAD-DALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLP 165

                         170
                  ....*....|
gi 1903802017 247 EGAIKTLQYR 256
Cdd:PRK09641  166 VGTVKTRIHR 175
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 87-265 1.18e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 78.56  E-value: 1.18e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  87 DSDQARMMDLVERA--------QAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRaLRRISTFTWQGRDF 158
Cdd:PRK12519    2 SAGDSAPTSLSSRSdaelfsalKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLS-LWRKSSYDPKRGSL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 159 GAWLVTIARNLVADHFKSSRFRLevttgEMLDANEVER---SPEDSVLESLSNAALLEAVR----KLNPQQQECVTLRFL 231
Cdd:PRK12519   81 SSYLLTLTRSRAIDRLRSRRSRQ-----RLLERWQQELlgeASEDTPLEQASLAERSQRVQtalaQLPESQRQVLELAYY 155

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1903802017 232 QGLSVAETARVMGKNEGAIKTLQYRAVRTLARLL 265
Cdd:PRK12519  156 EGLSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 95-265 6.55e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 76.69  E-value: 6.55e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  95 DLVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFtwQGR-DFGAWLVTIARnlvadh 173
Cdd:PRK12515   11 MLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQF--EGRsQVSTWLLSIAR------ 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 174 FKS----SRFRLEVTTGEmlDANEVE---RSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKN 246
Cdd:PRK12515   83 FKAlsalRRRKHEEIDDE--AAAAIEdgaDTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIP 160

                         170
                  ....*....|....*....
gi 1903802017 247 EGAIKTLQYRAVRTLARLL 265
Cdd:PRK12515  161 ESTVKTRMFYARKKLAELL 179
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 83-269 7.29e-17

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 76.23  E-value: 7.29e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  83 RPTADSDQarmmDLVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRDFGAWL 162
Cdd:PRK05602    1 RMDADPDE----ELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGEARFDTWL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 163 VTIARNLVADHFKSSRFRLEVTTGEMLDAnevERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARV 242
Cdd:PRK05602   77 HRVVLNLCYDRLRRRREVPVEDAPDVPDP---APGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAV 153

                         170       180
                  ....*....|....*....|....*..
gi 1903802017 243 MGKNEGAIKTLQYRAVRTLARLLPEDA 269
Cdd:PRK05602  154 MDISVDALESLLARGRRALRAQLADLP 180
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 111-180 3.41e-16

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: 71.08  E-value: 3.41e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1903802017 111 LYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTF-TWQGRDFGAWLVTIARNLVADHFKSSRFR 180
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFdPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 85-257 4.60e-16

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 74.31  E-value: 4.60e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  85 TADSDQARMMDLVERAQAGEAEAFGRLYDQYSDTVYRYIYYrVGGKATAEDLTSETFLRALRRISTFTwqGRDFG-AWLV 163
Cdd:PRK09649    3 ATASDDEAVTALALSAAKGNGRALEAFIKATQQDVWRFVAY-LSDVGSADDLTQETFLRAIGAIPRFS--ARSSArTWLL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 164 TIARNLVADHFKSSRFRLEVTTG----EMLDANEVERSPEDSVleslsnaALLEAVRKLNPQQQECVTLRFLQGLSVAET 239
Cdd:PRK09649   80 AIARHVVADHIRHVRSRPRTTRGarpeHLIDGDRHARGFEDLV-------EVTTMIADLTTDQREALLLTQLLGLSYADA 152

                         170
                  ....*....|....*...
gi 1903802017 240 ARVMGKNEGAIKTLQYRA 257
Cdd:PRK09649  153 AAVCGCPVGTIRSRVARA 170
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 84-257 2.15e-14

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 69.83  E-value: 2.15e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  84 PTADSDQArmmdLVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRdFGAWLV 163
Cdd:PRK11923    2 LTQEEDQQ----LVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSA-FYTWLY 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 164 TIARNLVADHFKSSRFR-----LEVTTGEMLDAN----EVErSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGL 234
Cdd:PRK11923   77 RIAINTAKNHLVSRGRRppdsdVSSEDAEFYDGDhalkDIE-SPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGL 155

                         170       180
                  ....*....|....*....|...
gi 1903802017 235 SVAETARVMGKNEGAIKTLQYRA 257
Cdd:PRK11923  156 SYEDIASVMQCPVGTVRSRIFRA 178
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 164-265 8.68e-14

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 67.30  E-value: 8.68e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 164 TIARNLVADHFKSSRFRLEVTTG-----------------EMLDANEVERSPEDSVLESLSNAALLEAVRKLNPQQQECV 226
Cdd:PRK09047   36 RILQNRIHDWFRRQKVRNTWVSLfssfsdddddddfdpleTLDSADEGAESPADKLERAQVLQLIEEAIQKLPARQREAF 115

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1903802017 227 TLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTLARLL 265
Cdd:PRK09047  116 LLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKAL 154
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 111-268 1.10e-13

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 67.21  E-value: 1.10e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 111 LYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQgrDFGAWLVTIARNLVADHFKSSRFRLEVTTgEMLD 190
Cdd:PRK09644    6 IYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ--KVKPWLFKVAYHTFIDFVRKEKKVSFVGT-DEIE 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1903802017 191 ANEVErSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTLARLLPED 268
Cdd:PRK09644   83 AIQAE-STEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEE 159
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 106-256 2.15e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 63.42  E-value: 2.15e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 106 EAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFtwQGRDFGAWLVTIARNLVADHFKSSRFRLEVTT 185
Cdd:PRK12541    5 QSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYY--KGEEIRPWLFTIAYNAFIDWYRKEKKYKTTTI 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1903802017 186 GEMLDANevERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYR 256
Cdd:PRK12541   83 EEFHLPN--VPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHR 151
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 100-257 3.42e-12

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 64.04  E-value: 3.42e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 100 AQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFtwQGRDFGAWLVTIARNLVADHFK-SSR 178
Cdd:PRK09647   22 GDKATMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNY--QPGTFEGWLHRITTNLFLDMVRrRAR 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 179 FRLEV--TTGEMLDANEVerSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYR 256
Cdd:PRK09647  100 IRMEAlpEDYDRVPGDEP--NPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHR 177


                  .
gi 1903802017 257 A 257
Cdd:PRK09647  178 G 178
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 110-257 8.57e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 62.40  E-value: 8.57e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 110 RLYDQ----YSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFtwqgRDFGA---WLVTIARNLVADHFKSSRFRLe 182
Cdd:PRK12517   23 RRYEAlvkaLHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSL----KDEKAakaWLITILRRENARRFERKQFDL- 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1903802017 183 VTTGEMLDANEVERSPEdsvlESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRA 257
Cdd:PRK12517   98 VDIEDDSIEDDASHSSE----EEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRA 168
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 88-265 3.03e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 60.87  E-value: 3.03e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  88 SDQARMMDLVERAQAGEAEAFGRLYDQ---YSDTVYRYIYYRVGGKAT-AEDLTSETFLRA-LRRistFTW-QGRDFGAW 161
Cdd:PRK12512    4 GREDEWTDLMRSANAGDAAAYRRLLKAvtpVLRAAARRGLARAGQPADqAEDIVQEILLAVhLKR---HTWdPGAPFAPW 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 162 LVTIARNLVADHFKSSRFRLEVTTGEMLDANEVERSPEDsvLESLSNAALLEAvrkLNPQQQECVTLRFLQGLSVAETAR 241
Cdd:PRK12512   81 LFAIARNKLIDALRRRGRRVFVDIDDFAETLPAEPATET--LPAGDVGRHLET---LPPRQRDVVQSISVEGASIKETAA 155

                         170       180
                  ....*....|....*....|....
gi 1903802017 242 VMGKNEGAIKTLQYRAVRTLARLL 265
Cdd:PRK12512  156 KLSMSEGAVRVALHRGLAALAAKF 179
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 208-261 1.40e-10

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: 55.57  E-value: 1.40e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1903802017 208 NAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTL 261
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 210-261 1.84e-10

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: 55.15  E-value: 1.84e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1903802017 210 ALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTL 261
Cdd:pfam08281   3 ALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 84-266 2.15e-10

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 58.57  E-value: 2.15e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  84 PTADSDQARMMDLVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRdFGAWLV 163
Cdd:PRK09643    5 PAVGFGERSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAA-VSSWLH 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 164 TIARNLVADHFKSSRFRLEVTTGemlDANEVERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVM 243
Cdd:PRK09643   84 RIVVNACLDRLRRAKARPTVPLD---DVYPVAQLERDPTARVETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARML 160

                         170       180
                  ....*....|....*....|...
gi 1903802017 244 GKNEGAIKTlqyRAVRTLARLLP 266
Cdd:PRK09643  161 GVAEGTVKS---RCARGRARLAE 180
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 103-261 2.63e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 58.21  E-value: 2.63e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 103 GEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTwQGRDFGAWLVTIARNLVADHFKSS--RFR 180
Cdd:PRK12543    4 GDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYD-SNRPFRFWLIGLVIKQIHSWRRKRwrRFR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 181 LEVTTGEMldANEVERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRT 260
Cdd:PRK12543   83 IFEKAEEQ--RKPVSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKK 160


                  .
gi 1903802017 261 L 261
Cdd:PRK12543  161 L 161
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 96-261 3.33e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 57.91  E-value: 3.33e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  96 LVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRDFGAWLVTIARNLVADHFK 175
Cdd:PRK12514    9 LIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPMTWLITIARNHAIDRLR 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 176 SSRfRLEVTTGEMLDANEVERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQY 255
Cdd:PRK12514   89 ARK-AVAVDIDEAHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLR 167


                  ....*.
gi 1903802017 256 RAVRTL 261
Cdd:PRK12514  168 RSLLKL 173
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 128-265 4.72e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 57.28  E-value: 4.72e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 128 GGKATAEDLTSETFLRALRRISTFTwQGRDFGAWLVTIARNLVADHFKSSRFRLEVTTGEMldANEVERSPEDSVleSLS 207
Cdd:PRK12540   27 GNGDRADDLVQETLLRALANIDSFQ-PGSNLPAWLFTILRNLFRSDYRKRRREVEDADGSY--AKTLKSQPGQNA--HLE 101

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1903802017 208 NAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTLARLL 265
Cdd:PRK12540  102 FEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALL 159
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 95-269 6.66e-10

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 57.26  E-value: 6.66e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  95 DLVERAQAG---EAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRdFGAWLVTIARNLVA 171
Cdd:PRK09640   12 ELVARVHVElfhVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSK-FKTWLYSITYNECI 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 172 DHFKSSRFRLEVTTGEMLDANEverSPEDSVLESLSNAALLEA-VRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAI 250
Cdd:PRK09640   91 TQYRKERRKRRLMDALSLDPLE---EASEEKAPKPEERGGLDRwLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSAT 167

                         170
                  ....*....|....*....
gi 1903802017 251 KTLQYRAVRTLARLLPEDA 269
Cdd:PRK09640  168 KMRYKRALDKLREKFAGLA 186
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 88-268 1.58e-09

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 56.08  E-value: 1.58e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  88 SDQArMMDLVERaqaGEAEAFGRLYDQYSDTVYRyIYYRVG-GKATAEDLTSETFLRALRRISTFTWQGRDFGAWLVTIA 166
Cdd:PRK13919    9 SDEA-LLALVAR---GEEEALRALFRRYAGAFLA-LARRMGlDGAAAEDVVQEVFIRVWKKAKEFDPRRGSARAWLLALA 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 167 RNLVADHFKSSRFR---LEVTTGEmldaNEVERSPEDSVLE--SLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETAR 241
Cdd:PRK13919   84 HHAAVDHVRRRAARpqpLEPDERE----PEAFDLPGPGLDEegHLDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQ 159

                         170       180
                  ....*....|....*....|....*..
gi 1903802017 242 VMGKNEGAIKTLQYRAVRTLARLLPED 268
Cdd:PRK13919  160 LLGLPLGTLKTRARRALSRLKEVLREP 186
SigZ TIGR02959
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 112-269 2.16e-09

RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).


Pssm-ID: 132004 [Multi-domain]  Cd Length: 170  Bit Score: 55.45  E-value: 2.16e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 112 YDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRdFGAWLVTIARNLVADHFKSSRFRLEVTTGEMLDA 191
Cdd:TIGR02959   1 WDEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDGQK-IQSWLYQIARNTIIDFYRSKSRSVELPESLLAAD 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1903802017 192 NEVERSPEDSVLESLSNaalleAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAvRTLARLLPEDA 269
Cdd:TIGR02959  80 SAREETFVKELSQCIPP-----MIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRG-RKKLKELLETC 151
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 83-268 3.53e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 55.74  E-value: 3.53e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  83 RPTADSDQarmmDLVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRdFGAWL 162
Cdd:PRK11922   11 PLSAASDR----ELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDAS-LSTWL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 163 VTIARNLVADHFKSSRFRLEVTT---------GEMLDANEVERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQG 233
Cdd:PRK11922   86 SRIVLNEALGRLRRRRRLVNLAEmvmastiagGERTPLADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRVVEE 165

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1903802017 234 LSVAETARVMGKNEGAIKTLQYRAVRTLARLLPED 268
Cdd:PRK11922  166 LSVEETAQALGLPEETVKTRLHRARRLLRESLARE 200
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 85-265 4.55e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 54.68  E-value: 4.55e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  85 TADSDQARMMDLVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRDFGAWLVT 164
Cdd:PRK12534    4 IPGHDDDETGRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGLTWLAM 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 165 IARNLVADHFKS-SRFRLEVTTGEMLDANEVERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVM 243
Cdd:PRK12534   84 IARNKAIDHLRAnAPQRRNVALDDAGELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAART 163

                         170       180
                  ....*....|....*....|..
gi 1903802017 244 GKNEGAIKTLQYRAVRTLARLL 265
Cdd:PRK12534  164 DTPIGTVKSWIRRGLAKLKACL 185
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 127-265 3.84e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 52.20  E-value: 3.84e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 127 VGGKATAEDLTSETFLRaLRRISTFTWQGR-DFGAWLVTIARNLVADHFKSSRfRLEVTTGEMLDANEVERSPEDSVLES 205
Cdd:PRK12524   47 LGDRAEAEDVTQEAMLR-LWRIAPDWRQGEaRVSTWLYRVVCNLCTDRLRRRR-RASVDLDDAPEPADAAPGAEEALIEG 124

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 206 LSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTLARLL 265
Cdd:PRK12524  125 DRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRALAALL 184
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 111-257 4.83e-08

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 53.00  E-value: 4.83e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 111 LYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRalrristftWQG------RDFGAWLVTIARNLVADHFKSSRFRLEVT 184
Cdd:PRK09636    9 EFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR---------WNNadraqiRDPRAWLTRVVTRLCLDRLRSARHRRETY 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1903802017 185 TGEMLDANEVERS--PEDSVL--ESLSNAALLeAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRA 257
Cdd:PRK09636   80 VGPWLPEPVVEELddPLEAVVaaEDLSLALML-ALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRA 155
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 96-265 8.77e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 50.87  E-value: 8.77e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  96 LVERAQAGEAEAFGRLYDQYSDTVyRYIYYRVGGKATAEDLTSETFLRALRRISTFtwQGRD-FGAWLVTIARNLVADhf 174
Cdd:PRK12518    1 LILRCQRGDRQSFRQLYRRYQQKV-RSTLYQLCGRELLDDLVQEVFLRVWKGLPKL--RNPAyFSTWLYRITWNVATD-- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 175 ksSRFRLevttgemldANEVERSPEDSVLESLSNAALLEAVRKLNPQ---QQECVTLRF----------LQGLSVAETAR 241
Cdd:PRK12518   76 --ARRQF---------AQRPSRIQDDSLNDQPSRPSDTPDLMQLHYQdlvQQGLQTLSLehravlvlhdLEDLPQKEIAE 144

                         170       180
                  ....*....|....*....|....
gi 1903802017 242 VMGKNEGAIKTLQYRAVRTLARLL 265
Cdd:PRK12518  145 ILNIPVGTVKSRLFYARRQLRKFL 168
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 86-265 1.05e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 50.82  E-value: 1.05e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  86 ADSDQARMMDLVERAQAGEAEAFGRLYDQYSDTVYRYIYYR-VGGKATAEDLTSETFLRALRRISTFTwQGRDFGAWLVT 164
Cdd:PRK12536    1 LSAAEARLRALLLRGLAGDAAAYRQFLSELAAHLRGFLRRRlPQLPDEVEDLVQEILLAVHNARHTYR-ADQPLTAWVHA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 165 IARNLVADHFKSsRFRLEVTTGEMLDANEVERSPEDSVLESLSN-AALLEavrKLNPQQQECVTLRFLQGLSVAETARVM 243
Cdd:PRK12536   80 IARYKLMDFLRS-RARREALHDPLDDESELFATSDDEAAEARRDlGKLLE---QLPDRQRLPIVHVKLEGLSVAETAQLT 155

                         170       180
                  ....*....|....*....|..
gi 1903802017 244 GKNEGAIKTLQYRAVRTLARLL 265
Cdd:PRK12536  156 GLSESAVKVGIHRGLKALAAKI 177
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
83-252 1.11e-07

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 50.82  E-value: 1.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  83 RPTADSDQARMMDLVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRDFGAWL 162
Cdd:PRK09646    7 MTGPPAESPDLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARGSALAWL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 163 VTIARNLVADHFKSSRF--RLEVTTGEMLDANEVERSPEdSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETA 240
Cdd:PRK09646   87 LTLAHRRAVDRVRSEQAasQREVRYGARNVDPAFDQVAE-EVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVA 165

                         170
                  ....*....|..
gi 1903802017 241 RVMGKNEGAIKT 252
Cdd:PRK09646  166 ERLAVPLGTVKT 177
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 111-256 1.28e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 50.25  E-value: 1.28e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 111 LYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQgRDFGAWLVTIARNLVADHFKSSRFRLEVTT----- 185
Cdd:PRK12522    8 LIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYV-ENYKKWITTICVRTFYDFYRKKKRWKDRILdlfhk 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1903802017 186 ---GEMLDANEVERSPEdsVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGaikTLQYR 256
Cdd:PRK12522   87 edgGEIEFADDVNISEE--FIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIG---TVKYR 155
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 124-259 1.35e-07

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 51.51  E-value: 1.35e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 124 YYRVGGKATAEDLTSETFLRALRRISTftwQGRDFGAWLVTIARNLVADHFKSSRFRLEVT--TGEMLDANEVERS--PE 199
Cdd:PRK09635   23 FRMVGDIGVAEDMVQEAFSRLLRAPVG---DIDDERGWLIVVTSRLCLDHIKSASTRRERPqdIAAWHDGDASVSSvdPA 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1903802017 200 DSV-LESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVR 259
Cdd:PRK09635  100 DRVtLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARR 160
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 214-261 1.53e-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. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 47.04  E-value: 1.53e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1903802017 214 AVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTL 261
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKL 48
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 95-251 1.74e-07

ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.


Pssm-ID: 254323 [Multi-domain]  Cd Length: 185  Bit Score: 50.11  E-value: 1.74e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  95 DLVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTS-----ETFLRALRRISTFTWQGRD-FGAWLVTIARN 168
Cdd:pfam07638   6 QLLQQVKDGDAAATEQLLPLVYDELRRLAGSKLQNERRGHTLQPtalvhEAFVRLVDTEDFPDWSGRGhFFAAAAEAMRR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 169 LVADHFKSSRFRL---EVTTGEMLDANEVERSPEDSVLESLSNAalLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGK 245
Cdd:pfam07638  86 ILIDHARRRQRQKrggDVQRRELDEVVDNGDSPNPDLLLDLDEA--LEQLFSLSPRQARLVELRFFAGLSNDEIAERLGV 163


                  ....*.
gi 1903802017 246 NEGAIK 251
Cdd:pfam07638 164 SERTVE 169
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 131-265 2.27e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 49.84  E-value: 2.27e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 131 ATAEDLTSETFLRALRRISTFTwQGRDFGAWLVTIARNLVADHFKSSRFRLEVTTGEMLdANEVERSPEDSVLEsLSNAA 210
Cdd:PRK12546   32 AVADDLVQDTIVKAWTNFDKFQ-EGTNLRAWLFTILRNTFYSDRRKHKREVPDPEGVHA-ASLAVKPAHDGRLA-MSDFR 108

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1903802017 211 llEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTLARLL 265
Cdd:PRK12546  109 --AAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 87-257 2.59e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 49.90  E-value: 2.59e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  87 DSDQARMMDLVERAQAGEAEAFGRLYDQYSDTVYRYIYYrVGGKATAEDLTSETFLRALRRISTFTwqGRDFG-AWLVTI 165
Cdd:PRK12535    6 ERDDAHVTDLALAAGRGDRAALTEFIRETQDDVWRLLAH-LGGHDIADDLTQETYLRVMSALPRFA--ARSSArTWLLSL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 166 ARNLVADHFKSSRFRLEVTTGEMLDANEVERSPEDSVL--ESLSNAALLEAvrkLNPQQQECVTLRFLQGLSVAETARVM 243
Cdd:PRK12535   83 ARRVWVDNIRHDMARPRKSATEYEDAAATTASNETTGSwsEWIDVRTLIDA---LPPERREALILTQVLGYTYEEAAKIA 159

                         170
                  ....*....|....
gi 1903802017 244 GKNEGAIKTLQYRA 257
Cdd:PRK12535  160 DVRVGTIRSRVARA 173
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 100-244 8.36e-07

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 47.92  E-value: 8.36e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 100 AQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTwqGRDFGAWLVTIARNLVADHFKssRF 179
Cdd:PRK12523    4 AQSPHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGRPELPT--PREPRAFLAAVAKGLMFDHFR--RA 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1903802017 180 RLE-VTTGEMLDANEVER-SPEDS--VLESLSnaALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMG 244
Cdd:PRK12523   80 ALEqAYLAELALVPEAEQpSPEEQhlILEDLK--AIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLG 146
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 83-270 1.50e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 47.93  E-value: 1.50e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  83 RPTADSDQARMMDLVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTftWQ-GR-DFGA 160
Cdd:PRK12538   40 PPVADAVFDEDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGR--WQhGRaKFST 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 161 WLVTIARNLVADHFKSSRFRLEVTTGEMLDAneveRSPEDSVLESLSNAALLE-AVRKLNPQQQECVTLRFLQGLSVAET 239
Cdd:PRK12538  118 WLYRVVSNRCIDLRRKPRTENVDAVPEVADG----KPDAVSVIERNELSDLLEaAMQRLPEQQRIAVILSYHENMSNGEI 193

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1903802017 240 ARVMGKNEGAIKTLQYRAVRTLARLLPEDAR 270
Cdd:PRK12538  194 AEVMDTTVAAVESLLKRGRQQLRDLLRRHER 224
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 113-244 2.31e-06

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 46.31  E-value: 2.31e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 113 DQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRIS-TFTWQGRdfgAWLVTIARNLVADHFKSSRFRlEVTTGEMLDA 191
Cdd:PRK12527    2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSsAQIEHPR---AFLYRTALNLVVDRHRRHRVR-QAEPLEVLDE 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1903802017 192 NEVERSPEDSVLESLSNA-ALLE-AVRKLNPQQQECVTLRFLQGLSVAETARVMG 244
Cdd:PRK12527   78 EERLHSPSPQTRLDLGQRlALLQrALAELPPACRDSFLLRKLEGLSHQQIAEHLG 132
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
93-270 3.15e-06

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 47.62  E-value: 3.15e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  93 MMDLVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFtwQGR-DFGAWLVTIARNLVA 171
Cdd:PRK08241    6 AAALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRF--EGRsSLRTWLYRIATNVCL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 172 DHFKSSRFR---LEVTTGEMLDANEVERSPEDSVLESLSNAALL-------------EAVR--------KLNPQQQECVT 227
Cdd:PRK08241   84 DALEGRARRplpTDLGAPAADPVDELVERPEVPWLEPYPDALLDpaaadpaarvvarESVRlafvaalqHLPPRQRAVLI 163

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1903802017 228 LRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTLARLLPEDAR 270
Cdd:PRK08241  164 LRDVLGWSAAEVAELLDTSVAAVNSALQRARATLAERGPSAAD 206
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 95-250 3.64e-06

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 46.47  E-value: 3.64e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  95 DLVERAQAGEAEAFGRLYDQYSDTVYrYIYYRVGGKATAEDLTSE----TFLRALRRISTFTWQGRDFGAWLVTIARNLV 170
Cdd:PRK06811    7 NFIKELKKKNEKALEFIVDTYGNLVK-KIVHKVLGTVNYSQLIEEcvndIFLSIWNNIDKFDEEKGSFKKWIAAISKYKA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 171 ADHFKSSRFRLEVTTGEMLDANEVERSPEDSVLESLSNaALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAI 250
Cdd:PRK06811   86 IDYKRKLTKNNEIDSIDEFILISEESIENEIILKENKE-EILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAI 164
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
96-270 1.80e-05

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 44.34  E-value: 1.80e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  96 LVERAQAGEAEAFGRLYDQYSDTV---YRYIYYRVGGKAT-AEDLTSETFLRALRRISTFTwQGRDFGAWLVTIARNLVA 171
Cdd:PRK12539   11 LMLASLDGDAAAHRALLERLSGHLrayYKGKLARIGRGAEeAEDLVQEALMAIHTRRHTYD-PEQPLTPWVYAIARYKLI 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 172 DHFKSSRFRLEVTTGEmlDANEVERSPEDSVLESLSNAALLeaVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIK 251
Cdd:PRK12539   90 DHLRRTRASLADVPID--DADELVAHDDHAAVESTLDLGRL--LARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVK 165

                         170
                  ....*....|....*....
gi 1903802017 252 TLQYRAVRTLARLLPEDAR 270
Cdd:PRK12539  166 VSVHRGLKALAALIGRETQ 184
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 95-261 2.47e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 44.15  E-value: 2.47e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  95 DLVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRDFGAWLVTIARNLVADHF 174
Cdd:PRK12531   16 ECMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKSALSTWIYTIIRNLCFDLL 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 175 KSSRFR-LEVTTGEMLDANE-----VER-SPEDSVLESlsnaALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNE 247
Cdd:PRK12531   96 RKQKGKdLHIHADDIWPSDYyppdlVDHySPEQDMLKE----QVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPL 171

                         170
                  ....*....|....
gi 1903802017 248 GAIKTLQYRAVRTL 261
Cdd:PRK12531  172 GTVKSRLRLAVEKL 185
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 96-264 6.12e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 42.87  E-value: 6.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  96 LVERAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTwqgRDFGA---WLVTIARNLVAD 172
Cdd:PRK12526   28 LILVAISRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYN---GDKGAattWVYTVMRNAAFD 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 173 HFKSSRFRLEVTTGEmlDANEVERSPEDSVLES------LSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKN 246
Cdd:PRK12526  105 MLRKIKAKKEQNLGD--DIWPIEQALAESQSESeefsdhLMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVP 182

                         170
                  ....*....|....*...
gi 1903802017 247 EGAIKTlqyRAVRTLARL 264
Cdd:PRK12526  183 LGTVKS---RLRLALAKL 197
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 99-270 6.48e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 42.79  E-value: 6.48e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017  99 RAQAGEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFtwQGRDFGAWLVTIARNlvaDHFKSSR 178
Cdd:PRK12533   11 MDAAARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSF--RGDNARPWLLAIVRH---TWYSEWR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 179 FRLEVTTGEMLDANEVERSPEDSVLESLSNAALL----------EAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEG 248
Cdd:PRK12533   86 RRANAHEVAAPDTLDDADSLDDWQPAGEDPLALLlraedvrlvnAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVG 165

                         170       180
                  ....*....|....*....|..
gi 1903802017 249 AIKTLQYRAVRTLARLLPEDAR 270
Cdd:PRK12533  166 TVMSRLARARRRLAALLGGASA 187
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 131-264 8.05e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 42.47  E-value: 8.05e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 131 ATAEDLTSETFLRALRRISTFTwQGRDFGAWLVTIARNLVADHFKSSRFRLEVTTGEMLDANEVERSPEDSvleSLSNAA 210
Cdd:PRK12511   29 AEAEDLVHDALVRALERRASFR-SGGNLRTWLMSILHNAFIDELRRRRVEARRADELAVLADASLPAAQEH---AVRLAQ 104

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1903802017 211 LLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGaikTLQYRAVRTLARL 264
Cdd:PRK12511  105 IRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIG---TLMSRIGRARAAL 155
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 111-244 9.77e-05

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 41.89  E-value: 9.77e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 111 LYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRdFGAWLVTIARNLVADHF-KSSRFrlevttgEML 189
Cdd:PRK09637    6 IWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSS-IKSWLYQIANNTIIDFYrKKNRS-------EEL 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1903802017 190 DANEV--ERSPEDSVLESLSnAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMG 244
Cdd:PRK09637   78 PDDLLfeDEEREENAKKELA-PCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLG 133
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 127-265 9.99e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 42.26  E-value: 9.99e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 127 VGGKATAEDLTSETFLRALRRISTFTwQGRDFGAWLVTIARN-LVADHFKSSRfrlEVTTGEMLDANEVERSPEDsvLES 205
Cdd:PRK12516   31 IGRHDRADDLVQDTIMKAWAKQDHFE-VGTNMKAWLFTILRNeFYSQMRKRGR---EVQDTDGMFTEQLAVHPSQ--YGT 104

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 206 LSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTLARLL 265
Cdd:PRK12516  105 LDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEIL 164
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 133-265 1.08e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 41.79  E-value: 1.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 133 AEDLTSETFLRALRRISTFTwQGRDFGAWLVTIARNLVADHFKSSRFRLEVTTGEMLDANEVERSPEDSV-LESLSnaal 211
Cdd:PRK12547   33 AEDLVQDTLMKAWAKQDSFE-MGTNLKAWLFTILRNEFYSQMRKRGREVQDSDGVFTARVAVHPAQYGSLdLQDFK---- 107

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1903802017 212 lEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTLARLL 265
Cdd:PRK12547  108 -KALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 106-265 1.48e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 41.58  E-value: 1.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 106 EAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFL---RALRRISTFTWQgrDFGAWLVTIARNLVADHFKSSRFR-- 180
Cdd:PRK12542    9 EKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFItlyKNLEKLHSLNTQ--ELKRYILRVAKNKAIDSYRKNKRHet 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 181 -LEVTTGEMLDAneVERSPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVR 259
Cdd:PRK12542   87 fLEEYERESIEA--VDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARK 164


                  ....*.
gi 1903802017 260 TLARLL 265
Cdd:PRK12542  165 RVQNMI 170
PRK06704 PRK06704
RNA polymerase subunit sigma-70;
111-268 1.99e-04

RNA polymerase subunit sigma-70;


Pssm-ID: 180663 [Multi-domain]  Cd Length: 228  Bit Score: 41.55  E-value: 1.99e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 111 LYDQYSDtVYRYIYYRVGGKATAEDLTSETFLRALRRISTftwqgRDFGAWLV-TIARNLVADHFKSSrfrlevTTGEML 189
Cdd:PRK06704   23 LIEQYGE-LKRYCTFLTKNKWDGEDLAQETVCKVLQKYSN-----KDICMTLVyKIARNRWLDQIKSK------SVHEKI 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 190 DANEVERSPEDSVleslsnAALLEAVRK----LNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTLARLL 265
Cdd:PRK06704   91 RDQITFEEPHEKI------ADLHEMVGKvlssLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVS 164


                  ...
gi 1903802017 266 PED 268
Cdd:PRK06704  165 EEG 167
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 197-244 2.26e-04

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


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 41.35  E-value: 2.26e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1903802017 197 SPEDSVLESLSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMG 244
Cdd:COG1191   166 DPEEELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLG 213
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 103-261 4.66e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 40.15  E-value: 4.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 103 GEAEAFGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWQGRDFGAWLVTIAR----NLVADHfkssr 178
Cdd:PRK12537   20 GDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARGSARGWIYSVTRhlalNVLRDT----- 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 179 fRLEVTTGEmlDANEVERSPE--DSVLESLSNAA-LLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQY 255
Cdd:PRK12537   95 -RREVVLDD--DAEETAQTLHeiIDDFDLWANSGkIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIK 171


                  ....*.
gi 1903802017 256 RAVRTL 261
Cdd:PRK12537  172 RSLKAL 177
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 109-267 5.16e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 39.93  E-value: 5.16e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 109 GRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWqgRDFGAWLVTIARNLVADHFKssRFRLEVTTGEM 188
Cdd:PRK12525   12 GQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI--REPRALLTTIARRLMYEGWR--RQDLERAYLQS 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 189 L-DANE-VERSPEDS--VLESLsnAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTLARL 264
Cdd:PRK12525   88 LaEAPEaVQPSPEEQwmVIETL--LAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQG 165


                  ...
gi 1903802017 265 LPE 267
Cdd:PRK12525  166 FQE 168
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 129-190 3.30e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 37.60  E-value: 3.30e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1903802017 129 GKATAEDLTSETFLRALRRISTFtwQGRD-FGAWLVTIARNLVADHFKSSRFRLEVTT---GEMLD 190
Cdd:PRK12532   29 HPDLAEDLVQETLLSAYSAGDSF--QGRAlVNSWLFAILKNKIIDALRQIGRQRKVFTlldDELLD 92
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 108-258 3.59e-03

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 37.48  E-value: 3.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1903802017 108 FGRLYDQYSDTVYRYIYYRVGGKATAEDLTSETFLRALRRISTFTWqgRDFGAWLVTIARNLVADHFKssRFRLEVTTGE 187
Cdd:PRK09651   12 FESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTI--RDPRSFLCTIAKRVMVDLFR--RNALEKAYLE 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1903802017 188 MLdANEVER---SPE--DSVLESLSNAALLeaVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAV 258
Cdd:PRK09651   88 ML-ALMPEGgapSPEerESQLETLQLLDSM--LDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAT 160
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
197-261 8.07e-03

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 36.85  E-value: 8.07e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1903802017 197 SPEDSVLES-LSNAALLEAVRKLNPQQQECVTLRFLQGLSVAETARVMGKNEGAIKTLQYRAVRTL 261
Cdd:PRK08215  188 SDEKNKDENwLEEIALKEAMKKLNDREKLILNLRFFQGKTQMEVAEEIGISQAQVSRLEKAALKHM 253
 
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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