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Conserved domains on  [gi|2276593057|ref|WP_255250719|]
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MULTISPECIES: sigma-70 family RNA polymerase sigma factor [Mycobacterium avium complex (MAC)]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 11484444)

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 Mycobacterium tuberculosis extracytoplasmic function (ECF) RNA polymerase sigma factor SigL

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
3-175 7.72e-98

ECF RNA polymerase sigma factor SigL;


:

Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 280.04  E-value: 7.72e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   3 RASGTAEAALMKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDTERSARAWLFTVARNMIIDDRRSA 82
Cdd:PRK09645    1 SGMATAEAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRSARAWLFTVARNLVIDERRSA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  83 RFRNVVGSTDTAGAPEQSTPDEVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVR 162
Cdd:PRK09645   81 RARPVEGGDDVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALR 160

                         170
                  ....*....|...
gi 2276593057 163 ALRLTLQELGVTR 175
Cdd:PRK09645  161 ALRLALQERGVTR 173
 
Name Accession Description Interval E-value
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
3-175 7.72e-98

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 280.04  E-value: 7.72e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   3 RASGTAEAALMKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDTERSARAWLFTVARNMIIDDRRSA 82
Cdd:PRK09645    1 SGMATAEAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRSARAWLFTVARNLVIDERRSA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  83 RFRNVVGSTDTAGAPEQSTPDEVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVR 162
Cdd:PRK09645   81 RARPVEGGDDVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALR 160

                         170
                  ....*....|...
gi 2276593057 163 ALRLTLQELGVTR 175
Cdd:PRK09645  161 ALRLALQERGVTR 173
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-174 3.16e-39

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: 131.66  E-value: 3.16e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   1 MSRASGTAEAALmKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIgDTERSARAWLFTVARNMIIDD-R 79
Cdd:COG1595     8 LERLRAGDEAAF-EELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSF-RGRGSFRAWLYRIARNLAIDHlR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  80 RSARFRNVVGSTDTAGAPEQSTPDE-VNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLH 158
Cdd:COG1595    86 KRRRRRELLDELAEELPDEAADPEEaLEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLS 165

                         170
                  ....*....|....*.
gi 2276593057 159 YAVRALRLTLQELGVT 174
Cdd:COG1595   166 RARKKLREALEEEGAL 181
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 15-168 1.50e-33

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: 116.29  E-value: 1.50e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  15 ALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIgDTERSARAWLFTVARNMIIDDRRSARFRNVVGSTDTA 94
Cdd:TIGR02937   5 ELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRF-DPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEE 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2276593057  95 GAPEQSTPDE-VNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTL 168
Cdd:TIGR02937  84 LLDSDPSPEEeLEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 16-85 9.73e-14

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: 62.61  E-value: 9.73e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2276593057  16 LYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVI-GDTERSARAWLFTVARNMIIDDRRSARFR 85
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFdPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 111-165 1.11e-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: 54.42  E-value: 1.11e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2276593057 111 RLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALR 165
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 135-164 7.22e-03

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 33.27  E-value: 7.22e-03
                           10        20        30
                   ....*....|....*....|....*....|
gi 2276593057  135 RGWTTAQIATDLGIAEGTVKSRLHYAVRAL 164
Cdd:smart00421  17 EGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
 
Name Accession Description Interval E-value
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
3-175 7.72e-98

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 280.04  E-value: 7.72e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   3 RASGTAEAALMKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDTERSARAWLFTVARNMIIDDRRSA 82
Cdd:PRK09645    1 SGMATAEAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRSARAWLFTVARNLVIDERRSA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  83 RFRNVVGSTDTAGAPEQSTPDEVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVR 162
Cdd:PRK09645   81 RARPVEGGDDVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALR 160

                         170
                  ....*....|...
gi 2276593057 163 ALRLTLQELGVTR 175
Cdd:PRK09645  161 ALRLALQERGVTR 173
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-174 3.16e-39

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: 131.66  E-value: 3.16e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   1 MSRASGTAEAALmKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIgDTERSARAWLFTVARNMIIDD-R 79
Cdd:COG1595     8 LERLRAGDEAAF-EELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSF-RGRGSFRAWLYRIARNLAIDHlR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  80 RSARFRNVVGSTDTAGAPEQSTPDE-VNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLH 158
Cdd:COG1595    86 KRRRRRELLDELAEELPDEAADPEEaLEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLS 165

                         170
                  ....*....|....*.
gi 2276593057 159 YAVRALRLTLQELGVT 174
Cdd:COG1595   166 RARKKLREALEEEGAL 181
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 15-168 1.50e-33

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: 116.29  E-value: 1.50e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  15 ALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIgDTERSARAWLFTVARNMIIDDRRSARFRNVVGSTDTA 94
Cdd:TIGR02937   5 ELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRF-DPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEE 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2276593057  95 GAPEQSTPDE-VNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTL 168
Cdd:TIGR02937  84 LLDSDPSPEEeLEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 16-169 7.21e-33

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 115.07  E-value: 7.21e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  16 LYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDtERSARAWLFTVARNMIIDDRRSARFRNVVGSTDTAG 95
Cdd:PRK11924   18 LFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNG-KGSARTWLLTIARNVCYDLLRRRRREKAVLSDDALE 96

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2276593057  96 APEQSTPDEVNAALDRL----LIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTLQ 169
Cdd:PRK11924   97 PEFAETAETPEAALLAKddlaRIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLE 174
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 14-165 1.33e-27

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: 101.10  E-value: 1.33e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  14 KALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIgDTERSARAWLFTVARNMIIDD-RRSARFRNVVGSTD 92
Cdd:TIGR02985   4 EQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETL-EISESIKAYLFTIVKNRCLNYlRHKQVEEKYQEELA 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2276593057  93 TAGAPEQSTPDEVNAALDR---LLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALR 165
Cdd:TIGR02985  83 EIEERELSEADPEEELEAKeleEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLR 158
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 16-171 5.40e-25

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 94.87  E-value: 5.40e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  16 LYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHpevIG--DTERSARAWLFTVARNMIIDDRRSARfRNVVGSTDT 93
Cdd:PRK09652   15 LVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRA---LHsfRGGAAFYTWLYRIARNTAINYLRKQG-RRPPASDVD 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  94 AGAPEQ----------STPDEVnaALDRLL---IADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYA 160
Cdd:PRK09652   91 AEEAEDfdladalrdiSTPENE--LLSAELeqrVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRA 168

                         170
                  ....*....|.
gi 2276593057 161 VRALRLTLQEL 171
Cdd:PRK09652  169 REALRAKLQPL 179
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 9-165 3.18e-24

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 92.78  E-value: 3.18e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   9 EAALMKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQH-----PEVIGDTersaraWLFTVARNMIIDD-RRSA 82
Cdd:PRK09638   16 DDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENlssfqGRSKFST------WLISIASRLYKDHlRKQK 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  83 RFRNVVGS-TDTAGAPEQSTPDEVNAALDRLLiaDAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAV 161
Cdd:PRK09638   90 REKLRLQRaKEETLRKEKWEAAIKGAEWSEML--DALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGI 167


                  ....
gi 2276593057 162 RALR 165
Cdd:PRK09638  168 KQLR 171
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 9-171 3.83e-24

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 93.20  E-value: 3.83e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   9 EAALMKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVigDTER-SARAWLFTVARNMIIDD----RRSAR 83
Cdd:PRK12519   27 QSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSSY--DPKRgSLSSYLLTLTRSRAIDRlrsrRSRQR 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  84 FRNVVGSTDTAGAPEQSTPDEVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRA 163
Cdd:PRK12519  105 LLERWQQELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLK 184


                  ....*...
gi 2276593057 164 LRLTLQEL 171
Cdd:PRK12519  185 LRELLQDL 192
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 9-175 5.59e-23

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 90.13  E-value: 5.59e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   9 EAALMKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLR------AWQHpevigdtERSARAWLFTVARNMIIDDRRSA 82
Cdd:PRK12513   24 DAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRviraraQYQP-------RARFRTWLYQIARNLLIDHWRRH 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  83 RFRNV----VGSTDTAGAPEQSTPD-EVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRL 157
Cdd:PRK12513   97 GARQApsldADEQLHALADDGAAPEqQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRL 176

                         170
                  ....*....|....*...
gi 2276593057 158 HYAVRALRLTLQELGVTR 175
Cdd:PRK12513  177 RYALQKLRELLAEEVAVA 194
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 9-170 7.36e-20

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 81.88  E-value: 7.36e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   9 EAALMKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDTERSARAWLFTVARNMIIDD--RRSARFRN 86
Cdd:PRK13919   21 EEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRGSARAWLLALAHHAAVDHvrRRAARPQP 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  87 VVGSTDTAGAPEQSTP--DEvNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRAL 164
Cdd:PRK13919  101 LEPDEREPEAFDLPGPglDE-EGHLDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRL 179


                  ....*.
gi 2276593057 165 RLTLQE 170
Cdd:PRK13919  180 KEVLRE 185
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 15-165 1.61e-19

RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.


Pssm-ID: 132028 [Multi-domain]  Cd Length: 162  Bit Score: 80.51  E-value: 1.61e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  15 ALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDtERSARAWLFTVARNMIIDDRRSARFRNVVgstdTA 94
Cdd:TIGR02983  10 AFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD-PDAPDAYVRRVLVNLARSRWRRRRLLELP----TR 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2276593057  95 GAPEQSTPDEVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALR 165
Cdd:TIGR02983  85 ELPDAAAPDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLR 155
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 34-173 3.81e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 77.07  E-value: 3.81e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  34 DASQSEDVVQETLLRAWQH-PEVIGDTERSAraWLFTVARNMIIDDRRSA---RFRNVVGSTDTAGAPEQSTPDevnaaL 109
Cdd:PRK12518   33 GRELLDDLVQEVFLRVWKGlPKLRNPAYFST--WLYRITWNVATDARRQFaqrPSRIQDDSLNDQPSRPSDTPD-----L 105

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2276593057 110 DRL----LIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTLQELGV 173
Cdd:PRK12518  106 MQLhyqdLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQGV 173
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 13-175 7.16e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 76.69  E-value: 7.16e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  13 MKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAW-QHPEVIGDTERSAraWLFTVARNMIIDDRRSARFRNVVGST 91
Cdd:PRK12515   24 MQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWrQAGQFEGRSQVST--WLLSIARFKALSALRRRKHEEIDDEA 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  92 DTAGAPEQSTPDevnAALDRLLIADAM----AQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLT 167
Cdd:PRK12515  102 AAAIEDGADTPE---VALQKSDTSAALraclAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAEL 178


                  ....*...
gi 2276593057 168 LQELGVTR 175
Cdd:PRK12515  179 LKAAGVER 186
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
15-174 2.36e-17

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 75.48  E-value: 2.36e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  15 ALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDTERSARAWLFTVARNMIIDDRRS---ARFRNV-VGS 90
Cdd:PRK09646   34 ELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARGSALAWLLTLAHRRAVDRVRSeqaASQREVrYGA 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  91 TDTAGAPEQSTpDEVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRltlQE 170
Cdd:PRK09646  114 RNVDPAFDQVA-EEVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGLIRLR---DC 189


                  ....
gi 2276593057 171 LGVT 174
Cdd:PRK09646  190 LGVS 193
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 16-165 3.53e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 71.51  E-value: 3.53e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  16 LYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDTErsARAWLFTVARNMIIDDRRSARFRNVVGSTDTAG 95
Cdd:PRK12541   10 IYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEE--IRPWLFTIAYNAFIDWYRKEKKYKTTTIEEFHL 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2276593057  96 APEQSTPDE--VNAALDRLLiaDAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALR 165
Cdd:PRK12541   88 PNVPSTEHEyfIKHEIASWL--DSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETK 157
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 11-170 3.29e-15

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 69.39  E-value: 3.29e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  11 ALMKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIgDTERSARAWLFTVARNMIIDDRRSARFRNVVGS 90
Cdd:PRK09415   16 DLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTY-KGKSSLKTWLYRIAINHCKDYLKSWHNKKVIVT 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  91 TDTA---GAPEQSTPDEVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLT 167
Cdd:PRK09415   95 EDIFtymESQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKG 174


                  ...
gi 2276593057 168 LQE 170
Cdd:PRK09415  175 LEE 177
SigZ TIGR02959
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 17-165 3.51e-15

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: 69.32  E-value: 3.51e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  17 YDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQH-PEVIGDTERsaRAWLFTVARNMIIDDRRSARFRNVVGSTDTA- 94
Cdd:TIGR02959   1 WDEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNlPSLKDGQKI--QSWLYQIARNTIIDFYRSKSRSVELPESLLAa 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2276593057  95 -GAPEQSTPDEVNAALDRLLiadamAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALR 165
Cdd:TIGR02959  79 dSAREETFVKELSQCIPPMI-----KELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLK 145
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 3-175 1.43e-14

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 67.75  E-value: 1.43e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   3 RASGTAEAALMKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDTERSARAWLFTVARNMIIDDRRSA 82
Cdd:PRK05602   12 ARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGEARFDTWLHRVVLNLCYDRLRRR 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  83 RFrnvvgsTDTAGAPEQstPDEVNAALDRL-------LIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKS 155
Cdd:PRK05602   92 RE------VPVEDAPDV--PDPAPGPDAGLearqrarRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALES 163

                         170       180
                  ....*....|....*....|
gi 2276593057 156 RLHYAVRALRLTLQELGVTR 175
Cdd:PRK05602  164 LLARGRRALRAQLADLPGSE 183
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 16-169 1.74e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 67.54  E-value: 1.74e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  16 LYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDTERSARAWLFTVARNMIIDDRRSARFRNVvgSTDTAG 95
Cdd:PRK12514   24 LYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPMTWLITIARNHAIDRLRARKAVAV--DIDEAH 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2276593057  96 APEQSTPD---EVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTLQ 169
Cdd:PRK12514  102 DLADPSPGpeaEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKLRECLS 178
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 11-160 6.37e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 66.25  E-value: 6.37e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  11 ALMKALYDEhaavLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDtERSARAWLFTVARnmiiddRRSAR------F 84
Cdd:PRK12517   27 ALVKALHAD----IYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKD-EKAAKAWLITILR------RENARrferkqF 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2276593057  85 RNVVGSTDTAGAPEQSTPDEvnaALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYA 160
Cdd:PRK12517   96 DLVDIEDDSIEDDASHSSEE---EMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRA 168
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 16-85 9.73e-14

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: 62.61  E-value: 9.73e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2276593057  16 LYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVI-GDTERSARAWLFTVARNMIIDDRRSARFR 85
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFdPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 19-169 1.99e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 64.86  E-value: 1.99e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  19 EHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDTErSARAWLFTVARNMIIDDRRSArfRNVVGSTDTAGAPE 98
Cdd:PRK12546   15 EHLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGT-NLRAWLFTILRNTFYSDRRKH--KREVPDPEGVHAAS 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2276593057  99 QSTPDEVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTLQ 169
Cdd:PRK12546   92 LAVKPAHDGRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 3-165 2.75e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 64.41  E-value: 2.75e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   3 RASGTAEAALMKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDTERSARAWLFTVAR----NMIIDD 78
Cdd:PRK12537   15 LACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARGSARGWIYSVTRhlalNVLRDT 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  79 RRSARFRNvvGSTDTAGAPEQSTPD-EVNAALDRllIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRL 157
Cdd:PRK12537   95 RREVVLDD--DAEETAQTLHEIIDDfDLWANSGK--IHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWI 170


                  ....*...
gi 2276593057 158 HYAVRALR 165
Cdd:PRK12537  171 KRSLKALR 178
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 26-170 3.75e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 64.44  E-value: 3.75e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  26 RYALRLTGDASQSEDVVQETLLRAWQHPEVIGDTERSARAWLFTVARNMIIDDRRSARFRNVVGSTD------TAGAPEQ 99
Cdd:PRK12526   53 RFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKGAATTWVYTVMRNAAFDMLRKIKAKKEQNLGDdiwpieQALAESQ 132

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2276593057 100 STPDEVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTLQE 170
Cdd:PRK12526  133 SESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMGE 203
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 16-170 9.88e-13

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 62.59  E-value: 9.88e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  16 LYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEviGDTERSARAWLFTVARNMIIDDRRSARfRNVVGSTDTAG 95
Cdd:PRK09644    6 IYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLE--DYDNQKVKPWLFKVAYHTFIDFVRKEK-KVSFVGTDEIE 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2276593057  96 APEQSTPDEVNAALD-RLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTLQE 170
Cdd:PRK09644   83 AIQAESTEEYVVAKNsYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 24-171 1.41e-12

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 62.79  E-value: 1.41e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  24 LWRYALRLTGDASQSEDVVQETLLRAWQHPEVIgDTERSARAWLFTVARNMIIDDRRSAR----FRNVVGSTD------T 93
Cdd:PRK09641   31 IYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSY-DINRKFSTWLYRIATNLTIDRLRKRKpdyyLDAEVAGTEgltmysQ 109

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2276593057  94 AGAPEQSTPDEVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTLQEL 171
Cdd:PRK09641  110 LAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREALRKQLRHL 187
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 5-165 1.51e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 62.44  E-value: 1.51e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   5 SGTAEAalMKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIgDTERSARAWLFTVARNMIIDDRRSA-- 82
Cdd:PRK12543    3 SGDQEA--FSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKY-DSNRPFRFWLIGLVIKQIHSWRRKRwr 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  83 RFRNVVGSTDTAGAPEQSTPDEVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVR 162
Cdd:PRK12543   80 RFRIFEKAEEQRKPVSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALK 159


                  ...
gi 2276593057 163 ALR 165
Cdd:PRK12543  160 KLR 162
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 14-171 1.82e-12

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 61.89  E-value: 1.82e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  14 KALYDEHAAVLWRYALRLTGDASQSEDVVQETLLR----AWQHPEVIGdtersarAWLFTVARNMIIDDRRSA--RFRNV 87
Cdd:PRK09639    6 EDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRlyrsDFKGIENEK-------GWLIKSARNVAYNYLRSEkrRRARI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  88 VGSTDTAGAPEQSTPDE-VNAALDRLLIADAMAQLSAEHRAV-IERsyYRGWTTAQIATDLGIAEGTVKSRLHYAVRALR 165
Cdd:PRK09639   79 LGEFQWQEVDNEPSPEEiWIRKEEITKVQEVLAKMTERDRTVlLLR--FSGYSYKEIAEALGIKESSVGTTLARAKKKFR 156


                  ....*.
gi 2276593057 166 LTLQEL 171
Cdd:PRK09639  157 KIYEQM 162
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 20-169 2.48e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 62.26  E-value: 2.48e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  20 HAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDTERSARAWLFTVARNMIIDDRRSARFRNVVGSTDTAGAPEQ 99
Cdd:PRK12531   36 YAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKSALSTWIYTIIRNLCFDLLRKQKGKDLHIHADDIWPSDY 115

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2276593057 100 STPDEVN--AALDRLLIADAMA---QLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTLQ 169
Cdd:PRK12531  116 YPPDLVDhySPEQDMLKEQVMKfldRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMD 190
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 24-165 6.57e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 60.57  E-value: 6.57e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  24 LWRYALRLTGDASQSEDVVQETLLRAWQHPEVIgDTERSARAWLFTVARNMIIDDRRSARFRNVVGSTdTAGAPEQSTPD 103
Cdd:PRK12511   17 LRRYARSLTRDSAEAEDLVHDALVRALERRASF-RSGGNLRTWLMSILHNAFIDELRRRRVEARRADE-LAVLADASLPA 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2276593057 104 EVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALR 165
Cdd:PRK12511   95 AQEHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALR 156
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 19-169 1.46e-11

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 59.31  E-value: 1.46e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  19 EHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVigDTERSARAWLFTVARNMIIDDRRSARFRNVVGSTDTAG--- 95
Cdd:PRK07037    6 DNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQ--DAVKQPVAYLFRIVRNLAIDHYRRQALENKYHGDEEDGldv 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2276593057  96 APEQSTPDEVNAALDRL-LIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTLQ 169
Cdd:PRK07037   84 PSPEASPEAALINRDTLrHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHCRKCLD 158
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 13-169 1.75e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 59.50  E-value: 1.75e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  13 MKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDTErSARAWLFTVARNMIIDD-RRSARFRNVVGST 91
Cdd:PRK12522    5 VEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE-NYKKWITTICVRTFYDFyRKKKRWKDRILDL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  92 -DTAGAPEQSTPDEVNAA------LDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRAL 164
Cdd:PRK12522   84 fHKEDGGEIEFADDVNISeefiqkVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQM 163


                  ....*
gi 2276593057 165 RLTLQ 169
Cdd:PRK12522  164 REHLE 168
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 16-169 1.80e-11

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 59.80  E-value: 1.80e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  16 LYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQhpEVIGDTERSARAWLFTVARNMIIDD-RRSARFRNVVGSTDTA 94
Cdd:PRK09647   33 LVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFR--SLQNYQPGTFEGWLHRITTNLFLDMvRRRARIRMEALPEDYD 110

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2276593057  95 GAP-EQSTPDEVNAalDRLLIAD---AMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTLQ 169
Cdd:PRK09647  111 RVPgDEPNPEQIYH--DARLDPDlqaALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 117-165 2.53e-11

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: 55.90  E-value: 2.53e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2276593057 117 AMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALR 165
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLR 49
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 27-171 2.84e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 58.73  E-value: 2.84e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  27 YALRLTGDASQSEDVVQETLLRAWQHPEVIgDTERSARAWLFTVARNMIIDDRRsaRFRNVVGSTDTAGAPEQSTPDEVN 106
Cdd:PRK12547   22 FAVSLSSKHDKAEDLVQDTLMKAWAKQDSF-EMGTNLKAWLFTILRNEFYSQMR--KRGREVQDSDGVFTARVAVHPAQY 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2276593057 107 AALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAvralRLTLQEL 171
Cdd:PRK12547   99 GSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRA----RNRLQEL 159
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 111-165 1.11e-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: 54.42  E-value: 1.11e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2276593057 111 RLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALR 165
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 1-169 1.52e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 57.94  E-value: 1.52e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   1 MSRASGTAEAALmKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDTERSARAWLFTVARNMIIDDRR 80
Cdd:PRK12538   54 LDRLATDDEAAF-RLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRAKFSTWLYRVVSNRCIDLRR 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  81 SARFRNVvgstDTAGAPEQSTPDEVnAALDR----LLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSR 156
Cdd:PRK12538  133 KPRTENV----DAVPEVADGKPDAV-SVIERnelsDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESL 207

                         170
                  ....*....|...
gi 2276593057 157 LHYAVRALRLTLQ 169
Cdd:PRK12538  208 LKRGRQQLRDLLR 220
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 7-162 1.63e-10

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 56.78  E-value: 1.63e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   7 TAEAALMKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVigDTERSARAWLFTVARNMIIDD-RRSARFR 85
Cdd:PRK12523    6 SPHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGRPEL--PTPREPRAFLAAVAKGLMFDHfRRAALEQ 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2276593057  86 NVVGSTDTAGAPEQSTPDEVNAALDRLLIADAM-AQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVR 162
Cdd:PRK12523   84 AYLAELALVPEAEQPSPEEQHLILEDLKAIDRLlGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLR 161
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 27-169 4.52e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 55.74  E-value: 4.52e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  27 YALRLTGDASQSEDVVQETLLRAWQHPEVIgDTERSARAWLFTVARNMIIDDRRSaRFRNvVGSTDTAGAPEQSTPDEVN 106
Cdd:PRK12516   26 FAVSLIGRHDRADDLVQDTIMKAWAKQDHF-EVGTNMKAWLFTILRNEFYSQMRK-RGRE-VQDTDGMFTEQLAVHPSQY 102

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2276593057 107 AALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTLQ 169
Cdd:PRK12516  103 GTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 13-171 1.35e-09

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 54.61  E-value: 1.35e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  13 MKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDTErSARAWLFTVARNMIIDDRRSaRFRNVVGSTD 92
Cdd:PRK09637    3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGS-SIKSWLYQIANNTIIDFYRK-KNRSEELPDD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  93 ---TAGAPEQSTPDEVNAALDRLLiadamAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRlhyaVRALRLTLQ 169
Cdd:PRK09637   81 llfEDEEREENAKKELAPCLRPFI-----DALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSR----VQRGRVKLK 151


                  ..
gi 2276593057 170 EL 171
Cdd:PRK09637  152 EL 153
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 12-164 1.84e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 54.20  E-value: 1.84e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  12 LMKALYDE-HAAV--LWRYALRLTGDASQSEDVVQETLLRAWQHPEVIgDTERSARAWLFTVARNMIIDDRRSARfRNVV 88
Cdd:PRK12540    3 LTDSLRDDiLAAVpsLRAFAISLSGNGDRADDLVQETLLRALANIDSF-QPGSNLPAWLFTILRNLFRSDYRKRR-REVE 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2276593057  89 GSTDTAGAPEQSTPDEvNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRAL 164
Cdd:PRK12540   81 DADGSYAKTLKSQPGQ-NAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKL 155
Sig70_famx1 TIGR02943
RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of ...
 24-92 2.44e-09

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: 54.00  E-value: 2.44e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  24 LWRYALRLTGDASQSEDVVQETLLRAWQHPEviGDTERSA-RAWLFTVARNMIIDDRRSARFRNVVGSTD 92
Cdd:TIGR02943  15 LLRFARLQLRDRDLAEDAVQETLLAALSHRD--SFAGRSAlKTWLFAILKNKIIDALRAKGREVKVSDLD 82
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 15-165 2.96e-09

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: 53.09  E-value: 2.96e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  15 ALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIgDTERSARAWLFTVARNMIIDDRRSARFRNVVGSTD-- 92
Cdd:TIGR02989   5 RLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQF-DPGTNFVAWARGIARNKVLNYRRKLGRDRLVFDDDll 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2276593057  93 TAGAPEQSTPDEVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALR 165
Cdd:TIGR02989  84 EALAAEAEPTEAERLSDDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSLR 156
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 16-156 5.39e-09

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 52.79  E-value: 5.39e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  16 LYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVI-GDTErsARAWLFTVARNMIIDDRRSARFRNVVgSTDTA 94
Cdd:PRK09643   32 LFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFrGDAA--VSSWLHRIVVNACLDRLRRAKARPTV-PLDDV 108

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2276593057  95 GAPEQSTPDEVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSR 156
Cdd:PRK09643  109 YPVAQLERDPTARVETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSR 170
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 4-170 5.40e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 53.14  E-value: 5.40e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   4 ASGTAEAALMKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDTERSARAWLFTVARNMIIDDRRS-A 82
Cdd:PRK12534   18 ATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGLTWLAMIARNKAIDHLRAnA 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  83 RFRNVVGSTDTAGAPE--QSTPDEVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYA 160
Cdd:PRK12534   98 PQRRNVALDDAGELRAadASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRG 177

                         170
                  ....*....|
gi 2276593057 161 VRALRLTLQE 170
Cdd:PRK12534  178 LAKLKACLER 187
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 30-171 6.97e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 52.26  E-value: 6.97e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  30 RLTGDASQSEDVVQETLLRAWQHPEVIgdTERSARAWLFTVARNMIIDD-RRSARFRNVVGSTdtAGAPE--QSTPDEVN 106
Cdd:PRK12525   28 RQLGCPHSAEDIASETFLQVLALPDPA--SIREPRALLTTIARRLMYEGwRRQDLERAYLQSL--AEAPEavQPSPEEQW 103

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2276593057 107 AALDRLLIADAM-AQLSAEHRAVIERSYYRGWTTAQIATDLGIAegtvKSRLH-YAVRALRLTLQEL 171
Cdd:PRK12525  104 MVIETLLAIDRLlDGLSGKARAAFLMSQLEGLTYVEIGERLGVS----LSRIHqYMVEAFKCCYQGF 166
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 111-164 8.49e-09

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: 49.38  E-value: 8.49e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2276593057 111 RLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRAL 164
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 35-164 1.83e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 51.24  E-value: 1.83e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  35 ASQSEDVVQETLL------RAWqhpevigDTERSARAWLFTVARNMIIDDRRSARFRNVVGSTDTAGAPEQSTPDEvnaA 108
Cdd:PRK12512   50 ADQAEDIVQEILLavhlkrHTW-------DPGAPFAPWLFAIARNKLIDALRRRGRRVFVDIDDFAETLPAEPATE---T 119

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2276593057 109 LDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRAL 164
Cdd:PRK12512  120 LPAGDVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGLAAL 175
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 2-164 4.02e-08

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 50.42  E-value: 4.02e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   2 SRASGTAEAALMKALYDEhaavLWRYALRLTgDASQSEDVVQETLLRAwqhpevIGDTER-----SARAWLFTVARNMII 76
Cdd:PRK09649   19 AKGNGRALEAFIKATQQD----VWRFVAYLS-DVGSADDLTQETFLRA------IGAIPRfsarsSARTWLLAIARHVVA 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  77 DDRRSARFRNvvgSTDTAGAPEQSTPDEVNAA--LDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVK 154
Cdd:PRK09649   88 DHIRHVRSRP---RTTRGARPEHLIDGDRHARgfEDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIR 164

                         170
                  ....*....|
gi 2276593057 155 SRLHYAVRAL 164
Cdd:PRK09649  165 SRVARARDAL 174
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
1-175 8.07e-08

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 50.71  E-value: 8.07e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   1 MSRASGTAEAALMkALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEviGDTERSA-RAWLFTVARN----MI 75
Cdd:PRK08241   10 LARAAAGDRDAFA-ALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYD--RFEGRSSlRTWLYRIATNvcldAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  76 IDDRRSARFRNVVGSTDTAGAPEQSTPDEV------NAALD----------------RLLIADAMAQLSAEHRAVIERSY 133
Cdd:PRK08241   87 EGRARRPLPTDLGAPAADPVDELVERPEVPwlepypDALLDpaaadpaarvvaresvRLAFVAALQHLPPRQRAVLILRD 166

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2276593057 134 YRGWTTAQIATDLGIAEGTVKSRLHyavRAlRLTLQELGVTR 175
Cdd:PRK08241  167 VLGWSAAEVAELLDTSVAAVNSALQ---RA-RATLAERGPSA 204
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 4-168 1.00e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 49.50  E-value: 1.00e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   4 ASGTAEAAlmKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDTERSARAWLFTVARNMIIDDRRSAR 83
Cdd:PRK12524   21 ANGDPAAA--RALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGEARVSTWLYRVVCNLCTDRLRRRR 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  84 frnvVGSTDTAGAPEqsTPDEVNAALDRLLIAD-------AMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSR 156
Cdd:PRK12524   99 ----RASVDLDDAPE--PADAAPGAEEALIEGDrmraldaALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESL 172

                         170
                  ....*....|..
gi 2276593057 157 LHYAVRALRLTL 168
Cdd:PRK12524  173 TARGKRALAALL 184
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 31-164 1.73e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 48.96  E-value: 1.73e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  31 LTGDASQSEDVVQETLLRAWQhpevIGDTER--SARAWLFTVARNMIIDDRRSARFRNVVGSTDTAGAPEqSTPDEVNAA 108
Cdd:PRK12533   38 LCGNASDADDVVQEACMRALR----FFDSFRgdNARPWLLAIVRHTWYSEWRRRANAHEVAAPDTLDDAD-SLDDWQPAG 112

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2276593057 109 LDRL----------LIADAMAQLSAEHRAVI-----ERSYYRgwttaQIATDLGIAEGTVKSRLHYAVRAL 164
Cdd:PRK12533  113 EDPLalllraedvrLVNAALAKLPVEYREVLvlrelEDMSYR-----EIAAIADVPVGTVMSRLARARRRL 178
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 5-85 1.74e-07

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 49.53  E-value: 1.74e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   5 SGTAEAAlmkALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEvigDTERSARAWLFTVARNMIIDDRRSARF 84
Cdd:PRK09636    1 MTMADAA---AEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLRWNNADR---AQIRDPRAWLTRVVTRLCLDRLRSARH 74


                  .
gi 2276593057  85 R 85
Cdd:PRK09636   75 R 75
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 11-162 2.64e-07

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 49.19  E-value: 2.64e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  11 ALMKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDTErsaRAWLFTVARNMIIDDRRSARFRN---- 86
Cdd:PRK09635    5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGDIDDE---RGWLIVVTSRLCLDHIKSASTRRerpq 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2276593057  87 VVGSTDTAGAPEQSTPDEVNAALD---RLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVR 162
Cdd:PRK09635   82 DIAAWHDGDASVSSVDPADRVTLDdevRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARR 160
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 34-174 5.99e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 47.65  E-value: 5.99e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  34 DASQSEDVVQETLLRAWQHpevIGDTERSAR--AWLFTVARNMIIDDRRSARFRNVVGSTDTAGAPEQSTPDEVNAALD- 110
Cdd:PRK11922   53 NDAEAEDVVQEAYLRAFRA---LGTFRGDASlsTWLSRIVLNEALGRLRRRRRLVNLAEMVMASTIAGGERTPLADPAEd 129

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2276593057 111 ----------RLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTL-QELGVT 174
Cdd:PRK11922  130 peraaarreiRALLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLLRESLaREIGPA 204
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 1-154 9.56e-07

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 46.34  E-value: 9.56e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   1 MSRASGTAEAALmKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAwqhpeVIGD---TERSARAWLFTVARNMIID 77
Cdd:PRK09651    1 SDRATTTASLTF-ESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRV-----MVSEtlsTIRDPRSFLCTIAKRVMVD 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  78 D-RRSA---RFRNVVGSTDTAGAPeqsTPDEVNAALDRLLIADAMAQ-LSAEHRAVIERSYYRGWTTAQIATDLGIAEGT 152
Cdd:PRK09651   75 LfRRNAlekAYLEMLALMPEGGAP---SPEERESQLETLQLLDSMLDgLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSS 151


                  ..
gi 2276593057 153 VK 154
Cdd:PRK09651  152 VK 153
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 40-175 4.98e-06

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 44.19  E-value: 4.98e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  40 DVVQETLLRAWQHpevIGDteRSARAW--LF-TVARNMIIDDRRSARFRNVVGSTDTAGAPEQ------------STPDE 104
Cdd:PRK09047    9 DIVQDAMIKLAEK---YGD--RPAAEWppLFqRILQNRIHDWFRRQKVRNTWVSLFSSFSDDDddddfdpletldSADEG 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2276593057 105 VNAALDRLLIADAMAQLSAEHRAVIERS-------YYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTLQELGVTR 175
Cdd:PRK09047   84 AESPADKLERAQVLQLIEEAIQKLPARQreafllrYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKGITL 161
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 23-174 2.47e-05

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 42.62  E-value: 2.47e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  23 VLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIgDTERSARAWLFTVARNMII----DDRRSARFRNVVGSTDTAGAPE 98
Cdd:PRK09640   38 TLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNF-EGKSKFKTWLYSITYNECItqyrKERRKRRLMDALSLDPLEEASE 116

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2276593057  99 QSTPD-EVNAALDRLLIadamaQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTLQELGVT 174
Cdd:PRK09640  117 EKAPKpEERGGLDRWLV-----HVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLREKFAGLAET 188
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 110-170 4.96e-05

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: 42.12  E-value: 4.96e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2276593057 110 DRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVkSRLH-YAVRALRLTLQE 170
Cdd:COG1191   176 LREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRV-SRLHkKALARLREYLKE 236
PRK12545 PRK12545
RNA polymerase factor sigma-70;
24-116 5.97e-05

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 41.87  E-value: 5.97e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  24 LWRYALRLTGDASQSEDVVQETLLRAWQHPEVIgDTERSARAWLFTVARNMIIDDRRsARFRNVvgstdTAGAPEQSTPD 103
Cdd:PRK12545   21 LLRFARLQLRDADAAEDAVQEALAAAWSQAGRF-AGQSAHKTWVFGILRNKLIDTLR-ARQRTV-----NLSALDAELDG 93

                          90
                  ....*....|...
gi 2276593057 104 EvnAALDRLLIAD 116
Cdd:PRK12545   94 E--ALLDRELFKD 104
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 13-160 1.22e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 40.81  E-value: 1.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  13 MKALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIG--DTERSARaWLFTVARNMIIDD-RRSARFRNVVG 89
Cdd:PRK12542   11 MEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHslNTQELKR-YILRVAKNKAIDSyRKNKRHETFLE 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2276593057  90 --STDTAGAPEQSTPDEVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYA 160
Cdd:PRK12542   90 eyERESIEAVDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERA 162
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 8-165 3.29e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 39.06  E-value: 3.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057   8 AEAALMKALYDEHAAVLWRYALRLTGDASQSEDVVQET---LLRAWQHPEVIgdterSARAWLFTVARNMIIDDRRSARF 84
Cdd:PRK12528    1 AHSATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTfvkVLVARETAQII-----EPRAFLTTIAKRVLCNHYRRQDL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  85 RNVVGSTdTAGAPEQSTPDEVNAA--------LDRLLiaDAMAQLSAehRAVIeRSYYRGWTTAQIATDLGIAEGTVKSR 156
Cdd:PRK12528   76 ERAYLEA-LAQLPERVAPSEEERAiiletlveLDQLL--DGLPPLVK--RAFL-LAQVDGLGYGEIATELGISLATVKRY 149


                  ....*....
gi 2276593057 157 LHYAvrALR 165
Cdd:PRK12528  150 LNKA--AMR 156
PRK12520 PRK12520
RNA polymerase sigma factor; Provisional
 15-120 4.90e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237126 [Multi-domain]  Cd Length: 191  Bit Score: 38.94  E-value: 4.90e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  15 ALYDEHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEVIGDtERSARAWLFTVARNMIIDDRRSARfRNVvgstdtA 94
Cdd:PRK12520    6 AQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAG-QSSLKTYLVGILKHKIIDAIRSGR-REV------R 77

                          90       100
                  ....*....|....*....|....*.
gi 2276593057  95 GAPEQSTPDEVNAALDRLLIADAMAQ 120
Cdd:PRK12520   78 LSLDDADEQSDDDLFDALFAADGHYR 103
PRK12544 PRK12544
RNA polymerase factor sigma-70;
26-80 5.48e-04

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 39.01  E-value: 5.48e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2276593057  26 RYALRLTGDASQSEDVVQETLLRAWQHPEVIGDteRSA-RAWLFTVARNMIIDDRR 80
Cdd:PRK12544   33 KFATLQLSDLHLAEDAVQEALIGALKNADSFAG--RAAfKTWVFAILKNKIIDLLR 86
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 24-169 7.00e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 38.76  E-value: 7.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  24 LWRYA-LRLTGDASQSEDVVQETLLRAWQHPEVIgdTERSA-RAWLFTVARNMIIDD-RRSARFRNV---VGSTD----- 92
Cdd:PRK12532   18 LLHFArLQLPDHPDLAEDLVQETLLSAYSAGDSF--QGRALvNSWLFAILKNKIIDAlRQIGRQRKVftlLDDELldeaf 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  93 -----------TAGAPEQ-STPDEVNAALDRLLIADAMAQLSAEHRA-VIERSYYRGWTTAQIATDLGIAEGTVKSRLHY 159
Cdd:PRK12532   96 eshfsqnghwtPEGQPQHwNTPEKSLNNNEFQKILQSCLYNLPENTArVFTLKEILGFSSDEIQQMCGISTSNYHTIMHR 175

                         170
                  ....*....|
gi 2276593057 160 AVRALRLTLQ 169
Cdd:PRK12532  176 ARESLRQCLQ 185
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 24-170 7.24e-04

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 38.22  E-value: 7.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  24 LWRYALRLTGDASQSEDVVQETLLRAWqhpEVIGDTE-RSARAWLFTVARNMIIDDRRSARFR-----NVVGSTDTAGAP 97
Cdd:PRK12527    8 LVRFLSARLGNRQAAEDVAHDAYLRVL---ERSSSAQiEHPRAFLYRTALNLVVDRHRRHRVRqaeplEVLDEEERLHSP 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2276593057  98 EQSTPDEVNAALDRLliADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTLQE 170
Cdd:PRK12527   85 SPQTRLDLGQRLALL--QRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQ 155
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
35-164 1.46e-03

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 37.40  E-value: 1.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  35 ASQSEDVVQETLLrAWQHPEVIGDTERSARAWLFTVARNMIIDDRRsaRFRNVVGSTDTAGAPEQSTPDEVNAALDRLLI 114
Cdd:PRK12539   49 AEEAEDLVQEALM-AIHTRRHTYDPEQPLTPWVYAIARYKLIDHLR--RTRASLADVPIDDADELVAHDDHAAVESTLDL 125

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 2276593057 115 ADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRAL 164
Cdd:PRK12539  126 GRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVKVSVHRGLKAL 175
PRK06704 PRK06704
RNA polymerase subunit sigma-70;
19-170 1.79e-03

RNA polymerase subunit sigma-70;


Pssm-ID: 180663 [Multi-domain]  Cd Length: 228  Bit Score: 37.70  E-value: 1.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  19 EHAAVLWRYALRLTGDASQSEDVVQETLLRAWQHPEvigdTERSARAWLFTVARNMIIDDRRSARFRNVVGSTDTAgape 98
Cdd:PRK06704   25 EQYGELKRYCTFLTKNKWDGEDLAQETVCKVLQKYS----NKDICMTLVYKIARNRWLDQIKSKSVHEKIRDQITF---- 96

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2276593057  99 qSTPDEVNAALDRlLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTLQE 170
Cdd:PRK06704   97 -EEPHEKIADLHE-MVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 34-99 1.81e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 37.44  E-value: 1.81e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2276593057  34 DASQSEDVVQETLLRAWQHPEVIgdTERSA-RAWLFTVARNMIID-DRRSARFRNvVGSTDTAGAPEQ 99
Cdd:PRK12530   30 DADLAEDVVQEALVSAYKNADSF--KGQSAlKTWIFAILKNKIIDlIRYRKRFVN-ESELIEEDSPNS 94
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 24-160 4.57e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 36.41  E-value: 4.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  24 LWRYALRLtGDASQSEDVVQETLLRawqhpeVIGDTER-----SARAWLFTVARNMIIDD--------RRSARFRNVVGS 90
Cdd:PRK12535   38 VWRLLAHL-GGHDIADDLTQETYLR------VMSALPRfaarsSARTWLLSLARRVWVDNirhdmarpRKSATEYEDAAA 110

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  91 TDTAGAPEQSTPDEVNAaldRLLIadamAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYA 160
Cdd:PRK12535  111 TTASNETTGSWSEWIDV---RTLI----DALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARA 173
PRK06930 PRK06930
positive control sigma-like factor; Validated
 72-160 4.84e-03

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 35.86  E-value: 4.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  72 RNMIIDDRRSARFRNVvgSTDTAGAPEQstPDEVNAALDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEG 151
Cdd:PRK06930   70 REVICDPLLIQRYFRS--MEDLEWDIEE--PESVISEWDKIRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKS 145


                  ....*....
gi 2276593057 152 TVKSRLHYA 160
Cdd:PRK06930  146 TVQSMIERA 154
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 30-169 5.04e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 36.18  E-value: 5.04e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057  30 RLTGDASQSEDVVQETLLrAWQHPEVIGDTERSARAWLFTVARNMIIDD-RRSARFRNVVGSTDTAGapEQSTPDEVNAA 108
Cdd:PRK12536   41 RLPQLPDEVEDLVQEILL-AVHNARHTYRADQPLTAWVHAIARYKLMDFlRSRARREALHDPLDDES--ELFATSDDEAA 117

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2276593057 109 LDRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTLQ 169
Cdd:PRK12536  118 EARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHRGLKALAAKIR 178
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 135-164 7.22e-03

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 33.27  E-value: 7.22e-03
                           10        20        30
                   ....*....|....*....|....*....|
gi 2276593057  135 RGWTTAQIATDLGIAEGTVKSRLHYAVRAL 164
Cdd:smart00421  17 EGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 110-169 8.04e-03

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 35.67  E-value: 8.04e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2276593057 110 DRLLIADAMAQLSAEHRAVIERSYYRGWTTAQIATDLGIAEGTVKSRLHYAVRALRLTLQ 169
Cdd:PRK07408  193 DRIRLQQALAQLEERTREVLEFVFLHDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQ 252
 
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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