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Conserved domains on  [gi|495112399|ref|WP_007837219|]
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RNA polymerase sigma factor [Phocaeicola dorei]

Protein Classification

RNA polymerase sigma factor( domain architecture ID 11446377)

RNA polymerase sigma factor plays a role in bacterial signal transduction and is regulated by anti-sigma factors. May belong to the ECF-type subfamily. Generally, sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.

CATH:  1.10.1740.10
Gene Ontology:  GO:0016987|GO:0006352|GO:0003677
PubMed:  28575802
SCOP:  4003741

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-175 4.46e-43

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: 141.67  E-value: 4.46e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399   1 MINEDKIREVWASDPERGFKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNEC 80
Cdd:COG1595    1 MSSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  81 LRFLNMRKEQAVSAEEVQEELMNKLMASDYVDYENEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTL 160
Cdd:COG1595   81 IDHLRKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTV 160

                        170
                 ....*....|....*
gi 495112399 161 KVNYHYAKEKIKEYM 175
Cdd:COG1595  161 KSRLSRARKKLREAL 175
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-175 4.46e-43

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: 141.67  E-value: 4.46e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399   1 MINEDKIREVWASDPERGFKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNEC 80
Cdd:COG1595    1 MSSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  81 LRFLNMRKEQAVSAEEVQEELMNKLMASDYVDYENEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTL 160
Cdd:COG1595   81 IDHLRKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTV 160

                        170
                 ....*....|....*
gi 495112399 161 KVNYHYAKEKIKEYM 175
Cdd:COG1595  161 KSRLSRARKKLREAL 175
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 19-173 2.04e-32

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 114.13  E-value: 2.04e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  19 FKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNeclRFLNM-RKEQ-----AV 92
Cdd:PRK09652  12 FALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARN---TAINYlRKQGrrppaSD 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  93 SAEEVQEELMNKLMASDYVDYENEMAVKF-----QQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYA 167
Cdd:PRK09652  89 VDAEEAEDFDLADALRDISTPENELLSAEleqrvRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRA 168


                 ....*.
gi 495112399 168 KEKIKE 173
Cdd:PRK09652 169 REALRA 174
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 19-175 8.52e-31

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: 109.36  E-value: 8.52e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399   19 FKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRKEQAVSAEEVQ 98
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLE 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 495112399   99 EELMNKLMASDYVDYENEMAVkFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKEYM 175
Cdd:TIGR02937  83 ELLDSDPSPEEELEQEEEREA-LREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 22-92 1.70e-13

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: 62.22  E-value: 1.70e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 495112399   22 LIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREE--SSLGTWIYRIATNECLRFLnmRKEQAV 92
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPErgVSFSTWLYTIIRNAIIDYL--RKQRRT 71
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 119-172 1.69e-06

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: 43.25  E-value: 1.69e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 495112399 119 VKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIK 172
Cdd:cd06171    2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-175 4.46e-43

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: 141.67  E-value: 4.46e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399   1 MINEDKIREVWASDPERGFKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNEC 80
Cdd:COG1595    1 MSSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  81 LRFLNMRKEQAVSAEEVQEELMNKLMASDYVDYENEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTL 160
Cdd:COG1595   81 IDHLRKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTV 160

                        170
                 ....*....|....*
gi 495112399 161 KVNYHYAKEKIKEYM 175
Cdd:COG1595  161 KSRLSRARKKLREAL 175
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 19-173 2.04e-32

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 114.13  E-value: 2.04e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  19 FKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNeclRFLNM-RKEQ-----AV 92
Cdd:PRK09652  12 FALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARN---TAINYlRKQGrrppaSD 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  93 SAEEVQEELMNKLMASDYVDYENEMAVKF-----QQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYA 167
Cdd:PRK09652  89 VDAEEAEDFDLADALRDISTPENELLSAEleqrvRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRA 168


                 ....*.
gi 495112399 168 KEKIKE 173
Cdd:PRK09652 169 REALRA 174
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 19-175 8.52e-31

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: 109.36  E-value: 8.52e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399   19 FKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRKEQAVSAEEVQ 98
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLE 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 495112399   99 EELMNKLMASDYVDYENEMAVkFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKEYM 175
Cdd:TIGR02937  83 ELLDSDPSPEEELEQEEEREA-LREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 6-175 4.90e-26

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 97.84  E-value: 4.90e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399   6 KIREVWASDpERGFKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLN 85
Cdd:PRK09641   8 LIKQVKKGD-QNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLR 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  86 MRKEQAVSAEEVQ--EEL-MNKLMASDYVDYEN-----EMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKV 157
Cdd:PRK09641  87 KRKPDYYLDAEVAgtEGLtMYSQLAADDALPEEqvvslELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPV 166

                        170
                 ....*....|....*...
gi 495112399 158 DTLKVNYHYAKEKIKEYM 175
Cdd:PRK09641 167 GTVKTRIHRGREALRKQL 184
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 17-173 1.33e-23

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 92.06  E-value: 1.33e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  17 RGFKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNEC---LRFLNMRKEQAVS 93
Cdd:PRK12513  26 AAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLidhWRRHGARQAPSLD 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  94 AEEVQEELMNKLMASDYVDYENEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKE 173
Cdd:PRK12513 106 ADEQLHALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLRE 185
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 19-173 1.57e-21

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 87.33  E-value: 1.57e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  19 FKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRKEQAVSAEEVQ 98
Cdd:PRK11922  32 FEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRRRRRLVNLAEMVM 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  99 EELMNKLM----ASDYVDYENEMAVK-----FQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKE 169
Cdd:PRK11922 112 ASTIAGGErtplADPAEDPERAAARReiralLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARR 191


                 ....
gi 495112399 170 KIKE 173
Cdd:PRK11922 192 LLRE 195
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 30-173 3.83e-21

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 85.02  E-value: 3.83e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  30 IYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRK-------------EQAVSAEE 96
Cdd:PRK11924  26 LLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRrekavlsddalepEFAETAET 105

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 495112399  97 VQEELMNKLMASDyvdyenemavkFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKE 173
Cdd:PRK11924 106 PEAALLAKDDLAR-----------IDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRE 171
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 38-175 9.04e-20

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 81.72  E-value: 9.04e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  38 VVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRKEQAV-SAEEVQEELMNKLMASDYVDYENE 116
Cdd:PRK09415  37 VKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSWHNKKViVTEDIFTYMESQKESVEEEVIQNA 116

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 495112399 117 MAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKEYM 175
Cdd:PRK09415 117 EDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 17-171 5.28e-19

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 79.85  E-value: 5.28e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  17 RGFKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRKEQA----V 92
Cdd:PRK11923  20 RAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHLVSRGRRPpdsdV 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  93 SAEEVQ----EELMNKLMASDYVDYENEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAK 168
Cdd:PRK11923 100 SSEDAEfydgDHALKDIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRAR 179


                 ...
gi 495112399 169 EKI 171
Cdd:PRK11923 180 EAI 182
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 19-168 4.99e-17

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: 73.75  E-value: 4.99e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399   19 FKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLnmRKEQAVsaEEVQ 98
Cdd:TIGR02985   3 FEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYL--RHKQVE--EKYQ 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 495112399   99 EELMNKLMAS-DYVDYENEMAVKFQQAILM-----LPEKQRVVFNLRYYDELEYEEISRITDTKVDTlkVNYHYAK 168
Cdd:TIGR02985  79 EELAEIEERElSEADPEEELEAKELEEIIEeaiekLPEQCREIFILSRFEGLSNKEIAEELGISVKT--VEYHITK 152
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 4-160 5.59e-17

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 74.30  E-value: 5.59e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399   4 EDKIREVWASDPErGFKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFRE-ESSLGTWIYRIATNECLR 82
Cdd:PRK05602   8 EELLARVAAGDPA-AFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPgEARFDTWLHRVVLNLCYD 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 495112399  83 FLNMRKEQAVsaeEVQEELMNKLMASDYVDYENEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTL 160
Cdd:PRK05602  87 RLRRRREVPV---EDAPDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDAL 161
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 17-173 1.07e-16

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 73.82  E-value: 1.07e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  17 RGFKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRflNMRKEQAVSAEE 96
Cdd:PRK09640  26 RAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECIT--QYRKERRKRRLM 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 495112399  97 VQEELMNKLMASDYVDYENEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKE 173
Cdd:PRK09640 104 DALSLDPLEEASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLRE 180
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 17-160 6.07e-16

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: 70.81  E-value: 6.07e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399   17 RGFKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNEClrfLNMRKEQAVSAEE 96
Cdd:TIGR02989   1 KAFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKV---LNYRRKLGRDRLV 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 495112399   97 VQEELMNKLMASDYVDYENEMAVKFQ---QAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTL 160
Cdd:TIGR02989  78 FDDDLLEALAAEAEPTEAERLSDDRQaleGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAV 144
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
33-88 2.73e-15

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 71.89  E-value: 2.73e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 495112399  33 HIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRK 88
Cdd:PRK08241  35 HCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNVCLDALEGRA 90
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 32-161 6.89e-15

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 68.97  E-value: 6.89e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  32 WHI-RRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRKEQ-AVSAEEVQEELMNklmASD 109
Cdd:PRK09643  41 WAVaRRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDRLRRAKARpTVPLDDVYPVAQL---ERD 117

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 495112399 110 YVDyENEMAVKFQQAILMLPEKQRVVFNLryYDELEY--EEISRITDTKVDTLK 161
Cdd:PRK09643 118 PTA-RVETALAVQRALMRLPVEQRAALVA--VDMQGYsvADAARMLGVAEGTVK 168
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 45-175 1.56e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 67.82  E-value: 1.56e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  45 EDILQEVFIRVFRHLPQFREESSLGTWIYRIATNEClrfLNMRKEQAVSAEEVQEELMNkLMASDYVDYENEMAVKFQ-- 122
Cdd:PRK12518  38 DDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVA---TDARRQFAQRPSRIQDDSLN-DQPSRPSDTPDLMQLHYQdl 113

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 495112399 123 --QAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKEYM 175
Cdd:PRK12518 114 vqQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 44-173 2.12e-14

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 67.35  E-value: 2.12e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  44 AEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRKEQAVSAEEVQEELMNKL---MASDYVDYENEMavk 120
Cdd:PRK09638  45 AEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHLRKQKREKLRLQRAKEETLRKEkweAAIKGAEWSEML--- 121

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 495112399 121 fqQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYA-KEKIKE 173
Cdd:PRK09638 122 --DALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGiKQLRKE 173
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 30-173 2.94e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 67.06  E-value: 2.94e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  30 IYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRKEQAVSAEEVQEelmnklMASD 109
Cdd:PRK12515  35 VYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSALRRRKHEEIDDEAAAA------IEDG 108

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 495112399 110 YVDYENEMAVKFQQAIL-----MLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKE 173
Cdd:PRK12515 109 ADTPEVALQKSDTSAALraclaKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAE 177
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 19-175 6.80e-14

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 65.74  E-value: 6.80e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  19 FKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHlpQFREESSLGTWIYRIATNECLRFLNMRKEQAVSAEEV- 97
Cdd:PRK09639   5 FEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKGIENEKGWLIKSARNVAYNYLRSEKRRRARILGEf 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 495112399  98 -QEELMNKLMASDYVdYENEMAVKFQQAILMLPEKQRVVFNLRYYDeLEYEEISRITDTKVDTLKVNYHYAKEKIKEYM 175
Cdd:PRK09639  83 qWQEVDNEPSPEEIW-IRKEEITKVQEVLAKMTERDRTVLLLRFSG-YSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 30-175 1.30e-13

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 65.96  E-value: 1.30e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  30 IYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREesslGT---WIYRIATNeclRFLNM-RKEQAVSAE---EVQEELM 102
Cdd:PRK09647  41 VYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP----GTfegWLHRITTN---LFLDMvRRRARIRMEalpEDYDRVP 113

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 495112399 103 NKLMASDYVDYENEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKEYM 175
Cdd:PRK09647 114 GDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 26-172 1.34e-13

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: 64.78  E-value: 1.34e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399   26 FQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESsLGTWIYRIATNEclrFLN-MRKEqaVSAEEVQEELMNK 104
Cdd:TIGR02950   4 YMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKDSS-IKPWLFRIARNA---FIDwYRKD--KKIQTIDDDAIGD 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 495112399  105 LMASDYVDYENEMAVKFQQAILM-----LPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIK 172
Cdd:TIGR02950  78 LEQHPVESPEHHLLIKIEQEEIThhlsrLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELK 150
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 22-92 1.70e-13

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: 62.22  E-value: 1.70e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 495112399   22 LIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREE--SSLGTWIYRIATNECLRFLnmRKEQAV 92
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPErgVSFSTWLYTIIRNAIIDYL--RKQRRT 71
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 12-157 2.57e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 65.65  E-value: 2.57e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  12 ASDPERGFKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFRE-ESSLGTWIYRIATNECLRFlnMRKEQ 90
Cdd:PRK12538  58 ATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHgRAKFSTWLYRVVSNRCIDL--RRKPR 135

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 495112399  91 AVSAEEVQEELMNKLMASDYVDyENEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKV 157
Cdd:PRK12538 136 TENVDAVPEVADGKPDAVSVIE-RNELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTV 201
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 42-161 4.67e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 63.93  E-value: 4.67e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  42 EDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRKEQAVSAEEVQEELMNKlmASDYVDYEN----EM 117
Cdd:PRK12519  54 QEAEDLTQEIFLSLWRKSSYDPKRGSLSSYLLTLTRSRAIDRLRSRRSRQRLLERWQQELLGE--ASEDTPLEQaslaER 131

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 495112399 118 AVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLK 161
Cdd:PRK12519 132 SQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVK 175
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 16-175 1.34e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 62.44  E-value: 1.34e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  16 ERGFKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRF-------LNMRK 88
Cdd:PRK12543   6 QEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSWrrkrwrrFRIFE 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  89 EQAVSAEEVQEELMNKLMasdyvdyENEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAK 168
Cdd:PRK12543  86 KAEEQRKPVSIDFSEDVL-------SKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAAL 158


                 ....*..
gi 495112399 169 EKIKEYM 175
Cdd:PRK12543 159 KKLRQKE 165
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 16-175 4.36e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 61.04  E-value: 4.36e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  16 ERGFKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRKE-----Q 90
Cdd:PRK12522   2 EEKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKKKRwkdriL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  91 AVSAEEVQEELMNKLMAS-DYVDYENEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKE 169
Cdd:PRK12522  82 DLFHKEDGGEIEFADDVNiSEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKK 161


                 ....*.
gi 495112399 170 KIKEYM 175
Cdd:PRK12522 162 QMREHL 167
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 26-177 4.50e-12

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 61.15  E-value: 4.50e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  26 FQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMR-KEQAVSAEEVQEELMNK 104
Cdd:PRK09637  10 YKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKnRSEELPDDLLFEDEERE 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 495112399 105 lmasdyVDYENEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKEYMIN 177
Cdd:PRK09637  90 ------ENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 35-161 1.10e-11

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: 59.71  E-value: 1.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399   35 RRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRKEQAVSAEEVQEelmnklMASDYVDYE 114
Cdd:TIGR02983  24 YLLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRRRRLLELPTRELPD------AAAPDPAPD 97

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 495112399  115 NEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLK 161
Cdd:TIGR02983  98 VALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVK 144
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 31-158 4.24e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 58.75  E-value: 4.24e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  31 YWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFRE-ESSLGTWIYRIATNECLRFLNMRKEQAVSAEEVqEELMNKLMASD 109
Cdd:PRK12524  40 LAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQgEARVSTWLYRVVCNLCTDRLRRRRRASVDLDDA-PEPADAAPGAE 118

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 495112399 110 YVDYENEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVD 158
Cdd:PRK12524 119 EALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVE 167
Sig70_famx3 TIGR02954
RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of ...
 41-175 1.04e-10

RNA polymerase sigma-70 factor, TIGR02954 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 certain Bacillus and Clostridium species.


Pssm-ID: 213752 [Multi-domain]  Cd Length: 169  Bit Score: 57.41  E-value: 1.04e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399   41 HEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRKEQAVSAEEVQEElmnKLMASDYVDYENEMAvk 120
Cdd:TIGR02954  40 EHDALDVIQETVYKAYLSIDKLKHPKYFNTWLTRILINECIDLLKKKKKVIPFDPNTSIE---KGECETHADSRLDLY-- 114

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 495112399  121 fqQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKEYM 175
Cdd:TIGR02954 115 --KAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167
SigZ TIGR02959
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 24-173 1.60e-10

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: 56.99  E-value: 1.60e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399   24 DFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRK------EQAVSAEEV 97
Cdd:TIGR02959   2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDGQKIQSWLYQIARNTIIDFYRSKSrsvelpESLLAADSA 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 495112399   98 QEELMNKlmasdyvdyenEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKE 173
Cdd:TIGR02959  82 REETFVK-----------ELSQCIPPMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKE 146
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 44-168 2.16e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 56.70  E-value: 2.16e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  44 AEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRKEQAVSAEEVQEELMN-----------------KLM 106
Cdd:PRK12530  34 AEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIRYRKRFVNESELIEEDSPNsffdekghwkpeyyepsEWQ 113

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 495112399 107 ASDYVDYENEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAK 168
Cdd:PRK12530 114 EVENTVYKEEFWLIFEACLNHLPAQQARVFMMREYLELSSEQICQECDISTSNLHVLLYRAR 175
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
16-161 1.29e-09

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 54.68  E-value: 1.29e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  16 ERGFKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFR-EESSLGTWIYRIATNECLRflNMRKEQAVSA 94
Cdd:PRK09646  29 QDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDpARGSALAWLLTLAHRRAVD--RVRSEQAASQ 106

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  95 EEVQEELMNKLMASDYVDYENEMAVKFQQ---AILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLK 161
Cdd:PRK09646 107 REVRYGARNVDPAFDQVAEEVEARLERERvrdCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVK 176
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 120-171 1.64e-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: 51.30  E-value: 1.64e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 495112399  120 KFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKI 171
Cdd:pfam08281   3 ALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 35-160 5.52e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 50.17  E-value: 5.52e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  35 RRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRKEQAVSAEEVQEelmnklMASDYVDYE 114
Cdd:PRK12511  22 RSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVEARRADELAV------LADASLPAA 95

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 495112399 115 NEMAVKFQQ---AILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTL 160
Cdd:PRK12511  96 QEHAVRLAQirdAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTL 144
Sig70_famx1 TIGR02943
RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of ...
 33-178 9.41e-08

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: 49.38  E-value: 9.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399   33 HIRRLVVSHED-AEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRKEQAVSA---EEVQEELMNKL--- 105
Cdd:TIGR02943  17 RFARLQLRDRDlAEDAVQETLLAALSHRDSFAGRSALKTWLFAILKNKIIDALRAKGREVKVSdldDELDDEAFNALftq 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  106 --------MASDYVDYENEMAVK-----FQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIK 172
Cdd:TIGR02943  97 nghwaqhgQPQHWNTPEKQLENKefwevFEACLYHLPEQTARVFMMREVLGFESDEICQELEISTSNCHVLLYRARLSLR 176


                  ....*.
gi 495112399  173 EYMINN 178
Cdd:TIGR02943 177 ACLSIN 182
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 36-161 1.79e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 48.90  E-value: 1.79e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  36 RLVVSHEDAEDILQEVFIRVFRHLPQFREESSLG-TWIYRIATNECLRFLNMRKEQAVS-----AEEVQEELMNKLMASD 109
Cdd:PRK12534  44 RMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGlTWLAMIARNKAIDHLRANAPQRRNvalddAGELRAADASPLERTE 123

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 495112399 110 YVDYENEMAVKFQQailMLPEKQRVVfNLRYYDELEYEEISRITDTKVDTLK 161
Cdd:PRK12534 124 RASTRRRIDHCLAE---LEPPRSELI-RTAFFEGITYEELAARTDTPIGTVK 171
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 30-178 1.96e-07

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 48.34  E-value: 1.96e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  30 IYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFrEESSLGTWIYRIATNECLRFlnMRKEQAVSAeeVQEELMNKLMASD 109
Cdd:PRK09644  14 VYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDY-DNQKVKPWLFKVAYHTFIDF--VRKEKKVSF--VGTDEIEAIQAES 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 495112399 110 YVDY--ENEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKEYMINN 178
Cdd:PRK09644  89 TEEYvvAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEE 159
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 19-175 1.98e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 48.77  E-value: 1.98e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  19 FKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFR-EESSLGTWIYRIATNECLRFLNMRK--EQAVSAE 95
Cdd:PRK12531  29 FALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDgQKSALSTWIYTIIRNLCFDLLRKQKgkDLHIHAD 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  96 EVQEELMNKLMASDYVDYENEM----AVKFqqaILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKI 171
Cdd:PRK12531 109 DIWPSDYYPPDLVDHYSPEQDMlkeqVMKF---LDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKL 185


                 ....
gi 495112399 172 KEYM 175
Cdd:PRK12531 186 RHSM 189
PRK09642 PRK09642
RNA polymerase sigma factor;
26-174 4.38e-07

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 47.40  E-value: 4.38e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  26 FQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFrEESSLGTWIYRIATNECLRF--LNMRKEQAVSAEEVQEELMN 103
Cdd:PRK09642   4 YRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNY-QFRGLKTWMARIATNHAIDYkrKKARENEELSLCKETEENIK 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 495112399 104 KLMASDYVDYENEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKEY 174
Cdd:PRK09642  83 SSHNIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKH 153
PRK12544 PRK12544
RNA polymerase factor sigma-70;
22-178 8.34e-07

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 47.10  E-value: 8.34e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  22 LIDFFQQPIYWHIRRLVVSHEdAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRKE----QAVSAEEV 97
Cdd:PRK12544  24 LEDLRKQMIKFATLQLSDLHL-AEDAVQEALIGALKNADSFAGRAAFKTWVFAILKNKIIDLLRQKKRhvsaSSLLRDEE 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  98 QEELMNKLM----------------ASDYVDYENEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLK 161
Cdd:PRK12544 103 EEEDFEELFdesghwqkderpqawgNPEESLEQEQFWRIFEACLDGLPAKYARVFMMREFIELETNEICHAVDLSVSNLN 182

                        170
                 ....*....|....*..
gi 495112399 162 VNYHYAKEKIKEYMINN 178
Cdd:PRK12544 183 VLLYRARLRLRECLENK 199
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 42-172 8.45e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 46.47  E-value: 8.45e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  42 EDAEDILQEVFIRVFRHLPQFREEsSLGTWIYRIATNECLRFlnMRKEQAVSAEEVQE-ELMNKLMASDYVDYENEMAVK 120
Cdd:PRK12541  30 HFAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFIDW--YRKEKKYKTTTIEEfHLPNVPSTEHEYFIKHEIASW 106

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 495112399 121 FQQAILMLPEKQRVVFnLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIK 172
Cdd:PRK12541 107 LDSLSSLPLERRNVLL-LRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETK 157
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 37-175 8.87e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 46.88  E-value: 8.87e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  37 LVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNEClrFLNMRKeqavSAEEVQEE--LMNKLMASDYVDYE 114
Cdd:PRK12516  30 LIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEF--YSQMRK----RGREVQDTdgMFTEQLAVHPSQYG 103

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 495112399 115 NEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKEYM 175
Cdd:PRK12516 104 TLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEIL 164
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 119-172 1.69e-06

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: 43.25  E-value: 1.69e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 495112399 119 VKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIK 172
Cdd:cd06171    2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 35-159 2.02e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 46.26  E-value: 2.02e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  35 RRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLgTWIYRIATN----EClrflnmRKEQAVSAEEVQEELMNKLMASDY 110
Cdd:PRK12533  36 RWLCGNASDADDVVQEACMRALRFFDSFRGDNAR-PWLLAIVRHtwysEW------RRRANAHEVAAPDTLDDADSLDDW 108

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 495112399 111 VDY---------ENEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDT 159
Cdd:PRK12533 109 QPAgedplalllRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGT 166
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 44-175 2.13e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 45.60  E-value: 2.13e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  44 AEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNEclrFLNMRKEQAVSAEEVQEELMNKLmaSDYVDYENEMAVK-FQ 122
Cdd:PRK12546  34 ADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNT---FYSDRRKHKREVPDPEGVHAASL--AVKPAHDGRLAMSdFR 108

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 495112399 123 QAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKEYM 175
Cdd:PRK12546 109 AAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 35-173 2.30e-06

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 45.68  E-value: 2.30e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  35 RRLVVSHEDAEDILQEVFIRVFRHLPQFR-EESSLGTWIYRIATNECLRFLNMR--KEQAVSAEEVQEELMNklMASDYV 111
Cdd:PRK13919  41 RRMGLDGAAAEDVVQEVFIRVWKKAKEFDpRRGSARAWLLALAHHAAVDHVRRRaaRPQPLEPDEREPEAFD--LPGPGL 118

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 495112399 112 DYENEM-AVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKE 173
Cdd:PRK13919 119 DEEGHLdRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKE 181
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 36-159 2.39e-06

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 46.45  E-value: 2.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  36 RLVVSHEDAEDILQEVFIRVFR-HLPQFREessLGTWIYRIATNECLRFLN---MRKEQAVSA---EEVQEELMNKLmAS 108
Cdd:PRK09636  23 RMLGSVADAEDIVQEAWLRWNNaDRAQIRD---PRAWLTRVVTRLCLDRLRsarHRRETYVGPwlpEPVVEELDDPL-EA 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 495112399 109 DYVDYENEMAvkfqqAILM---LPEKQRVVFNLRYYDELEYEEISRITDTKVDT 159
Cdd:PRK09636  99 VVAAEDLSLA-----LMLAlerLSPLERAAFLLHDVFGVPFDEIASTLGRSPAA 147
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 44-175 2.96e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 45.34  E-value: 2.96e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  44 AEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRKEQAVSAE-EVQEELMNKLMASDYVDYEnemavKFQ 122
Cdd:PRK12540  32 ADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRSDYRKRRREVEDADgSYAKTLKSQPGQNAHLEFE-----EFR 106

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 495112399 123 QAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKEYM 175
Cdd:PRK12540 107 AALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALL 159
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 37-173 3.22e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 44.87  E-value: 3.22e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  37 LVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNEClrFLNMRKeqavSAEEVQEE--LMNKLMASDYVDYE 114
Cdd:PRK12547  26 LSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEF--YSQMRK----RGREVQDSdgVFTARVAVHPAQYG 99

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 495112399 115 NEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKE 173
Cdd:PRK12547 100 SLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQE 158
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 35-161 5.84e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 44.38  E-value: 5.84e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  35 RRLVVSHEDAEDILQEVFIRVFRHLPQFreESSLGT---WIYRIATNECLRFLNMRKEQAVSAEEVQEELMNKLMASDYV 111
Cdd:PRK12537  41 RRIVRDRALAEDIVHDAFIKIWTGAASF--DPARGSargWIYSVTRHLALNVLRDTRREVVLDDDAEETAQTLHEIIDDF 118

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 495112399 112 DYENEMAvKFQQAILML-PEKQRVVFNlRYYDELEYEEISRITDTKVDTLK 161
Cdd:PRK12537 119 DLWANSG-KIHRCLEQLePARRNCILH-AYVDGCSHAEIAQRLGAPLGTVK 167
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 44-173 1.77e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 43.38  E-value: 1.77e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  44 AEDILQEVFIRVFRHLPQFREESSLGTWIYRIATNECLRFLNMRKEQAVSAEEVQEELMNKLMAS--------------- 108
Cdd:PRK12532  33 AEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQIGRQRKVFTLLDDELLDEAFEShfsqnghwtpegqpq 112

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399 109 DYVDYE-----NEMAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKE 173
Cdd:PRK12532 113 HWNTPEkslnnNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRARESLRQ 182
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 43-178 3.57e-05

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 43.03  E-value: 3.57e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  43 DAEDILQEVFIRVFRhlPQFREESSLGTWIYRIATNECL---RFLNMRKE--QAVSAEEVQEELMNKLMASDYVDYENEM 117
Cdd:PRK09635  31 VAEDMVQEAFSRLLR--APVGDIDDERGWLIVVTSRLCLdhiKSASTRRErpQDIAAWHDGDASVSSVDPADRVTLDDEV 108

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 495112399 118 AVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKEYMINN 178
Cdd:PRK09635 109 RLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKINESRIAA 169
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 22-172 3.71e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 42.35  E-value: 3.71e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  22 LIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESS--LGTWIYRIATNECLRFLNMRKEQAVSAEEVQE 99
Cdd:PRK12542  14 LYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTqeLKRYILRVAKNKAIDSYRKNKRHETFLEEYER 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 495112399 100 ELMnKLMASDYVDYENEMAVKFQQAILM--LPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIK 172
Cdd:PRK12542  94 ESI-EAVDENIEEWEKRKMSEVQIDTLLkeLNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRVQ 167
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 16-175 4.88e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 42.10  E-value: 4.88e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  16 ERGFKLLIDFFQQPIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGT-WIYRIATNEC---LRFLNMRKEQA 91
Cdd:PRK12526  37 KQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKGAATtWVYTVMRNAAfdmLRKIKAKKEQN 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  92 VS------AEEVQEELMNKLMASDYVDYENEMAVkfqqaILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYH 165
Cdd:PRK12526 117 LGddiwpiEQALAESQSESEEFSDHLMDKQILSY-----IEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLR 191

                        170
                 ....*....|
gi 495112399 166 YAKEKIKEYM 175
Cdd:PRK12526 192 LALAKLKVQM 201
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 32-161 2.08e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 40.27  E-value: 2.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  32 WHIRRLVVSHEDAEDILQEVFIRVFRHLPQFREESSLGTWIYRIATN---ECLRFLNMR-KEQAVSAEEVQEELMNKLMA 107
Cdd:PRK12535  39 WRLLAHLGGHDIADDLTQETYLRVMSALPRFAARSSARTWLLSLARRvwvDNIRHDMARpRKSATEYEDAAATTASNETT 118

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 495112399 108 SDYVDYenemaVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLK 161
Cdd:PRK12535 119 GSWSEW-----IDVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIR 167
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
29-167 5.54e-04

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 38.91  E-value: 5.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  29 PIYWHIRRLVVSHEDAEDILQEVFIRVFRHLPQF-REESSLGTWIYRIATNecLRFLNMRKEQAVSAEEVQEELMNKLMA 107
Cdd:PRK09645  21 PLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLaDTGRSARAWLFTVARN--LVIDERRSARARPVEGGDDVLGVPEQS 98

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 495112399 108 S-DYVDYENEmAVKFQQAILMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYA 167
Cdd:PRK09645  99 ApDEVDRALD-RLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYA 158
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
33-172 1.07e-03

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 38.03  E-value: 1.07e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  33 HIRRLVV------------SHEDAEDILQEVFIRVFRHLPQFREES-SLGTWIYRIATN---ECLRflNMRKEQAVSAEE 96
Cdd:PRK09648  32 IIRPLVVrycrarlggverPGLSADDVAQEVCLAVITALPRYRDQGrPFLAFVYGIAAHkvaDAHR--AAGRDKAVPTEE 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  97 VQEElmnklmASD-------YVDYE--NEMAVKFQqailMLPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYA 167
Cdd:PRK09648 110 VPER------PSDdagpeerALRSEssNRMRELLD----TLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRA 179


                 ....*
gi 495112399 168 KEKIK 172
Cdd:PRK09648 180 LARLR 184
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 128-173 1.88e-03

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: 34.71  E-value: 1.88e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 495112399  128 LPEKQRVVFNLRYYDELEYEEISRITDTKVDTLKVNYHYAKEKIKE 173
Cdd:pfam04545   5 LPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 43-175 2.93e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 36.72  E-value: 2.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495112399  43 DAEDILQEVFIRVFRHLPQFR-EESSLGTWIYRIATNECLRFLNMRKEQAVSAEEVQEelmnklMASDYVDYEnemavkf 121
Cdd:PRK12514  45 EAEEALQDVYVKIWTKADRFAvSGLSPMTWLITIARNHAIDRLRARKAVAVDIDEAHD------LADPSPGPE------- 111

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 495112399 122 qQAILMLPEKQRVVFNLR-------------YYDELEYEEISRITDTKVDTLKVNYHYAKEKIKEYM 175
Cdd:PRK12514 112 -AEVIAGDEGQRIDACLEelekdraaavrraYLEGLSYKELAERHDVPLNTMRTWLRRSLLKLRECL 177
 
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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