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Conserved domains on  [gi|2309718997|ref|WP_261397953|]
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sigma-70 family RNA polymerase sigma factor [Maritimibacter alkaliphilus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK12514 super family cl30921
RNA polymerase sigma factor; Provisional
 18-185 2.51e-82

RNA polymerase sigma factor; Provisional


The actual alignment was detected with superfamily member PRK12514:

Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 241.26  E-value: 2.51e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGYSPMTWLITIARNHAIDRLRKRR 97
Cdd:PRK12514   12 RVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPMTWLITIARNHAIDRLRARK 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  98 SGSAPLEDADTVPDGAPGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLM 177
Cdd:PRK12514   92 AVAVDIDEAHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLL 171


                  ....*...
gi 2309718997 178 KLRECLTR 185
Cdd:PRK12514  172 KLRECLSR 179
 
Name Accession Description Interval E-value
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 18-185 2.51e-82

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 241.26  E-value: 2.51e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGYSPMTWLITIARNHAIDRLRKRR 97
Cdd:PRK12514   12 RVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPMTWLITIARNHAIDRLRARK 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  98 SGSAPLEDADTVPDGAPGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLM 177
Cdd:PRK12514   92 AVAVDIDEAHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLL 171


                  ....*...
gi 2309718997 178 KLRECLTR 185
Cdd:PRK12514  172 KLRECLSR 179
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 18-185 5.15e-40

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: 133.97  E-value: 5.15e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGySPMTWLITIARNHAIDRLRKRR 97
Cdd:COG1595    10 RLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRG-SFRAWLYRIARNLAIDHLRKRR 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  98 SGSAPLED-ADTVPDGAPGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSL 176
Cdd:COG1595    89 RRRELLDElAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRAR 168


                  ....*....
gi 2309718997 177 MKLRECLTR 185
Cdd:COG1595   169 KKLREALEE 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 25-183 1.75e-32

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: 113.98  E-value: 1.75e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  25 AAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVvGYSPMTWLITIARNHAIDRLRKRRSGSAPLE 104
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDP-EGSFKAWLFRIARNLILDYLRRKRRLRRELD 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2309718997 105 DADTVPDGAPGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLRECL 183
Cdd:TIGR02937  80 LLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 30-97 5.17e-12

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: 58.37  E-value: 5.17e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2309718997  30 LYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRV-VGYSPMTWLITIARNHAIDRLRKRR 97
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPeRGVSFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 126-180 3.30e-04

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: 37.08  E-value: 3.30e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2309718997 126 RAALMRCLGEL-ERQRaEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLR 180
Cdd:cd06171     1 RERLEEALDKLpERER-EVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 18-185 2.51e-82

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 241.26  E-value: 2.51e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGYSPMTWLITIARNHAIDRLRKRR 97
Cdd:PRK12514   12 RVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPMTWLITIARNHAIDRLRARK 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  98 SGSAPLEDADTVPDGAPGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLM 177
Cdd:PRK12514   92 AVAVDIDEAHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLL 171


                  ....*...
gi 2309718997 178 KLRECLTR 185
Cdd:PRK12514  172 KLRECLSR 179
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 19-185 1.65e-44

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 145.58  E-value: 1.65e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  19 TAMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGYSPMTWLITIARNHAIDRLRKR-- 96
Cdd:PRK12534   19 TAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGLTWLAMIARNKAIDHLRANap 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  97 RSGSAPLEDADTVPDGAPGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSL 176
Cdd:PRK12534   99 QRRNVALDDAGELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGL 178


                  ....*....
gi 2309718997 177 MKLRECLTR 185
Cdd:PRK12534  179 AKLKACLER 187
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 18-185 5.15e-40

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: 133.97  E-value: 5.15e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGySPMTWLITIARNHAIDRLRKRR 97
Cdd:COG1595    10 RLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRG-SFRAWLYRIARNLAIDHLRKRR 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  98 SGSAPLED-ADTVPDGAPGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSL 176
Cdd:COG1595    89 RRRELLDElAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRAR 168


                  ....*....
gi 2309718997 177 MKLRECLTR 185
Cdd:COG1595   169 KKLREALEE 177
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 22-185 7.98e-34

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 118.15  E-value: 7.98e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  22 GDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGySPMTWLITIARNHAIDRLRKRRSGSA 101
Cdd:PRK11924   10 GDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKG-SARTWLLTIARNVCYDLLRRRRREKA 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997 102 PLEDADTVPDGA---PGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMK 178
Cdd:PRK11924   89 VLSDDALEPEFAetaETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQL 168


                  ....*..
gi 2309718997 179 LRECLTR 185
Cdd:PRK11924  169 LRECLEA 175
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 25-183 1.75e-32

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: 113.98  E-value: 1.75e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  25 AAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVvGYSPMTWLITIARNHAIDRLRKRRSGSAPLE 104
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDP-EGSFKAWLFRIARNLILDYLRRKRRLRRELD 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2309718997 105 DADTVPDGAPGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLRECL 183
Cdd:TIGR02937  80 LLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
18-183 2.12e-32

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 114.77  E-value: 2.12e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGYSPMTWLITIARNHAIDRLRKRR 97
Cdd:PRK09646   23 RVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARGSALAWLLTLAHRRAVDRVRSEQ 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  98 SGSA--PLEDADTVPDGAPGPEAAVLASSERAALMRCLGEL-ERQRaEAVQRAYLLGETYAELAARYSVPVNTMRTWLRR 174
Cdd:PRK09646  103 AASQreVRYGARNVDPAFDQVAEEVEARLERERVRDCLDALtDTQR-ESVTLAYYGGLTYREVAERLAVPLGTVKTRMRD 181


                  ....*....
gi 2309718997 175 SLMKLRECL 183
Cdd:PRK09646  182 GLIRLRDCL 190
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 22-183 2.02e-26

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 99.36  E-value: 2.02e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  22 GDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIW----CNADRyrvvgYSPMTWLITIARNHAIDRLRKRR 97
Cdd:PRK12519   26 GQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWrkssYDPKR-----GSLSSYLLTLTRSRAIDRLRSRR 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  98 SGSAPLEDADTVPDGAPGPEAAV--LASSERAALMR-CLGEL-ERQRaEAVQRAYLLGETYAELAARYSVPVNTMRTWLR 173
Cdd:PRK12519  101 SRQRLLERWQQELLGEASEDTPLeqASLAERSQRVQtALAQLpESQR-QVLELAYYEGLSQSEIAKRLGIPLGTVKARAR 179

                         170
                  ....*....|
gi 2309718997 174 RSLMKLRECL 183
Cdd:PRK12519  180 QGLLKLRELL 189
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 20-184 3.06e-26

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 98.70  E-value: 3.06e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  20 AMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGYSPMTWLITIARNHAIDRLRKRRSg 99
Cdd:PRK12537   18 ARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARGSARGWIYSVTRHLALNVLRDTRR- 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997 100 SAPLEDADTvpDGAPGPEAAV---LASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSL 176
Cdd:PRK12537   97 EVVLDDDAE--ETAQTLHEIIddfDLWANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSL 174


                  ....*...
gi 2309718997 177 MKLRECLT 184
Cdd:PRK12537  175 KALRECMG 182
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 18-185 7.58e-23

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 90.10  E-value: 7.58e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGYSPMTWLITIARNHAIDRLRKRR 97
Cdd:PRK05602   13 RVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGEARFDTWLHRVVLNLCYDRLRRRR 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  98 sgSAPLEDADTVPDGAPGPEAAVLASSERAALMRCLGEL-ERQRaEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSL 176
Cdd:PRK05602   93 --EVPVEDAPDVPDPAPGPDAGLEARQRARRVEQALAALpERQR-EAIVLQYYQGLSNIEAAAVMDISVDALESLLARGR 169


                  ....*....
gi 2309718997 177 MKLRECLTR 185
Cdd:PRK05602  170 RALRAQLAD 178
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 20-183 4.03e-22

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 88.05  E-value: 4.03e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  20 AMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGYSPMTWLITIARNHAIDRLRKRRSG 99
Cdd:PRK13919   18 ARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRGSARAWLLALAHHAAVDHVRRRAAR 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997 100 SAPLEDADTVPDG--APGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLM 177
Cdd:PRK13919   98 PQPLEPDEREPEAfdLPGPGLDEEGHLDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALS 177


                  ....*.
gi 2309718997 178 KLRECL 183
Cdd:PRK13919  178 RLKEVL 183
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 18-185 5.27e-22

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 87.86  E-value: 5.27e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRvvGYSPM-TWLITIARNHAIDRLRKR 96
Cdd:PRK12515   15 RIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFE--GRSQVsTWLLSIARFKALSALRRR 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  97 RSGSAPLEDADTVPDGAPGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSL 176
Cdd:PRK12515   93 KHEEIDDEAAAAIEDGADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYAR 172


                  ....*....
gi 2309718997 177 MKLRECLTR 185
Cdd:PRK12515  173 KKLAELLKA 181
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 18-181 9.79e-22

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 86.78  E-value: 9.79e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRvVGYSPMTWLITIARNHAIDRLRKRR 97
Cdd:PRK09652    3 RVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR-GGAAFYTWLYRIARNTAINYLRKQG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  98 ----SGSAPLEDADTVPDGA-----PGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTM 168
Cdd:PRK09652   82 rrppASDVDAEEAEDFDLADalrdiSTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTV 161

                         170
                  ....*....|...
gi 2309718997 169 RTWLRRSLMKLRE 181
Cdd:PRK09652  162 RSRIFRAREALRA 174
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 22-180 9.58e-18

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 76.66  E-value: 9.58e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  22 GDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRvVGYSPMTWLITIARNHAIDRLRKRR---- 97
Cdd:PRK09641   15 GDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYD-INRKFSTWLYRIATNLTIDRLRKRKpdyy 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  98 -----SGSAPLEDADTVPDGAPGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWL 172
Cdd:PRK09641   94 ldaevAGTEGLTMYSQLAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRI 173


                  ....*...
gi 2309718997 173 RRSLMKLR 180
Cdd:PRK09641  174 HRGREALR 181
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 18-183 3.62e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 75.11  E-value: 3.62e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGySPMTWLITIARNHAIDRLRKRR 97
Cdd:PRK12513   19 RYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRA-RFRTWLYQIARNLLIDHWRRHG 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  98 SGSAPLEDAD----TVPDGAPGPEAAVLASSERAALMRCLGEL-ERQRAEAVQRAYlLGETYAELAARYSVPVNTMRTWL 172
Cdd:PRK12513   98 ARQAPSLDADeqlhALADDGAAPEQQLSLFRDRRRLQAALETLpDEQREVFLLREH-GDLELEEIAELTGVPEETVKSRL 176

                         170
                  ....*....|.
gi 2309718997 173 RRSLMKLRECL 183
Cdd:PRK12513  177 RYALQKLRELL 187
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 20-165 2.22e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 73.39  E-value: 2.22e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  20 AMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGYSPMTWLITIARNHAIDRLRKRRSG 99
Cdd:PRK12524   21 ANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGEARVSTWLYRVVCNLCTDRLRRRRRA 100

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2309718997 100 SAPLEDADTVPDGAPGPEAAVLASSERAALMRCLGEL-ERQRAEAVQRaYLLGETYAELAARYSVPV 165
Cdd:PRK12524  101 SVDLDDAPEPADAAPGAEEALIEGDRMRALDAALAALpERQRQAVVLR-HIEGLSNPEIAEVMEIGV 166
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 26-183 1.04e-15

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: 70.67  E-value: 1.04e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  26 AFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVgYSPMTWLITIARNHAIDRLRKRR-------S 98
Cdd:TIGR02985   2 AFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEIS-ESIKAYLFTIVKNRCLNYLRHKQveekyqeE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  99 GSAPLEDADTVPDgapgPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMK 178
Cdd:TIGR02985  81 LAEIEERELSEAD----PEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKF 156


                  ....*
gi 2309718997 179 LRECL 183
Cdd:TIGR02985 157 LRKEL 161
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 18-185 5.90e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 67.30  E-value: 5.90e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRvvGYSP-MTWLITIARNHAIDRLRKR 96
Cdd:PRK11922   23 RVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFR--GDASlSTWLSRIVLNEALGRLRRR 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  97 RSGSAPLEDAD----------TVPDGAPGPEAAVLASSERAALMRCLGEL-ERQRAEAVQRAyLLGETYAELAARYSVPV 165
Cdd:PRK11922  101 RRLVNLAEMVMastiaggertPLADPAEDPERAAARREIRALLERAIDALpDAFRAVFVLRV-VEELSVEETAQALGLPE 179

                         170       180
                  ....*....|....*....|
gi 2309718997 166 NTMRTWLRRSLMKLRECLTR 185
Cdd:PRK11922  180 ETVKTRLHRARRLLRESLAR 199
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 23-180 8.29e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 66.49  E-value: 8.29e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  23 DRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGYSPMTWLITIARNHAIDRLRKRRSGSAP 102
Cdd:PRK12531   25 DKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKSALSTWIYTIIRNLCFDLLRKQKGKDLH 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997 103 LEDADTVPDGAPGPEAAVLASSERAAL----MRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMK 178
Cdd:PRK12531  105 IHADDIWPSDYYPPDLVDHYSPEQDMLkeqvMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEK 184


                  ..
gi 2309718997 179 LR 180
Cdd:PRK12531  185 LR 186
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 27-181 1.02e-12

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 62.66  E-value: 1.02e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  27 FGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRvvgYSPMTWLITIARNHAIDRLRK------RRSGS 100
Cdd:PRK09639    5 FEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRSDFKGI---ENEKGWLIKSARNVAYNYLRSekrrraRILGE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997 101 APLEDADTVPDgapgPEAAVLASSERAALMRCLGEL-ERQRAEAVQRayLLGETYAELAARYSVPVNTMRTWLRRSLMKL 179
Cdd:PRK09639   82 FQWQEVDNEPS----PEEIWIRKEEITKVQEVLAKMtERDRTVLLLR--FSGYSYKEIAEALGIKESSVGTTLARAKKKF 155


                  ..
gi 2309718997 180 RE 181
Cdd:PRK09639  156 RK 157
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 18-184 1.76e-12

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 62.80  E-value: 1.76e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRvvGYSPM-TWLITIARNHAIDRLRKR 96
Cdd:PRK09643   20 AHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFR--GDAAVsSWLHRIVVNACLDRLRRA 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  97 RS-GSAPLEDADTVPDGAPGPEAAV-LASSERAALMRCLGElerQRAeAVQRAYLLGETYAELAARYSVPVNTMRTWLRR 174
Cdd:PRK09643   98 KArPTVPLDDVYPVAQLERDPTARVeTALAVQRALMRLPVE---QRA-ALVAVDMQGYSVADAARMLGVAEGTVKSRCAR 173

                         170
                  ....*....|
gi 2309718997 175 SLMKLRECLT 184
Cdd:PRK09643  174 GRARLAELLG 183
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 30-97 5.17e-12

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: 58.37  E-value: 5.17e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2309718997  30 LYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRV-VGYSPMTWLITIARNHAIDRLRKRR 97
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPeRGVSFSTWLYTIIRNAIIDYLRKQR 69
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 22-180 1.57e-11

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 59.65  E-value: 1.57e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  22 GDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYR-VVGYSpmTWLITIARNHAIDRLRKRRSGS 100
Cdd:PRK09638   15 GDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQgRSKFS--TWLISIASRLYKDHLRKQKREK 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997 101 APLEDADTVPDGAPGPEAAVlASSERAALMRCLGEL-ERQRAEAVQRAYlLGETYAELAARYSVPVNTMRTWLRRSLMKL 179
Cdd:PRK09638   93 LRLQRAKEETLRKEKWEAAI-KGAEWSEMLDALSKLdPEFRAPVILKHY-YGYTYEEIAKMLNIPEGTVKSRVHHGIKQL 170


                  .
gi 2309718997 180 R 180
Cdd:PRK09638  171 R 171
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
30-180 2.53e-11

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 59.32  E-value: 2.53e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  30 LYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGYSPMTWLITIARNHAIDRLRKRRSgsaplEDADTV 109
Cdd:PRK09645   14 LYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRSARAWLFTVARNLVIDERRSARA-----RPVEGG 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2309718997 110 PDGAPGPEAAVLASSERAA----LMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLR 180
Cdd:PRK09645   89 DDVLGVPEQSAPDEVDRALdrllVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALR 163
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 26-182 2.55e-11

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: 58.87  E-value: 2.55e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  26 AFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVvGYSPMTWLITIARNHAIDRLRKRRSGSAPLED 105
Cdd:TIGR02989   2 AFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDP-GTNFVAWARGIARNKVLNYRRKLGRDRLVFDD 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2309718997 106 aDTVPDGAPGPEAAVLASSE--RAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLREC 182
Cdd:TIGR02989  81 -DLLEALAAEAEPTEAERLSddRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSLREC 158
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 18-185 3.34e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 59.87  E-value: 3.34e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGYSPMTWLITIARNHAIDRLRKRR 97
Cdd:PRK12538   56 RLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRAKFSTWLYRVVSNRCIDLRRKPR 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  98 SgsaplEDADTVPDGAPGPEAAVlASSERAALMRCLGE----LERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLR 173
Cdd:PRK12538  136 T-----ENVDAVPEVADGKPDAV-SVIERNELSDLLEAamqrLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLK 209

                         170
                  ....*....|..
gi 2309718997 174 RSLMKLRECLTR 185
Cdd:PRK12538  210 RGRQQLRDLLRR 221
PRK09642 PRK09642
RNA polymerase sigma factor;
38-175 2.37e-10

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 56.26  E-value: 2.37e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  38 LFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGYSpmTWLITIARNHAIDRLRKRRSGSAPL---EDADTVPDGAP 114
Cdd:PRK09642    8 IFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFRGLK--TWMARIATNHAIDYKRKKARENEELslcKETEENIKSSH 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2309718997 115 GPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRS 175
Cdd:PRK09642   86 NIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRA 146
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
18-120 3.32e-10

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 57.64  E-value: 3.32e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGySPMTWLITIARNHAIDRL--RK 95
Cdd:PRK08241   12 RAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGRS-SLRTWLYRIATNVCLDALegRA 90

                          90       100
                  ....*....|....*....|....*
gi 2309718997  96 RRSGSAPLEDADTVPDGAPGPEAAV 120
Cdd:PRK08241   91 RRPLPTDLGAPAADPVDELVERPEV 115
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 52-183 6.07e-09

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 52.83  E-value: 6.07e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  52 AEDALQEIYVKIWCNADRYRvvGYSPM-TWLITIARNHAIDRLRK--RRSGSAPLEDADTVPDGAPGPEAAVLASSERAA 128
Cdd:PRK09415   43 AEDLTQEIFVKCYKSLHTYK--GKSSLkTWLYRIAINHCKDYLKSwhNKKVIVTEDIFTYMESQKESVEEEVIQNAEDER 120

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2309718997 129 LMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLRECL 183
Cdd:PRK09415  121 LASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 35-185 6.95e-09

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 53.25  E-value: 6.95e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  35 SAKLFGICLRVLSKEQEAEDALQEIYVKIwcnadrYRVV-GYSPMT---WLITIARNHAIDRLRKR---RSGSAPlEDAD 107
Cdd:PRK09647   38 ADRVYRLAYRLSGNQHDAEDLTQETFIRV------FRSLqNYQPGTfegWLHRITTNLFLDMVRRRariRMEALP-EDYD 110

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2309718997 108 TVPDGAPGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLRECLTR 185
Cdd:PRK09647  111 RVPGDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAA 188
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 23-181 1.10e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 52.50  E-value: 1.10e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  23 DRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGYSPMTWLITIARNHAIDRLRKRRSGSA- 101
Cdd:PRK12526   36 DKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKGAATTWVYTVMRNAAFDMLRKIKAKKEq 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997 102 -------PLEDADTVPDGAPGPEAAVLassERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRR 174
Cdd:PRK12526  116 nlgddiwPIEQALAESQSESEEFSDHL---MDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRL 192


                  ....*..
gi 2309718997 175 SLMKLRE 181
Cdd:PRK12526  193 ALAKLKV 199
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 18-175 1.31e-08

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 52.11  E-value: 1.31e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAMGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRvvGYSPM-TWL----ITIARNHAIDR 92
Cdd:PRK11923   13 RVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFR--GDSAFyTWLyriaINTAKNHLVSR 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  93 LRKRRSGSAPLEDADTVP-DGA----PGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNT 167
Cdd:PRK11923   91 GRRPPDSDVSSEDAEFYDgDHAlkdiESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGT 170


                  ....*...
gi 2309718997 168 MRTWLRRS 175
Cdd:PRK11923  171 VRSRIFRA 178
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 44-184 6.54e-08

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 49.98  E-value: 6.54e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  44 RVlSKEQEAEDALQEIYVKIWCNADRYRVVGySPMTWLITIARNHAIDRLRKrRSGSAPLEDADTVPDGAPGPEAavlas 123
Cdd:PRK09637   21 RV-SNEADVDDLLQEVLIKTHSNLHSLKDGS-SIKSWLYQIANNTIIDFYRK-KNRSEELPDDLLFEDEEREENA----- 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2309718997 124 seRAALMRCL----GELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLRECLT 184
Cdd:PRK09637   93 --KKELAPCLrpfiDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE 155
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 30-175 2.04e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 48.89  E-value: 2.04e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  30 LYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVGYSPMT-WLITIARNHAIDRLRKRRSGSAPLED--- 105
Cdd:PRK12542   14 LYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKrYILRVAKNKAIDSYRKNKRHETFLEEyer 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2309718997 106 --ADTVPDGAPGPEAAVLASSERAALMRCLGELERQraeAVQRAYLLGETYAELAARYSVPVNTMRTWLRRS 175
Cdd:PRK12542   94 esIEAVDENIEEWEKRKMSEVQIDTLLKELNESNRQ---VFKYKVFYNLTYQEISSVMGITEANVRKQFERA 162
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 18-179 3.14e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 48.16  E-value: 3.14e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAM-GDRAAFGRLYQLTSAKLFGI----CLRVLSKEQEAEDALQEIYVKIWCNADRYRVVG-YSPmtWLITIARNHAID 91
Cdd:PRK12512   14 RSANaGDAAAYRRLLKAVTPVLRAAarrgLARAGQPADQAEDIVQEILLAVHLKRHTWDPGApFAP--WLFAIARNKLID 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  92 RLRKR-RSGSAPLED-ADTVPDGAPGPeaavlaSSERAALMRCLGEL-ERQRaEAVQRAYLLGETYAELAARYSVPVNTM 168
Cdd:PRK12512   92 ALRRRgRRVFVDIDDfAETLPAEPATE------TLPAGDVGRHLETLpPRQR-DVVQSISVEGASIKETAAKLSMSEGAV 164

                         170
                  ....*....|.
gi 2309718997 169 RTWLRRSLMKL 179
Cdd:PRK12512  165 RVALHRGLAAL 175
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 23-181 5.54e-07

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 47.63  E-value: 5.54e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  23 DRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRvvGYSPM-TWLITIARNHAIDRLRKRRSGSA 101
Cdd:PRK09640   24 VTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFE--GKSKFkTWLYSITYNECITQYRKERRKRR 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997 102 PLEDADTVPDGAPGPEAAVlASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLRE 181
Cdd:PRK09640  102 LMDALSLDPLEEASEEKAP-KPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLRE 180
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 28-182 7.34e-07

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 47.15  E-value: 7.34e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  28 GRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIwcnADRYRVVG-YSPMTWLITIARNHAIDRLRKRRSGSAPLEDA 106
Cdd:PRK12523   13 GALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRL---LGRPELPTpREPRAFLAAVAKGLMFDHFRRAALEQAYLAEL 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2309718997 107 DTVPDGA-PGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSlmkLREC 182
Cdd:PRK12523   90 ALVPEAEqPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQG---LRQC 163
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 30-183 9.44e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 46.41  E-value: 9.44e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  30 LYQLTSAKLFGICLrvLSKEQEAEDALQEIYVKIWCNADRYRVvGYSPMTWLITIARNHAIDRLRKRRSgsaPLEDADTV 109
Cdd:PRK12547   13 LLALPALRAFAVSL--SSKHDKAEDLVQDTLMKAWAKQDSFEM-GTNLKAWLFTILRNEFYSQMRKRGR---EVQDSDGV 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2309718997 110 PDGAPGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLRECL 183
Cdd:PRK12547   87 FTARVAVHPAQYGSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 126-179 9.69e-07

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 43.98  E-value: 9.69e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2309718997 126 RAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKL 179
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 20-183 5.69e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 44.57  E-value: 5.69e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  20 AMGDRAAFGR--LYQLTSAKLFGICLrvLSKEQEAEDALQEIYVKIWCNADRYRVvGYSPMTWLITIARNHAIDRLRKRr 97
Cdd:PRK12516    5 SVEGTPPFKRelLAALPSLRAFAVSL--IGRHDRADDLVQDTIMKAWAKQDHFEV-GTNMKAWLFTILRNEFYSQMRKR- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  98 sgSAPLEDADTVPDGAPGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLM 177
Cdd:PRK12516   81 --GREVQDTDGMFTEQLAVHPSQYGTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQ 158


                  ....*.
gi 2309718997 178 KLRECL 183
Cdd:PRK12516  159 RLQEIL 164
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 46-185 7.28e-06

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 44.10  E-value: 7.28e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  46 LSKEQE-AEDALQEIYVKIWCNADRYRVVGYSPmtWLITIARNHAIDRLRK-RRSGSAPLEDADTVPdgAPGPEAAVLAS 123
Cdd:PRK09644   21 LTKSHHaAEDLLQETFYRAYIYLEDYDNQKVKP--WLFKVAYHTFIDFVRKeKKVSFVGTDEIEAIQ--AESTEEYVVAK 96

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2309718997 124 SERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLRECLTR 185
Cdd:PRK09644   97 NSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 36-183 1.37e-05

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 43.14  E-value: 1.37e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  36 AKLFGICLRVLSKEQEAEDALQEIYVKI--WCNADRYRvvgySPMTWLITIARNHAIDRLRKR---RSGSAPLEDADTVP 110
Cdd:PRK07037    9 SMLVKIAARIVGCRSRAEDVVQDAFVKLveAPNQDAVK----QPVAYLFRIVRNLAIDHYRRQaleNKYHGDEEDGLDVP 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2309718997 111 DGAPGPEAAVLASSERAALMRCLGEL-ERQRAeAVQRAYLLGETYAELAARYSVP---VNTMrtwLRRSLMKLRECL 183
Cdd:PRK07037   85 SPEASPEAALINRDTLRHVADALSELpARTRY-AFEMYRLHGETQKDIARELGVSptlVNFM---IRDALVHCRKCL 157
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 22-181 2.00e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 43.18  E-value: 2.00e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  22 GDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIW---CNADRYRvvgySPMTWLITIA-------RNHAID 91
Cdd:PRK12543    4 GDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWeslRKYDSNR----PFRFWLIGLVikqihswRRKRWR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  92 RLR---KRRSGSAPLEDADtvpdgapgpEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTM 168
Cdd:PRK12543   80 RFRifeKAEEQRKPVSIDF---------SEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTV 150

                         170
                  ....*....|...
gi 2309718997 169 RTWLRRSLMKLRE 181
Cdd:PRK12543  151 KSRIHAALKKLRQ 163
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 39-180 2.02e-05

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 43.00  E-value: 2.02e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  39 FGICLRVLSK---EQEAEDALQEIYVKIWCNADRYRVVGYSPMTWLITIARNHAIDRLRK-RRSGSAPLEDADTVPDGAP 114
Cdd:PRK06811   32 KKIVHKVLGTvnySQLIEECVNDIFLSIWNNIDKFDEEKGSFKKWIAAISKYKAIDYKRKlTKNNEIDSIDEFILISEES 111

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2309718997 115 GpEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLR 180
Cdd:PRK06811  112 I-ENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQ 176
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 49-181 2.13e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 42.85  E-value: 2.13e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  49 EQEAEDALQEIYVKIWCNADRYRVvGYSPMTWLITIARNHAIDRLRKRRSGSAPLEDADTVPDGA--PGPEAAVLASSER 126
Cdd:PRK12511   28 SAEAEDLVHDALVRALERRASFRS-GGNLRTWLMSILHNAFIDELRRRRVEARRADELAVLADASlpAAQEHAVRLAQIR 106

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2309718997 127 AALMRClgeLERQRAeAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLRE 181
Cdd:PRK12511  107 DAFFDL---PEEQRA-ALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
51-169 3.69e-05

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 42.41  E-value: 3.69e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  51 EAEDALQEIYVKIWCNADRYRVVgySPMT-WLITIARNHAIDRLRKRRSGSA--PLEDADTVpdGAPGPEAAVLASSERA 127
Cdd:PRK12539   51 EAEDLVQEALMAIHTRRHTYDPE--QPLTpWVYAIARYKLIDHLRRTRASLAdvPIDDADEL--VAHDDHAAVESTLDLG 126

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2309718997 128 ALMRCLGELERQRAEAVQrayLLGETYAELAARY-----SVPVNTMR 169
Cdd:PRK12539  127 RLLARLPEKMRLAIQAVK---LEGLSVAEAATRSgmsesAVKVSVHR 170
PRK12545 PRK12545
RNA polymerase factor sigma-70;
52-184 5.27e-05

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 42.25  E-value: 5.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  52 AEDALQEIYVKIWCNADRYrvVGYSP-MTWLITIARNHAIDRLRKRR------------SGSAPLE----------DADT 108
Cdd:PRK12545   35 AEDAVQEALAAAWSQAGRF--AGQSAhKTWVFGILRNKLIDTLRARQrtvnlsaldaelDGEALLDrelfkdnghwAAHA 112

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2309718997 109 VPDGAPGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLRECLT 184
Cdd:PRK12545  113 KPRPWPKPETILQQQQFWTLFETCLDHLPEQIGRVFMMREFLDFEIDDICTELTLTANHCSVLLYRARTRLRTCLS 188
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 21-158 5.76e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 41.46  E-value: 5.76e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  21 MGDRAAFGRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRvvGYSPMTWLITIARNHAIDRLRK-RRSG 99
Cdd:PRK12541    1 MKRKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYK--GEEIRPWLFTIAYNAFIDWYRKeKKYK 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2309718997 100 SAPLEDADTVPdgAPGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELA 158
Cdd:PRK12541   79 TTTIEEFHLPN--VPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIA 135
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 18-175 1.43e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 40.65  E-value: 1.43e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAMGDRAAFGRLYQLTSAKLFGIcLRVLSKEQEAEDALQEIYVKIWCNADRYrVVGYSPMTWLITIARNHAIDRLR--- 94
Cdd:PRK12535   18 AAGRGDRAALTEFIRETQDDVWRL-LAHLGGHDIADDLTQETYLRVMSALPRF-AARSSARTWLLSLARRVWVDNIRhdm 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  95 -KRRSGSAPLEDADtvpDGAPGPEAAVLASsERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLR 173
Cdd:PRK12535   96 aRPRKSATEYEDAA---ATTASNETTGSWS-EWIDVRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVA 171


                  ..
gi 2309718997 174 RS 175
Cdd:PRK12535  172 RA 173
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 18-117 2.03e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 40.09  E-value: 2.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAMGDRAAFGRLYQLTSAK----LFGICLRVLskeqeAEDALQEIYVKIWCNADRYRVVGYSPmTWLITIARNHAIDRl 93
Cdd:PRK12518    4 RCQRGDRQSFRQLYRRYQQKvrstLYQLCGREL-----LDDLVQEVFLRVWKGLPKLRNPAYFS-TWLYRITWNVATDA- 76

                          90       100
                  ....*....|....*....|....
gi 2309718997  94 RKRRSGSAPLEDADTVPDGAPGPE 117
Cdd:PRK12518   77 RRQFAQRPSRIQDDSLNDQPSRPS 100
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 52-185 2.28e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 40.30  E-value: 2.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  52 AEDALQEIYVKIWCNADRYRvvGYSPM-TWLITIARNHAIDRLRKR---RSGSAPLEDADT--------------VPDGA 113
Cdd:PRK12532   33 AEDLVQETLLSAYSAGDSFQ--GRALVnSWLFAILKNKIIDALRQIgrqRKVFTLLDDELLdeafeshfsqnghwTPEGQ 110

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2309718997 114 PG----PEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLRECLTR 185
Cdd:PRK12532  111 PQhwntPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQI 186
PRK12544 PRK12544
RNA polymerase factor sigma-70;
46-183 2.40e-04

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 40.17  E-value: 2.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  46 LSKEQEAEDALQEIYVKIWCNADRYRvvGYSPM-TWLITIARNHAIDRLRKRR---SGSAPLEDADT------------- 108
Cdd:PRK12544   39 LSDLHLAEDAVQEALIGALKNADSFA--GRAAFkTWVFAILKNKIIDLLRQKKrhvSASSLLRDEEEeedfeelfdesgh 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997 109 -VPDGAP----GPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLRECL 183
Cdd:PRK12544  117 wQKDERPqawgNPEESLEQEQFWRIFEACLDGLPAKYARVFMMREFIELETNEICHAVDLSVSNLNVLLYRARLRLRECL 196
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 126-180 3.30e-04

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: 37.08  E-value: 3.30e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2309718997 126 RAALMRCLGEL-ERQRaEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLR 180
Cdd:cd06171     1 RERLEEALDKLpERER-EVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
18-140 3.58e-04

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 39.57  E-value: 3.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  18 RTAMGDRAAFGRLYQLTSAKLFGIC-LRVLSKEQ---EAEDALQEIYVKIWCNADRYRVVGYSPMTWLITIARNHAIDRL 93
Cdd:PRK09648   17 EAVAGDRRALREVLEIIRPLVVRYCrARLGGVERpglSADDVAQEVCLAVITALPRYRDQGRPFLAFVYGIAAHKVADAH 96

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2309718997  94 RKR-RSGSAPLEDADTVPDGAPGPEAAVLASSERAALMRCLGEL-ERQR 140
Cdd:PRK09648   97 RAAgRDKAVPTEEVPERPSDDAGPEERALRSESSNRMRELLDTLpEKQR 145
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 20-175 4.13e-04

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 39.25  E-value: 4.13e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  20 AMGDRAAFGRLYQLTSAKLFGIcLRVLSKEQEAEDALQEIYVKIWCNADRYRvvGYSP-MTWLITIARNHAIDRLRKrrs 98
Cdd:PRK09649   19 AKGNGRALEAFIKATQQDVWRF-VAYLSDVGSADDLTQETFLRAIGAIPRFS--ARSSaRTWLLAIARHVVADHIRH--- 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  99 gsapledADTVPDGAPGPEAAVLASSERAA--------LMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRT 170
Cdd:PRK09649   93 -------VRSRPRTTRGARPEHLIDGDRHArgfedlveVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRS 165


                  ....*
gi 2309718997 171 WLRRS 175
Cdd:PRK09649  166 RVARA 170
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 30-178 4.71e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 39.06  E-value: 4.71e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  30 LYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVVgySPMTWLITIARNHAIDRLRKRRSGSAPLEDAdtv 109
Cdd:PRK12528    9 LYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQII--EPRAFLTTIAKRVLCNHYRRQDLERAYLEAL--- 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2309718997 110 pdgAPGPEAAVLASSERAALMRCLGELER---QRAEAVQRAYLL----GETYAELAARYSVPVNTMRTWLRRSLMK 178
Cdd:PRK12528   84 ---AQLPERVAPSEEERAIILETLVELDQlldGLPPLVKRAFLLaqvdGLGYGEIATELGISLATVKRYLNKAAMR 156
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 28-176 7.96e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 38.39  E-value: 7.96e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  28 GRLYQLTSAKLFGICLRVLSKEQEAEDALQEIYVKIWCNADRYRVvgYSPMTWLITIARNHAIDRLRKRRSGSAPLEDAD 107
Cdd:PRK12525   12 GQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI--REPRALLTTIARRLMYEGWRRQDLERAYLQSLA 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997 108 TVPDG-APGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSL 176
Cdd:PRK12525   90 EAPEAvQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAF 159
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 52-183 1.25e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 37.90  E-value: 1.25e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  52 AEDALQEIYVKIWCNADRYRvVGYSPMTWLITIARNHAIDRLRKRRSgsaPLEDADTVPDGA----PGPEAAVLASSERA 127
Cdd:PRK12546   34 ADDLVQDTIVKAWTNFDKFQ-EGTNLRAWLFTILRNTFYSDRRKHKR---EVPDPEGVHAASlavkPAHDGRLAMSDFRA 109

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2309718997 128 AlmrcLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLRECL 183
Cdd:PRK12546  110 A----FAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 50-184 1.81e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 37.79  E-value: 1.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  50 QEAEDALQEIYVKIWCNADRYRvvGYSPMTWLITIARNHAIDRLRKRRSGSA-----PLEDADTVPDGAPGPE--AAVLA 122
Cdd:PRK12533   43 SDADDVVQEACMRALRFFDSFR--GDNARPWLLAIVRHTWYSEWRRRANAHEvaapdTLDDADSLDDWQPAGEdpLALLL 120

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2309718997 123 SSERAALM-RCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLRECLT 184
Cdd:PRK12533  121 RAEDVRLVnAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRRLAALLG 183
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 37-159 1.96e-03

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 37.98  E-value: 1.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  37 KLFGICLRVLSKEQEAEDALQEIYVKiWCNADRYRVvgYSPMTWLITIARNHAIDRLR----KRRSGSAPLEDADTVPDG 112
Cdd:PRK09636   16 HLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI--RDPRAWLTRVVTRLCLDRLRsarhRRETYVGPWLPEPVVEEL 92

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2309718997 113 APGPEAAVLASSERAALMRCLgelerQRAEAVQR-AYLL----GETYAELAA 159
Cdd:PRK09636   93 DDPLEAVVAAEDLSLALMLAL-----ERLSPLERaAFLLhdvfGVPFDEIAS 139
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 52-185 2.05e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 37.44  E-value: 2.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  52 AEDALQEIYVKIWCNADRYRvvGYSPM-TWLITIARNHAID--RLRKRRSGSAPLEDADT----------------VPDG 112
Cdd:PRK12530   34 AEDVVQEALVSAYKNADSFK--GQSALkTWIFAILKNKIIDliRYRKRFVNESELIEEDSpnsffdekghwkpeyyEPSE 111

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2309718997 113 APGPEAAVLASSERAALMRCLGELERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLRECLTR 185
Cdd:PRK12530  112 WQEVENTVYKEEFWLIFEACLNHLPAQQARVFMMREYLELSSEQICQECDISTSNLHVLLYRARLQLQACLSK 184
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 30-183 4.60e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 36.48  E-value: 4.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2309718997  30 LYQLTSAKLFGICLRvlSKEQEAEDALQEIYVKIWCNADRYRVvGYSPMTWLITIARNHAIDRLRKRRSgsaPLEDAD-- 107
Cdd:PRK12540   12 LAAVPSLRAFAISLS--GNGDRADDLVQETLLRALANIDSFQP-GSNLPAWLFTILRNLFRSDYRKRRR---EVEDADgs 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2309718997 108 --TVPDGAPGPEAAVLASSERAALMRclgeLERQRAEAVQRAYLLGETYAELAARYSVPVNTMRTWLRRSLMKLRECL 183
Cdd:PRK12540   86 yaKTLKSQPGQNAHLEFEEFRAALDK----LPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALL 159
 
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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