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Conserved domains on  [gi|446424305|ref|WP_000502160|]
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MULTISPECIES: sigma-70 family RNA polymerase sigma factor [Bacillus cereus group]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SigBFG super family cl37200
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 24-240 4.74e-25

RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.


The actual alignment was detected with superfamily member TIGR02980:

Pssm-ID: 274373 [Multi-domain]  Cd Length: 227  Bit Score: 100.38  E-value: 4.74e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305   24 KKYSRLVYYYVNKYFSNiakaieqetNLNMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRD-SQKIR 102
Cdd:TIGR02980  10 ELNLPLVRSIARRFRNR---------GEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDdTWAVR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  103 ITNEVYEIKGKISRMKlhdEE----------VESIAKLLEVSVRDVKTAKEF--NPRTISLQTPLnKEVNKEKVTLENTL 170
Cdd:TIGR02980  81 VPRRLKELGVKINKAT---EEltqrlgrsptIAEIAERLGVSEEEVVEALEAgnAYQALSLDASI-EDDDGDPIALLDTL 156

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446424305  171 IDKKtsMTLDDVIKKMIITAFLSTLCSKEKFVWEL-HAKNMTQAAIGKRLGVTQTQISRILKGIYKKAEEY 240
Cdd:TIGR02980 157 GDED--DALETVEDRLALKPLLAALPERERRILLLrFFEDKTQSEIAERLGISQMHVSRLLRRALKKLREQ 225
 
Name Accession Description Interval E-value
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 24-240 4.74e-25

RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.


Pssm-ID: 274373 [Multi-domain]  Cd Length: 227  Bit Score: 100.38  E-value: 4.74e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305   24 KKYSRLVYYYVNKYFSNiakaieqetNLNMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRD-SQKIR 102
Cdd:TIGR02980  10 ELNLPLVRSIARRFRNR---------GEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDdTWAVR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  103 ITNEVYEIKGKISRMKlhdEE----------VESIAKLLEVSVRDVKTAKEF--NPRTISLQTPLnKEVNKEKVTLENTL 170
Cdd:TIGR02980  81 VPRRLKELGVKINKAT---EEltqrlgrsptIAEIAERLGVSEEEVVEALEAgnAYQALSLDASI-EDDDGDPIALLDTL 156

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446424305  171 IDKKtsMTLDDVIKKMIITAFLSTLCSKEKFVWEL-HAKNMTQAAIGKRLGVTQTQISRILKGIYKKAEEY 240
Cdd:TIGR02980 157 GDED--DALETVEDRLALKPLLAALPERERRILLLrFFEDKTQSEIAERLGISQMHVSRLLRRALKKLREQ 225
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 20-236 9.92e-25

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


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 99.51  E-value: 9.92e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  20 DDFMKKYSRLVYYYVNKYfsnIAKAIEQetnlnMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRDSQ 99
Cdd:COG1191   18 EELIEEYLPLVKKIASRL---AGRLPAE-----LDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYLRDED 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305 100 KI-----RITNEVYEIKGKISRMKLHDEEVESIAKLLEVSVRDVKTAKE--FNPRTISLQTPLNkevnkEKVTLENTLID 172
Cdd:COG1191   90 WVprsvrELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEaaNAYQLLSLDEPLE-----DGDDLLDLLES 164

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446424305 173 KKTSMTLDDVIKKMIITAFLSTLCSKEKFVWELHA-KNMTQAAIGKRLGVTQTQISRILKGIYKK 236
Cdd:COG1191  165 GDPEEELEHEELREALAEAIEQLPERERLVLSLYYfEELTLKEIAEVLGVSESRVSRLHKKALAR 229
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
54-240 1.24e-17

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 80.79  E-value: 1.24e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  54 DDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRDSQKIRITNEVYEIKGKISRMKlhDE---------EV 124
Cdd:PRK05572  60 DDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDGTVKVSRSLKETANKIRKDK--DElskelgrepTI 137

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305 125 ESIAKLLEVSVRDVKTAKEFNPRTISLQtplnkevnkeKVTLEN-----TLIDKKTSMTLDDVIKKMIITAFLSTLCSKE 199
Cdd:PRK05572 138 EELAEYLGVTPEEVVLAQEASRSPQSIH----------ETVHENdgdpiTLLDQIADQSEEDWFDKIALKEAIRELDERE 207

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 446424305 200 KFVWEL-HAKNMTQAAIGKRLGVTQTQISRILKGIYKKAEEY 240
Cdd:PRK05572 208 RLIVYLrYFKDKTQSEVAKRLGISQVQVSRLEKKILKQMKEK 249
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 22-101 2.68e-10

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: 55.67  E-value: 2.68e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305   22 FMKKYSRLVYYYVNKYFSNiakaieqetNLNMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRDSQKI 101
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGD---------GADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
207-235 1.29e-03

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 36.34  E-value: 1.29e-03
                           10        20
                   ....*....|....*....|....*....
gi 446424305   207 AKNMTQAAIGKRLGVTQTQISRILKGIYK 235
Cdd:smart00530   8 EKGLTQEELAEKLGVSRSTLSRIENGKRK 36
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 207-235 3.94e-03

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 35.22  E-value: 3.94e-03
                         10        20
                 ....*....|....*....|....*....
gi 446424305 207 AKNMTQAAIGKRLGVTQTQISRILKGIYK 235
Cdd:cd00093   10 EKGLTQEELAEKLGVSRSTISRIENGKRN 38
 
Name Accession Description Interval E-value
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 24-240 4.74e-25

RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.


Pssm-ID: 274373 [Multi-domain]  Cd Length: 227  Bit Score: 100.38  E-value: 4.74e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305   24 KKYSRLVYYYVNKYFSNiakaieqetNLNMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRD-SQKIR 102
Cdd:TIGR02980  10 ELNLPLVRSIARRFRNR---------GEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDdTWAVR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  103 ITNEVYEIKGKISRMKlhdEE----------VESIAKLLEVSVRDVKTAKEF--NPRTISLQTPLnKEVNKEKVTLENTL 170
Cdd:TIGR02980  81 VPRRLKELGVKINKAT---EEltqrlgrsptIAEIAERLGVSEEEVVEALEAgnAYQALSLDASI-EDDDGDPIALLDTL 156

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446424305  171 IDKKtsMTLDDVIKKMIITAFLSTLCSKEKFVWEL-HAKNMTQAAIGKRLGVTQTQISRILKGIYKKAEEY 240
Cdd:TIGR02980 157 GDED--DALETVEDRLALKPLLAALPERERRILLLrFFEDKTQSEIAERLGISQMHVSRLLRRALKKLREQ 225
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 20-236 9.92e-25

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


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 99.51  E-value: 9.92e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  20 DDFMKKYSRLVYYYVNKYfsnIAKAIEQetnlnMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRDSQ 99
Cdd:COG1191   18 EELIEEYLPLVKKIASRL---AGRLPAE-----LDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYLRDED 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305 100 KI-----RITNEVYEIKGKISRMKLHDEEVESIAKLLEVSVRDVKTAKE--FNPRTISLQTPLNkevnkEKVTLENTLID 172
Cdd:COG1191   90 WVprsvrELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEaaNAYQLLSLDEPLE-----DGDDLLDLLES 164

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446424305 173 KKTSMTLDDVIKKMIITAFLSTLCSKEKFVWELHA-KNMTQAAIGKRLGVTQTQISRILKGIYKK 236
Cdd:COG1191  165 GDPEEELEHEELREALAEAIEQLPERERLVLSLYYfEELTLKEIAEVLGVSESRVSRLHKKALAR 229
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 50-222 9.12e-18

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 81.25  E-value: 9.12e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  50 NLNMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRDSQK-IRI-TNEVYEIKgKISRMK-------LH 120
Cdd:COG0568   54 GLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRtIRLpVHMAETLN-KLRRAKrqllqelGR 132

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305 121 DEEVESIAKLLEVSVRDVKTAKEFNPRTISLQTPLNKEvnkEKVTLENTLIDKKTSMTLDDVIKKMI---ITAFLSTLCS 197
Cdd:COG0568  133 EPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDD---EDSELGDLLEDEEAPSPEEALEEELLreeLREALDTLTE 209

                        170       180       190
                 ....*....|....*....|....*....|
gi 446424305 198 KEKFVWEL-----HAKNMTQAAIGKRLGVT 222
Cdd:COG0568  210 REREILRLrfgldDGEPHTLEEIGKEFGVS 239
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
54-240 1.24e-17

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 80.79  E-value: 1.24e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  54 DDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRDSQKIRITNEVYEIKGKISRMKlhDE---------EV 124
Cdd:PRK05572  60 DDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDGTVKVSRSLKETANKIRKDK--DElskelgrepTI 137

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305 125 ESIAKLLEVSVRDVKTAKEFNPRTISLQtplnkevnkeKVTLEN-----TLIDKKTSMTLDDVIKKMIITAFLSTLCSKE 199
Cdd:PRK05572 138 EELAEYLGVTPEEVVLAQEASRSPQSIH----------ETVHENdgdpiTLLDQIADQSEEDWFDKIALKEAIRELDERE 207

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 446424305 200 KFVWEL-HAKNMTQAAIGKRLGVTQTQISRILKGIYKKAEEY 240
Cdd:PRK05572 208 RLIVYLrYFKDKTQSEVAKRLGISQVQVSRLEKKILKQMKEK 249
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 3-239 5.29e-17

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 78.97  E-value: 5.29e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305   3 DEQKDLIE--QEDVLMMTDDDFMKKYSRLVYYYVNKYFSNiaKAIEqetnlnmDDLIQSGMLGLVTARRDFKTELGFKFT 80
Cdd:PRK08583  13 EEVNKWIAeyQENQDEEAQEKLVKHYKNLVESLAYKYSKG--QSHH-------EDLVQVGMVGLLGAIRRYDPSFGRSFE 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  81 TFAVPRILGYIRKAVRD-SQKIRITNEVYEIKGKISRM--KLHDE-----EVESIAKLLEVSVRDVKTAKEF--NPRTIS 150
Cdd:PRK08583  84 AFAVPTIIGEIKRYLRDkTWSVHVPRRIKELGPKIKKAvdELTTElqrspKISEIADRLGVSEEEVLEAMEMgkSYQALS 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305 151 LQTPLnkEVNKEKVTLenTLID--KKTSMTLDDVIKKMIITAFLSTLCSKEKFVWEL-HAKNMTQAAIGKRLGVTQTQIS 227
Cdd:PRK08583 164 VDHSI--EADSDGSTV--TLLDivGQQEDGYELTEQRMILEKILPVLSDREKSIIQCtFIENLSQKETGERLGISQMHVS 239

                        250
                 ....*....|..
gi 446424305 228 RILKGIYKKAEE 239
Cdd:PRK08583 240 RLQRQAIKKLRE 251
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 22-236 1.90e-16

RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.


Pssm-ID: 274153 [Multi-domain]  Cd Length: 224  Bit Score: 76.93  E-value: 1.90e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305   22 FMKKYSRLVYYYVNKYFSNIAKAIEQetnlnmDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILG----YIRK---- 93
Cdd:TIGR02479   1 LIRRYLPLVKRIAGRLSVGLPSSVEL------DDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGamldELRRldwv 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305   94 --AVRDSQKiRITNEVYEIKGKISRMKlhdeEVESIAKLLEVSVRDVKTAKE--FNPRTISLQTPLNKEVnkEKVTLENT 169
Cdd:TIGR02479  75 prSLRQKAR-KLERAIRELEARLGREP----TEEEIAEELGMDLKEYRQALNeiNALSLVSLDELLESGD--DGGSLIDR 147

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446424305  170 LIDKKT---SMTLDDVIKKMIITAFLSTLCSKEKFVWEL-HAKNMTQAAIGKRLGVTQTQISRILKGIYKK 236
Cdd:TIGR02479 148 IEDDKSedpEEELEREELREALAEAIESLSEREQLVLSLyYYEELNLKEIGEVLGLTESRVSQIHSQALKK 218
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 52-230 2.19e-15

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 74.43  E-value: 2.19e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  52 NMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRD-SQKIRITNEVYEIKGKISR------MKL-HDEE 123
Cdd:PRK07122  66 PRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDnSWSVKVPRRLKELHLRLGRataelsQRLgRAPT 145

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305 124 VESIAKLLEVSVRDVK----TAKEFNprTISLQTPLNKEvNKEKVTLENTLIDkkTSMTLDDVIKKMIITAFLSTLCSKE 199
Cdd:PRK07122 146 ASELAAELGMDREEVVeglvAGSAYN--TLSIDSGGGSG-DDDARAIADTLGD--VDAGLDQIENREALRPLLAALPERE 220

                        170       180       190
                 ....*....|....*....|....*....|..
gi 446424305 200 KFVWELH-AKNMTQAAIGKRLGVTQTQISRIL 230
Cdd:PRK07122 221 RTVLVLRfFESMTQTQIAERVGISQMHVSRLL 252
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
52-240 2.10e-14

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 71.52  E-value: 2.10e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  52 NMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRDSQKIRITNEVYEI-------KGKISRMKLHDEEV 124
Cdd:PRK08215  63 NVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIaykalqvREKLINENSKEPTV 142

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305 125 ESIAKLLEVSVRDVKTAKEFNPRTISLQTP--------------LNKEVNKEKVTLENtlidkktsMTLDDVIKKmiita 190
Cdd:PRK08215 143 EEIAKELEVPREEVVFALDAIQDPVSLFEPiyhdggdpiyvmdqISDEKNKDENWLEE--------IALKEAMKK----- 209

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446424305 191 flstLCSKEKFVWELH-AKNMTQAAIGKRLGVTQTQISRILKGIYKKAEEY 240
Cdd:PRK08215 210 ----LNDREKLILNLRfFQGKTQMEVAEEIGISQAQVSRLEKAALKHMRKY 256
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 20-229 1.46e-13

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 69.33  E-value: 1.46e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  20 DDFMKKYSRLVYYYVNKYFSNIAKAIEQetnlnmDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILG---------- 89
Cdd:PRK06288  34 EYLILKYSPLVKYVAGRIAVGMPQNVEF------DDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGaifdelrsid 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  90 YIRKAVRdsQKIRITNEVYEI-KGKISRmKLHDEEvesIAKLLEVSVRDVKT--AKEFNPRTISLQTPLNKEVNKEKVTL 166
Cdd:PRK06288 108 WIPRSVR--QKARQIERAIAMlEARLGR-TPSDEE---IADELGISLEEYNSllSKLSGTSVVSLNDLWFGGDEGDEVSL 181

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446424305 167 ENTLidkKTSMTLDDV-------IKKMIITAfLSTLCSKEKFVWELHA-KNMTQAAIGKRLGVTQTQISRI 229
Cdd:PRK06288 182 MDTL---ESPAALNPDeiaereeIKRVIVEA-IKTLPEREKKVLILYYyEDLTLKEIGKVLGVTESRISQL 248
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
1-229 1.30e-11

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 63.53  E-value: 1.30e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305   1 MGDEQK---DLIEQEDvlMMTDDDFMKKYSRLVYYYVNKYFSNIAKAIEQetnlnmDDLIQSGMLGLVTARRDFKTELGF 77
Cdd:PRK07670   5 TYEEQKlwdRWKEERD--PDAADELIRRYMPLVHYHVQRISVGLPKSVSK------DDLKSLGMLGLYDALEKFDPSRDL 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  78 KFTTFAVPRILGYI----RK------AVRD-SQKIRITNEVYEikgkisRMKLHDEEVESIAKLLEVSVRDVKTAKE--F 144
Cdd:PRK07670  77 KFDTYASFRIRGAIidglRKedwlprSMREkTKKVEAAIEKLE------QRYMRNVTPKEVAAELGMTEEEVEATMNegF 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305 145 NPRTISLQTPLNKEVNKEKVTLenTLIDKKTSMTLDDVIKKMII---TAFLSTLCSKEKFVWELHAKN-MTQAAIGKRLG 220
Cdd:PRK07670 151 FANLLSIDEKTHDQDDGENVSV--TIRDDKTPTPEEKLLKEELIeelAEKIKQLSEKEQLVISLFYKEeLTLTEIGQVLN 228


                 ....*....
gi 446424305 221 VTQTQISRI 229
Cdd:PRK07670 229 LSTSRISQI 237
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 28-229 2.51e-11

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 63.65  E-value: 2.51e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  28 RLVYYYVNKYfsniakaieQETNLNMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRD-SQKIRITNE 106
Cdd:PRK07406 147 RLVVSIAKKY---------MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADqSRTIRLPVH 217

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305 107 VYEikgKISRMK----LHDEEV------ESIAKLLEVSVRDVKTAKEFNPRTISLQTPLNKEvnkEKVTLENtLIDKKTS 176
Cdd:PRK07406 218 LYE---TISRIKkttkVLSQEFgrkpteEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKE---EDSRLGD-FIEADGE 290

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446424305 177 MTLDDVIKKMI---ITAFLSTLCSKEKFVWELH-----AKNMTQAAIGKRLGVTQTQISRI 229
Cdd:PRK07406 291 TPEDDVAKNLLredLEGVLATLSPRERDVLRLRyglddGRMKTLEEIGQIFNVTRERIRQI 351
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 20-240 2.68e-10

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: 58.13  E-value: 2.68e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305   20 DDFMKKYSRLVYYYVNKYFSNIAKAieqetnlnmDDLIQSGMLGLVTARRDFKTELGFKftTFAVPRILGYIRKAVRDSQ 99
Cdd:TIGR02937   4 EELYERYLPLVYRYARRYLGDDADA---------EDLVQEAFLKLLEALDRFDPEGSFK--AWLFRIARNLILDYLRRKR 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  100 KIRITNEVYEikgkisrmklhdeevesiakllevsvrdvktakefnprtislqtplnkevnkekvtlENTLIDKKTSMTL 179
Cdd:TIGR02937  73 RLRRELDLLE---------------------------------------------------------ELLDSDPSPEEEL 95

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446424305  180 DDVIKKMIITAFLSTLCSKEKFVWELHA-KNMTQAAIGKRLGVTQTQISRILKGIYKKAEEY 240
Cdd:TIGR02937  96 EQEEEREALREALEKLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 22-101 2.68e-10

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: 55.67  E-value: 2.68e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305   22 FMKKYSRLVYYYVNKYFSNiakaieqetNLNMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRDSQKI 101
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGD---------GADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 53-236 7.17e-09

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 55.24  E-value: 7.17e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  53 MDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILG----YIRK------AVRDSQKiRITNEVYEIKGKISRmKLHDE 122
Cdd:PRK06986  38 LDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGamldELRSldwvprSVRRNAR-EVAQAIRQLEQELGR-EPTDT 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305 123 EVesiAKLLEVSVRDVKTAK--EFNPRTISLQTpLNKEVNKEKVTLENTLIDKKTSMTLDDVIKKMIITAfLSTLCSKEK 200
Cdd:PRK06986 116 EV---AEKLGLSLEEYREMLldTNISQLFSIDE-LRGEHGDSILVTEDHQDEDPLQQLEDEELREALVEA-IESLPEREQ 190

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 446424305 201 FVWEL---HAKNMTQaaIGKRLGVTQTQISRILKGIYKK 236
Cdd:PRK06986 191 LVLSLyyqEELNLKE--IGAVLGVSESRVSQIHSQAIKR 227
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 55-229 2.05e-08

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 54.58  E-value: 2.05e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  55 DLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRD-SQKIRIT-------NEVYEIKGKISRMKLHDEEVES 126
Cdd:PRK05657 115 DLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNqTRTIRLPvhvvkelNVYLRAARELEHKLDHEPSAEE 194

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305 127 IAKLLEVSVRDVKTAKEFNPRTISLQTPLNKEVNKekvTLENTLIDKKTS----MTLDDVIKKMiITAFLSTLCSKEKFV 202
Cdd:PRK05657 195 IAELLDKPVDDVSRMLALNERITSLDTPLGGDPEK---SLLDILADEQENgpedTTQDDDMKQS-IVKWLFELNDKQREV 270

                        170       180       190
                 ....*....|....*....|....*....|..
gi 446424305 203 WE-----LHAKNMTQAAIGKRLGVTQTQISRI 229
Cdd:PRK05657 271 LArrfglLGYEAATLEDVAREIGLTRERVRQI 302
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 52-233 2.64e-08

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 53.77  E-value: 2.64e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  52 NMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRD-SQKIRITN---EVYEIKGKIS---RMKLH---- 120
Cdd:PRK07408  52 PYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDkSPTVRIPRrwqELQRQAKKVRqelRQELGrqpt 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305 121 DEEvesIAKLLEVSV---RDVKTAKEfNPRTISLQTPLNKEVNkEKVTLENTLIDKKT-SMTL--DDVIKkmiITAFLST 194
Cdd:PRK07408 132 DQE---IAQALDISLeewQEIKLALQ-NRTPLSLDAPVNQDED-GSTSLGDLLPDPRYrSFQLaqEDRIR---LQQALAQ 203

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 446424305 195 LCSKEK------FVWELhaknmTQAAIGKRLGVTQTQISR-ILKGI 233
Cdd:PRK07408 204 LEERTRevlefvFLHDL-----TQKEAAERLGISPVTVSRrVKKGL 244
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 55-236 5.44e-08

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 53.58  E-value: 5.44e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  55 DLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRD-SQKIRITNEVYEIKGKISRMK--LH--------DEE 123
Cdd:PRK07921 115 DLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADqSRTIRLPVHLVEQVNKLARIKreLHqqlgreatDEE 194

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305 124 V--------ESIAKLLEVSvRDvktakefnprTISLQTPLNKEvnkEKVTLENTLIDKKTSMTLDDVIKKMI---ITAFL 192
Cdd:PRK07921 195 LaeesgipeEKIADLLEHS-RD----------PVSLDMPVGSD---EEAPLGDFIEDSEATSAENAVIAGLLhtdIRSVL 260

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 446424305 193 STLCSKEKFVWELH-----AKNMTQAAIGKRLGVTQTQISRILKGIYKK 236
Cdd:PRK07921 261 ATLDEREQQVIRLRfglddGQPRTLDQIGKLFGLSRERVRQIEREVMSK 309
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 28-162 6.12e-08

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 53.72  E-value: 6.12e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  28 RLVYYYVNKYfsniakaieQETNLNMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAV-RDSQKIR---- 102
Cdd:PRK07598 186 RLVVSVAKKY---------QNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIaTQSRTIRlpvh 256

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446424305 103 ITNEVYEIKG---KISRMKLHDEEVESIAKLLEVSVRDVKTAKEFNPRTISLQTPLNKEVNKE 162
Cdd:PRK07598 257 ITEKLNKIKKaqrKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTE 319
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 55-158 2.06e-06

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 48.83  E-value: 2.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  55 DLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRD-SQKIRITNEVYEIKGK---ISRMKLHD----EEVES 126
Cdd:PRK09210 158 DLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADqARTIRIPVHMVETINKlirVQRQLLQElgrePTPEE 237

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 446424305 127 IAKLLEVS---VRDV-KTAKEfnprTISLQTPLNKE 158
Cdd:PRK09210 238 IAEEMDMPpekVREIlKIAQE----PVSLETPIGEE 269
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
28-236 2.42e-06

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 47.63  E-value: 2.42e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  28 RLVYYYVNKYfSNiakaieqeTNLNMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRDSQKIRitNEV 107
Cdd:PRK05803  60 RLVAHIVKKF-EN--------TGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTK--KEV 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305 108 YeikgkisrmkLHDEevesiakllevsvrdVKTAKEFNPrtISLQTPLNKEvnkekvtlENTLIDK-KTSMTLDDVIKKm 186
Cdd:PRK05803 129 S----------LQDP---------------IGVDKEGNE--ISLIDILGSE--------EDDVIEQvELKMEVEKLYKK- 172

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446424305 187 iitafLSTLCSKEKFVWEL-----HAKNMTQAAIGKRLGVTQTQISRILKGIYKK 236
Cdd:PRK05803 173 -----IDILDEREKEVIEMryglgNGKEKTQREIAKALGISRSYVSRIEKRALKK 222
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
22-243 3.83e-05

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 43.74  E-value: 3.83e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  22 FMKKYSRLVYYYVNKYFSNIAkaiEQEtnlnmdDLIQSGMLGLVTARRDFKTELGFKFTTFA---VPR-ILGYIRKAVRd 97
Cdd:PRK08295  29 LIEKYKNFVRAKARSYFLIGA---DRE------DIVQEGMIGLYKAIRDYDKDKLSSFKSFAelcITRqIITAIKTANR- 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  98 sQKIRITNEVYEIKGKIsrmklHDEEVESiaKLLEVsvrdVKTAKEFNPrtislqtplnkevnkekvtlENTLIDKKtsm 177
Cdd:PRK08295  99 -QKHIPLNSYVSLDKPI-----YDEESDR--TLLDV----ISEAKVTDP--------------------EELIISKE--- 143

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446424305 178 TLDDVIKKMiitafLSTLCSKEKFVWELHAKNMTQAAIGKRLGVTQTQISRILKGIYKKAEEYGNK 243
Cdd:PRK08295 144 ELEDIEEKI-----EELLSELEKEVLELYLDGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYLEN 204
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 9-229 6.86e-04

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 40.37  E-value: 6.86e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305   9 IEQEDVLMmtddDFmkkYSRLVYYYVNKYFSNIAkaieqeTNLNMDDLIQSGMLGLVTARRDFKTELGFKFTTFAvpriL 88
Cdd:PRK05911  22 IEYRDVLI----EF---YLPLVKNVAHRLISGMP------SHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYA----L 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  89 GYIRKAVRDSQKIR--ITNEVYEIKGKIS------RMKLHDEEVE-SIAKLLEVSVRDVktAKEFNPRTISLQTPLNKEV 159
Cdd:PRK05911  85 FLIKAAIIDDLRKQdwVPRSVHQKANKLAdamdslRQSLGKEPTDgELCEYLNISQQEL--SGWFSSARPALILSLNEEF 162

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446424305 160 -----NKEKVTLENTLIDKKTSMTLDDVIKK---MIITAFLSTLCSKEKFVWEL-HAKNMTQAAIGKRLGVTQTQISRI 229
Cdd:PRK05911 163 pcqsdDEAGLALEERIADERAETGYDVVDKKefsSILAEAILALEEKERKVMALyYYEELVLKEIGKILGVSESRVSQI 241
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
207-235 1.29e-03

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 36.34  E-value: 1.29e-03
                           10        20
                   ....*....|....*....|....*....
gi 446424305   207 AKNMTQAAIGKRLGVTQTQISRILKGIYK 235
Cdd:smart00530   8 EKGLTQEELAEKLGVSRSTLSRIENGKRK 36
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 51-229 2.03e-03

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 39.25  E-value: 2.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  51 LNMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVprilGYIRKAVRD---------------SQKI------RITNEVYE 109
Cdd:PRK07500  65 LPMNDLIQEGYVGLLEAAARFEPDREVRFSTYAT----WWIRASIQDyilrnwsivrggtssAQKAlffnlrRLRARLAQ 140

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305 110 IKGKISRMKLHdeevESIAKLLEVSVRDVKTAK-EFNPRTISLQTPL--NKEVNKEKV-TLENT--LIDKKTSMTLDDVI 183
Cdd:PRK07500 141 ADEELTKQEIH----REIATALGVSLSDVEMMDaRLSGPDASLNAPQseEDEGRSERMdFLVDDspLPDEQVESSIDGER 216

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 446424305 184 KKMIITAFLSTLCSKEKFVWE---LHAKNMTQAAIGKRLGVTQTQISRI 229
Cdd:PRK07500 217 RRRWLTQALQTLNERELRIIRerrLREDGATLEALGEELGISKERVRQI 265
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 198-232 2.19e-03

Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms];


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 36.71  E-value: 2.19e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 446424305 198 KEKFvweLHAKNMTQAAIGKRLGVTQTQISRILKG 232
Cdd:COG3093   14 REEF---LEPLGLSQTELAKALGVSRQRISEILNG 45
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 28-116 3.17e-03

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 38.67  E-value: 3.17e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  28 RLVYYYVNKYfsniakaieQETNLNMDDLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAV-RDSQKIRITNE 106
Cdd:PRK05949 102 RLVVAIAKKY---------QKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIaQQARTIRLPIH 172

                         90
                 ....*....|
gi 446424305 107 VYEIKGKISR 116
Cdd:PRK05949 173 ITEKLNKIKK 182
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 207-235 3.94e-03

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 35.22  E-value: 3.94e-03
                         10        20
                 ....*....|....*....|....*....
gi 446424305 207 AKNMTQAAIGKRLGVTQTQISRILKGIYK 235
Cdd:cd00093   10 EKGLTQEELAEKLGVSRSTISRIENGKRN 38
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
207-235 5.53e-03

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 34.82  E-value: 5.53e-03
                         10        20
                 ....*....|....*....|....*....
gi 446424305 207 AKNMTQAAIGKRLGVTQTQISRILKGIYK 235
Cdd:COG1476   15 ERGLTQEELAELLGVSRQTISAIENGKYN 43
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 40-158 5.86e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 38.05  E-value: 5.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446424305  40 NIAKaieQETNLNMD--DLIQSGMLGLVTARRDFKTELGFKFTTFAVPRILGYIRKAVRD-SQKIRI---TNEVYEIKGK 113
Cdd:PRK05901 286 SLAK---RYTNRGLSflDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADqARTIRIpvhMVETINKLGR 362

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446424305 114 ISRMKLHD-------EEvesIAKLLEVSVRDVKTAKEFNPRTISLQTPLNKE 158
Cdd:PRK05901 363 IERELLQElgreptpEE---LAKEMGFTPEKVREIQKYNREPISLDKTIGKE 411
AF0184 COG2522
Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];
204-232 6.36e-03

Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];


Pssm-ID: 442012 [Multi-domain]  Cd Length: 99  Bit Score: 35.57  E-value: 6.36e-03
                         10        20
                 ....*....|....*....|....*....
gi 446424305 204 ELHAKNMTQAAIGKRLGVTQTQISRILKG 232
Cdd:COG2522   23 ELVERGLSQSEIAKLLGITQAAVSQYLSG 51
COG5606 COG5606
Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];
205-232 6.58e-03

Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];


Pssm-ID: 444337  Cd Length: 105  Bit Score: 35.63  E-value: 6.58e-03
                         10        20
                 ....*....|....*....|....*...
gi 446424305 205 LHAKNMTQAAIGKRLGVTQTQISRILKG 232
Cdd:COG5606   41 IKERGLTQAEAAELLGITQPRVSDLLRG 68
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 104-162 6.63e-03

Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.


Pssm-ID: 427997 [Multi-domain]  Cd Length: 78  Bit Score: 34.89  E-value: 6.63e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 446424305  104 TNEVYEIKGKISRMKLHDEEVESIAKLLEVSVRDVKTAKEFNPRTISLQTPLNKEVNKE 162
Cdd:pfam04539   3 LNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGE 61
 
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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