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Conserved domains on  [gi|524784949|emb|CDE77498|]
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rNA polymerase sigma factor sigma-70 family [Ruminococcus sp. CAG:353]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK08295 super family cl32289
RNA polymerase sporulation sigma factor SigH;
18-198 8.82e-32

RNA polymerase sporulation sigma factor SigH;


The actual alignment was detected with superfamily member PRK08295:

Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 114.24  E-value: 8.82e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  18 SLSSCSDEELVERCRGGrlSVPAASELIYRYFGFIKSKAASMCGSASVCDDFVQEGVLGFLSAIRHYSSDKGTAFSSYAY 97
Cdd:PRK08295   5 DYDELEDEELVELARSG--DKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  98 SCVVNRMKTAAAKLSR-----LQST--------EEGSD--------EDKGEDnltPENIIIQRELFRELEDT----LSPM 152
Cdd:PRK08295  83 LCITRQIITAIKTANRqkhipLNSYvsldkpiyDEESDrtlldvisEAKVTD---PEELIISKEELEDIEEKieelLSEL 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 524784949 153 EYEIFRLSITGLTSEEIAKKLNISVKSAENAVSRARRKLKGKIADE 198
Cdd:PRK08295 160 EKEVLELYLDGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYLENR 205
 
Name Accession Description Interval E-value
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
18-198 8.82e-32

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 114.24  E-value: 8.82e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  18 SLSSCSDEELVERCRGGrlSVPAASELIYRYFGFIKSKAASMCGSASVCDDFVQEGVLGFLSAIRHYSSDKGTAFSSYAY 97
Cdd:PRK08295   5 DYDELEDEELVELARSG--DKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  98 SCVVNRMKTAAAKLSR-----LQST--------EEGSD--------EDKGEDnltPENIIIQRELFRELEDT----LSPM 152
Cdd:PRK08295  83 LCITRQIITAIKTANRqkhipLNSYvsldkpiyDEESDrtlldvisEAKVTD---PEELIISKEELEDIEEKieelLSEL 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 524784949 153 EYEIFRLSITGLTSEEIAKKLNISVKSAENAVSRARRKLKGKIADE 198
Cdd:PRK08295 160 EKEVLELYLDGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYLENR 205
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 23-198 2.78e-30

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: 109.70  E-value: 2.78e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  23 SDEELVERCRGGRLSvpAASELIYRYFGFIKSKAASMCGSASVCDDFVQEGvlgFLSAIRHYSS-DKGTAFSSYAYSCVV 101
Cdd:COG1595    3 SDEELLERLRAGDEA--AFEELYERYRPRLYRYARRLLGDRADAEDLVQET---FLRLWRKLDSfRGRGSFRAWLYRIAR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949 102 NRMKTAAAKLSRLQSTEEGSDEDKGEDNLTPENIIIQRELFRELE---DTLSPMEYEIFRLS-ITGLTSEEIAKKLNISV 177
Cdd:COG1595   78 NLAIDHLRKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLaalERLPPRQREVLVLRyLEGLSYAEIAEILGISE 157

                        170       180
                 ....*....|....*....|.
gi 524784949 178 KSAENAVSRARRKLKGKIADE 198
Cdd:COG1595  158 GTVKSRLSRARKKLREALEEE 178
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 40-195 2.67e-24

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: 93.57  E-value: 2.67e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949   40 AASELIYRYFGFIKSKAASMCGSASVCDDFVQEGVLGFLSAIRHYSSDKgtAFSSYAYSCVVNRMKTAAAKLSRLQSTEE 119
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDYLRRKRRLRRELD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  120 gSDEDKGEDNLTPENIIIQRELFRELE---DTLSPMEYEIFRLS-ITGLTSEEIAKKLNISVKSAENAVSRARRKLKGKI 195
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. ...
 44-113 1.08e-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: 60.68  E-value: 1.08e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949   44 LIYRYFGFIKSKAASMCGSASVCDDFVQEGVLGFLSAIRHYSSDKGTAFSSYAYSCVVNRMKTAAAKLSR 113
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 147-192 6.05e-10

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 52.91  E-value: 6.05e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 524784949   147 DTLSPMEYEIFRLSITGLTSEEIAKKLNISVKSAENAVSRARRKLK 192
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 139-192 1.03e-06

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 44.02  E-value: 1.03e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 524784949 139 RELFRELEDTLSPMEYEIFRLS-ITGLTSEEIAKKLNISVKSAENAVSRARRKLK 192
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRfGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
18-198 8.82e-32

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 114.24  E-value: 8.82e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  18 SLSSCSDEELVERCRGGrlSVPAASELIYRYFGFIKSKAASMCGSASVCDDFVQEGVLGFLSAIRHYSSDKGTAFSSYAY 97
Cdd:PRK08295   5 DYDELEDEELVELARSG--DKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  98 SCVVNRMKTAAAKLSR-----LQST--------EEGSD--------EDKGEDnltPENIIIQRELFRELEDT----LSPM 152
Cdd:PRK08295  83 LCITRQIITAIKTANRqkhipLNSYvsldkpiyDEESDrtlldvisEAKVTD---PEELIISKEELEDIEEKieelLSEL 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 524784949 153 EYEIFRLSITGLTSEEIAKKLNISVKSAENAVSRARRKLKGKIADE 198
Cdd:PRK08295 160 EKEVLELYLDGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYLENR 205
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 23-198 2.78e-30

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: 109.70  E-value: 2.78e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  23 SDEELVERCRGGRLSvpAASELIYRYFGFIKSKAASMCGSASVCDDFVQEGvlgFLSAIRHYSS-DKGTAFSSYAYSCVV 101
Cdd:COG1595    3 SDEELLERLRAGDEA--AFEELYERYRPRLYRYARRLLGDRADAEDLVQET---FLRLWRKLDSfRGRGSFRAWLYRIAR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949 102 NRMKTAAAKLSRLQSTEEGSDEDKGEDNLTPENIIIQRELFRELE---DTLSPMEYEIFRLS-ITGLTSEEIAKKLNISV 177
Cdd:COG1595   78 NLAIDHLRKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLaalERLPPRQREVLVLRyLEGLSYAEIAEILGISE 157

                        170       180
                 ....*....|....*....|.
gi 524784949 178 KSAENAVSRARRKLKGKIADE 198
Cdd:COG1595  158 GTVKSRLSRARKKLREALEEE 178
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 40-195 2.67e-24

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: 93.57  E-value: 2.67e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949   40 AASELIYRYFGFIKSKAASMCGSASVCDDFVQEGVLGFLSAIRHYSSDKgtAFSSYAYSCVVNRMKTAAAKLSRLQSTEE 119
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDYLRRKRRLRRELD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  120 gSDEDKGEDNLTPENIIIQRELFRELE---DTLSPMEYEIFRLS-ITGLTSEEIAKKLNISVKSAENAVSRARRKLKGKI 195
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. ...
 44-113 1.08e-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: 60.68  E-value: 1.08e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949   44 LIYRYFGFIKSKAASMCGSASVCDDFVQEGVLGFLSAIRHYSSDKGTAFSSYAYSCVVNRMKTAAAKLSR 113
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 43-192 2.18e-10

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: 56.80  E-value: 2.18e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949   43 ELIYR-YFGFIKSKAASMCGSASVCDDFVQEGvlgFLSAIRHYSS-DKGTAFSSYAYSCVVNRmktAAAKLSRLQSTEEG 120
Cdd:TIGR02985   4 EQLYRrYYPKLCAFARRYVKDEEDAEDIVQDV---FLKLWENRETlEISESIKAYLFTIVKNR---CLNYLRHKQVEEKY 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  121 SDE--DKGEDNLT---PENIIIQRELFRELEDTLS--PMEY-EIFRLSIT-GLTSEEIAKKLNISVKSAENAVSRARRKL 191
Cdd:TIGR02985  78 QEElaEIEERELSeadPEEELEAKELEEIIEEAIEklPEQCrEIFILSRFeGLSNKEIAEELGISVKTVEYHITKALKFL 157


                  .
gi 524784949  192 K 192
Cdd:TIGR02985 158 R 158
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 147-192 6.05e-10

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 52.91  E-value: 6.05e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 524784949   147 DTLSPMEYEIFRLSITGLTSEEIAKKLNISVKSAENAVSRARRKLK 192
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
149-191 3.87e-09

DNA-binding transcriptional regulator, CsgD family [Transcription];


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 53.99  E-value: 3.87e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 524784949 149 LSPMEYEIFRLSITGLTSEEIAKKLNISVKSAENAVSRARRKL 191
Cdd:COG2771  128 LTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKL 170
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 140-191 4.85e-09

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 52.59  E-value: 4.85e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 524784949 140 ELFRELedtLSPMEYEIFRLSITGLTSEEIAKKLNISVKSAENAVSRARRKL 191
Cdd:COG2197   64 EALRRL---LTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKL 112
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 25-197 1.11e-08

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: 53.29  E-value: 1.11e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  25 EELVERCRGGRLSvpAASELIYRYFGFIKSKAASMCG--SASVcDDFVQEGVLGFLSAIRHYSSDKGTAFSSYAYSCVVN 102
Cdd:COG1191    3 EELLRRYQEGDEE--AREELIEEYLPLVKKIASRLAGrlPAEL-DDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949 103 RMK-------------------------TAAAKLSRLQSTEE-------------------------------GSDEDKG 126
Cdd:COG1191   80 AILdylrdedwvprsvrelarkieeaieELEQELGREPTDEEiaeelgisleevqealeaanayqllsldeplEDGDDLL 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949 127 E--DNLTPENIIIQRELFRELE---DTLSPMEyeifRLSIT-----GLTSEEIAKKLNISVKSAENAVSRARRKLKGKIA 196
Cdd:COG1191  160 DllESGDPEEELEHEELREALAeaiEQLPERE----RLVLSlyyfeELTLKEIAEVLGVSESRVSRLHKKALARLREYLK 235


                 .
gi 524784949 197 D 197
Cdd:COG1191  236 E 236
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 23-198 1.31e-08

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 52.35  E-value: 1.31e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  23 SDEELVERCRGGRlsVPAASELIYRYFGFIKSKAASMCGSASVCDDFVQEGvlgFLSAIRHYSS-DKGTA-FSSYAYSCV 100
Cdd:PRK05602   6 PDEELLARVAAGD--PAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQET---FLRIWKQAPSwRPGEArFDTWLHRVV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949 101 VNRMktaaakLSRLQSTEEGSDEDKGE---DNLTPENIIIQRELFRELEDTLSPMEyEIFRLSIT-----GLTSEEIAKK 172
Cdd:PRK05602  81 LNLC------YDRLRRRREVPVEDAPDvpdPAPGPDAGLEARQRARRVEQALAALP-ERQREAIVlqyyqGLSNIEAAAV 153

                        170       180
                 ....*....|....*....|....*.
gi 524784949 173 LNISVKSAENAVSRARRKLKGKIADE 198
Cdd:PRK05602 154 MDISVDALESLLARGRRALRAQLADL 179
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 139-191 5.06e-08

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 48.42  E-value: 5.06e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 524784949 139 RELFRELEDTLSPMEYEIFRLSITGLTSEEIAKKLNISVKSAENAVSRARRKL 191
Cdd:COG5905    3 PSSSTSHPSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKL 55
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 12-193 8.95e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 50.06  E-value: 8.95e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  12 SEDPCDSLSSCSDEELVERCRGGRlsvPAASELIY-RYFGFIKSKAASMCGSASVCDDFVQEGvlgFLSAIRH--YSSDK 88
Cdd:PRK12519   4 GDSAPTSLSSRSDAELFSALKAGQ---SAALGVLYdRHAGLVYGLALKILGNSQEAEDLTQEI---FLSLWRKssYDPKR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  89 GtAFSSY----AYSCVVNRMKtaaAKLSRLQSTEEGSDEDKGE--DNLTPENIII--QRELFRELEDTLSPMEYEIFRLS 160
Cdd:PRK12519  78 G-SLSSYlltlTRSRAIDRLR---SRRSRQRLLERWQQELLGEasEDTPLEQASLaeRSQRVQTALAQLPESQRQVLELA 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 524784949 161 I-TGLTSEEIAKKLNI---SVKsaenavSRARR---KLKG 193
Cdd:PRK12519 154 YyEGLSQSEIAKRLGIplgTVK------ARARQgllKLRE 187
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
67-176 1.01e-07

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 50.33  E-value: 1.01e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  67 DDFVQEGVLGFLSAIRHYSSDKGTAFSSYAYSCVVNR--MKTAAAKLSRLQ-STEE--GSDEDKGE----DNLTPENIII 137
Cdd:PRK05803  77 DDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEilMHLRNLKKTKKEvSLQDpiGVDKEGNEisliDILGSEEDDV 156

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 524784949 138 ---------QRELFRELeDTLSPMEYEIFRLSItGL------TSEEIAKKLNIS 176
Cdd:PRK05803 157 ieqvelkmeVEKLYKKI-DILDEREKEVIEMRY-GLgngkekTQREIAKALGIS 208
GerE pfam00196
Bacterial regulatory proteins, luxR family;
147-192 1.17e-07

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 46.81  E-value: 1.17e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 524784949  147 DTLSPMEYEIFRLSITGLTSEEIAKKLNISVKSAENAVSRARRKLK 192
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLN 46
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 122-194 3.73e-07

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 48.40  E-value: 3.73e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 524784949 122 DEDKGEDNLTPENIIIQ---RELFRELEDTLSPMEYEIF-RLSITGLTSEEIAKKLNISVKSAENAVSRARRKLKGK 194
Cdd:PRK06811 102 DEFILISEESIENEIILkenKEEILKLINDLEKLDREIFiRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 139-191 4.53e-07

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 45.14  E-value: 4.53e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 524784949  139 RELFRELEDTLSPMEYEIFRLS-ITGLTSEEIAKKLNISVKSAENAVSRARRKL 191
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRyLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 139-192 1.03e-06

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 44.02  E-value: 1.03e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 524784949 139 RELFRELEDTLSPMEYEIFRLS-ITGLTSEEIAKKLNISVKSAENAVSRARRKLK 192
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRfGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 28-197 1.18e-06

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 46.72  E-value: 1.18e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  28 VERCRGGRlsvPAASELIYRYF-GFIKSKAASMCGSASVCDDFVQEGvlgFLSAIRHYSS-DKGTAFSSYAYSCVVNRMK 105
Cdd:PRK09652   1 VERVQRGD---RAAFALLVRRYqPRVKRLLSRLTRDPADAEDLVQET---FIKAYRALHSfRGGAAFYTWLYRIARNTAI 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949 106 TAAAKLSRLQSTEEGSDEDK--------GEDNLTPENIIIQRELFRELEDT---LSPMEYEIFRLS-ITGLTSEEIAKKL 173
Cdd:PRK09652  75 NYLRKQGRRPPASDVDAEEAedfdladaLRDISTPENELLSAELEQRVRAAiesLPEELRTAITLReIEGLSYEEIAEIM 154

                        170       180
                 ....*....|....*....|....*..
gi 524784949 174 NIS---VKSaenAVSRARRKLKGKIAD 197
Cdd:PRK09652 155 GCPigtVRS---RIFRAREALRAKLQP 178
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 149-192 1.21e-06

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 44.06  E-value: 1.21e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 524784949 149 LSPMEYEIFRLSITGLTSEEIAKKLNISVKSAENAVSRARRKLK 192
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLG 44
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 23-197 1.36e-06

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 46.86  E-value: 1.36e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  23 SDEELVERCRGGRLSVPAA-SELIYRYFGFIKSKAASMCGSASVCDDFVQEGVLGFLSAIRHYssDKGTAFSSYAYSCVV 101
Cdd:PRK09640   9 NDEELVARVHVELFHVTRAyEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNF--EGKSKFKTWLYSITY 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949 102 NRMKTAAAKL---SRLQSTEEGSDEDKGEDNLTPEniIIQRELFRELEDTLSPMEYEIFRLS-ITGLTSEEIAKKLNISV 177
Cdd:PRK09640  87 NECITQYRKErrkRRLMDALSLDPLEEASEEKAPK--PEERGGLDRWLVHVNPIDREILVLRfVAELEFQEIADIMHMGL 164

                        170       180
                 ....*....|....*....|
gi 524784949 178 KSAENAVSRARRKLKGKIAD 197
Cdd:PRK09640 165 SATKMRYKRALDKLREKFAG 184
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 24-192 2.50e-06

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 45.78  E-value: 2.50e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  24 DEELVERCRGGrlSVPAASELIYRYFGFIKSKAASMCGSASVCDDFVQEGvlgFLSAIRHYSSDKGTA-FSSYAYSCVVN 102
Cdd:PRK09638   5 EKELIQKAKKG--DDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQET---MLKAIENLSSFQGRSkFSTWLISIASR 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949 103 RMKTAAAKLSRLQSTEEgSDEDKGEDNLTPENIIIQRElFRELEDTLSPMEYEiFRLSIT-----GLTSEEIAKKLNI-- 175
Cdd:PRK09638  80 LYKDHLRKQKREKLRLQ-RAKEETLRKEKWEAAIKGAE-WSEMLDALSKLDPE-FRAPVIlkhyyGYTYEEIAKMLNIpe 156

                        170
                 ....*....|....*....
gi 524784949 176 -SVKS-AENAVSRARRKLK 192
Cdd:PRK09638 157 gTVKSrVHHGIKQLRKEWG 175
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 12-199 4.99e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 45.27  E-value: 4.99e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  12 SEDPCDSLSSCSDEELVERCRGGRLSvpAASELIYRYFGFIKSKAASMCGSASVCDDFVQEGVLGFLSAIRHYSSDKGTA 91
Cdd:PRK12524   1 MTMPFDALSDVSDEALLVLYANGDPA--AARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGEARV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  92 fSSYAYSCVVNrMKTAAAKLSRLQSTEEGSDEDKGEDNLTPENIIIQRELFRELEDTLSPM-----EYEIFRlSITGLTS 166
Cdd:PRK12524  79 -STWLYRVVCN-LCTDRLRRRRRASVDLDDAPEPADAAPGAEEALIEGDRMRALDAALAALperqrQAVVLR-HIEGLSN 155

                        170       180       190
                 ....*....|....*....|....*....|...
gi 524784949 167 EEIAKKLNISVKSAENAVSRARRKLKGKIADEK 199
Cdd:PRK12524 156 PEIAEVMEIGVEAVESLTARGKRALAALLAGQR 188
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 68-199 1.88e-05

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: 43.89  E-value: 1.88e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  68 DFVQEGVLGFLSAIRHYSSDKGTAFSSYAY---------------SCV---------VNRMKTAAAKLS----RLQSTEE 119
Cdd:COG0568   59 DLIQEGNLGLMKAVEKFDPERGFRFSTYATwwirqaitraiadqwRTIrlpvhmaetLNKLRRAKRQLLqelgREPTPEE 138

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949 120 -----------------------------GSDEDK-------GEDNLTPENIIIQRELFRELE---DTLSPMEYEIFRL- 159
Cdd:COG0568  139 iaeelgvpeekvremlrlarepvsldapvGDDEDSelgdlleDEEAPSPEEALEEELLREELRealDTLTEREREILRLr 218

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 524784949 160 ----SITGLTSEEIAKKLNIsvkSAEnavsRAR-------RKLKGKIADEK 199
Cdd:COG0568  219 fgldDGEPHTLEEIGKEFGV---SRE----RVRqieakalRKLRHPLRSRK 262
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 138-191 2.01e-05

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 43.55  E-value: 2.01e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 524784949 138 QRELFRELEDTLSPMEYEIFRLSITGLTSEEIAKKLNISVKSAEnaVSRAR--RKL 191
Cdd:COG4566  127 RRAELRARLASLTPREREVLDLVVAGLSNKQIARELGISPRTVE--VHRANvmEKL 180
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 18-192 1.11e-04

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 41.05  E-value: 1.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  18 SLSSCSDEELVERCRGGRLSvpAASELIYRYFGFIKSKAASMCGSASVCDDFVQEGVLGFLSAIRHYSSDKGTAFS---S 94
Cdd:PRK13919   4 PLESLSDEALLALVARGEEE--ALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRGSARAwllA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  95 YAYSCVVNRMKTAAAKLSRLQSTEE----------GSDEDKGEDNLTpeniiIQRELfreleDTLSPMEYEIFR-LSITG 163
Cdd:PRK13919  82 LAHHAAVDHVRRRAARPQPLEPDERepeafdlpgpGLDEEGHLDRTR-----LGRAL-----KALSPEERRVIEvLYYQG 151

                        170       180
                 ....*....|....*....|....*....
gi 524784949 164 LTSEEIAKKLNISVKSAENAVSRARRKLK 192
Cdd:PRK13919 152 YTHREAAQLLGLPLGTLKTRARRALSRLK 180
PRK06930 PRK06930
positive control sigma-like factor; Validated
 121-197 2.25e-04

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 40.10  E-value: 2.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949 121 SDEDKGEDNLTPENIIIQRELFReLED---TLSPMEYEIFRLSIT-GLTSEEIAKKLNISVKSAENAVSRARRKLKGKIA 196
Cdd:PRK06930  85 SMEDLEWDIEEPESVISEWDKIR-IEDalsVLTEREKEVYLMHRGyGLSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163


                 .
gi 524784949 197 D 197
Cdd:PRK06930 164 E 164
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 27-192 2.49e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 40.09  E-value: 2.49e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  27 LVERC-RGGRLSVpaaSELIYRYFGFIKSKAASMCGSASVcDDFVQEGvlgFLSAIRHYSSDKGTA-FSSYAY----SCV 100
Cdd:PRK12518   1 LILRCqRGDRQSF---RQLYRRYQQKVRSTLYQLCGRELL-DDLVQEV---FLRVWKGLPKLRNPAyFSTWLYritwNVA 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949 101 VNRMKTAAAKLSRLQ--STEEGSDEDKGEDNLTPENI--IIQRELfreleDTLSPMEYEIFRL-SITGLTSEEIAKKLNI 175
Cdd:PRK12518  74 TDARRQFAQRPSRIQddSLNDQPSRPSDTPDLMQLHYqdLVQQGL-----QTLSLEHRAVLVLhDLEDLPQKEIAEILNI 148

                        170
                 ....*....|....*..
gi 524784949 176 SVKSAENAVSRARRKLK 192
Cdd:PRK12518 149 PVGTVKSRLFYARRQLR 165
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 45-199 2.92e-04

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 39.86  E-value: 2.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  45 IYRYFgfikskaASMCGSASVCDDFVQEGvlgFLSAIRHYSSDKGTAFSSYAYSCVVNRMKTAAAKLSRLQSTeeGSDED 124
Cdd:PRK09644  14 VYRYL-------FSLTKSHHAAEDLLQET---FYRAYIYLEDYDNQKVKPWLFKVAYHTFIDFVRKEKKVSFV--GTDEI 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 524784949 125 KGEDNLTPENIIIQRELFRELE---DTLSPMEYEIFRL-SITGLTSEEIAKKLNISVKSAENAVSRARRKLKGKIADEK 199
Cdd:PRK09644  82 EAIQAESTEEYVVAKNSYEKLIqiiHTLPVIEAQAILLcDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEEK 160
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 67-177 5.39e-04

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 39.67  E-value: 5.39e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  67 DDFVQEGVLGFLSAIRHYSSDKGTAFSSYAyscvVNRMKTAAAklsrlqsteegsDEDKGEDNLtPENIiiqRELFRELE 146
Cdd:PRK06288  62 DDLVSYGVFGLIDAIEKFDPEREIKFKTYA----VTRIRGAIF------------DELRSIDWI-PRSV---RQKARQIE 121

                         90       100       110
                 ....*....|....*....|....*....|.
gi 524784949 147 DTLSPMEYEIFRlsitGLTSEEIAKKLNISV 177
Cdd:PRK06288 122 RAIAMLEARLGR----TPSDEEIADELGISL 148
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 68-192 5.56e-04

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 38.78  E-value: 5.56e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  68 DFVQEGVLGFL-SAIRHYSSDKGTAFSSYAYScVVNRMKTAAaklsRLQSTEEGS-DEDKGEDNLTPENIIIQRELFREL 145
Cdd:PRK09639  32 DLAQEVFLRLYrSDFKGIENEKGWLIKSARNV-AYNYLRSEK----RRRARILGEfQWQEVDNEPSPEEIWIRKEEITKV 106

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 524784949 146 EDTLSPM---EYEIFRLSITGLTSEEIAKKLNISVKSAENAVSRARRKLK 192
Cdd:PRK09639 107 QEVLAKMterDRTVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKKKFR 156
SigX4 TIGR02957
RNA polymerase sigma-70 factor, TIGR02957 family; This group of sigma factors are members of ...
 54-191 5.65e-04

RNA polymerase sigma-70 factor, TIGR02957 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.


Pssm-ID: 132002 [Multi-domain]  Cd Length: 281  Bit Score: 39.64  E-value: 5.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949   54 SKAASMCGSASVCDDFVQEGVLgflsaiRHYSSDKGTAFSSYAYSCVV------NRMKTAAAKlsRLQSTEEGSDEDKGE 127
Cdd:TIGR02957  12 SLAYRMLGSVADAEDIVQETFL------RWQEADRAQIENPKAYLTKVvtrrciDVLRSARAR--REVYVGPWLPEPLLT 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  128 DNLTPENIIIQRE-----LFRELEdTLSPMEYEIFRLS-ITGLTSEEIAKKLNISVKSAENAVSRARRKL 191
Cdd:TIGR02957  84 TSADPAESVELAEslsmaYLLLLE-RLSPLERAVFVLReVFDYPYEEIASIVGKSEANCRQLVSRARRHL 152
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
61-192 7.27e-04

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 38.80  E-value: 7.27e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  61 GSASVCDDFVQEGVLGFLSAIRHYsSDKGTAFSSYAYSCVVNRMKTAAAKLSRLQS--TEEGSDEDKGEDnlTPENIIIQ 138
Cdd:PRK09648  50 RPGLSADDVAQEVCLAVITALPRY-RDQGRPFLAFVYGIAAHKVADAHRAAGRDKAvpTEEVPERPSDDA--GPEERALR 126

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 524784949 139 REL---FRELEDTLSPMEYEIFRLS-ITGLTSEEIAKKLNISVKSAENAVSRARRKLK 192
Cdd:PRK09648 127 SESsnrMRELLDTLPEKQREILILRvVVGLSAEETAEAVGSTPGAVRVAQHRALARLR 184
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 56-176 1.00e-03

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 38.13  E-value: 1.00e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  56 AASMCGSASVCDDFVQEGvlgFLSAIRHYSSDKGTAFSSYAYSCVVNrmktAAAKLSRLQSTEE--GSDEDKGED----N 129
Cdd:PRK07037  15 AARIVGCRSRAEDVVQDA---FVKLVEAPNQDAVKQPVAYLFRIVRN----LAIDHYRRQALENkyHGDEEDGLDvpspE 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 524784949 130 LTPENIIIQRELFRELEDTLSPM------EYEIFRLSitGLTSEEIAKKLNIS 176
Cdd:PRK07037  88 ASPEAALINRDTLRHVADALSELpartryAFEMYRLH--GETQKDIARELGVS 138
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 40-198 1.24e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 38.03  E-value: 1.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  40 AASELIYRYFGFIKSKAASMCGSASVCDDFVQEGvlgFLSAIRHYSS--DKGTAfSSYAYSCVVNRMKTAAAKLSRLQST 117
Cdd:PRK11924  14 AFSELFRPHAPDLLRYARRQLGDRALAEDAVQEA---FLRAWRKADLfnGKGSA-RTWLLTIARNVCYDLLRRRRREKAV 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949 118 EEgSDEDKGEDNLTPENI------IIQRELFRELEDTLSPMEYEIFRLS-ITGLTSEEIAKKLNISVKSAENAVSRARRK 190
Cdd:PRK11924  90 LS-DDALEPEFAETAETPeaallaKDDLARIDRCLDALPVKQREVFLLRyVEGLSYREIAEILGVPVGTVKSRLRRARQL 168


                 ....*...
gi 524784949 191 LKGKIADE 198
Cdd:PRK11924 169 LRECLEAQ 176
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 149-191 1.53e-03

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 38.28  E-value: 1.53e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 524784949 149 LSPMEYEIFRLSITGLTSEEIAKKLNISVKSAENAVSRARRKL 191
Cdd:PRK10840 151 LSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKL 193
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 67-96 1.89e-03

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 37.98  E-value: 1.89e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 524784949  67 DDFVQEGVLGFLSAIRHYSSDKGTAFSSYA 96
Cdd:PRK07408  54 EDLVQVGSLGLIRAIERFDPSKGHAFSSFA 83
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 127-197 2.08e-03

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 37.27  E-value: 2.08e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 524784949 127 EDNLTPENIIIQRELFRELEDTLSPM------EY-EIFRLS-ITGLTSEEIAKKLNISVKSAENAVSRARRKLKGKIAD 197
Cdd:PRK09637  78 PDDLLFEDEEREENAKKELAPCLRPFidalpeKYaEALRLTeLEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 63-96 2.15e-03

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 37.90  E-value: 2.15e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 524784949  63 ASV-CDDFVQEGVLGFLSAIRHYSSDKGTAFSSYA 96
Cdd:PRK06986  34 ASVdLDDLIQAGMIGLLEAARRYDGEQGASFETYA 68
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 147-192 2.55e-03

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 34.71  E-value: 2.55e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 524784949  147 DTLSPMEYEIFRLS-ITGLTSEEIAKKLNIS---VKSAEnavSRARRKLK 192
Cdd:pfam04545   3 ASLPPRERQVLVLRyGEGLTLEEIGERLGISrerVRQIE---KRALRKLR 49
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 68-192 2.87e-03

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 37.93  E-value: 2.87e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  68 DFVQEGVLGFLSAIRHYSSDKGTAFSSYAYSCV------------------------VNRMKTAAAKLS----RLQSTEE 119
Cdd:PRK07598 204 DLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIrqgitraiatqsrtirlpvhitekLNKIKKAQRKISqekgRTPTIED 283

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949 120 -----------------------------GSDEDK--GE----DNLTPENIIIQRELFRELE---DTLSPMEYEIFRLSI 161
Cdd:PRK07598 284 iaqelemtptqvrevllrvprsvsletkvGKDKDTelGDlletDDISPEEMLMRESLQRDLQhllADLTSRERDVIRMRF 363

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 524784949 162 tGLTS------EEIAKKLNISVKSAENAVSRARRKLK 192
Cdd:PRK07598 364 -GLADghtyslAEIGRALDLSRERVRQIESKALQKLR 399
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 62-192 2.96e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 37.22  E-value: 2.96e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  62 SASVCDDFVQEGVLGFLSAIRHYSSDkgTAFSSYAYSCVVNRMKTAAAKLSR---LQSTEEGSDEDKGEDNL-------- 130
Cdd:PRK12532  29 HPDLAEDLVQETLLSAYSAGDSFQGR--ALVNSWLFAILKNKIIDALRQIGRqrkVFTLLDDELLDEAFESHfsqnghwt 106

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 524784949 131 ---------TPENIIIQRELFRELEDTLSPMEYEIFRL----SITGLTSEEIAKKLNISVKSAENAVSRARRKLK 192
Cdd:PRK12532 107 pegqpqhwnTPEKSLNNNEFQKILQSCLYNLPENTARVftlkEILGFSSDEIQQMCGISTSNYHTIMHRARESLR 181
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 52-191 5.43e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 36.10  E-value: 5.43e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 524784949  52 IKSKAASMCGSASVCDDFVQEGVLGFLSAIRHYSSdkGTAFSSYAYSCVVNRMKTAAAKLSRLQSTEEGSDEDKGEDNLT 131
Cdd:PRK12540  18 LRAFAISLSGNGDRADDLVQETLLRALANIDSFQP--GSNLPAWLFTILRNLFRSDYRKRRREVEDADGSYAKTLKSQPG 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 524784949 132 pENIIIQRELFRELEDTLSPMEYEIFRL-SITGLTSEEIAKKLNISVKSAENAVSRARRKL 191
Cdd:PRK12540  96 -QNAHLEFEEFRAALDKLPQDQREALILvGASGFSYEDAAAICGCAVGTIKSRVNRARSKL 155
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
158-191 5.88e-03

ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 36.22  E-value: 5.88e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 524784949 158 RLSITGLTSEEIAKKLNISVKSAENAVSRARRKL 191
Cdd:COG2909  132 RLLAEGLSNKEIAERLFISVNTVKTHLRNIYRKL 165
 
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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