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Conserved domains on  [gi|488811343|ref|WP_002723749|]
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MULTISPECIES: sigma-70 family RNA polymerase sigma factor [Leptospira]

Protein Classification

RNA polymerase sigma factor( domain architecture ID 11446377)

RNA polymerase sigma factor is an initiation factor that promotes the attachment of RNA polymerase to specific initiation sites and is then released

Gene Ontology:  GO:0006352|GO:0016987
PubMed:  16285916|9818380
SCOP:  8103616

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 12-171 3.48e-35

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: 121.25  E-value: 3.48e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  12 FDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPsKGNETSWMFTIAKNQFLDLIRKKdtseKREVEN 91
Cdd:COG1595   19 FEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRG-RGSFRAWLYRIARNLAIDHLRKR----RRRREL 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  92 SHKVLEFISKKEIEYEE---DKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRK 168
Cdd:COG1595   94 LDELAEELPDEAADPEEaleAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLRE 173


                 ...
gi 488811343 169 KLQ 171
Cdd:COG1595  174 ALE 176
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 12-171 3.48e-35

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: 121.25  E-value: 3.48e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  12 FDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPsKGNETSWMFTIAKNQFLDLIRKKdtseKREVEN 91
Cdd:COG1595   19 FEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRG-RGSFRAWLYRIARNLAIDHLRKR----RRRREL 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  92 SHKVLEFISKKEIEYEE---DKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRK 168
Cdd:COG1595   94 LDELAEELPDEAADPEEaleAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLRE 173


                 ...
gi 488811343 169 KLQ 171
Cdd:COG1595  174 ALE 176
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 11-170 3.50e-29

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: 105.51  E-value: 3.50e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343   11 DFDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPsKGNETSWMFTIAKNQFLDLIRKKDtSEKREVE 90
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDP-EGSFKAWLFRIARNLILDYLRRKR-RLRRELD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343   91 NSHKVLEFISKKEiEYEEDKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRKKL 170
Cdd:TIGR02937  80 LLEELLDSDPSPE-EELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 12-175 7.05e-21

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 84.64  E-value: 7.05e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  12 FDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDpSKGNETSWMFTIAKNQFLDLIRKKDT-SEKREVE 90
Cdd:PRK11924  15 FSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN-GKGSARTWLLTIARNVCYDLLRRRRReKAVLSDD 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  91 NSHKVLEFISKKEIEYEEDKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRKKL 170
Cdd:PRK11924  94 ALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECL 173


                 ....*
gi 488811343 171 QNSNF 175
Cdd:PRK11924 174 EAQWE 178
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 15-82 1.47e-16

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: 70.31  E-value: 1.47e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488811343   15 LYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKGNE-TSWMFTIAKNQFLDLIRKKD 82
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSfSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 113-157 2.69e-05

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: 40.17  E-value: 2.69e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 488811343 113 LDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNR 157
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQ 45
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 132-174 2.53e-04

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 37.51  E-value: 2.53e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 488811343   132 ILRFLRN-YTIKETAEKLGISARTVnrKTYVSLIFlrKKLQNSN 174
Cdd:smart00421  11 VLRLLAEgLTNKEIAERLGISEKTV--KTHLSNIM--RKLGVRS 50
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 12-171 3.48e-35

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: 121.25  E-value: 3.48e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  12 FDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPsKGNETSWMFTIAKNQFLDLIRKKdtseKREVEN 91
Cdd:COG1595   19 FEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRG-RGSFRAWLYRIARNLAIDHLRKR----RRRREL 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  92 SHKVLEFISKKEIEYEE---DKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRK 168
Cdd:COG1595   94 LDELAEELPDEAADPEEaleAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLRE 173


                 ...
gi 488811343 169 KLQ 171
Cdd:COG1595  174 ALE 176
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 11-170 3.50e-29

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: 105.51  E-value: 3.50e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343   11 DFDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPsKGNETSWMFTIAKNQFLDLIRKKDtSEKREVE 90
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDP-EGSFKAWLFRIARNLILDYLRRKR-RLRRELD 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343   91 NSHKVLEFISKKEiEYEEDKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRKKL 170
Cdd:TIGR02937  80 LLEELLDSDPSPE-EELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 12-175 7.05e-21

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 84.64  E-value: 7.05e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  12 FDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDpSKGNETSWMFTIAKNQFLDLIRKKDT-SEKREVE 90
Cdd:PRK11924  15 FSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN-GKGSARTWLLTIARNVCYDLLRRRRReKAVLSDD 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  91 NSHKVLEFISKKEIEYEEDKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRKKL 170
Cdd:PRK11924  94 ALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECL 173


                 ....*
gi 488811343 171 QNSNF 175
Cdd:PRK11924 174 EAQWE 178
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 12-170 1.15e-19

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: 80.68  E-value: 1.15e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343   12 FDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKgNETSWMFTIAKNQFLDLIRKKDTSEKR-EVE 90
Cdd:TIGR02985   3 FEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISE-SIKAYLFTIVKNRCLNYLRHKQVEEKYqEEL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343   91 NSHKVLEFISKKEIEYEEDKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRKKL 170
Cdd:TIGR02985  82 AEIEERELSEADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 15-82 1.47e-16

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: 70.31  E-value: 1.47e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488811343   15 LYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKGNE-TSWMFTIAKNQFLDLIRKKD 82
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSfSTWLYTIIRNAIIDYLRKQR 69
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 12-170 1.65e-16

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 73.13  E-value: 1.65e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  12 FDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKGNETsWMFTIAKNQFLDLIRKKDTSEKRE--- 88
Cdd:PRK09638  20 LTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFST-WLISIASRLYKDHLRKQKREKLRLqra 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  89 -VENSHKVLEFISKKEIEYEEdkhQLDLLNAslenLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLR 167
Cdd:PRK09638  99 kEETLRKEKWEAAIKGAEWSE---MLDALSK----LDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLR 171


                 ...
gi 488811343 168 KKL 170
Cdd:PRK09638 172 KEW 174
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 11-151 3.13e-16

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 71.90  E-value: 3.13e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  11 DFDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNwdkfDP-SKGNETSWMFTIAKNQFLDLIRKKDTSEKREV 89
Cdd:PRK09639   4 TFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS----DFkGIENEKGWLIKSARNVAYNYLRSEKRRRARIL 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488811343  90 ENS--HKVLEFISKKEIEYEedKHQLDLLNASLENLPHLEKNIIILRFlRNYTIKETAEKLGIS 151
Cdd:PRK09639  80 GEFqwQEVDNEPSPEEIWIR--KEEITKVQEVLAKMTERDRTVLLLRF-SGYSYKEIAEALGIK 140
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 12-155 1.19e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 70.35  E-value: 1.19e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  12 FDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFdpsKGNETS-WMFTIAKNQFLDLIRKKDTSEKREVE 90
Cdd:PRK12541   7 LEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYY---KGEEIRpWLFTIAYNAFIDWYRKEKKYKTTTIE 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488811343  91 NSHkvLEFISKKEIEYEEdKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTV 155
Cdd:PRK12541  84 EFH--LPNVPSTEHEYFI-KHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKV 145
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 12-171 2.87e-15

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 69.84  E-value: 2.87e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  12 FDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPsKGNETSWMFTIAKNQFLDLIRKKdtseKREVEN 91
Cdd:PRK09652  12 FALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRG-GAAFYTWLYRIARNTAINYLRKQ----GRRPPA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  92 SHkvlefISKKEIEYEEDKHQL----------------DLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTV 155
Cdd:PRK09652  87 SD-----VDAEEAEDFDLADALrdistpenellsaeleQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTV 161

                        170       180
                 ....*....|....*....|.
gi 488811343 156 NrktyvSLIF-----LRKKLQ 171
Cdd:PRK09652 162 R-----SRIFrareaLRAKLQ 177
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 12-155 1.40e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 68.18  E-value: 1.40e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  12 FDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPsKGNETSWMFTIAKNQFLDLIRKKDtsekreven 91
Cdd:PRK12513  28 FEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQP-RARFRTWLYQIARNLLIDHWRRHG--------- 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  92 shkvleFISKKEIEYEEDKH-----------QLDL------LNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISART 154
Cdd:PRK12513  98 ------ARQAPSLDADEQLHaladdgaapeqQLSLfrdrrrLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEET 171


                 .
gi 488811343 155 V 155
Cdd:PRK12513 172 V 172
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 21-172 9.93e-13

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 63.18  E-value: 9.93e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  21 EKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKGNETsWMFTIAKNQFLDLIRKK--DTSEKREVENSHKVLEF 98
Cdd:PRK09641  29 DKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFST-WLYRIATNLTIDRLRKRkpDYYLDAEVAGTEGLTMY 107

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488811343  99 --ISKKEIEYEEDKHQLDL---LNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRKKLQN 172
Cdd:PRK09641 108 sqLAADDALPEEQVVSLELqetIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREALRKQLRH 186
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 23-172 3.13e-12

RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).


Pssm-ID: 274379 [Multi-domain]  Cd Length: 159  Bit Score: 61.18  E-value: 3.13e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343   23 IYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSkGNETSWMFTIAKNQFLDLIRKKDTSekREVENShKVLEFISKK 102
Cdd:TIGR02989  14 LRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPG-TNFVAWARGIARNKVLNYRRKLGRD--RLVFDD-DLLEALAAE 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488811343  103 --EIEYEEDKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVnrktYVSLIFLRKKLQN 172
Cdd:TIGR02989  90 aePTEAERLSDDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAV----YKALQRIRVSLRE 157
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 13-171 1.24e-11

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 59.89  E-value: 1.24e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  13 DGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKgnETSWMFTIAKNQFLDLIRKkdtsEKREVENS 92
Cdd:PRK09644   4 EEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQK--VKPWLFKVAYHTFIDFVRK----EKKVSFVG 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  93 HKVLEFISKKEIE-YEEDKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGIsartvNRKTYVSLIFL-RKKL 170
Cdd:PRK09644  78 TDEIEAIQAESTEeYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDL-----KLNTYKSHLFRgRKRL 152


                 .
gi 488811343 171 Q 171
Cdd:PRK09644 153 K 153
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 12-171 9.65e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 57.52  E-value: 9.65e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  12 FDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKGNETSWMFTIAKNQFLDLIRKKDTSEKrEVEN 91
Cdd:PRK12514  21 FSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPMTWLITIARNHAIDRLRARKAVAV-DIDE 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  92 SHKVLEFISKKEIE-YEEDKHQldLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRKKL 170
Cdd:PRK12514 100 AHDLADPSPGPEAEvIAGDEGQ--RIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKLRECL 177


                 .
gi 488811343 171 Q 171
Cdd:PRK12514 178 S 178
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 11-162 2.37e-10

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


Pssm-ID: 132028 [Multi-domain]  Cd Length: 162  Bit Score: 56.24  E-value: 2.37e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343   11 DFDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFdPSKGNETSWMFTIAKNQFLDLIRKKdtsekREVE 90
Cdd:TIGR02983   7 EFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRI-RDPDAPDAYVRRVLVNLARSRWRRR-----RLLE 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488811343   91 NSHKVLEFISKKEIEYEEDKHQlDLLNAsLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVnrKTYVS 162
Cdd:TIGR02983  81 LPTRELPDAAAPDPAPDVALRA-ALARA-LRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTV--KSRLS 148
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 37-159 3.54e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 56.39  E-value: 3.54e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  37 AEETCQETFIKVLNNWDKFDPSKgNETSWMFTIAKNQFLDLIRKKdtseKREVENSHKVL-EFISKKEieyEEDKH-QLD 114
Cdd:PRK12546  34 ADDLVQDTIVKAWTNFDKFQEGT-NLRAWLFTILRNTFYSDRRKH----KREVPDPEGVHaASLAVKP---AHDGRlAMS 105

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 488811343 115 LLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKT 159
Cdd:PRK12546 106 DFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRA 150
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
12-170 4.78e-10

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 55.83  E-value: 4.78e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  12 FDGLYSRNYEKIYRFLLSKGaskeEAEETCQETFIKVLNNWDKFDPSKGNETSWMFTIAKNQFLDLIRKKDTSEKREVE- 90
Cdd:PRK09646  36 YDRTSSRVYGLVRRVLRDPG----YSEETTQEVYLEVWRTASRFDPARGSALAWLLTLAHRRAVDRVRSEQAASQREVRy 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  91 ---NSHKVLEFISkKEIEYEEDKHQldlLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLR 167
Cdd:PRK09646 112 garNVDPAFDQVA-EEVEARLERER---VRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGLIRLR 187


                 ...
gi 488811343 168 KKL 170
Cdd:PRK09646 188 DCL 190
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 14-170 5.25e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 55.89  E-value: 5.25e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  14 GLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDpSKGNETSWMFTIAKNQFLDLIRKK-----DTSEKRE 88
Cdd:PRK12515  26 TLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFE-GRSQVSTWLLSIARFKALSALRRRkheeiDDEAAAA 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  89 VENSHKVLEFISKKeieyeedKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVnrKTyvSLIFLRK 168
Cdd:PRK12515 105 IEDGADTPEVALQK-------SDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTV--KT--RMFYARK 173


                 ..
gi 488811343 169 KL 170
Cdd:PRK12515 174 KL 175
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 22-172 1.45e-09

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 54.56  E-value: 1.45e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  22 KIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKGNETSWMFTIAKNQFLDLIRK-KDTSEKREVENSHKVLEFIS 100
Cdd:PRK06811  33 KIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKGSFKKWIAAISKYKAIDYKRKlTKNNEIDSIDEFILISEESI 112

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488811343 101 KKEIEYEEDKHQLDLLnasLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRKKLQN 172
Cdd:PRK06811 113 ENEIILKENKEEILKL---INDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKLN 181
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 26-171 1.50e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 54.11  E-value: 1.50e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  26 FLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKgNETSWMFTIAKNQFLDLIRKKdtseKREVENSHKVleFISKKEIe 105
Cdd:PRK12547  22 FAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT-NLKAWLFTILRNEFYSQMRKR----GREVQDSDGV--FTARVAV- 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488811343 106 YEEDKHQLDL--LNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVnrKTYVSLIflRKKLQ 171
Cdd:PRK12547  94 HPAQYGSLDLqdFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTI--KSRVSRA--RNRLQ 157
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 26-157 2.44e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 53.81  E-value: 2.44e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  26 FLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKgNETSWMFTIAKNQFLDLIRKKdtseKREVENSHKVLEFISKKE-- 103
Cdd:PRK12540  21 FAISLSGNGDRADDLVQETLLRALANIDSFQPGS-NLPAWLFTILRNLFRSDYRKR----RREVEDADGSYAKTLKSQpg 95

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488811343 104 ----IEYEEdkhqldlLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISART----VNR 157
Cdd:PRK12540  96 qnahLEFEE-------FRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTiksrVNR 150
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 25-155 5.75e-09

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 52.68  E-value: 5.75e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  25 RFLLSKGASKEEAEETCQETFIKVLNNWDKFDpSKGNETSWMFTIAKNQFLDLIRKKDTSEKREVEnshkvlEFISKKEI 104
Cdd:PRK09637  16 AFLHSRVSNEADVDDLLQEVLIKTHSNLHSLK-DGSSIKSWLYQIANNTIIDFYRKKNRSEELPDD------LLFEDEER 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 488811343 105 EYEEDKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTV 155
Cdd:PRK09637  89 EENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGA 139
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 31-170 8.59e-09

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 52.61  E-value: 8.59e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  31 GASKEEAEETCQETFIKVLNNWDKFDPSKGNETSWMFTIAKNQFLDLIRKKdtsekrevENSHKVLEFISKKEIEYE--- 107
Cdd:PRK13919  44 GLDGAAAEDVVQEVFIRVWKKAKEFDPRRGSARAWLLALAHHAAVDHVRRR--------AARPQPLEPDEREPEAFDlpg 115

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488811343 108 ---EDKHQLD--LLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRKKL 170
Cdd:PRK13919 116 pglDEEGHLDrtRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVL 183
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 26-171 1.11e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 52.27  E-value: 1.11e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  26 FLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKgNETSWMFTIAKNQFLDLIRKKDtsekREVENSHKVLefiSKKEIE 105
Cdd:PRK12516  26 FAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT-NMKAWLFTILRNEFYSQMRKRG----REVQDTDGMF---TEQLAV 97

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488811343 106 YEEDKHQLDL--LNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVnrKTYVSLIflRKKLQ 171
Cdd:PRK12516  98 HPSQYGTLDLqdFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTI--KSRVNRA--RQRLQ 161
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 12-171 1.64e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 51.59  E-value: 1.64e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  12 FDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKGNETSWMFTIAKNQFLDLIRKKdTSEKREV-- 89
Cdd:PRK12534  27 FEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGLTWLAMIARNKAIDHLRAN-APQRRNVal 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  90 -------ENSHKVLEfiskkEIEYEEDKHQLDLLNASLENlPHLEknIIILRFLRNYTIKETAEKLGISARTVNRKTYVS 162
Cdd:PRK12534 106 ddagelrAADASPLE-----RTERASTRRRIDHCLAELEP-PRSE--LIRTAFFEGITYEELAARTDTPIGTVKSWIRRG 177


                 ....*....
gi 488811343 163 LIFLRKKLQ 171
Cdd:PRK12534 178 LAKLKACLE 186
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 12-172 2.27e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 51.27  E-value: 2.27e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  12 FDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKGNETsWMFTIAKNQ-----------FLDLIRK 80
Cdd:PRK12543   9 FSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRF-WLIGLVIKQihswrrkrwrrFRIFEKA 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  81 KDTSEKREVENSHKVLEFISKKEieyeedkhqldlLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTY 160
Cdd:PRK12543  88 EEQRKPVSIDFSEDVLSKESNQE------------LIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIH 155

                        170
                 ....*....|..
gi 488811343 161 VSLIFLRKKLQN 172
Cdd:PRK12543 156 AALKKLRQKEQI 167
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 22-170 3.73e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 50.95  E-value: 3.73e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  22 KIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKGNETSWMFTIAKNQFLDLIRK-KDTSEKREVENSHKVLEFIS 100
Cdd:PRK12526  50 KIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKGAATTWVYTVMRNAAFDMLRKiKAKKEQNLGDDIWPIEQALA 129

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488811343 101 KKEIEYEE-DKHQLDL-LNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRKKL 170
Cdd:PRK12526 130 ESQSESEEfSDHLMDKqILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
15-171 4.32e-08

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 50.46  E-value: 4.32e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  15 LYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKGNETSWMFTIAKNQFLDLIRkkdTSEKREVENSHK 94
Cdd:PRK09645  14 LYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRSARAWLFTVARNLVIDERR---SARARPVEGGDD 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  95 VLEFISKKeieyEEDKHQ--LD--LLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRKKL 170
Cdd:PRK09645  91 VLGVPEQS----APDEVDraLDrlLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALRLAL 166


                 .
gi 488811343 171 Q 171
Cdd:PRK09645 167 Q 167
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 15-171 7.73e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 50.06  E-value: 7.73e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  15 LYSRNYEKIYRFLLSKGASKEEAEETCQETFikvLNNWDK--FDPSKGNETSWMFTIAKNQFLDLIRKKDTSEK--REVE 90
Cdd:PRK12519  34 LYDRHAGLVYGLALKILGNSQEAEDLTQEIF---LSLWRKssYDPKRGSLSSYLLTLTRSRAIDRLRSRRSRQRllERWQ 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  91 NSHKV-------LEFISKKEIEYEedkhqldlLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSL 163
Cdd:PRK12519 111 QELLGeasedtpLEQASLAERSQR--------VQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGL 182


                 ....*...
gi 488811343 164 IFLRKKLQ 171
Cdd:PRK12519 183 LKLRELLQ 190
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 37-167 2.57e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 48.23  E-value: 2.57e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  37 AEETCQETFIKVLNNWDKFDPSKGNETSWMFTIAKNQFLDLIRKKDtsekREV------ENSHKVLEFISkKEIEYEEDK 110
Cdd:PRK12537  50 AEDIVHDAFIKIWTGAASFDPARGSARGWIYSVTRHLALNVLRDTR----REVvldddaEETAQTLHEII-DDFDLWANS 124

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 488811343 111 HQLDllnASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLR 167
Cdd:PRK12537 125 GKIH---RCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALR 178
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 36-174 3.61e-07

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 48.01  E-value: 3.61e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  36 EAEETCQETFIKVLNNWDKFDpSKGNETSWMFTIAKNQFLDLIRKkdtsEKREvensHKVLEFISKKEIEYEEDKHQLDL 115
Cdd:PRK09640  52 DADDVCQEVMLKVLYGLKNFE-GKSKFKTWLYSITYNECITQYRK----ERRK----RRLMDALSLDPLEEASEEKAPKP 122

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488811343 116 -----LNASLENLPHLEKNIIILRFLRNYTIKETAE--KLGISARTVNRKTyvSLIFLRKKLQNSN 174
Cdd:PRK09640 123 eerggLDRWLVHVNPIDREILVLRFVAELEFQEIADimHMGLSATKMRYKR--ALDKLREKFAGLA 186
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 33-171 5.57e-07

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 47.43  E-value: 5.57e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  33 SKEEAEETCQETFIKVLNNWDKFDpSKGNETSWMFTIAKNQFLDLI-----RKKDTSEKREvENSHKVLEFISKKEIEYE 107
Cdd:PRK09415  39 NKEVAEDLTQEIFVKCYKSLHTYK-GKSSLKTWLYRIAINHCKDYLkswhnKKVIVTEDIF-TYMESQKESVEEEVIQNA 116

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488811343 108 EDKHqldlLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRKKLQ 171
Cdd:PRK09415 117 EDER----LASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLE 176
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 95-171 1.01e-06

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: 47.22  E-value: 1.01e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488811343   95 VLEFISKKEIEYEEDKHQLdLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRKKLQ 171
Cdd:TIGR02980 152 LLDTLGDEDDALETVEDRL-ALKPLLAALPERERRILLLRFFEDKTQSEIAERLGISQMHVSRLLRRALKKLREQLL 227
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 103-171 1.76e-06

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 46.69  E-value: 1.76e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488811343 103 EIEYEEDKHQLDLLnasLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRKKLQ 171
Cdd:PRK07122 199 GLDQIENREALRPL---LAALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKTLARLRDQLE 264
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 120-157 1.99e-06

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: 42.80  E-value: 1.99e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 488811343  120 LENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNR 157
Cdd:pfam04545   2 LASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQ 39
Sig-70_X6 TIGR02999
RNA polymerase sigma factor, TIGR02999 family; This group of sigma factors are members of the ...
 76-157 3.17e-06

RNA polymerase sigma factor, TIGR02999 family; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.


Pssm-ID: 132044 [Multi-domain]  Cd Length: 183  Bit Score: 45.39  E-value: 3.17e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343   76 DLIRKKdTSEKReveNSHKVLEFISKKEIEYEEDKH-QLDLLNASLENL----PHLEkNIIILRFLRNYTIKETAEKLGI 150
Cdd:TIGR02999  88 DHARRR-RAQKR---GGGAVRVPLDEVLPDAEADLDeELLDLDDALDKLaqvdPRQA-EVVELRFFAGLTVEEIAELLGV 162


                  ....*..
gi 488811343  151 SARTVNR 157
Cdd:TIGR02999 163 SVRTVER 169
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 21-172 7.89e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 44.09  E-value: 7.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  21 EKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKgNETSWMFTIAKNQFLDLIRKK-----------DTSEKREV 89
Cdd:PRK12522  14 QQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE-NYKKWITTICVRTFYDFYRKKkrwkdrildlfHKEDGGEI 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  90 ENSHKVLefISKKEIEYEEDKhqldLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRKK 169
Cdd:PRK12522  93 EFADDVN--ISEEFIQKVEAE----MIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREH 166


                 ...
gi 488811343 170 LQN 172
Cdd:PRK12522 167 LEG 169
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 1-162 1.00e-05

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 43.65  E-value: 1.00e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343   1 MSQNSESQIFDFDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNwDKF----DPSkgnetSWMFTIAKNQFLD 76
Cdd:PRK09651   1 SDRATTTASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLstirDPR-----SFLCTIAKRVMVD 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  77 LIRkKDTSEKREVENSHKVLEFISKKEIEYEEDKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVn 156
Cdd:PRK09651  75 LFR-RNALEKAYLEMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSV- 152


                 ....*.
gi 488811343 157 rKTYVS 162
Cdd:PRK09651 153 -KKYVA 157
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 105-171 1.09e-05

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


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 44.04  E-value: 1.09e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488811343 105 EYEEDKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNR-KTYVsLIFLRKKLQ 171
Cdd:COG1191  169 EELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRlHKKA-LARLREYLK 235
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 113-170 1.34e-05

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: 40.90  E-value: 1.34e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 488811343  113 LDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVnrKTYVSLIflRKKL 170
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTV--KSRLSRA--RKKL 54
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 25-155 1.68e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 43.15  E-value: 1.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  25 RFLLSKGASKEEAEETCQETFIKV---LNNWDKFDPSKgnetSWMFTIAKNQFLDLIRKKDtsekREVENShkVLEFISK 101
Cdd:PRK12512  41 RGLARAGQPADQAEDIVQEILLAVhlkRHTWDPGAPFA----PWLFAIARNKLIDALRRRG----RRVFVD--IDDFAET 110

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 488811343 102 KEIEYEEDKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTV 155
Cdd:PRK12512 111 LPAEPATETLPAGDVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAV 164
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 113-157 2.69e-05

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: 40.17  E-value: 2.69e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 488811343 113 LDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNR 157
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQ 45
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 12-155 2.89e-05

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 42.77  E-value: 2.89e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  12 FDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFdpsKGNE--TSWMFTIAKNQFLDLIRKKDTSEKREV 89
Cdd:PRK09643  29 FGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSF---RGDAavSSWLHRIVVNACLDRLRRAKARPTVPL 105

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488811343  90 ENSHKVLEFISKKeieYEEDKHQLDLLNAsLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTV 155
Cdd:PRK09643 106 DDVYPVAQLERDP---TARVETALAVQRA-LMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTV 167
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 107-175 6.32e-05

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 42.21  E-value: 6.32e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488811343 107 EEDKHQLDLLNASLEnlphlEKNIIILR--FLRNYTIKETAEKLGISARTVNRKTYVSLIFLRKKLQNSNF 175
Cdd:PRK07408 191 QEDRIRLQQALAQLE-----ERTREVLEfvFLHDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQPEDD 256
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 13-81 1.24e-04

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 40.92  E-value: 1.24e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488811343  13 DGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPskGNETSWMFTIAKNQFLDLIRKK 81
Cdd:PRK09647  31 EELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--GTFEGWLHRITTNLFLDMVRRR 97
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
107-170 1.60e-04

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 40.51  E-value: 1.60e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488811343 107 EEDKHQLDLLNASLENLPHLEKNIIILrFLRNYTIKETAEKLGISARTVnrKTYVSLIflRKKL 170
Cdd:COG2771  112 ALLLAALARLLARAPGLTPREREVLRL-LAEGLTLKEIARILGISERTV--RTHLKRI--YRKL 170
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 109-176 1.66e-04

ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.


Pssm-ID: 254323 [Multi-domain]  Cd Length: 185  Bit Score: 40.48  E-value: 1.66e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488811343  109 DKHQLDL---LNASLENLPHLEKNI---IILRFLRNYTIKETAEKLGISARTVNRKtyvsLIFLRKKLQNSNFD 176
Cdd:pfam07638 116 DSPNPDLlldLDEALEQLFSLSPRQarlVELRFFAGLSNDEIAERLGVSERTVERN----WALARAWLHRELRD 185
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
17-155 2.39e-04

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 40.10  E-value: 2.39e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  17 SRNYEKIYRFLLSK-GASKEEAEETCQETFIKVLNNWDKFDPSKgNETSWMFTIAKNQFLDLIRKKDTSEKR-EVENSHK 94
Cdd:PRK12539  31 SGHLRAYYKGKLARiGRGAEEAEDLVQEALMAIHTRRHTYDPEQ-PLTPWVYAIARYKLIDHLRRTRASLADvPIDDADE 109

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488811343  95 VLEFISKKEIEYEEDKHQLdllnasLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTV 155
Cdd:PRK12539 110 LVAHDDHAAVESTLDLGRL------LARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAV 164
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 132-174 2.53e-04

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 37.51  E-value: 2.53e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 488811343   132 ILRFLRN-YTIKETAEKLGISARTVnrKTYVSLIFlrKKLQNSN 174
Cdd:smart00421  11 VLRLLAEgLTNKEIAERLGISEKTV--KTHLSNIM--RKLGVRS 50
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 132-171 2.55e-04

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: 39.11  E-value: 2.55e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 488811343 132 ILRFL-RNYTIKETAEKLGISARTVnrKTYVSLIFlrKKLQ 171
Cdd:COG2197   77 VLRLLaEGLSNKEIAERLGISERTV--KTHVSNIL--RKLG 113
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
24-79 3.33e-04

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 39.92  E-value: 3.33e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 488811343  24 YRFLlskgASKEEAEETCQETFIKVLNNWDKFDpSKGNETSWMFTIAKNQFLDLIR 79
Cdd:PRK08241  37 YRML----GSVHDAEDAVQETLLRAWRGYDRFE-GRSSLRTWLYRIATNVCLDALE 87
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 12-146 3.52e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 39.84  E-value: 3.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  12 FDGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKGNETSWMFTIAKNQFLDLIRKKDTsekrevEN 91
Cdd:PRK12538  65 FRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRAKFSTWLYRVVSNRCIDLRRKPRT------EN 138

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  92 SHKVLEFISKKE-----IEYEEDKHqldLLNASLENLPHLEKNIIILRFLRNYTIKETAE 146
Cdd:PRK12538 139 VDAVPEVADGKPdavsvIERNELSD---LLEAAMQRLPEQQRIAVILSYHENMSNGEIAE 195
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 15-158 3.56e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 39.65  E-value: 3.56e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  15 LYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKGNE-TSWMFTIAKNQFLDLIRKKDTSEKREVENSH 93
Cdd:PRK12542  14 LYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQElKRYILRVAKNKAIDSYRKNKRHETFLEEYER 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488811343  94 KVLEFISKKEIEYEEDKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRK 158
Cdd:PRK12542  94 ESIEAVDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQ 158
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 22-81 3.92e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 39.53  E-value: 3.92e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  22 KIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKGNETSWMFTIAKNQFLDLIRKK 81
Cdd:PRK12531  39 KLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKSALSTWIYTIIRNLCFDLLRKQ 98
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 13-157 4.65e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 39.06  E-value: 4.65e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  13 DGLYSRNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKfdPSKGNETSWMFTIAKNQFLDLIRKKDtsekreVENS 92
Cdd:PRK12528   7 EGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARET--AQIIEPRAFLTTIAKRVLCNHYRRQD------LERA 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  93 H-KVLEFISKKEIEYEEDK----HQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNR 157
Cdd:PRK12528  79 YlEALAQLPERVAPSEEERaiilETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKR 148
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 95-173 5.50e-04

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 39.29  E-value: 5.50e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488811343  95 VLEFISKKEIEYEEDKHQLdLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRKKLQNS 173
Cdd:PRK08583 179 LLDIVGQQEDGYELTEQRM-ILEKILPVLSDREKSIIQCTFIENLSQKETGERLGISQMHVSRLQRQAIKKLREAAFLD 256
PRK06704 PRK06704
RNA polymerase subunit sigma-70;
18-174 8.06e-04

RNA polymerase subunit sigma-70;


Pssm-ID: 180663 [Multi-domain]  Cd Length: 228  Bit Score: 38.85  E-value: 8.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  18 RNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSkgneTSWMFTIAKNQFLDLIRKKDTSEKREvenshkvle 97
Cdd:PRK06704  25 EQYGELKRYCTFLTKNKWDGEDLAQETVCKVLQKYSNKDIC----MTLVYKIARNRWLDQIKSKSVHEKIR--------- 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  98 fiskKEIEYEEDKHQL----DLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNrktyVSLIFLRKKLQNS 173
Cdd:PRK06704  92 ----DQITFEEPHEKIadlhEMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVK----ASLFRSRNRLKTV 163


                 .
gi 488811343 174 N 174
Cdd:PRK06704 164 S 164
HTH_23 pfam13384
Homeodomain-like domain;
131-157 9.66e-04

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 35.71  E-value: 9.66e-04
                          10        20
                  ....*....|....*....|....*..
gi 488811343  131 IILRFLRNYTIKETAEKLGISARTVNR 157
Cdd:pfam13384  10 ALLLLAEGLSVKEIAELLGVSRRTVYR 36
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 36-89 9.81e-04

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 38.09  E-value: 9.81e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 488811343  36 EAEETCQETFIKVLNNWDKFDPSKGNETSWMFTIAKNQFLDLIRKkdtseKREV 89
Cdd:PRK05602  46 EAEDVAQETFLRIWKQAPSWRPGEARFDTWLHRVVLNLCYDRLRR-----RREV 94
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 20-157 1.72e-03

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 37.06  E-value: 1.72e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  20 YEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDkfDPSKGNETSWMFTIAKNQFLDLIRKK--DTSEKREVENSHKVLE 97
Cdd:PRK12527   5 YRELVRFLSARLGNRQAAEDVAHDAYLRVLERSS--SAQIEHPRAFLYRTALNLVVDRHRRHrvRQAEPLEVLDEEERLH 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  98 FISKKEIEYEedKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNR 157
Cdd:PRK12527  83 SPSPQTRLDL--GQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEK 140
PRK09642 PRK09642
RNA polymerase sigma factor;
23-175 1.95e-03

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 37.00  E-value: 1.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  23 IYRFLLSKGASKEEAEETCQETFIKVLNNWDKFDpSKGNETsWMFTIAKNQFLDLIRKKdTSEKREVENSHKVLEFI-SK 101
Cdd:PRK09642   8 IFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQ-FRGLKT-WMARIATNHAIDYKRKK-ARENEELSLCKETEENIkSS 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488811343 102 KEIE-YEEDKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYVSLIFLRKKLQNSNF 175
Cdd:PRK09642  85 HNIEdLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEEEF 159
PRK12544 PRK12544
RNA polymerase factor sigma-70;
25-175 2.13e-03

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 37.47  E-value: 2.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  25 RFLLSKGASKEEAEETCQETFIKVLNNWDKFDPSKGNETsWMFTIAKNQFLDLIRKKdtseKREVENSHKVLEFISKKEI 104
Cdd:PRK12544  33 KFATLQLSDLHLAEDAVQEALIGALKNADSFAGRAAFKT-WVFAILKNKIIDLLRQK----KRHVSASSLLRDEEEEEDF 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343 105 EY--------------------EEDKHQLD---LLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNRKTYV 161
Cdd:PRK12544 108 EElfdesghwqkderpqawgnpEESLEQEQfwrIFEACLDGLPAKYARVFMMREFIELETNEICHAVDLSVSNLNVLLYR 187

                        170
                 ....*....|....
gi 488811343 162 SLIFLRKKLQNSNF 175
Cdd:PRK12544 188 ARLRLRECLENKWF 201
HTH_28 pfam13518
Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is ...
 131-155 2.72e-03

Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is likely to be DNA-binding.


Pssm-ID: 463908 [Multi-domain]  Cd Length: 52  Bit Score: 34.49  E-value: 2.72e-03
                          10        20
                  ....*....|....*....|....*
gi 488811343  131 IILRFLRNYTIKETAEKLGISARTV 155
Cdd:pfam13518   5 IVLLALEGESIKEAARLFGISRSTV 29
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
105-157 3.32e-03

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 36.87  E-value: 3.32e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 488811343 105 EYEEDKHQLDLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTVNR 157
Cdd:PRK05572 185 QSEEDWFDKIALKEAIRELDERERLIVYLRYFKDKTQSEVAKRLGISQVQVSR 237
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 37-81 3.72e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 36.67  E-value: 3.72e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 488811343  37 AEETCQETFIKVLNNWDKFDPSKGNETsWMFTIAKNQFLDLIRKK 81
Cdd:PRK12530  34 AEDVVQEALVSAYKNADSFKGQSALKT-WIFAILKNKIIDLIRYR 77
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 18-155 6.37e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 36.10  E-value: 6.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488811343  18 RNYEKIYRFLLSKGASKEEAEETCQETFIKVLNNWDKFdpsKGNE--TSWMFTIAKNQFLDLIRK-KDTSEKREVENSHK 94
Cdd:PRK11922  38 RHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTF---RGDAslSTWLSRIVLNEALGRLRRrRRLVNLAEMVMAST 114

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488811343  95 VLEFISKKE------IEYEEDKHQL-DLLNASLENLPHLEKNIIILRFLRNYTIKETAEKLGISARTV 155
Cdd:PRK11922 115 IAGGERTPLadpaedPERAAARREIrALLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETV 182
 
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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