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Conserved domains on  [gi|2730672382|ref|WP_344792955|]
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sigma-70 family RNA polymerase sigma factor [Gryllotalpicola daejeonensis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SigH_actino super family cl31274
RNA polymerase sigma-70 factor, TIGR02947 family; This group of sigma factors are members of ...
 9-196 4.32e-103

RNA polymerase sigma-70 factor, TIGR02947 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.


The actual alignment was detected with superfamily member TIGR02947:

Pssm-ID: 131992 [Multi-domain]  Cd Length: 193  Bit Score: 295.34  E-value: 4.32e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382   9 NEAPRELTFEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQRE 88
Cdd:TIGR02947   5 TKTQRAQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPGTNLKAWLYRILTNTYINSYRKAQRR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  89 PFQTPIEDLEDWQLGGAESTTARASRSAEAEAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTV 168
Cdd:TIGR02947  85 PQQSDDDDIEDWQLAKAASHTSNGLRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTV 164

                         170       180
                  ....*....|....*....|....*...
gi 2730672382 169 MSRLHRGRRMLRDLLSDYARDRGSAAQT 196
Cdd:TIGR02947 165 MSRLHRGRKQLRKQLVDVAGERGFGPRA 192
 
Name Accession Description Interval E-value
SigH_actino TIGR02947
RNA polymerase sigma-70 factor, TIGR02947 family; This group of sigma factors are members of ...
 9-196 4.32e-103

RNA polymerase sigma-70 factor, TIGR02947 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.


Pssm-ID: 131992 [Multi-domain]  Cd Length: 193  Bit Score: 295.34  E-value: 4.32e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382   9 NEAPRELTFEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQRE 88
Cdd:TIGR02947   5 TKTQRAQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPGTNLKAWLYRILTNTYINSYRKAQRR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  89 PFQTPIEDLEDWQLGGAESTTARASRSAEAEAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTV 168
Cdd:TIGR02947  85 PQQSDDDDIEDWQLAKAASHTSNGLRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTV 164

                         170       180
                  ....*....|....*....|....*...
gi 2730672382 169 MSRLHRGRRMLRDLLSDYARDRGSAAQT 196
Cdd:TIGR02947 165 MSRLHRGRKQLRKQLVDVAGERGFGPRA 192
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 10-189 1.55e-71

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 214.67  E-value: 1.55e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  10 EAPRELTFEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREP 89
Cdd:PRK09652    5 QRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQGRRP 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  90 FQT--PIEDLEDWQLGGAESTTArasrSAEAEAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGT 167
Cdd:PRK09652   85 PASdvDAEEAEDFDLADALRDIS----TPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGT 160

                         170       180
                  ....*....|....*....|..
gi 2730672382 168 VMSRLHRGRRMLRDLLSDYARD 189
Cdd:PRK09652  161 VRSRIFRAREALRAKLQPLLDE 182
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-189 5.94e-46

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: 149.76  E-value: 5.94e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382   1 MTDDLELSNEAPR--ELTFEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTF 78
Cdd:COG1595     1 MSSDEELLERLRAgdEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  79 INNYRKKQREPfqtpiEDLEDwqlggAESTTARASRSAEAEAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIA 158
Cdd:COG1595    81 IDHLRKRRRRR-----ELLDE-----LAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIA 150

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2730672382 159 DIMKTPIGTVMSRLHRGRRMLRDLLSDYARD 189
Cdd:COG1595   151 EILGISEGTVKSRLSRARKKLREALEEEGAL 181
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 24-88 2.33e-15

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: 67.61  E-value: 2.33e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2730672382  24 FMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFH--QGTNLKAWLYRILTNTFINNYRKKQRE 88
Cdd:pfam04542   5 YLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDpeRGVSFSTWLYTIIRNAIIDYLRKQRRT 71
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 128-180 6.04e-12

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: 58.27  E-value: 6.04e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2730672382 128 DVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLR 180
Cdd:cd06171     3 RLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
SigH_actino TIGR02947
RNA polymerase sigma-70 factor, TIGR02947 family; This group of sigma factors are members of ...
 9-196 4.32e-103

RNA polymerase sigma-70 factor, TIGR02947 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.


Pssm-ID: 131992 [Multi-domain]  Cd Length: 193  Bit Score: 295.34  E-value: 4.32e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382   9 NEAPRELTFEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQRE 88
Cdd:TIGR02947   5 TKTQRAQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPGTNLKAWLYRILTNTYINSYRKAQRR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  89 PFQTPIEDLEDWQLGGAESTTARASRSAEAEAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTV 168
Cdd:TIGR02947  85 PQQSDDDDIEDWQLAKAASHTSNGLRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTV 164

                         170       180
                  ....*....|....*....|....*...
gi 2730672382 169 MSRLHRGRRMLRDLLSDYARDRGSAAQT 196
Cdd:TIGR02947 165 MSRLHRGRKQLRKQLVDVAGERGFGPRA 192
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 10-189 1.55e-71

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 214.67  E-value: 1.55e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  10 EAPRELTFEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREP 89
Cdd:PRK09652    5 QRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQGRRP 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  90 FQT--PIEDLEDWQLGGAESTTArasrSAEAEAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGT 167
Cdd:PRK09652   85 PASdvDAEEAEDFDLADALRDIS----TPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGT 160

                         170       180
                  ....*....|....*....|..
gi 2730672382 168 VMSRLHRGRRMLRDLLSDYARD 189
Cdd:PRK09652  161 VRSRIFRAREALRAKLQPLLDE 182
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-189 5.94e-46

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: 149.76  E-value: 5.94e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382   1 MTDDLELSNEAPR--ELTFEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTF 78
Cdd:COG1595     1 MSSDEELLERLRAgdEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  79 INNYRKKQREPfqtpiEDLEDwqlggAESTTARASRSAEAEAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIA 158
Cdd:COG1595    81 IDHLRKRRRRR-----ELLDE-----LAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIA 150

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2730672382 159 DIMKTPIGTVMSRLHRGRRMLRDLLSDYARD 189
Cdd:COG1595   151 EILGISEGTVKSRLSRARKKLREALEEEGAL 181
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 26-200 1.69e-36

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 126.44  E-value: 1.69e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  26 DQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTnLKAWLYRILTNTFINNYRKKQREPFQTPIEDledwqlggA 105
Cdd:PRK09647   39 DRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQPGT-FEGWLHRITTNLFLDMVRRRARIRMEALPED--------Y 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 106 ESTTARASRSAEAEAIDHLpDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLLSD 185
Cdd:PRK09647  110 DRVPGDEPNPEQIYHDARL-DPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAA 188

                         170
                  ....*....|....*
gi 2730672382 186 YARDRGSAAQTSSAR 200
Cdd:PRK09647  189 HAPHAECAALLNPAR 203
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 17-185 4.26e-36

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 124.70  E-value: 4.26e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  17 FEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPFQTPIED 96
Cdd:PRK11924   15 FSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKAVLSDDA 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  97 LEDWQLGGAESTTARASRSAEAEAIDhlpdsdvkNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGR 176
Cdd:PRK11924   95 LEPEFAETAETPEAALLAKDDLARID--------RCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRAR 166


                  ....*....
gi 2730672382 177 RMLRDLLSD 185
Cdd:PRK11924  167 QLLRECLEA 175
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 17-183 6.23e-33

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: 115.91  E-value: 6.23e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  17 FEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPFQtpIED 96
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRE--LDL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  97 LEDWqlggaesttARASRSAEAEAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGR 176
Cdd:TIGR02937  81 LEEL---------LDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRAR 151


                  ....*..
gi 2730672382 177 RMLRDLL 183
Cdd:TIGR02937 152 KKLRELL 158
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 25-183 2.22e-28

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 104.92  E-value: 2.22e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  25 MDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREpfqtpIEDledwqlgg 104
Cdd:PRK12546   17 LPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKRE-----VPD-------- 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 105 aeSTTARASRSAEAEAID-HLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLL 183
Cdd:PRK12546   84 --PEGVHAASLAVKPAHDgRLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 26-185 1.05e-27

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 103.24  E-value: 1.05e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  26 DQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQrepfqtPIEDLEDwQLGGA 105
Cdd:PRK09641   29 DKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRKRK------PDYYLDA-EVAGT 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 106 ESTT-----ARASRSAEAEAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLR 180
Cdd:PRK09641  102 EGLTmysqlAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREALR 181


                  ....*
gi 2730672382 181 DLLSD 185
Cdd:PRK09641  182 KQLRH 186
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 17-184 4.26e-27

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 101.11  E-value: 4.26e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  17 FEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREpfqtpIED 96
Cdd:PRK12547    8 FKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKRGRE-----VQD 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  97 LEDwqlggaeSTTARASRSAEAEAIDHLpdSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGR 176
Cdd:PRK12547   83 SDG-------VFTARVAVHPAQYGSLDL--QDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRAR 153


                  ....*...
gi 2730672382 177 RMLRDLLS 184
Cdd:PRK12547  154 NRLQELLK 161
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 29-180 5.95e-27

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 101.02  E-value: 5.95e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  29 YAAALrmTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPFQT-PIEDLEDWQLGGAES 107
Cdd:PRK12511   20 YARSL--TRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVEARRAdELAVLADASLPAAQE 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2730672382 108 TTARASRsaeaeaidhlpdsdVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLR 180
Cdd:PRK12511   98 HAVRLAQ--------------IRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALR 156
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 27-185 1.15e-26

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 100.44  E-value: 1.15e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  27 QLYAAALR---MTR--NPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQRepfQTPIEDLEDWQ 101
Cdd:PRK09637    8 SEYKAQLKaflHSRvsNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKNR---SEELPDDLLFE 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 102 LGGAESttarasrSAEAEAIDHLpdsdvKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRD 181
Cdd:PRK09637   85 DEEREE-------NAKKELAPCL-----RPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152


                  ....
gi 2730672382 182 LLSD 185
Cdd:PRK09637  153 LLEG 156
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 34-185 2.14e-26

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 99.88  E-value: 2.14e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  34 RMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPFQT--PIEDLEDWQLGGAESTTAR 111
Cdd:PRK11923   39 RFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHLVSRGRRPPDSdvSSEDAEFYDGDHALKDIES 118

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2730672382 112 ASRSAEAEAIDHLpdsdVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGR----RMLRDLLSD 185
Cdd:PRK11923  119 PERALLRDEIEGT----VHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRAReaidKALQPLLQE 192
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 12-183 5.47e-26

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 98.50  E-value: 5.47e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  12 PRELTFEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREpfq 91
Cdd:PRK12540    2 PLTDSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRSDYRKRRRE--- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  92 tpIEDLEdwqlgGAESTTARASRSAEAeaidHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSR 171
Cdd:PRK12540   79 --VEDAD-----GSYAKTLKSQPGQNA----HLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSR 147

                         170
                  ....*....|..
gi 2730672382 172 LHRGRRMLRDLL 183
Cdd:PRK12540  148 VNRARSKLSALL 159
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 28-185 1.68e-25

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 97.01  E-value: 1.68e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  28 LYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREpfqtpiedledWQLGGAES 107
Cdd:PRK09638   31 LYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHLRKQKRE-----------KLRLQRAK 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2730672382 108 TTARASRSAEAeAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLLSD 185
Cdd:PRK09638  100 EETLRKEKWEA-AIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEWGQ 176
SigZ TIGR02959
RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a ...
 24-185 2.14e-25

RNA polymerase sigma factor, SigZ family; This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).


Pssm-ID: 132004 [Multi-domain]  Cd Length: 170  Bit Score: 96.67  E-value: 2.14e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  24 FMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPFqtpIEDLEDWQLG 103
Cdd:TIGR02959   4 FRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDGQKIQSWLYQIARNTIIDFYRSKSRSVE---LPESLLAADS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 104 GAESTtarasrsAEAEAIDHLPdsdvkNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLL 183
Cdd:TIGR02959  81 AREET-------FVKELSQCIP-----PMIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148


                  ..
gi 2730672382 184 SD 185
Cdd:TIGR02959 149 ET 150
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 17-199 2.40e-25

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 96.96  E-value: 2.40e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  17 FEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREpfqtpIED 96
Cdd:PRK12516   12 FKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRGRE-----VQD 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  97 LEdwqlggAESTTARASRSAEAEAIDHlpdSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGR 176
Cdd:PRK12516   87 TD------GMFTEQLAVHPSQYGTLDL---QDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRAR 157

                         170       180
                  ....*....|....*....|....*...
gi 2730672382 177 RMLRDLL-----SDYARDRGSAAQTSSA 199
Cdd:PRK12516  158 QRLQEILqiegeADYGPDADSARATSRA 185
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 9-203 1.37e-24

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 95.95  E-value: 1.37e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382   9 NEAPRELTFEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHqGTNLKAWLYRILTNTFINNYRKKqRE 88
Cdd:PRK12533   12 DAAARGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFR-GDNARPWLLAIVRHTWYSEWRRR-AN 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  89 PFQTPIED-------LEDWQLGGAESttarasrsaEAEAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIM 161
Cdd:PRK12533   90 AHEVAAPDtlddadsLDDWQPAGEDP---------LALLLRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIA 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2730672382 162 KTPIGTVMSRLHRGRRMLRDLLSDYARDRGSAAQTSSARSER 203
Cdd:PRK12533  161 DVPVGTVMSRLARARRRLAALLGGASAAQAAPGERAAGRPRR 202
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 24-183 3.84e-24

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 93.40  E-value: 3.84e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  24 FMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQRepFQTPIEDLEDWQLG 103
Cdd:PRK12522   12 YKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKKKR--WKDRILDLFHKEDG 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 104 GaESTTARASRSAEaEAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLL 183
Cdd:PRK12522   90 G-EIEFADDVNISE-EFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHL 167
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 24-183 7.76e-24

RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot:


Pssm-ID: 274361 [Multi-domain]  Cd Length: 154  Bit Score: 92.13  E-value: 7.76e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  24 FMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFhQGTNLKAWLYRILTNTFINNYRKKQREPFqTPIEDLEDWQLG 103
Cdd:TIGR02950   4 YMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSF-KDSSIKPWLFRIARNAFIDWYRKDKKIQT-IDDDAIGDLEQH 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 104 GAESTTARASRSAEAEAIDHLpdsdvknaLQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLL 183
Cdd:TIGR02950  82 PVESPEHHLLIKIEQEEITHH--------LSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 25-189 1.35e-20

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 85.68  E-value: 1.35e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  25 MDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQG-TNLKAWLYRILTNTFINNYRKKQREPFQTPIEdledwqlg 103
Cdd:PRK12538   73 IDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGrAKFSTWLYRVVSNRCIDLRRKPRTENVDAVPE-------- 144

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 104 gAESTTARASRSAEAEAIDHLpdsdVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLL 183
Cdd:PRK12538  145 -VADGKPDAVSVIERNELSDL----LEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219


                  ....*.
gi 2730672382 184 SDYARD 189
Cdd:PRK12538  220 RRHERD 225
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 28-183 6.18e-20

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: 82.44  E-value: 6.18e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  28 LYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPFqtPIEDLEDwqlggaes 107
Cdd:TIGR02983  19 LLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRRRRLLEL--PTRELPD-------- 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2730672382 108 ttarasRSAEAEAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLL 183
Cdd:TIGR02983  89 ------AAAPDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELL 158
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 26-194 1.08e-19

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 82.45  E-value: 1.08e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  26 DQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPfQTPIEDLEDWqlggA 105
Cdd:PRK09643   38 RRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDRLRRAKARP-TVPLDDVYPV----A 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 106 ESTTARASRSAEAeaidhlpdSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLLSd 185
Cdd:PRK09643  113 QLERDPTARVETA--------LAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRARLAELLG- 183


                  ....*....
gi 2730672382 186 YARDRGSAA 194
Cdd:PRK09643  184 YLRAGGNAS 192
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 13-182 2.23e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 80.75  E-value: 2.23e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  13 RELTFEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAwAQFHQGTNLKAWLYRILTNTFINNYRKKQREPFQT 92
Cdd:PRK12541    3 RKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVH-IDYYKGEEIRPWLFTIAYNAFIDWYRKEKKYKTTT 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  93 piedLEDWQLGGAESTTARASRSAEaeaIDHLPDSdvknaLQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRL 172
Cdd:PRK12541   82 ----IEEFHLPNVPSTEHEYFIKHE---IASWLDS-----LSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIEL 149

                         170
                  ....*....|
gi 2730672382 173 HRGRRMLRDL 182
Cdd:PRK12541  150 HRGRKETKSI 159
SigX5 TIGR02960
RNA polymerase sigma-70 factor, TIGR02960 family; This group of sigma factors are members of ...
 17-181 3.83e-19

RNA polymerase sigma-70 factor, TIGR02960 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.


Pssm-ID: 132005 [Multi-domain]  Cd Length: 324  Bit Score: 83.37  E-value: 3.83e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  17 FEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPfqTPIED 96
Cdd:TIGR02960   7 FTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGRSSVRTWLYRIATNACLDALEARQRRP--RPVGL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  97 LEDWQLGGAESTTARASRSAE-------AEAIDHLPDSDVK------------NALQAIPEDFRMAVYFADVEGFSYQEI 157
Cdd:TIGR02960  85 GAPSADGTAAASEAAEVTWLEplpdltlDLDDPAAADPSVAagsresvrlafvAAIQYLPPRQRAVLLLRDVLGWRAAET 164

                         170       180
                  ....*....|....*....|....
gi 2730672382 158 ADIMKTPIGTVMSRLHRGRRMLRD 181
Cdd:TIGR02960 165 AELLGTSTASVNSALQRARATLDE 188
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 28-184 1.43e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 80.39  E-value: 1.43e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  28 LYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQR------EPFQTPIEDLEDWQ 101
Cdd:PRK11922   43 LYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRRRRRlvnlaeMVMASTIAGGERTP 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 102 LGGAESTTARASRSAEAEAIdhlpdsdVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRD 181
Cdd:PRK11922  123 LADPAEDPERAAARREIRAL-------LERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLLRE 195


                  ...
gi 2730672382 182 LLS 184
Cdd:PRK11922  196 SLA 198
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 42-183 9.63e-18

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 77.10  E-value: 9.63e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  42 AQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNT---FINN--YRKKQrepfqtPIEDLEDwqlggaesTTARASRSA 116
Cdd:PRK09415   43 AEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHckdYLKSwhNKKVI------VTEDIFT--------YMESQKESV 108

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2730672382 117 EAEAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLL 183
Cdd:PRK09415  109 EEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 44-183 1.64e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 76.30  E-value: 1.64e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  44 DLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPFQTPIEdledwqlggaeSTTARASRSAEAEAIDH 123
Cdd:PRK12518   39 DLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRQFAQRPSRIQDD-----------SLNDQPSRPSDTPDLMQ 107

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2730672382 124 LPDSD-VKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLL 183
Cdd:PRK12518  108 LHYQDlVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 25-193 9.54e-17

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 74.30  E-value: 9.54e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  25 MDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQG-TNLKAWLYRILTNTFINNYRKKQREPFQTPiEDLEDWQLG 103
Cdd:PRK05602   30 LPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGeARFDTWLHRVVLNLCYDRLRRRREVPVEDA-PDVPDPAPG 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 104 GAESTTARASRSAeaeaidhlpdsdVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLL 183
Cdd:PRK05602  109 PDAGLEARQRARR------------VEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQL 176

                         170
                  ....*....|
gi 2730672382 184 SDYARDRGSA 193
Cdd:PRK05602  177 ADLPGSEDDR 186
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 15-191 1.10e-16

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 73.76  E-value: 1.10e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  15 LTFEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQF-HQgtNLKAWLYRILTNTFINNYRKKQREPFQTp 93
Cdd:PRK09644    1 MEIEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYdNQ--KVKPWLFKVAYHTFIDFVRKEKKVSFVG- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  94 iedleDWQLGGAESTTArasrsaeaEAIDHLPDSDVK--NALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSR 171
Cdd:PRK09644   78 -----TDEIEAIQAEST--------EEYVVAKNSYEKliQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSH 144

                         170       180
                  ....*....|....*....|
gi 2730672382 172 LHRGRRMLRDLlsdYARDRG 191
Cdd:PRK09644  145 LFRGRKRLKAL---LKEEKS 161
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
1-195 2.23e-16

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 75.74  E-value: 2.23e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382   1 MTDDLELSNEAPRELTFEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFIN 80
Cdd:PRK08241    5 AAAALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATNVCLD 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  81 NYRKKQREPFQTpieDLedwqlgGAESTTARASRSAEAEAI------DHLPDSDVKN-----------------ALQAIP 137
Cdd:PRK08241   85 ALEGRARRPLPT---DL------GAPAADPVDELVERPEVPwlepypDALLDPAAADpaarvvaresvrlafvaALQHLP 155

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2730672382 138 EDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDL---LSDYARDRGSAAQ 195
Cdd:PRK08241  156 PRQRAVLILRDVLGWSAAEVAELLDTSVAAVNSALQRARATLAERgpsAADTLREPDDPEE 216
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 24-88 2.33e-15

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: 67.61  E-value: 2.33e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2730672382  24 FMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFH--QGTNLKAWLYRILTNTFINNYRKKQRE 88
Cdd:pfam04542   5 YLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDpeRGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 28-186 3.52e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 70.49  E-value: 3.52e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  28 LYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRkkqREPFQTPIEDLEDWQLGGAes 107
Cdd:PRK12513   39 LYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWR---RHGARQAPSLDADEQLHAL-- 113

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2730672382 108 ttARASRSAEAEAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLLSDY 186
Cdd:PRK12513  114 --ADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLRELLAEE 190
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
17-190 4.93e-14

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 67.03  E-value: 4.93e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  17 FEEQALPfmdqLYAAALRMTRNPADAQDLVQETFVKAFAAWAQF-HQGTNLKAWLYRILTNTFINNYRKKQREPfqtpie 95
Cdd:PRK09645   15 YDEHAAP----LWRYALRLTGDRARAEDVVQETLLRAWQHPEVLaDTGRSARAWLFTVARNLVIDERRSARARP------ 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  96 dledwQLGGAEsTTARASRSAEAEAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRG 175
Cdd:PRK09645   85 -----VEGGDD-VLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYA 158

                         170
                  ....*....|....*
gi 2730672382 176 RRMLRDLLSDYARDR 190
Cdd:PRK09645  159 LRALRLALQERGVTR 173
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 14-183 6.62e-14

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 66.51  E-value: 6.62e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  14 ELTFEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAwaQFHQGTNLKAWLYRILTNTFINNYRKKQREpfQTP 93
Cdd:PRK09639    2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKGIENEKGWLIKSARNVAYNYLRSEKRR--RAR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  94 IEDLEDWQLGGAESttarasrSAEAEAIDHLPDSDVKNALQAIPEDFRMaVYFADVEGFSYQEIADIMKTPIGTVMSRLH 173
Cdd:PRK09639   78 ILGEFQWQEVDNEP-------SPEEIWIRKEEITKVQEVLAKMTERDRT-VLLLRFSGYSYKEIAEALGIKESSVGTTLA 149

                         170
                  ....*....|
gi 2730672382 174 RGRRMLRDLL 183
Cdd:PRK09639  150 RAKKKFRKIY 159
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 17-187 1.17e-13

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 66.12  E-value: 1.17e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  17 FEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPFQTPIED 96
Cdd:PRK09640   28 YEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKERRKRRLMDALS 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  97 LEDWQlggaESTTARASRSAEAEAIDHLPDSdvknaLQAIPEDFRMAVYFADVEgfsYQEIADIMKTPIGTVMSRLHRGR 176
Cdd:PRK09640  108 LDPLE----EASEEKAPKPEERGGLDRWLVH-----VNPIDREILVLRFVAELE---FQEIADIMHMGLSATKMRYKRAL 175

                         170
                  ....*....|.
gi 2730672382 177 RMLRDLLSDYA 187
Cdd:PRK09640  176 DKLREKFAGLA 186
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 29-184 4.69e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 62.00  E-value: 4.69e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  29 YAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREpfQTPIEDLEDWQLGGAEST 108
Cdd:PRK12519   43 YGLALKILGNSQEAEDLTQEIFLSLWRKSSYDPKRGSLSSYLLTLTRSRAIDRLRSRRSR--QRLLERWQQELLGEASED 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 109 TARASRSAEAEAidhlpdSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRG----RRMLRDLLS 184
Cdd:PRK12519  121 TPLEQASLAERS------QRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGllklRELLQDLLE 194
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 128-180 6.04e-12

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: 58.27  E-value: 6.04e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2730672382 128 DVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLR 180
Cdd:cd06171     3 RLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 11-184 3.27e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 59.90  E-value: 3.27e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  11 APRELTfeEQALPfmdQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQG-TNLKAWLYRILTNTFINNYRKKQREP 89
Cdd:PRK12524   27 AARALT--LRLAP---RALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGeARVSTWLYRVVCNLCTDRLRRRRRAS 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  90 F-QTPIEDLEDWQLGGAESTTARASRSAeaeaidhlpdsdVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTV 168
Cdd:PRK12524  102 VdLDDAPEPADAAPGAEEALIEGDRMRA------------LDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAV 169

                         170
                  ....*....|....*.
gi 2730672382 169 MSRLHRGRRMLRDLLS 184
Cdd:PRK12524  170 ESLTARGKRALAALLA 185
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 28-191 3.77e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 59.31  E-value: 3.77e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  28 LYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNtfiNNYRKKQREPFQTpiEDLEDwqlggaES 107
Cdd:PRK12517   36 IYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLITILRR---ENARRFERKQFDL--VDIED------DS 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 108 TTARASRSAEAEAIDHLpdsdVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLLSDYA 187
Cdd:PRK12517  105 IEDDASHSSEEEMEQEW----LRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKPD 180


                  ....
gi 2730672382 188 RDRG 191
Cdd:PRK12517  181 VQRG 184
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 27-184 9.41e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 58.29  E-value: 9.41e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  27 QLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFH-QGTNLKAWLYRILTNTFINNYRKkqREPFQTPIEDLEDwqlgga 105
Cdd:PRK12514   31 KLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAvSGLSPMTWLITIARNHAIDRLRA--RKAVAVDIDEAHD------ 102

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2730672382 106 estTARASRSAEAEAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLLS 184
Cdd:PRK12514  103 ---LADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKLRECLS 178
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 129-179 9.65e-11

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: 55.15  E-value: 9.65e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2730672382 129 VKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRML 179
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09642 PRK09642
RNA polymerase sigma factor;
28-180 2.02e-10

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 57.03  E-value: 2.02e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  28 LYAAALRMTRNPADAQDLVQETFVKAFAAWAQFhQGTNLKAWLYRILTNTFINNYRKKQREPfqtpiedlEDWQLGGAES 107
Cdd:PRK09642    8 IFQVIFSILRHEEDAKDVTQEVFVKIHASLPNY-QFRGLKTWMARIATNHAIDYKRKKAREN--------EELSLCKETE 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2730672382 108 TTARASRSAEAEAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLR 180
Cdd:PRK09642   79 ENIKSSHNIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIK 151
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 27-181 6.40e-10

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: 55.40  E-value: 6.40e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  27 QLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTfINNYRKKQREPFQTPIEDLEDWQLGGAE 106
Cdd:TIGR02989  13 ALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNK-VLNYRRKLGRDRLVFDDDLLEALAAEAE 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2730672382 107 STTAR---ASRSAEAEAIDHLPDSDvknalqaipEDFRMAVYFadvEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRD 181
Cdd:TIGR02989  92 PTEAErlsDDRQALEGCLEKLPERQ---------RELLDLRYQ---RGQKATALAEQTGRTVNAVYKALQRIRVSLRE 157
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 38-196 6.64e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 56.06  E-value: 6.64e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  38 NPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPFQTPIEdLEDwqlgGAESTTARASRSAE 117
Cdd:PRK12535   47 GHDIADDLTQETYLRVMSALPRFAARSSARTWLLSLARRVWVDNIRHDMARPRKSATE-YED----AAATTASNETTGSW 121

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 118 AEAIDhlpdsdVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLLS--DYARDRGSAAQ 195
Cdd:PRK12535  122 SEWID------VRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARADLIAATAtgQASAERGKSAQ 195


                  .
gi 2730672382 196 T 196
Cdd:PRK12535  196 G 196
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 28-180 6.10e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 53.20  E-value: 6.10e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  28 LYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTfINNYRKKQREPFQ--TPIEDL-EDWQLGG 104
Cdd:PRK12543   20 VYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQ-IHSWRRKRWRRFRifEKAEEQrKPVSIDF 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2730672382 105 AESTTARASRSAEAEAIDHLPDSdvknalqaipedFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLR 180
Cdd:PRK12543   99 SEDVLSKESNQELIELIHKLPYK------------LRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLR 162
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 27-183 9.28e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 52.86  E-value: 9.28e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  27 QLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGT-NLKAWLYRILTNTFINNYRKKQREpfqTPIEDledwqlGGA 105
Cdd:PRK12537   35 RLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARgSARGWIYSVTRHLALNVLRDTRRE---VVLDD------DAE 105

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2730672382 106 ESTTARASRSAEAEAIDHLpdSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLL 183
Cdd:PRK12537  106 ETAQTLHEIIDDFDLWANS--GKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRECM 181
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 29-193 2.91e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 51.66  E-value: 2.91e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  29 YAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPF-QTPIEDLEDwqlgGAES 107
Cdd:PRK12515   36 YRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSALRRRKHEEIdDEAAAAIED----GADT 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 108 TTARASRSAEAEAIdhlpdsdvKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLLSDYA 187
Cdd:PRK12515  112 PEVALQKSDTSAAL--------RACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLKAAG 183


                  ....*.
gi 2730672382 188 RDRGSA 193
Cdd:PRK12515  184 VERGWP 189
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 39-179 3.19e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 51.24  E-value: 3.19e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  39 PADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPFqTPIEDLedwqlggAESTTArasrsaeA 118
Cdd:PRK12512   50 ADQAEDIVQEILLAVHLKRHTWDPGAPFAPWLFAIARNKLIDALRRRGRRVF-VDIDDF-------AETLPA-------E 114

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2730672382 119 EAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRML 179
Cdd:PRK12512  115 PATETLPAGDVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGLAAL 175
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 18-189 4.32e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 50.82  E-value: 4.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  18 EEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFH--QGTNLKAWLYRILTNTFINNYRKKQR-EPFqtpi 94
Cdd:PRK12542   12 EELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHslNTQELKRYILRVAKNKAIDSYRKNKRhETF---- 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  95 edLEDWQlggAESTTARASRSAEAEAiDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHR 174
Cdd:PRK12542   88 --LEEYE---RESIEAVDENIEEWEK-RKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFER 161

                         170
                  ....*....|....*
gi 2730672382 175 GRRMLRDLLSDYARD 189
Cdd:PRK12542  162 ARKRVQNMIGGIQHD 176
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 7-183 1.15e-07

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 49.91  E-value: 1.15e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382   7 LSNEAPRELTF--EEQALPFMDQLYAAAL-----RMTRNPADAQDLVQETFVKAFAAWAQFH-QGTNLKAWLYRILTNTF 78
Cdd:PRK13919    8 LSDEALLALVArgEEEALRALFRRYAGAFlalarRMGLDGAAAEDVVQEVFIRVWKKAKEFDpRRGSARAWLLALAHHAA 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  79 INNYRKKQREPfqTPIEDLEDwqlggaesttarasrsaEAEAID----------HLPDSDVKNALQAIPEDFRMAVYFAD 148
Cdd:PRK13919   88 VDHVRRRAARP--QPLEPDER-----------------EPEAFDlpgpgldeegHLDRTRLGRALKALSPEERRVIEVLY 148

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 2730672382 149 VEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLL 183
Cdd:PRK13919  149 YQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVL 183
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 40-189 1.59e-07

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 49.27  E-value: 1.59e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  40 ADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPFQTpiedledwqLGGAESTTARASRsaEAE 119
Cdd:PRK09649   48 GSADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVADHIRHVRSRPRTT---------RGARPEHLIDGDR--HAR 116

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 120 AIDHLpdSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMlrdLLSDYARD 189
Cdd:PRK09649  117 GFEDL--VEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDA---LLADAEPD 181
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
34-184 5.15e-07

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 47.80  E-value: 5.15e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  34 RMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPFQTPIEDLEDWqlggAESTTARAS 113
Cdd:PRK12539   44 RIGRGAEEAEDLVQEALMAIHTRRHTYDPEQPLTPWVYAIARYKLIDHLRRTRASLADVPIDDADEL----VAHDDHAAV 119

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2730672382 114 RSAEaeaidhlpdsDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLLS 184
Cdd:PRK12539  120 ESTL----------DLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVKVSVHRGLKALAALIG 180
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 27-183 5.92e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 47.74  E-value: 5.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  27 QLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFH-QGTNLKAWLYRILTNTFINNYRKKQREPFQTPIEDLEDWQLGGA 105
Cdd:PRK12534   37 KLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDpSRARGLTWLAMIARNKAIDHLRANAPQRRNVALDDAGELRAADA 116

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2730672382 106 eSTTARASRSAEAEAIDHlpdsdVKNALQAIPEDFRMAVYFadvEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDLL 183
Cdd:PRK12534  117 -SPLERTERASTRRRIDH-----CLAELEPPRSELIRTAFF---EGITYEELAARTDTPIGTVKSWIRRGLAKLKACL 185
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 34-179 1.05e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 46.97  E-value: 1.05e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  34 RMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKK-QREPFQTPIEDLEDWqLGGAESTTARA 112
Cdd:PRK12536   41 RLPQLPDEVEDLVQEILLAVHNARHTYRADQPLTAWVHAIARYKLMDFLRSRaRREALHDPLDDESEL-FATSDDEAAEA 119

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2730672382 113 SRsaeaeaidhlpdsDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRML 179
Cdd:PRK12536  120 RR-------------DLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHRGLKAL 173
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 132-181 2.71e-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: 2.71e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2730672382 132 ALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRD 181
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 26-183 4.78e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 45.31  E-value: 4.78e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  26 DQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPFQTPIEDLED------ 99
Cdd:PRK12532   17 LLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQIGRQRKVFTLLDDELldeafe 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 100 --------WQLGGAESTTARASRSAEAEAIDHLPDSdvknALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSR 171
Cdd:PRK12532   97 shfsqnghWTPEGQPQHWNTPEKSLNNNEFQKILQS----CLYNLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTI 172

                         170
                  ....*....|..
gi 2730672382 172 LHRGRRMLRDLL 183
Cdd:PRK12532  173 MHRARESLRQCL 184
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 37-99 5.70e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 45.14  E-value: 5.70e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2730672382  37 RNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPFQTPIEDLED 99
Cdd:PRK12530   29 KDADLAEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIRYRKRFVNESELIEEDS 91
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 24-158 1.58e-05

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 43.52  E-value: 1.58e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  24 FMD---QLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLkAWLYRILTNTFINNYRKKQRE-PFQTPIEDLED 99
Cdd:PRK07037    4 FVDnrsMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKQPV-AYLFRIVRNLAIDHYRRQALEnKYHGDEEDGLD 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2730672382 100 WQLGGAESTTARASRsaeaeaiDHLpdSDVKNALQAIPEDFRMAVYFADVEGFSYQEIA 158
Cdd:PRK07037   83 VPSPEASPEAALINR-------DTL--RHVADALSELPARTRYAFEMYRLHGETQKDIA 132
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 18-180 2.51e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 43.38  E-value: 2.51e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  18 EEQALPFMDQLYAAALRM-----TRNPADAQDLVQETFVkafAAWAQFH----QGTNLKAWLYRILTNTFINNYRKKQRE 88
Cdd:PRK12531   25 DKQAFALVFSYYAPKLKQfamkhVGNEQVAMEMVQETMS---TVWQKAHlfdgQKSALSTWIYTIIRNLCFDLLRKQKGK 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  89 PFQTPIEDLedWqlggaesttarASRSAEAEAIDHL-PDSD-----VKNALQAIPEDFRMAVYFADVEGFSYQEIADIMK 162
Cdd:PRK12531  102 DLHIHADDI--W-----------PSDYYPPDLVDHYsPEQDmlkeqVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFD 168

                         170
                  ....*....|....*...
gi 2730672382 163 TPIGTVMSRLHRGRRMLR 180
Cdd:PRK12531  169 IPLGTVKSRLRLAVEKLR 186
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 36-186 3.09e-05

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 42.65  E-value: 3.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  36 TRNPADAQDLVQETFVKAFAAWAQfHQGTNLKAWLYRILTNTFINNYRK-KQREPFQT---------------PIEDLED 99
Cdd:PRK09047    1 VRDDDAALDIVQDAMIKLAEKYGD-RPAAEWPPLFQRILQNRIHDWFRRqKVRNTWVSlfssfsdddddddfdPLETLDS 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 100 wQLGGAESTTARASRSAEAEAIDhlpdsdvkNALQAIP----EDFRMAVYfadvEGFSYQEIADIMKTPIGTVMSRLHRG 175
Cdd:PRK09047   80 -ADEGAESPADKLERAQVLQLIE--------EAIQKLParqrEAFLLRYW----EDMDVAETAAAMGCSEGSVKTHCSRA 146

                         170
                  ....*....|.
gi 2730672382 176 RRMLRDLLSDY 186
Cdd:PRK09047  147 THALAKALEAK 157
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
29-183 8.70e-05

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 41.58  E-value: 8.70e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  29 YAAALRMTRNPADAQDLVQETFVKAFAAWAQFH--QGTNLkAWLYRILTNTFINNYRKKQ----REpfqtpiedledwQL 102
Cdd:PRK09646   44 YGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDpaRGSAL-AWLLTLAHRRAVDRVRSEQaasqRE------------VR 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 103 GGAESTTARASRSAEaEAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRRMLRDL 182
Cdd:PRK09646  111 YGARNVDPAFDQVAE-EVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189


                  .
gi 2730672382 183 L 183
Cdd:PRK09646  190 L 190
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 38-172 2.27e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 40.55  E-value: 2.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  38 NPADAQDLVQETFVKAfaaWAQFHQGTNLKA----WLYRILTNTFINNYRKKQREPFQTPIEDLedWQLGGAESTtaraS 113
Cdd:PRK12526   61 NEAQANELVQETMSNV---WRKAHLYNGDKGaattWVYTVMRNAAFDMLRKIKAKKEQNLGDDI--WPIEQALAE----S 131

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2730672382 114 RSAEAEAIDHLPDSDVKNALQAIPEDFRMAV---YFADVegfSYQEIADIMKTPIGTVMSRL 172
Cdd:PRK12526  132 QSESEEFSDHLMDKQILSYIEKLPEAQQTVVkgvYFQEL---SQEQLAQQLNVPLGTVKSRL 190
PRK12544 PRK12544
RNA polymerase factor sigma-70;
31-185 3.96e-04

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 39.78  E-value: 3.96e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  31 AALRMTRNPAdAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPFQTPIEDLEDwqlgGAESTTA 110
Cdd:PRK12544   35 ATLQLSDLHL-AEDAVQEALIGALKNADSFAGRAAFKTWVFAILKNKIIDLLRQKKRHVSASSLLRDEE----EEEDFEE 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382 111 RASRSA-----EAEAIDHLPDSDVKNA---------LQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGR 176
Cdd:PRK12544  110 LFDESGhwqkdERPQAWGNPEESLEQEqfwrifeacLDGLPAKYARVFMMREFIELETNEICHAVDLSVSNLNVLLYRAR 189


                  ....*....
gi 2730672382 177 RMLRDLLSD 185
Cdd:PRK12544  190 LRLRECLEN 198
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 27-161 7.91e-04

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 39.13  E-value: 7.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  27 QLYAAALRMTRNPADAQDLVQETFVKafaaWAQFHQGT--NLKAWLYRILTNTFINNYR--KKQREPFQTP------IED 96
Cdd:PRK09636   16 HLLSVAYRMLGSVADAEDIVQEAWLR----WNNADRAQirDPRAWLTRVVTRLCLDRLRsaRHRRETYVGPwlpepvVEE 91

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2730672382  97 LEDWQLGG--AESTTARASRsaeaeaidhlpdsdvknALQAIPEDFRMAVYFADVEGFSYQEIADIM 161
Cdd:PRK09636   92 LDDPLEAVvaAEDLSLALML-----------------ALERLSPLERAAFLLHDVFGVPFDEIASTL 141
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 32-177 1.57e-03

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 38.41  E-value: 1.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  32 ALRMTRNPADAQDLVQETFVKAfaAWAQFHQGTNLKAWLYRILTNTFINNYR--KKQREPFQtpieDLEDWqlggaESTT 109
Cdd:PRK09635   22 AFRMVGDIGVAEDMVQEAFSRL--LRAPVGDIDDERGWLIVVTSRLCLDHIKsaSTRRERPQ----DIAAW-----HDGD 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2730672382 110 ARASRSAEAEAIDHlpDSDVKNALQAIPEDF----RMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHRGRR 177
Cdd:PRK09635   91 ASVSSVDPADRVTL--DDEVRLALLIMLERLgpaeRVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARR 160
PRK12520 PRK12520
RNA polymerase sigma factor; Provisional
 16-99 1.96e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237126 [Multi-domain]  Cd Length: 191  Bit Score: 37.79  E-value: 1.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  16 TFEEQALPFMDQLYAAALRMTRNPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQREPFQTPIE 95
Cdd:PRK12520    3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQSSLKTYLVGILKHKIIDAIRSGRREVRLSLDD 82


                  ....
gi 2730672382  96 DLED 99
Cdd:PRK12520   83 ADEQ 86
PRK12545 PRK12545
RNA polymerase factor sigma-70;
23-87 5.98e-03

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 36.47  E-value: 5.98e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2730672382  23 PFMDQLYAAALRMTR----NPADAQDLVQETFVKAFAAWAQFHQGTNLKAWLYRILTNTFINNYRKKQR 87
Cdd:PRK12545   12 AYLAQLRHDLLRFARlqlrDADAAEDAVQEALAAAWSQAGRFAGQSAHKTWVFGILRNKLIDTLRARQR 80
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 39-174 7.36e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 35.59  E-value: 7.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2730672382  39 PADAQDLVQETFVKAFAAwAQFHQGTNLKAWLYRILTNTFINNYRKkqrepfqtpiEDLEDWQLGGAESTTARASRSAEA 118
Cdd:PRK12528   28 PQSAADLAQDTFVKVLVA-RETAQIIEPRAFLTTIAKRVLCNHYRR----------QDLERAYLEALAQLPERVAPSEEE 96

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2730672382 119 EAIDHLPDSDVKNALQAIPEDFRMAVYFADVEGFSYQEIADIMKTPIGTVMSRLHR 174
Cdd:PRK12528   97 RAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNK 152
 
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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