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Conserved domains on  [gi|1681988327|dbj|BBL14745|]
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DNA-directed RNA polymerase sigma-70 factor [Alistipes communis]

Protein Classification

RNA polymerase sigma factor( domain architecture ID 11446377)

RNA polymerase sigma factor plays a role in bacterial signal transduction and is regulated by anti-sigma factors. May belong to the ECF-type subfamily. Generally, sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.

CATH:  1.10.1740.10
Gene Ontology:  GO:0016987|GO:0006352|GO:0003677
PubMed:  28575802
SCOP:  4003741

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]; ...
 1-179 2.78e-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: 2.78e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327   1 MSMEERILaERCKAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFswRGEGSLRAWMERIAV 80
Cdd:COG1595     1 MSSDEELL-ERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSF--RGRGSFRAWLYRIAR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  81 NVSLEALRQKRRL--HYPTTVDRLPERYEEPTSDEMERLPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISE 158
Cdd:COG1595    78 NLAIDHLRKRRRRreLLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISE 157

                         170       180
                  ....*....|....*....|.
gi 1681988327 159 KTSSSQLFRAKALLARRIKEY 179
Cdd:COG1595   158 GTVKSRLSRARKKLREALEEE 178
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-179 2.78e-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: 2.78e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327   1 MSMEERILaERCKAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFswRGEGSLRAWMERIAV 80
Cdd:COG1595     1 MSSDEELL-ERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSF--RGRGSFRAWLYRIAR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  81 NVSLEALRQKRRL--HYPTTVDRLPERYEEPTSDEMERLPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISE 158
Cdd:COG1595    78 NLAIDHLRKRRRRreLLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISE 157

                         170       180
                  ....*....|....*....|.
gi 1681988327 159 KTSSSQLFRAKALLARRIKEY 179
Cdd:COG1595   158 GTVKSRLSRARKKLREALEEE 178
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 10-182 1.65e-33

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 117.21  E-value: 1.65e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  10 ERCKAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFswRGEGSLRAWMERIAVNVSLEALRQ 89
Cdd:PRK09652    2 ERVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSF--RGGAAFYTWLYRIARNTAINYLRK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  90 KRRLHYPTTVDR----------LPERYEEPTSDEMERLPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEK 159
Cdd:PRK09652   80 QGRRPPASDVDAeeaedfdladALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIG 159

                         170       180
                  ....*....|....*....|...
gi 1681988327 160 TSSSQLFRAKALLARRIKEYVKD 182
Cdd:PRK09652  160 TVRSRIFRAREALRAKLQPLLDE 182
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 18-176 3.53e-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: 115.52  E-value: 3.53e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  18 DARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFswRGEGSLRAWMERIAVNVSLEALRQKRRLH-YP 96
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRF--DPEGSFKAWLFRIARNLILDYLRRKRRLRrEL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  97 TTVDRLPERYEEPTSDEMERLPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALLARRI 176
Cdd:TIGR02937  79 DLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 23-92 4.34e-14

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: 63.76  E-value: 4.34e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  23 LYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFSWRGEGSLRAWMERIAVNVSLEALRQKRR 92
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 120-172 3.32e-08

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: 47.87  E-value: 3.32e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1681988327 120 DDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALL 172
Cdd:cd06171     2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-179 2.78e-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: 2.78e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327   1 MSMEERILaERCKAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFswRGEGSLRAWMERIAV 80
Cdd:COG1595     1 MSSDEELL-ERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSF--RGRGSFRAWLYRIAR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  81 NVSLEALRQKRRL--HYPTTVDRLPERYEEPTSDEMERLPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISE 158
Cdd:COG1595    78 NLAIDHLRKRRRRreLLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISE 157

                         170       180
                  ....*....|....*....|.
gi 1681988327 159 KTSSSQLFRAKALLARRIKEY 179
Cdd:COG1595   158 GTVKSRLSRARKKLREALEEE 178
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 10-182 1.65e-33

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 117.21  E-value: 1.65e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  10 ERCKAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFswRGEGSLRAWMERIAVNVSLEALRQ 89
Cdd:PRK09652    2 ERVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSF--RGGAAFYTWLYRIARNTAINYLRK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  90 KRRLHYPTTVDR----------LPERYEEPTSDEMERLPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEK 159
Cdd:PRK09652   80 QGRRPPASDVDAeeaedfdladALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIG 159

                         170       180
                  ....*....|....*....|...
gi 1681988327 160 TSSSQLFRAKALLARRIKEYVKD 182
Cdd:PRK09652  160 TVRSRIFRAREALRAKLQPLLDE 182
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 18-176 3.53e-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: 115.52  E-value: 3.53e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  18 DARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFswRGEGSLRAWMERIAVNVSLEALRQKRRLH-YP 96
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRF--DPEGSFKAWLFRIARNLILDYLRRKRRLRrEL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  97 TTVDRLPERYEEPTSDEMERLPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALLARRI 176
Cdd:TIGR02937  79 DLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 15-172 6.76e-32

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 113.14  E-value: 6.76e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  15 GDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFswRGEGSLRAWMERIAVNVSLEALRQKRRLH 94
Cdd:PRK11924   10 GDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLF--NGKGSARTWLLTIARNVCYDLLRRRRREK 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  95 YPTTVDRL-PERYEEPTSDEMERLPYDDLKRL---IAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKA 170
Cdd:PRK11924   88 AVLSDDALePEFAETAETPEAALLAKDDLARIdrcLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQ 167


                  ..
gi 1681988327 171 LL 172
Cdd:PRK11924  168 LL 169
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 22-178 1.12e-26

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 99.82  E-value: 1.12e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  22 ELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFswRGEGSLRAWMERIAVNVSLEALRQKRRLHYPTTVDR 101
Cdd:PRK09415   20 EIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTY--KGKSSLKTWLYRIAINHCKDYLKSWHNKKVIVTEDI 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327 102 LPERYEEPTSDEMERLPYDDLKRL---IAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALLARRIKE 178
Cdd:PRK09415   98 FTYMESQKESVEEEVIQNAEDERLasaVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 4-172 2.08e-25

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 97.73  E-value: 2.08e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327   4 EERILAERCKAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFswRGEGSLRAWMERIAVNVS 83
Cdd:PRK11922   16 SDRELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTF--RGDASLSTWLSRIVLNEA 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  84 LEALRQKRRLHYPTTVDRLPEryEEPTSDEMERLPYDD-------------LKRLIAELPDGYRTVFNLYCIEELSHREI 150
Cdd:PRK11922   94 LGRLRRRRRLVNLAEMVMAST--IAGGERTPLADPAEDperaaarreiralLERAIDALPDAFRAVFVLRVVEELSVEET 171

                         170       180
                  ....*....|....*....|..
gi 1681988327 151 AERLGISEKTSSSQLFRAKALL 172
Cdd:PRK11922  172 AQALGLPEETVKTRLHRARRLL 193
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 21-168 3.47e-24

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: 92.62  E-value: 3.47e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  21 RELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFaaIDRFSWRGEGSLRAWMERIAVNVSLEALR-QKRRLHYPTTV 99
Cdd:TIGR02985   4 EQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLW--ENRETLEISESIKAYLFTIVKNRCLNYLRhKQVEEKYQEEL 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1681988327 100 DRLPERYEEPTSDEMErLPYDDLKRLIAE----LPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRA 168
Cdd:TIGR02985  82 AEIEERELSEADPEEE-LEAKELEEIIEEaiekLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKA 153
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 8-172 8.35e-20

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 81.69  E-value: 8.35e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327   8 LAERCKAGDNDARRELYTRFGGRLLSIcLRYVGDRATAEDLLHDCFIKVFAAIDRFswRGEGSLRAWMERIAVNVSLEAL 87
Cdd:PRK12518    1 LILRCQRGDRQSFRQLYRRYQQKVRST-LYQLCGRELLDDLVQEVFLRVWKGLPKL--RNPAYFSTWLYRITWNVATDAR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  88 RQ----KRRLHYPTTVDRLPEryeEPTSDEMERLPYDDL-KRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSS 162
Cdd:PRK12518   78 RQfaqrPSRIQDDSLNDQPSR---PSDTPDLMQLHYQDLvQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVK 154

                         170
                  ....*....|
gi 1681988327 163 SQLFRAKALL 172
Cdd:PRK12518  155 SRLFYARRQL 164
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 1-176 1.50e-18

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 78.58  E-value: 1.50e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327   1 MSMEERILAERCKAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRF--SWRgegsLRAWMERI 78
Cdd:PRK09641    1 MDLLIKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYdiNRK----FSTWLYRI 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  79 AVNVSLEALRQKRRLHY----------PTTVDRLPERYEEPTSDEMERLPYDDLKRLIAELPDGYRTVFNLYCIEELSHR 148
Cdd:PRK09641   77 ATNLTIDRLRKRKPDYYldaevagtegLTMYSQLAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLK 156

                         170       180
                  ....*....|....*....|....*...
gi 1681988327 149 EIAERLGISEKTSSSQLFRAKALLARRI 176
Cdd:PRK09641  157 EISEILDLPVGTVKTRIHRGREALRKQL 184
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 5-177 1.22e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 73.61  E-value: 1.22e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327   5 ERILAERCKAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFSWRGEGSlrAWMERIAVNVSL 84
Cdd:PRK12515    9 DEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVS--TWLLSIARFKAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  85 EALRQKRRLHY-PTTVDRLPERYEEPTSDEMERLPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSS 163
Cdd:PRK12515   87 SALRRRKHEEIdDEAAAAIEDGADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKT 166

                         170
                  ....*....|....
gi 1681988327 164 QLFRAKALLARRIK 177
Cdd:PRK12515  167 RMFYARKKLAELLK 180
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 22-172 2.81e-16

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 72.90  E-value: 2.81e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  22 ELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFSwrgEGSLRAWMERIAVNVSLEALRQKRRLHYpttvDR 101
Cdd:PRK09647   32 ELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQ---PGTFEGWLHRITTNLFLDMVRRRARIRM----EA 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1681988327 102 LPERYEEPTSDEM--ERLPYD-----DLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALL 172
Cdd:PRK09647  105 LPEDYDRVPGDEPnpEQIYHDarldpDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQL 182
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 8-175 3.10e-16

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 72.38  E-value: 3.10e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327   8 LAERCKAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDrfSWR-GEGSLRAWMERIAVNVSLEA 86
Cdd:PRK05602   10 LLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAP--SWRpGEARFDTWLHRVVLNLCYDR 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  87 LRqKRRLHyptTVDRLPER-YEEPTSDemERLPYDDLKRLI----AELPDGYRTVFNLYCIEELSHREIAERLGISEKTS 161
Cdd:PRK05602   88 LR-RRREV---PVEDAPDVpDPAPGPD--AGLEARQRARRVeqalAALPERQREAIVLQYYQGLSNIEAAAVMDISVDAL 161

                         170
                  ....*....|....*...
gi 1681988327 162 SSQLFRA----KALLARR 175
Cdd:PRK05602  162 ESLLARGrralRAQLADL 179
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 4-180 6.65e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 72.03  E-value: 6.65e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327   4 EERILAeRCKAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRfsWRGEGSLRAWMERIAVNVS 83
Cdd:PRK12513   13 DEALML-RYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQ--YQPRARFRTWLYQIARNLL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  84 LEALR-QKRRLH----YPTTVDRLPERYEEPTSDEMERLPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISE 158
Cdd:PRK12513   90 IDHWRrHGARQApsldADEQLHALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPE 169

                         170       180
                  ....*....|....*....|..
gi 1681988327 159 KTSSSQLFRAKALLARRIKEYV 180
Cdd:PRK12513  170 ETVKSRLRYALQKLRELLAEEV 191
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 1-168 1.87e-15

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 70.43  E-value: 1.87e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327   1 MSMEERILAERCKAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFSwrGEGSLRAWMERIAV 80
Cdd:PRK09638    1 MQMDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQ--GRSKFSTWLISIAS 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  81 NVSLEALRQKRRlhypttVDRLPERYEEPTSDEMER------LPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERL 154
Cdd:PRK09638   79 RLYKDHLRKQKR------EKLRLQRAKEETLRKEKWeaaikgAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKML 152

                         170
                  ....*....|....
gi 1681988327 155 GISEKTSSSQLFRA 168
Cdd:PRK09638  153 NIPEGTVKSRVHHG 166
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 24-176 1.89e-15

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: 69.79  E-value: 1.89e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  24 YTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDrfSWRGEgSLRAWMERIAVNVSLEALRQKRRLHYpTTVDRLP 103
Cdd:TIGR02950   1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLH--SFKDS-SIKPWLFRIARNAFIDWYRKDKKIQT-IDDDAIG 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1681988327 104 ER----YEEPTSDEMERLPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALLARRI 176
Cdd:TIGR02950  77 DLeqhpVESPEHHLLIKIEQEEITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL 153
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 15-173 1.91e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 70.69  E-value: 1.91e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  15 GDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVF-AAIDrfsWR-GEGSLRAWMERIAVNVSLEALRQKRR 92
Cdd:PRK12524   23 GDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWrIAPD---WRqGEARVSTWLYRVVCNLCTDRLRRRRR 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  93 LHypTTVDRLPERYEEPTSDE---MERLPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAK 169
Cdd:PRK12524  100 AS--VDLDDAPEPADAAPGAEealIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGK 177


                  ....
gi 1681988327 170 ALLA 173
Cdd:PRK12524  178 RALA 181
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 12-155 2.92e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 69.81  E-value: 2.92e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  12 CKAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFSwRGEGSLRAWMERIAVNVSLEALRQKR 91
Cdd:PRK12537   17 CARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFD-PARGSARGWIYSVTRHLALNVLRDTR 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1681988327  92 RLHYPTTVDRLPERYEEPTSDEMERLpyDDLKRLIAEL----PDGYRTVFNLYcIEELSHREIAERLG 155
Cdd:PRK12537   96 REVVLDDDAEETAQTLHEIIDDFDLW--ANSGKIHRCLeqlePARRNCILHAY-VDGCSHAEIAQRLG 160
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 14-176 3.18e-15

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 70.12  E-value: 3.18e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  14 AGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFswRGEGSLRAWMERIAVNVSLEALRQKR-R 92
Cdd:PRK09643   23 AGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSF--RGDAAVSSWLHRIVVNACLDRLRRAKaR 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  93 LHYPT-TVDRLPERYEEPTS-DEMERlpydDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKA 170
Cdd:PRK09643  101 PTVPLdDVYPVAQLERDPTArVETAL----AVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRA 176


                  ....*.
gi 1681988327 171 LLARRI 176
Cdd:PRK09643  177 RLAELL 182
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 8-182 4.15e-15

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 69.83  E-value: 4.15e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327   8 LAERCKAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFswRGEGSLRAWMERIAVNVSLEAL 87
Cdd:PRK11923   10 LVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNF--RGDSAFYTWLYRIAINTAKNHL 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  88 RQKRRLHYPTTVD----------------RLPERyeEPTSDEMErlpyDDLKRLIAELPDGYRTVFNLYCIEELSHREIA 151
Cdd:PRK11923   88 VSRGRRPPDSDVSsedaefydgdhalkdiESPER--ALLRDEIE----GTVHRTIQQLPEDLRTALTLREFDGLSYEDIA 161

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1681988327 152 ERLGISEKTSSSQLFRAKALLARRIKEYVKD 182
Cdd:PRK11923  162 SVMQCPVGTVRSRIFRAREAIDKALQPLLQE 192
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 27-172 1.74e-14

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 67.70  E-value: 1.74e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  27 FGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDrfSWRGEGSLRAWMERIAVNVSLEALRQKRRLhypttvDRLPER- 105
Cdd:PRK09637   10 YKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLH--SLKDGSSIKSWLYQIANNTIIDFYRKKNRS------EELPDDl 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1681988327 106 --YEEPTSDEMERLPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALL 172
Cdd:PRK09637   82 lfEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKL 150
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 23-92 4.34e-14

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: 63.76  E-value: 4.34e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  23 LYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFSWRGEGSLRAWMERIAVNVSLEALRQKRR 92
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 8-168 6.64e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 63.69  E-value: 6.64e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327   8 LAERCKAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFSwRGEGSLRAWMERIAVNVSLEAL 87
Cdd:PRK12514    9 LIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFA-VSGLSPMTWLITIARNHAIDRL 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  88 RQKRrlhyPTTVDrLPERY---EEPTSDEMERLPYDDLKRLIA---ELP-DGYRTVFNLYcIEELSHREIAERLGISEKT 160
Cdd:PRK12514   88 RARK----AVAVD-IDEAHdlaDPSPGPEAEVIAGDEGQRIDAcleELEkDRAAAVRRAY-LEGLSYKELAERHDVPLNT 161


                  ....*...
gi 1681988327 161 SSSQLFRA 168
Cdd:PRK12514  162 MRTWLRRS 169
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
14-179 1.78e-12

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 62.40  E-value: 1.78e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  14 AGDNDAR--RELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFSwRGEGSLRAWMERIAVNVSLEAlRQKR 91
Cdd:PRK09645    3 MATAEAAlmRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLA-DTGRSARAWLFTVARNLVIDE-RRSA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  92 RLHYPTTVDRLPERYEEPTSDEMER-LPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKA 170
Cdd:PRK09645   81 RARPVEGGDDVLGVPEQSAPDEVDRaLDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALR 160


                  ....*....
gi 1681988327 171 LLARRIKEY 179
Cdd:PRK09645  161 ALRLALQER 169
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 119-172 1.25e-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: 57.08  E-value: 1.25e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1681988327 119 YDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALL 172
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 13-172 1.94e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 59.69  E-value: 1.94e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  13 KAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFSWRgeGSLRAWMERIAVNVSLEALRQKRR 92
Cdd:PRK12519   24 KAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSSYDPKR--GSLSSYLLTLTRSRAIDRLRSRRS 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  93 LHypttvdRLPERY------EEPTSDEMERLPYDDL----KRLIAELPDGYRTVFNLYCIEELSHREIAERLGI---SEK 159
Cdd:PRK12519  102 RQ------RLLERWqqellgEASEDTPLEQASLAERsqrvQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIplgTVK 175

                         170
                  ....*....|....
gi 1681988327 160 TSSSQ-LFRAKALL 172
Cdd:PRK12519  176 ARARQgLLKLRELL 189
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 41-172 2.23e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 59.41  E-value: 2.23e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  41 DRATAEDLLHDCFIKVFAAidRFSWRGEGSLRAWMERIAVNVSLEALRQKR-RLHYPTTVDRLPERYEEPTSDEMERLPy 119
Cdd:PRK12511   27 DSAEAEDLVHDALVRALER--RASFRSGGNLRTWLMSILHNAFIDELRRRRvEARRADELAVLADASLPAAQEHAVRLA- 103

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1681988327 120 dDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALL 172
Cdd:PRK12511  104 -QIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAAL 155
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 31-157 3.27e-11

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 58.63  E-value: 3.27e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  31 LLSICLRYVGDRATAEDLLHDCFIKVfaaIDRFSWRGEGSLRAWMERIAVNVSLEALRQKR-RLHYPTTVDRLPERYEEP 109
Cdd:PRK12527    8 LVRFLSARLGNRQAAEDVAHDAYLRV---LERSSSAQIEHPRAFLYRTALNLVVDRHRRHRvRQAEPLEVLDEEERLHSP 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1681988327 110 TSDEMERLP--YDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGIS 157
Cdd:PRK12527   85 SPQTRLDLGqrLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGIS 134
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 31-181 7.06e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 57.96  E-value: 7.06e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  31 LLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFSWrgEGSLRAWMERIAVNVSLEALRQKRRLhypttVDRLPERYEEPT 110
Cdd:PRK12522   16 IYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSY--VENYKKWITTICVRTFYDFYRKKKRW-----KDRILDLFHKED 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327 111 SDEME-------------RLPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALLarriK 177
Cdd:PRK12522   89 GGEIEfaddvniseefiqKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQM----R 164


                  ....
gi 1681988327 178 EYVK 181
Cdd:PRK12522  165 EHLE 168
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
8-175 1.09e-10

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 59.18  E-value: 1.09e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327   8 LAERCKAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFswRGEGSLRAWMERIAVNVSLEAL 87
Cdd:PRK08241    9 LLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRF--EGRSSLRTWLYRIATNVCLDAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  88 RQKRR------LHYP--TTVDRLPERYE----EPTSDemERLPYDDLK-----------RL--IA---ELPDGYRTVFNL 139
Cdd:PRK08241   87 EGRARrplptdLGAPaaDPVDELVERPEvpwlEPYPD--ALLDPAAADpaarvvaresvRLafVAalqHLPPRQRAVLIL 164

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 1681988327 140 YCIEELSHREIAERLGISEKTSSSQLFRAKALLARR 175
Cdd:PRK08241  165 RDVLGWSAAEVAELLDTSVAAVNSALQRARATLAER 200
PRK09642 PRK09642
RNA polymerase sigma factor;
45-178 2.75e-10

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 56.26  E-value: 2.75e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  45 AEDLLHDCFIKVFAAIDRFSWRGegsLRAWMERIAVNVSLEALRQKRRLHYPTTVDRLPERYEEPTSDEMERLPYDDLKR 124
Cdd:PRK09642   22 AKDVTQEVFVKIHASLPNYQFRG---LKTWMARIATNHAIDYKRKKARENEELSLCKETEENIKSSHNIEDLLLTKEQKL 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1681988327 125 LIA----ELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALLARRIKE 178
Cdd:PRK09642   99 LIAqklrELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKE 156
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 41-178 3.74e-10

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 56.04  E-value: 3.74e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  41 DRATAEDLLHDCFIKVFAAIDRFSwrgEGSLRAWMERIAVNVSLEALRQKRRLHYPTTVDRLPERYEEPTSDEMERLPYD 120
Cdd:PRK09644   24 SHHAAEDLLQETFYRAYIYLEDYD---NQKVKPWLFKVAYHTFIDFVRKEKKVSFVGTDEIEAIQAESTEEYVVAKNSYE 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1681988327 121 DLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALLARRIKE 178
Cdd:PRK09644  101 KLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 39-172 4.40e-10

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 55.73  E-value: 4.40e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  39 VGDRATAEDLLHDCFIKVFaaidRFSWRGEGSLRAWMERIAVNVSLEALR-QKRRLHYPTTVDRLPERYEEPTSDEM--E 115
Cdd:PRK09639   24 VKDRTQAEDLAQEVFLRLY----RSDFKGIENEKGWLIKSARNVAYNYLRsEKRRRARILGEFQWQEVDNEPSPEEIwiR 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1681988327 116 RLPYDDLKRLIAELPDGYRTVFNLYcIEELSHREIAERLGISEKTSSSQLFRAKALL 172
Cdd:PRK09639  100 KEEITKVQEVLAKMTERDRTVLLLR-FSGYSYKEIAEALGIKESSVGTTLARAKKKF 155
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 15-178 5.89e-10

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 55.69  E-value: 5.89e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  15 GDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFSWRgEGSLRAWMERIAVNVSLEALRQKRRLH 94
Cdd:PRK13919   20 GEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPR-RGSARAWLLALAHHAAVDHVRRRAARP 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  95 YPTTVD-RLPERYEEPTS--DEMERLPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKAL 171
Cdd:PRK13919   99 QPLEPDeREPEAFDLPGPglDEEGHLDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSR 178


                  ....*..
gi 1681988327 172 LARRIKE 178
Cdd:PRK13919  179 LKEVLRE 185
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 41-173 1.38e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 54.85  E-value: 1.38e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  41 DRATAEDLLHDCFIKVFAAIDRFSwrgEGS-LRAWMERIAVNVSLEALRQKRRLHYPTTVDRLPERYEEPTSDemERLPY 119
Cdd:PRK12546   30 NVAVADDLVQDTIVKAWTNFDKFQ---EGTnLRAWLFTILRNTFYSDRRKHKREVPDPEGVHAASLAVKPAHD--GRLAM 104

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1681988327 120 DDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALLA 173
Cdd:PRK12546  105 SDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLA 158
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 14-172 4.29e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 53.52  E-value: 4.29e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  14 AGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFS-WRGEGslRAWMERIAVNVSLEALRQKRR 92
Cdd:PRK12534   21 GGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDpSRARG--LTWLAMIARNKAIDHLRANAP 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  93 LHYPTTVD---RLPERYEEPTSDEMERLPYDDLKRLIAEL--PDG--YRTVFnlycIEELSHREIAERLGISEKTSSSQL 165
Cdd:PRK12534   99 QRRNVALDdagELRAADASPLERTERASTRRRIDHCLAELepPRSelIRTAF----FEGITYEELAARTDTPIGTVKSWI 174


                  ....*..
gi 1681988327 166 FRAKALL 172
Cdd:PRK12534  175 RRGLAKL 181
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 45-178 6.88e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 52.78  E-value: 6.88e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  45 AEDLLHDCFIKVFaaIDRFSWRGEGSLRAWMERIAVNVSLEALRQKRRlHYPTTVDRLPERYeePTSDEMERLPYDDLKR 124
Cdd:PRK12512   53 AEDIVQEILLAVH--LKRHTWDPGAPFAPWLFAIARNKLIDALRRRGR-RVFVDIDDFAETL--PAEPATETLPAGDVGR 127

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1681988327 125 LIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALLARRIKE 178
Cdd:PRK12512  128 HLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGLAALAAKFRS 181
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 4-182 8.02e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 53.32  E-value: 8.02e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327   4 EERILAERCKAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAaiDRFSWR-GEGSLRAWMERIAVNV 82
Cdd:PRK12538   49 EDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWT--HRGRWQhGRAKFSTWLYRVVSNR 126

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  83 SLEALRQKRRLH---YPTTVDRLPERYEEPTSDEMERLpyddLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEK 159
Cdd:PRK12538  127 CIDLRRKPRTENvdaVPEVADGKPDAVSVIERNELSDL----LEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVA 202

                         170       180
                  ....*....|....*....|...
gi 1681988327 160 TSSSQLFRAKALLARRIKEYVKD 182
Cdd:PRK12538  203 AVESLLKRGRQQLRDLLRRHERD 225
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 30-157 1.56e-08

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 51.61  E-value: 1.56e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  30 RLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFSWRGEgslRAWMERIAVNVSLEALR-QKRRLHYPTTVDRLPERYEE 108
Cdd:PRK07037   10 MLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKQP---VAYLFRIVRNLAIDHYRrQALENKYHGDEEDGLDVPSP 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1681988327 109 PTSDEMERLPYDDLKRL---IAELPDGYRTVFNLYCIEELSHREIAERLGIS 157
Cdd:PRK07037   87 EASPEAALINRDTLRHVadaLSELPARTRYAFEMYRLHGETQKDIARELGVS 138
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 120-172 3.32e-08

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: 47.87  E-value: 3.32e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1681988327 120 DDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALL 172
Cdd:cd06171     2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 10-165 1.18e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 49.54  E-value: 1.18e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  10 ERCKAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFSWRgEGSLRAWMERIAVNVSLEALR- 88
Cdd:PRK12531   19 EKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQ-KSALSTWIYTIIRNLCFDLLRk 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  89 QKRRLHYPTTVDRLPERYEEPTSDEMERLPYDDLK----RLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQ 164
Cdd:PRK12531   98 QKGKDLHIHADDIWPSDYYPPDLVDHYSPEQDMLKeqvmKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSR 177


                  .
gi 1681988327 165 L 165
Cdd:PRK12531  178 L 178
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 16-152 2.00e-07

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 48.78  E-value: 2.00e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  16 DNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFSWRgeGSLRAWMERIAVNVSLEALRQ---KRR 92
Cdd:PRK09640   24 VTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSITYNECITQYRKerrKRR 101

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  93 LHYPTTVDRLPERYEEPTSDEMERlpyDDLKRLIAELPDGYRTVFNLYCIEELSHREIAE 152
Cdd:PRK09640  102 LMDALSLDPLEEASEEKAPKPEER---GGLDRWLVHVNPIDREILVLRFVAELEFQEIAD 158
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 13-169 1.23e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 46.58  E-value: 1.23e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  13 KAGDNDARR--ELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFSWRGEGSLRAWMERIAVNVSLEALRQK 90
Cdd:PRK12542    2 KVTNNDYEKmeELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKN 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  91 RRL------HYPTTVDRLPERYEEPTSDEMERLPYDdlkRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQ 164
Cdd:PRK12542   82 KRHetfleeYERESIEAVDENIEEWEKRKMSEVQID---TLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQ 158


                  ....*
gi 1681988327 165 LFRAK 169
Cdd:PRK12542  159 FERAR 163
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 100-182 1.78e-06

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: 46.36  E-value: 1.78e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327 100 DRLPERYEEPTSDEMERLpyDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTsSSQLfRAKALLarRIKEY 179
Cdd:COG1191   160 DLLESGDPEEELEHEELR--EALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESR-VSRL-HKKALA--RLREY 233


                  ...
gi 1681988327 180 VKD 182
Cdd:COG1191   234 LKE 236
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
14-158 2.39e-06

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 45.49  E-value: 2.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  14 AGDNDARRELYTRFGGRLLSIC---LRYVGDRAT-AEDLLHDCFIKVFaaIDRFSWRGEGSLRAWMERIAVNVSLEALRQ 89
Cdd:PRK12539   17 DGDAAAHRALLERLSGHLRAYYkgkLARIGRGAEeAEDLVQEALMAIH--TRRHTYDPEQPLTPWVYAIARYKLIDHLRR 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1681988327  90 KRRLHYPTTVDRLPERYEEPTSDEMERlpYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISE 158
Cdd:PRK12539   95 TRASLADVPIDDADELVAHDDHAAVES--TLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSE 161
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 22-178 2.66e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 45.31  E-value: 2.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  22 ELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDrfSWRGEgSLRAWMERIAVNVSLEALRQKRRlhYPTTVDR 101
Cdd:PRK12541    9 EIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHID--YYKGE-EIRPWLFTIAYNAFIDWYRKEKK--YKTTTIE 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1681988327 102 LPERYEEPTSDEMERLPYDDLKRL--IAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALLaRRIKE 178
Cdd:PRK12541   84 EFHLPNVPSTEHEYFIKHEIASWLdsLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKET-KSIKE 161
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 37-157 3.90e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 44.94  E-value: 3.90e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  37 RYVGDRATAEDLLHDCFIKVFAAIDRFSWRgegSLRAWMERIAVNVSLEALRQKR-RLHYPTTVDRLPERYEePTSDEME 115
Cdd:PRK12525   28 RQLGCPHSAEDIASETFLQVLALPDPASIR---EPRALLTTIARRLMYEGWRRQDlERAYLQSLAEAPEAVQ-PSPEEQW 103

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1681988327 116 RL--PYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGIS 157
Cdd:PRK12525  104 MVieTLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVS 147
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 40-172 4.48e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 45.06  E-value: 4.48e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  40 GDRATAEDLLHDCFIKVFAAIDrfSWRGEGSLRAWMerIAVNVSLEALRQKRRLHYPTTVDRLPERYEEPTSDEMErLPY 119
Cdd:PRK12517   45 KDKHIAEDLVQETFLRAWRSLD--SLKDEKAAKAWL--ITILRRENARRFERKQFDLVDIEDDSIEDDASHSSEEE-MEQ 119

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1681988327 120 DDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALL 172
Cdd:PRK12517  120 EWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQL 172
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 23-157 5.05e-06

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 44.46  E-value: 5.05e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  23 LYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAaidRFSWRGEGSLRAWMERIAVNVSLEALRQKR-RLHYPTTVDR 101
Cdd:PRK12523   15 LYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLG---RPELPTPREPRAFLAAVAKGLMFDHFRRAAlEQAYLAELAL 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1681988327 102 LPERyEEPtSDEMERLPYDDLK---RLIAELPDGYRTVFNLYCIEELSHREIAERLGIS 157
Cdd:PRK12523   92 VPEA-EQP-SPEEQHLILEDLKaidRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVS 148
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 38-173 6.57e-06

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 44.65  E-value: 6.57e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  38 YVGDRATAEDLLHDCFIKVFAAIDRFSwrGEGSLRAWMERIAVNVSLEALRQKRRlHYPTTVDRLPERYEEptSDEMERl 117
Cdd:PRK09649   43 YLSDVGSADDLTQETFLRAIGAIPRFS--ARSSARTWLLAIARHVVADHIRHVRS-RPRTTRGARPEHLID--GDRHAR- 116

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327 118 PYDDL---KRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAK-ALLA 173
Cdd:PRK09649  117 GFEDLvevTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARdALLA 176
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 40-174 8.32e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 44.34  E-value: 8.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  40 GDRATAEDLLHDCFIKVFAAIDRFswRGEGSlRAWMERIAVNVSLEALRQKRRLH---YPTTVD---RLPERYEEPTSDE 113
Cdd:PRK12533   40 GNASDADDVVQEACMRALRFFDSF--RGDNA-RPWLLAIVRHTWYSEWRRRANAHevaAPDTLDdadSLDDWQPAGEDPL 116

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1681988327 114 MERLPYDDLKRL---IAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALLAR 174
Cdd:PRK12533  117 ALLLRAEDVRLVnaaLAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRRLAA 180
COG4941 COG4941
Predicted RNA polymerase sigma factor, contains C-terminal TPR domain [Transcription];
21-178 6.55e-05

Predicted RNA polymerase sigma factor, contains C-terminal TPR domain [Transcription];


Pssm-ID: 443968 [Multi-domain]  Cd Length: 412  Bit Score: 42.39  E-value: 6.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  21 RELYtrfgGRLLSICLRYVGDRATAEDLLHDCFIkvfAAIDRfsWRGEG---SLRAWMERIAVNVSLEALR--QKRRLHY 95
Cdd:COG4941    13 REES----GRLVAALARRFGDLDLAEDAVQDAFL---AALEQ--WPRDGvpdNPAAWLYTVARRRAIDRLRreARRRRKE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  96 PTTVDRLPERYEEPTSDEmERLPyDDLKRLI-----AELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKa 170
Cdd:COG4941    84 AELAADLEAEAPAEDADD-DDIP-DDRLRLLftcchPALSPEAQVALTLRLVGGLTTAEIARAFLVPEATMAQRIVRAK- 160


                  ....*...
gi 1681988327 171 llaRRIKE 178
Cdd:COG4941   161 ---RKIRE 165
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 43-172 3.99e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 39.53  E-value: 3.99e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  43 ATAEDLLHDCFIKVFAAIDRFSwrGEGSLRAWMERIAVNVSLEALRQK-RRLHYPTTVDR-------------------- 101
Cdd:PRK12532   31 DLAEDLVQETLLSAYSAGDSFQ--GRALVNSWLFAILKNKIIDALRQIgRQRKVFTLLDDelldeafeshfsqnghwtpe 108

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1681988327 102 -LPERYEEPTSDEMERLPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALL 172
Cdd:PRK12532  109 gQPQHWNTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRARESL 180
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 125-168 4.31e-04

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: 36.64  E-value: 4.31e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1681988327 125 LIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRA 168
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRA 44
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 39-172 9.17e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 38.41  E-value: 9.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  39 VGDRATAEDLLHDCFIKVFAAIDRFSWrgEGSLRAWMERIAVNVSLEALRQKRRL------HYPTTVDRLPERYEEptsd 112
Cdd:PRK12516   31 IGRHDRADDLVQDTIMKAWAKQDHFEV--GTNMKAWLFTILRNEFYSQMRKRGREvqdtdgMFTEQLAVHPSQYGT---- 104

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327 113 emerLPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALL 172
Cdd:PRK12516  105 ----LDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRL 160
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
8-165 1.43e-03

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 37.73  E-value: 1.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327   8 LAERCKAGDNDARRELYTRFGGRLLSICLRYVGDRATAEDLLHDCFIKVFAAIDRFSwRGEGSLRAWM----ERIAVNVS 83
Cdd:PRK09646   20 LLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFD-PARGSALAWLltlaHRRAVDRV 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  84 LEALRQKRRLHYPTTVDRLPErYEEpTSDEME-RLPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSS 162
Cdd:PRK09646   99 RSEQAASQREVRYGARNVDPA-FDQ-VAEEVEaRLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVK 176


                  ...
gi 1681988327 163 SQL 165
Cdd:PRK09646  177 TRM 179
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 30-173 1.52e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 37.64  E-value: 1.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  30 RLLSICLRYVGDRAtaEDLLHDCFIKVFAAIDRFswRGEGSLRAWMERIAVNVSLEALRQKRRL------HYPTTVDRLP 103
Cdd:PRK12540   19 RAFAISLSGNGDRA--DDLVQETLLRALANIDSF--QPGSNLPAWLFTILRNLFRSDYRKRRREvedadgSYAKTLKSQP 94

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327 104 eryeeptsDEMERLPYDDLKRLIAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKALLA 173
Cdd:PRK12540   95 --------GQNAHLEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLS 156
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 31-170 1.73e-03

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 38.02  E-value: 1.73e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  31 LLSICLRYVGDRATAEDLLHDCFIKVFAA----IDrfswrgegSLRAWMERIAVNVSLEALRQKR-RLHYPTTVDRLPER 105
Cdd:PRK09635   18 LVDLAFRMVGDIGVAEDMVQEAFSRLLRApvgdID--------DERGWLIVVTSRLCLDHIKSAStRRERPQDIAAWHDG 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1681988327 106 YEEPTS-DEMERLPYDDLKRL-----IAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKA 170
Cdd:PRK09635   90 DASVSSvDPADRVTLDDEVRLallimLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARR 160
PRK12544 PRK12544
RNA polymerase factor sigma-70;
39-183 3.55e-03

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 36.70  E-value: 3.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327  39 VGDRATAEDLLHDCFIKVFAAIDRFSwrGEGSLRAWMERIAVNVSLEALRQKRRLHYPTTVDRLPE-------------- 104
Cdd:PRK12544   39 LSDLHLAEDAVQEALIGALKNADSFA--GRAAFKTWVFAILKNKIIDLLRQKKRHVSASSLLRDEEeeedfeelfdesgh 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1681988327 105 --RYEEPTS----DEMerLPYDDLKRL----IAELPDGYRTVFNLYCIEELSHREIAERLGISEKTSSSQLFRAKAllar 174
Cdd:PRK12544  117 wqKDERPQAwgnpEES--LEQEQFWRIfeacLDGLPAKYARVFMMREFIELETNEICHAVDLSVSNLNVLLYRARL---- 190


                  ....*....
gi 1681988327 175 RIKEYVKDK 183
Cdd:PRK12544  191 RLRECLENK 199
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 121-169 5.22e-03

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 36.59  E-value: 5.22e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1681988327 121 DLKRLIAE----LPDGYRTVFNLYCIEELSHREIAERLGISEK------TSSSQLFRAK 169
Cdd:PRK06288  201 EIKRVIVEaiktLPEREKKVLILYYYEDLTLKEIGKVLGVTESrisqlhTKAVLQLRAK 259
 
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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