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Conserved domains on  [gi|933374904|emb|CUN66735|]
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RNA polymerase%2C sigma subunit%2C SigV [Hungatella hathewayi]

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]; ...
 15-158 1.31e-35

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


:

Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 121.64  E-value: 1.31e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  15 ANQKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIVSDEPLGEEAAYV 94
Cdd:COG1595   25 RYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAEELPDE 104

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 933374904  95 EPGYGET-------EGFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:COG1595  105 AADPEEAleaeellEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREAL 175
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 15-158 1.31e-35

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 121.64  E-value: 1.31e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  15 ANQKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIVSDEPLGEEAAYV 94
Cdd:COG1595   25 RYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAEELPDE 104

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 933374904  95 EPGYGET-------EGFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:COG1595  105 AADPEEAleaeellEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREAL 175
Sig70_famx3 TIGR02954
RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of ...
 13-158 7.33e-32

RNA polymerase sigma-70 factor, TIGR02954 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. This family is found in certain Bacillus and Clostridium species.


Pssm-ID: 213752 [Multi-domain]  Cd Length: 169  Bit Score: 111.73  E-value: 7.33e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904   13 IIANQKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIVSDEPLGEEAA 92
Cdd:TIGR02954  22 IKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPKYFNTWLTRILINECIDLLKKKKKVIPFDPNTSIEKG 101

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 933374904   93 YVEPGYGETEGFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:TIGR02954 102 ECETHADSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 17-158 3.98e-24

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 92.18  E-value: 3.98e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  17 QKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIVSDEPLGEEAAYVEP 96
Cdd:PRK09652  20 QPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQGRRPPASDVDAEEAEDFDL 99

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 933374904  97 GYGETE----------GFFEE-----LDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK09652 100 ADALRDistpenellsAELEQrvraaIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 106-155 1.80e-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: 58.66  E-value: 1.80e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 933374904 106 EELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLK 155
Cdd:cd06171    6 EALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 108-154 2.26e-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: 55.54  E-value: 2.26e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 933374904  108 LDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLL 154
Cdd:pfam08281   8 LEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 15-158 1.31e-35

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 121.64  E-value: 1.31e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  15 ANQKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIVSDEPLGEEAAYV 94
Cdd:COG1595   25 RYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAEELPDE 104

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 933374904  95 EPGYGET-------EGFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:COG1595  105 AADPEEAleaeellEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREAL 175
Sig70_famx3 TIGR02954
RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of ...
 13-158 7.33e-32

RNA polymerase sigma-70 factor, TIGR02954 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. This family is found in certain Bacillus and Clostridium species.


Pssm-ID: 213752 [Multi-domain]  Cd Length: 169  Bit Score: 111.73  E-value: 7.33e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904   13 IIANQKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIVSDEPLGEEAA 92
Cdd:TIGR02954  22 IKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPKYFNTWLTRILINECIDLLKKKKKVIPFDPNTSIEKG 101

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 933374904   93 YVEPGYGETEGFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:TIGR02954 102 ECETHADSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 13-158 8.89e-28

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: 100.88  E-value: 8.89e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904   13 IIANQKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIVSDEPLGEEAA 92
Cdd:TIGR02937   7 YERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEELLD 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 933374904   93 YVEPGYGETEG------FFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:TIGR02937  87 SDPSPEEELEQeeereaLREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 17-158 3.98e-24

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 92.18  E-value: 3.98e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  17 QKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIVSDEPLGEEAAYVEP 96
Cdd:PRK09652  20 QPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQGRRPPASDVDAEEAEDFDL 99

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 933374904  97 GYGETE----------GFFEE-----LDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK09652 100 ADALRDistpenellsAELEQrvraaIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 17-158 3.10e-23

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: 89.54  E-value: 3.10e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904   17 QKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVK-KRNREIVSDEPLGEEAAYVE 95
Cdd:TIGR02985  11 YPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRhKQVEEKYQEELAEIEERELS 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 933374904   96 PGYGETEGFFEEL--------DRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:TIGR02985  91 EADPEEELEAKELeeiieeaiEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 21-159 8.78e-22

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 86.18  E-value: 8.78e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  21 YRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNRE---IVSDEPLGEEAAYVE-P 96
Cdd:PRK11924  27 LRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREkavLSDDALEPEFAETAEtP 106

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 933374904  97 GYG-----ETEGFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEELV 159
Cdd:PRK11924 107 EAAllakdDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLE 174
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 12-158 1.67e-19

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: 79.74  E-value: 1.67e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904   12 YIIANQKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIVSDEPLGEEA 91
Cdd:TIGR02983  11 FVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRRRRLLELPTRELPDAA 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 933374904   92 AyVEPGYGETE--GFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:TIGR02983  91 A-PDPAPDVALraALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELL 158
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 15-158 1.80e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 78.85  E-value: 1.80e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  15 ANQKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIVSDEPlgeEAAYV 94
Cdd:PRK11922  38 RHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRRRRRLVNLAEM---VMAST 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  95 EPGY------------------GETEGFFEE-LDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLK 155
Cdd:PRK11922 115 IAGGertpladpaedperaaarREIRALLERaIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLLR 194


                 ...
gi 933374904 156 EEL 158
Cdd:PRK11922 195 ESL 197
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 22-159 1.73e-16

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 72.47  E-value: 1.73e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  22 RLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVK-----------KRNREIVSDEPLGEE 90
Cdd:PRK09415  31 QLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKswhnkkvivteDIFTYMESQKESVEE 110

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 933374904  91 AAYVEpgyGETEGFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEELV 159
Cdd:PRK09415 111 EVIQN---AEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLE 176
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 17-158 2.56e-16

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 72.04  E-value: 2.56e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  17 QKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNRE---------------- 80
Cdd:PRK09641  28 KDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRKRKPDyyldaevagtegltmy 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  81 --IVSDEPLGEEAayVEpgYGETEGFF-EELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEE 157
Cdd:PRK09641 108 sqLAADDALPEEQ--VV--SLELQETIqEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183


                 .
gi 933374904 158 L 158
Cdd:PRK09641 184 L 184
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 13-149 9.95e-14

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 65.21  E-value: 9.95e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  13 IIANQKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIVSDEPLGEEAA 92
Cdd:PRK11923  26 VLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHLVSRGRRPPDSDVSSEDAE 105

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 933374904  93 YVEPGYG--------------ETEG-FFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYR 149
Cdd:PRK11923 106 FYDGDHAlkdiesperallrdEIEGtVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFR 177
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 19-158 4.18e-13

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 63.52  E-value: 4.18e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  19 KFYRLAYTYVRNENDALDIVQNAICSALEHYESIRE-ISYIKTWFYRVLVHESLNYVKKRnREIVSDEPLgeEAAYVEPG 97
Cdd:PRK05602  32 RLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPgEARFDTWLHRVVLNLCYDRLRRR-REVPVEDAP--DVPDPAPG 108

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 933374904  98 YGETEGFFEELDR-------LPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK05602 109 PDAGLEARQRARRveqalaaLPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQL 176
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 17-158 1.47e-12

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 62.26  E-value: 1.47e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  17 QKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNRE-----IVSDEPLGEEA 91
Cdd:PRK09640  36 QRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKERRKrrlmdALSLDPLEEAS 115

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 933374904  92 AYVEPGYGETEGFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK09640 116 EEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLREKF 182
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 106-155 1.80e-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: 58.66  E-value: 1.80e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 933374904 106 EELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLK 155
Cdd:cd06171    6 EALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 28-158 7.40e-12

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 60.00  E-value: 7.40e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  28 VRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNReivSDEPLGEEAAYVEPgygETEGFFEE 107
Cdd:PRK09637  22 VSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKNR---SEELPDDLLFEDEE---REENAKKE 95

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 933374904 108 L--------DRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK09637  96 LapclrpfiDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 108-154 2.26e-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: 55.54  E-value: 2.26e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 933374904  108 LDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLL 154
Cdd:pfam08281   8 LEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 22-156 2.49e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 58.64  E-value: 2.49e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  22 RLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIVSDEPLGEEAAYVEPGYGET 101
Cdd:PRK12511  19 RYARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVEARRADELAVLADASLPAAQEH 98

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 933374904 102 --------EGFFeeldRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKE 156
Cdd:PRK12511  99 avrlaqirDAFF----DLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 34-160 4.09e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 58.44  E-value: 4.09e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  34 ALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIVSDEPLGEEAAYVEPG-YG--ETEGFFEELDR 110
Cdd:PRK12516  37 ADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRGREVQDTDGMFTEQLAVHPSqYGtlDLQDFRAALDQ 116

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 933374904 111 LPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEELVI 160
Cdd:PRK12516 117 LPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQI 166
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 3-159 9.54e-11

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 56.95  E-value: 9.54e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904   3 QDHYDIVVNYIIanqkkfyrlayTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIV 82
Cdd:PRK09638  25 QQHYSFLYKYLL-----------KLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHLRKQKREKL 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  83 SDEPLGEEAAYVEPGYGETEG-----FFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEE 157
Cdd:PRK09638  94 RLQRAKEETLRKEKWEAAIKGaewseMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173


                 ..
gi 933374904 158 LV 159
Cdd:PRK09638 174 WG 175
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 21-156 1.22e-10

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 56.81  E-value: 1.22e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  21 YRLAYTYVRNENDALDIVQNAICSALEHYESiREISYIKTWFYRVLVHESLNYVKKRNREI-VSDEPLGEEAAYVEPGYG 99
Cdd:PRK09644  15 YRYLFSLTKSHHAAEDLLQETFYRAYIYLED-YDNQKVKPWLFKVAYHTFIDFVRKEKKVSfVGTDEIEAIQAESTEEYV 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 933374904 100 ETEGFFEELDR----LPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKE 156
Cdd:PRK09644  94 VAKNSYEKLIQiihtLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKA 154
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 19-149 2.52e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 56.31  E-value: 2.52e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  19 KFYRLAytyVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIVSDEPLGEE---AAYVE 95
Cdd:PRK12530  22 KFATLQ---LKDADLAEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIRYRKRFVNESELIEEDspnSFFDE 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 933374904  96 PGYGETEGF--------------------FEE-LDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYR 149
Cdd:PRK12530  99 KGHWKPEYYepsewqeventvykeefwliFEAcLNHLPAQQARVFMMREYLELSSEQICQECDISTSNLHVLLYR 173
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 24-160 3.08e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 55.65  E-value: 3.08e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  24 AYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIV-SDEPLGEEAAYVEPGYG--E 100
Cdd:PRK12547  23 AVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKRGREVQdSDGVFTARVAVHPAQYGslD 102

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904 101 TEGFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEELVI 160
Cdd:PRK12547 103 LQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKV 162
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 108-156 7.18e-10

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: 51.66  E-value: 7.18e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 933374904  108 LDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKE 156
Cdd:pfam04545   2 LASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 21-158 5.49e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 52.94  E-value: 5.49e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  21 YRLAYTYVRNENDALDIVQNAICSALEH---YESIReiSYIKTWFYRVLVHESLNYVKK---RNREIVSDEPLGEEAAYV 94
Cdd:PRK12538  77 YAIALRIVGNRADAEDVVQDTMLKVWTHrgrWQHGR--AKFSTWLYRVVSNRCIDLRRKprtENVDAVPEVADGKPDAVS 154

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 933374904  95 EPGYGETEGFFEE-LDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK12538 155 VIERNELSDLLEAaMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 13-160 7.97e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 51.89  E-value: 7.97e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  13 IIANQKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIVSDEPLGEEAA 92
Cdd:PRK12540  11 ILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRSDYRKRRREVEDADGSYAKTL 90

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 933374904  93 YVEPGYG---ETEGFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEELVI 160
Cdd:PRK12540  91 KSQPGQNahlEFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYV 161
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 28-158 1.17e-08

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 51.12  E-value: 1.17e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  28 VRNENDALDIVQNAICSALEHYeSIREISYIKTWFYRVLVHESLNYVKK---RNR--EIVSDEPLGEEAAY------VEP 96
Cdd:PRK09047   1 VRDDDAALDIVQDAMIKLAEKY-GDRPAAEWPPLFQRILQNRIHDWFRRqkvRNTwvSLFSSFSDDDDDDDfdpletLDS 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 933374904  97 GYGETEGFFEELDR-------------LPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK09047  80 ADEGAESPADKLERaqvlqlieeaiqkLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKAL 154
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 24-158 1.25e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 51.38  E-value: 1.25e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  24 AYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREiVSDePLGEEAA--YVEP---GY 98
Cdd:PRK12546  24 AISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKRE-VPD-PEGVHAAslAVKPahdGR 101

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  99 GETEGFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK12546 102 LAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161
PRK12520 PRK12520
RNA polymerase sigma factor; Provisional
 22-158 1.40e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237126 [Multi-domain]  Cd Length: 191  Bit Score: 51.27  E-value: 1.40e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  22 RLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREI----VSDEPLGEEAA----- 92
Cdd:PRK12520  17 RFARLQLRDPALAEDAVSETLLAVLEHPERFAGQSSLKTYLVGILKHKIIDAIRSGRREVrlslDDADEQSDDDLfdalf 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  93 -----YVEP--GYGETEG------FFEEL----DRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLK 155
Cdd:PRK12520  97 aadghYREPpsDWGDPDAalsrreFFEVLqacvDRLPPRTGRVFMMREWLELETEEICQELQITATNAWVLLYRARMRLR 176


                 ...
gi 933374904 156 EEL 158
Cdd:PRK12520 177 ECL 179
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 21-158 2.69e-08

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 50.94  E-value: 2.69e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  21 YRLAYTYVRNENDALDIVQNA---ICSALEHYESireiSYIKTWFYRVLVHESLNYVKKRNReiVSDEPLGEEAAYVEPG 97
Cdd:PRK09647  42 YRLAYRLSGNQHDAEDLTQETfirVFRSLQNYQP----GTFEGWLHRITTNLFLDMVRRRAR--IRMEALPEDYDRVPGD 115

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 933374904  98 YGETEGFFEE----------LDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK09647 116 EPNPEQIYHDarldpdlqaaLDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 28-156 3.13e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 50.55  E-value: 3.13e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  28 VRNENDALDIVQNAICSALEH---YESIREISyiKTWFYRVLVHESLNYVKKRNREIVSDEPlGEEAAYVEPGYGETEGF 104
Cdd:PRK12537  44 VRDRALAEDIVHDAFIKIWTGaasFDPARGSA--RGWIYSVTRHLALNVLRDTRREVVLDDD-AEETAQTLHEIIDDFDL 120

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904 105 FEELDRL--------PAdTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKE 156
Cdd:PRK12537 121 WANSGKIhrcleqlePA-RRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 13-158 3.25e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 50.70  E-value: 3.25e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  13 IIANQKKFYRLAYTYVRNEND-ALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREI-----VSDEP 86
Cdd:PRK12532  11 LIESRKLLLHFARLQLPDHPDlAEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQIGRQRkvftlLDDEL 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  87 LGE--EAAYVEPG----------YGETEGFFEE----------LDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVK 144
Cdd:PRK12532  91 LDEafESHFSQNGhwtpegqpqhWNTPEKSLNNnefqkilqscLYNLPENTARVFTLKEILGFSSDEIQQMCGISTSNYH 170

                        170
                 ....*....|....
gi 933374904 145 SKLYRGLKLLKEEL 158
Cdd:PRK12532 171 TIMHRARESLRQCL 184
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 19-147 6.18e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 49.93  E-value: 6.18e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  19 KFYRLAYTYVRNENDALDIVQNAICSALEH---YESirEISYIKTWFY---RVLVHESLNYVKKRNREIVSDEPLGEEaa 92
Cdd:PRK12531  39 KLKQFAMKHVGNEQVAMEMVQETMSTVWQKahlFDG--QKSALSTWIYtiiRNLCFDLLRKQKGKDLHIHADDIWPSD-- 114

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 933374904  93 YVEPG----YGETEGFFEE-----LDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKL 147
Cdd:PRK12531 115 YYPPDlvdhYSPEQDMLKEqvmkfLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRL 178
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 20-155 9.13e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 48.78  E-value: 9.13e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  20 FYRLAYTYVRNENDALDIVQNAICSALEHYESIREiSYIKTWFYRVLVHESLN-YVKKRNREIVSDE-------PLGEEA 91
Cdd:PRK12541  18 LFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKG-EEIRPWLFTIAYNAFIDwYRKEKKYKTTTIEefhlpnvPSTEHE 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 933374904  92 AYVEpgyGETEGFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLK 155
Cdd:PRK12541  97 YFIK---HEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETK 157
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 15-80 1.20e-07

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: 46.43  E-value: 1.20e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 933374904   15 ANQKKFYRLAYTYVRNENDALDIVQNA---ICSALEHYESIREISyIKTWFYRVLVHESLNYVKKRNRE 80
Cdd:pfam04542   4 RYLPLVYSLARRYLGDGADAEDLVQEGflgLWRAIERFDPERGVS-FSTWLYTIIRNAIIDYLRKQRRT 71
PRK12544 PRK12544
RNA polymerase factor sigma-70;
17-158 1.36e-07

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 49.03  E-value: 1.36e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  17 QKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIVSDEPLGEE------ 90
Cdd:PRK12544  28 RKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGRAAFKTWVFAILKNKIIDLLRQKKRHVSASSLLRDEeeeedf 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  91 -AAYVEPGY----------GETEGFFEE----------LDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYR 149
Cdd:PRK12544 108 eELFDESGHwqkderpqawGNPEESLEQeqfwrifeacLDGLPAKYARVFMMREFIELETNEICHAVDLSVSNLNVLLYR 187


                 ....*....
gi 933374904 150 GLKLLKEEL 158
Cdd:PRK12544 188 ARLRLRECL 196
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 21-158 2.15e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 48.35  E-value: 2.15e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  21 YRLAYTYVRNENDALDIVQNAICSALEHYESIRE-ISYIKTWFYRVLVHESLNYVKKRNREIVS--------DEPLGEEA 91
Cdd:PRK12524  40 LAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQgEARVSTWLYRVVCNLCTDRLRRRRRASVDlddapepaDAAPGAEE 119

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 933374904  92 AYVEPGygETEGFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK12524 120 ALIEGD--RMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRALAALL 184
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 59-158 2.26e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 48.15  E-value: 2.26e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  59 KTWFYRVlVHESLN--YVKKRNREIVSDEPLGEEAAYVEPGYGETEGFFEELDR---------LPADTQNVIRLRFYEEM 127
Cdd:PRK12513  78 RTWLYQI-ARNLLIdhWRRHGARQAPSLDADEQLHALADDGAAPEQQLSLFRDRrrlqaaletLPDEQREVFLLREHGDL 156

                         90       100       110
                 ....*....|....*....|....*....|.
gi 933374904 128 SLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK12513 157 ELEEIAELTGVPEETVKSRLRYALQKLRELL 187
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 106-154 3.85e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 47.80  E-value: 3.85e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 933374904 106 EELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLL 154
Cdd:PRK12533 130 AALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRRL 178
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 17-158 3.93e-07

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 47.25  E-value: 3.93e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  17 QKKFYRLAYTyVRNENDALDIVQNAICSALEhyESIREISYIKTWFYRVLVHESLNYVKK----RNREI-------VSDE 85
Cdd:PRK09639  14 PDVVQQIFYI-VKDRTQAEDLAQEVFLRLYR--SDFKGIENEKGWLIKSARNVAYNYLRSekrrRARILgefqwqeVDNE 90

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 933374904  86 PLGEEAAYVEPgygETEGFFEELDRLPADTQNVIRLRFyEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK09639  91 PSPEEIWIRKE---EITKVQEVLAKMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 106-158 3.97e-07

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: 47.90  E-value: 3.97e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 933374904 106 EELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVkSKLY-RGLKLLKEEL 158
Cdd:COG1191  182 EAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRV-SRLHkKALARLREYL 234
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 17-158 4.97e-07

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 47.01  E-value: 4.97e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  17 QKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYV-KKRNREIVSDEPLGEEAAYVE 95
Cdd:PRK09643  37 HRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDRLrRAKARPTVPLDDVYPVAQLER 116

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 933374904  96 PGYGETE---GFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK09643 117 DPTARVEtalAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRARLAELL 182
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
21-158 5.68e-07

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 46.61  E-value: 5.68e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  21 YRLAYTYVRNENDALDIVQNAICSALEHYESI-REISYIKTWFYRV---LVHESLNYVKKRNREiVSDEPLGEEAAYVEP 96
Cdd:PRK09645  23 WRYALRLTGDRARAEDVVQETLLRAWQHPEVLaDTGRSARAWLFTVarnLVIDERRSARARPVE-GGDDVLGVPEQSAPD 101

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 933374904  97 GYG---ETEGFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLY---RGLKLLKEEL 158
Cdd:PRK09645 102 EVDralDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHyalRALRLALQER 169
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 60-158 3.81e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 44.79  E-value: 3.81e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  60 TWFYRVLVHES---LNYVKKRNREIVSDE--PLGEEAAYVEPgygETEGFFEEL---------DRLPADTQNVIRLRFYE 125
Cdd:PRK12526  92 TWVYTVMRNAAfdmLRKIKAKKEQNLGDDiwPIEQALAESQS---ESEEFSDHLmdkqilsyiEKLPEAQQTVVKGVYFQ 168

                         90       100       110
                 ....*....|....*....|....*....|...
gi 933374904 126 EMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK12526 169 ELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 2-158 7.10e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 43.91  E-value: 7.10e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904   2 KQDHYDIVVNyiiANQKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREI 81
Cdd:PRK12517  21 KQRRYEALVK---ALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLITILRRENARRFERKQFDL 97

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 933374904  82 V--SDEPLGEEAAYVEPGYGETEGFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK12517  98 VdiEDDSIEDDASHSSEEEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 106-158 8.44e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 43.90  E-value: 8.44e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 933374904 106 EELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK12519 137 TALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 59-159 1.01e-05

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 43.36  E-value: 1.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  59 KTWFYRVLVHESLNYVKKRNREIVSDEP-LGEEAAYVEPGYGETEgfFEELDR---------LPADTQNVIRLRFYEEMS 128
Cdd:PRK13919  76 RAWLLALAHHAAVDHVRRRAARPQPLEPdEREPEAFDLPGPGLDE--EGHLDRtrlgralkaLSPEERRVIEVLYYQGYT 153

                         90       100       110
                 ....*....|....*....|....*....|.
gi 933374904 129 LQEIAAVMELSVNTVKSKLYRGLKLLKEELV 159
Cdd:PRK13919 154 HREAAQLLGLPLGTLKTRARRALSRLKEVLR 184
PRK12545 PRK12545
RNA polymerase factor sigma-70;
12-149 1.48e-05

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 43.02  E-value: 1.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  12 YIIANQKKFYRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNR------------ 79
Cdd:PRK12545  13 YLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQSAHKTWVFGILRNKLIDTLRARQRtvnlsaldaeld 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  80 -EIVSDEPL----GEEAAYVEP-GYGETEGFFEE----------LDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTV 143
Cdd:PRK12545  93 gEALLDRELfkdnGHWAAHAKPrPWPKPETILQQqqfwtlfetcLDHLPEQIGRVFMMREFLDFEIDDICTELTLTANHC 172


                 ....*.
gi 933374904 144 KSKLYR 149
Cdd:PRK12545 173 SVLLYR 178
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 106-157 1.81e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 42.80  E-value: 1.81e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 933374904 106 EELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEE 157
Cdd:PRK12543 113 ELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQK 164
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 21-158 1.97e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 42.80  E-value: 1.97e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  21 YRLAYTYVRNENDALDIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNYVKKRNREIVSDEplgeEAAYVEPGYGE 100
Cdd:PRK12515  36 YRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSALRRRKHEEIDDE----AAAAIEDGADT 111

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 933374904 101 TEGFFEE----------LDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK12515 112 PEVALQKsdtsaalracLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179
PRK09642 PRK09642
RNA polymerase sigma factor;
21-156 2.53e-05

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 42.01  E-value: 2.53e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  21 YRLAYTYVRNENDALDIVQNA---ICSALEHYEsireISYIKTWFYRVLVHESLNYVKKRNREIVSDEPLGEEAAYVEPG 97
Cdd:PRK09642   9 FQVIFSILRHEEDAKDVTQEVfvkIHASLPNYQ----FRGLKTWMARIATNHAIDYKRKKARENEELSLCKETEENIKSS 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 933374904  98 YGETEGFF---------EELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKE 156
Cdd:PRK09642  85 HNIEDLLLtkeqklliaQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKK 152
PRK06704 PRK06704
RNA polymerase subunit sigma-70;
4-157 3.36e-05

RNA polymerase subunit sigma-70;


Pssm-ID: 180663 [Multi-domain]  Cd Length: 228  Bit Score: 42.32  E-value: 3.36e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904   4 DHYDIvvNYIIANQKKFYRLAYTYVRNENDALDIVQNAICSALEHYeSIREISYikTWFYRVLVHESLNYVKKRNREivs 83
Cdd:PRK06704  16 NHSNI--NFLIEQYGELKRYCTFLTKNKWDGEDLAQETVCKVLQKY-SNKDICM--TLVYKIARNRWLDQIKSKSVH--- 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  84 dEPLGEEAAYVEPgYGETEGFFEE----LDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRG---LKLLKE 156
Cdd:PRK06704  88 -EKIRDQITFEEP-HEKIADLHEMvgkvLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSrnrLKTVSE 165


                 .
gi 933374904 157 E 157
Cdd:PRK06704 166 E 166
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 36-158 5.50e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 41.24  E-value: 5.50e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  36 DIVQNAICSALEHYESIREISYIKTWFYRVLVHESLNY----VKKRNREIVSDEPLGEEAAYVEPGYGETEgfFEELDR- 110
Cdd:PRK12518  39 DLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDArrqfAQRPSRIQDDSLNDQPSRPSDTPDLMQLH--YQDLVQq 116

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 933374904 111 ----LPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK12518 117 glqtLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 21-158 2.25e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 39.47  E-value: 2.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904  21 YRLAYTYVRNENDALDIVQNaicSALEHYESIREISYIKT---WFYRVLVHESLNYVKKRNR--EIVSD---EPLGEEAA 92
Cdd:PRK12522  17 YSLCYKLAKTKEDAEDIFQE---TWIKVFSSRHQLSYVENykkWITTICVRTFYDFYRKKKRwkDRILDlfhKEDGGEIE 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 933374904  93 YVEPG--------YGETEGFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKLYRGLKLLKEEL 158
Cdd:PRK12522  94 FADDVniseefiqKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHL 167
Sig-70_X6 TIGR02999
RNA polymerase sigma factor, TIGR02999 family; This group of sigma factors are members of the ...
 63-144 2.62e-03

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


Pssm-ID: 132044 [Multi-domain]  Cd Length: 183  Bit Score: 36.53  E-value: 2.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 933374904   63 YRVLV-HESLNYVKKRNREIVsDEPLGEEAAYVEPGYGET----EGFFEELDRLPADTQNVIRLRFYEEMSLQEIAAVME 137
Cdd:TIGR02999  83 RRILVdHARRRRAQKRGGGAV-RVPLDEVLPDAEADLDEElldlDDALDKLAQVDPRQAEVVELRFFAGLTVEEIAELLG 161


                  ....*..
gi 933374904  138 LSVNTVK 144
Cdd:TIGR02999 162 VSVRTVE 168
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 105-139 3.96e-03

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 36.36  E-value: 3.96e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 933374904 105 FEELDRLPADTQNVIRLRFYEEMSLQEIAAVMELS 139
Cdd:PRK06986 179 VEAIESLPEREQLVLSLYYQEELNLKEIGAVLGVS 213
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 106-147 9.29e-03

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


Pssm-ID: 254323 [Multi-domain]  Cd Length: 185  Bit Score: 35.09  E-value: 9.29e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 933374904  106 EELDRLPADTQNVIRLRFYEEMSLQEIAAVMELSVNTVKSKL 147
Cdd:pfam07638 131 EQLFSLSPRQARLVELRFFAGLSNDEIAERLGVSERTVERNW 172
 
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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