NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|15598481|ref|NP_251975|]
View 

ECF subfamily sigma-70 factor [Pseudomonas aeruginosa PAO1]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 4-200 3.99e-40

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: 134.74  E-value: 3.99e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   4 PTDAELLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIGRSHT-EEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAK 82
Cdd:COG1595   2 SSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADaEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAI 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481  83 SRLRQVRREVFLDDLPGPHgtvddqrfaadghwsqppHAWHEDSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQG 162
Cdd:COG1595  82 DHLRKRRRRRELLDELAEE------------------LPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEG 143

                       170       180       190
                ....*....|....*....|....*....|....*...
gi 15598481 163 LELEEIRDLLDITLSNVRVLLHRARLKVFATLEHFEET 200
Cdd:COG1595 144 LSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGAL 181
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 4-200 3.99e-40

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: 134.74  E-value: 3.99e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   4 PTDAELLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIGRSHT-EEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAK 82
Cdd:COG1595   2 SSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADaEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAI 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481  83 SRLRQVRREVFLDDLPGPHgtvddqrfaadghwsqppHAWHEDSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQG 162
Cdd:COG1595  82 DHLRKRRRRRELLDELAEE------------------LPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEG 143

                       170       180       190
                ....*....|....*....|....*....|....*...
gi 15598481 163 LELEEIRDLLDITLSNVRVLLHRARLKVFATLEHFEET 200
Cdd:COG1595 144 LSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGAL 181
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 1-188 1.69e-28

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 106.59  E-value: 1.69e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    1 MAAPTDAELLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIGR-SHTEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITAN 79
Cdd:PRK11922  12 LSAASDRELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNdAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLN 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   80 TAKSRLRQVRREVFLDDLPGPHGTVDDQRFaadghwsqpPHAWHEDSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRE 159
Cdd:PRK11922  92 EALGRLRRRRRLVNLAEMVMASTIAGGERT---------PLADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRV 162

                        170       180
                 ....*....|....*....|....*....
gi 15598481  160 RQGLELEEIRDLLDITLSNVRVLLHRARL 188
Cdd:PRK11922 163 VEELSVEETAQALGLPEETVKTRLHRARR 191
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 19-190 1.41e-25

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: 96.65  E-value: 1.41e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    19 RAFRELVGAYQGAMRAVAWAIIGRSHT-EEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSRLRQVRREVFLDDL 97
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADaEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    98 pgphgtvDDQRFAADghwsqpphawheDSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLS 177
Cdd:TIGR02937  81 -------LEELLDSD------------PSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVG 141

                         170
                  ....*....|...
gi 15598481   178 NVRVLLHRARLKV 190
Cdd:TIGR02937 142 TVKRRLKRARKKL 154
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 137-190 7.42e-10

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: 52.49  E-value: 7.42e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15598481 137 RDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRARLKV 190
Cdd:cd06171   1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 137-190 2.60e-09

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: 51.30  E-value: 2.60e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 15598481   137 RDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRARLKV 190
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 4-200 3.99e-40

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: 134.74  E-value: 3.99e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   4 PTDAELLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIGRSHT-EEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAK 82
Cdd:COG1595   2 SSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADaEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAI 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481  83 SRLRQVRREVFLDDLPGPHgtvddqrfaadghwsqppHAWHEDSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQG 162
Cdd:COG1595  82 DHLRKRRRRRELLDELAEE------------------LPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEG 143

                       170       180       190
                ....*....|....*....|....*....|....*...
gi 15598481 163 LELEEIRDLLDITLSNVRVLLHRARLKVFATLEHFEET 200
Cdd:COG1595 144 LSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGAL 181
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 1-188 1.69e-28

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 106.59  E-value: 1.69e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    1 MAAPTDAELLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIGR-SHTEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITAN 79
Cdd:PRK11922  12 LSAASDRELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNdAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLN 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   80 TAKSRLRQVRREVFLDDLPGPHGTVDDQRFaadghwsqpPHAWHEDSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRE 159
Cdd:PRK11922  92 EALGRLRRRRRLVNLAEMVMASTIAGGERT---------PLADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRV 162

                        170       180
                 ....*....|....*....|....*....
gi 15598481  160 RQGLELEEIRDLLDITLSNVRVLLHRARL 188
Cdd:PRK11922 163 VEELSVEETAQALGLPEETVKTRLHRARR 191
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 12-187 6.32e-28

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 103.73  E-value: 6.32e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   12 RLLAGEQRAFRELVGAYQgamRAVAwAIIGR-----SHTEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSRLR 86
Cdd:PRK09652   3 RVQRGDRAAFALLVRRYQ---PRVK-RLLSRltrdpADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   87 QVRREVflddlpgphGTVDDQRFAADGhWSQPPHAWHEDSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQGLELE 166
Cdd:PRK09652  79 KQGRRP---------PASDVDAEEAED-FDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYE 148

                        170       180
                 ....*....|....*....|.
gi 15598481  167 EIRDLLDITLSNVRVLLHRAR 187
Cdd:PRK09652 149 EIAEIMGCPIGTVRSRIFRAR 169
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 46-195 1.33e-27

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 103.09  E-value: 1.33e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   46 EEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSRLRQVRREVFLDDLPGPHGTVD--DQRFAADGHWSQPPHAWH 123
Cdd:PRK12532  34 EDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQIGRQRKVFTLLDDELLDEafESHFSQNGHWTPEGQPQH 113

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15598481  124 EDSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRARLKVFATLE 195
Cdd:PRK12532 114 WNTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 19-196 1.87e-26

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 99.66  E-value: 1.87e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   19 RAFRELVGAYQGAMRAVAWAIIGRSHT-EEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSRLRQVRRE--VFLD 95
Cdd:PRK11924  13 EAFSELFRPHAPDLLRYARRQLGDRALaEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREkaVLSD 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   96 DLPgphgtvddqrfaadghwsQPPHAWHEDSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDIT 175
Cdd:PRK11924  93 DAL------------------EPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVP 154

                        170       180
                 ....*....|....*....|.
gi 15598481  176 LSNVRVLLHRARLKVFATLEH 196
Cdd:PRK11924 155 VGTVKSRLRRARQLLRECLEA 175
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 19-190 1.41e-25

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: 96.65  E-value: 1.41e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    19 RAFRELVGAYQGAMRAVAWAIIGRSHT-EEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSRLRQVRREVFLDDL 97
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADaEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    98 pgphgtvDDQRFAADghwsqpphawheDSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLS 177
Cdd:TIGR02937  81 -------LEELLDSD------------PSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVG 141

                         170
                  ....*....|...
gi 15598481   178 NVRVLLHRARLKV 190
Cdd:TIGR02937 142 TVKRRLKRARKKL 154
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 5-187 1.73e-25

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 97.46  E-value: 1.73e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    5 TDAELLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIGRSH-TEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKS 83
Cdd:PRK09641   4 LIKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHeAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTID 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   84 RLRQVRREVFLDD-LPGPHGTVDDQRFAADghwsqpphawhEDSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQG 162
Cdd:PRK09641  84 RLRKRKPDYYLDAeVAGTEGLTMYSQLAAD-----------DALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIED 152

                        170       180
                 ....*....|....*....|....*
gi 15598481  163 LELEEIRDLLDITLSNVRVLLHRAR 187
Cdd:PRK09641 153 LSLKEISEILDLPVGTVKTRIHRGR 177
PRK12520 PRK12520
RNA polymerase sigma factor; Provisional
 32-195 1.39e-24

RNA polymerase sigma factor; Provisional


Pssm-ID: 237126 [Multi-domain]  Cd Length: 191  Bit Score: 95.18  E-value: 1.39e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   32 MRAVAWAiigrshtEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSRLRQVRREVFLDDLPGPH---GTVDDQR 108
Cdd:PRK12520  23 LRDPALA-------EDAVSETLLAVLEHPERFAGQSSLKTYLVGILKHKIIDAIRSGRREVRLSLDDADEqsdDDLFDAL 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481  109 FAADGHWSQPPHAWheDSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRARL 188
Cdd:PRK12520  96 FAADGHYREPPSDW--GDPDAALSRREFFEVLQACVDRLPPRTGRVFMMREWLELETEEICQELQITATNAWVLLYRARM 173


                 ....*..
gi 15598481  189 KVFATLE 195
Cdd:PRK12520 174 RLRECLD 180
PRK12544 PRK12544
RNA polymerase factor sigma-70;
44-195 8.35e-23

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 91.02  E-value: 8.35e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   44 HTEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSRLRQVRREVFLDDL-PGPHGTVD-DQRFAADGHW--SQPP 119
Cdd:PRK12544  44 LAEDAVQEALIGALKNADSFAGRAAFKTWVFAILKNKIIDLLRQKKRHVSASSLlRDEEEEEDfEELFDESGHWqkDERP 123

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15598481  120 HAWHedSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRARLKVFATLE 195
Cdd:PRK12544 124 QAWG--NPEESLEQEQFWRIFEACLDGLPAKYARVFMMREFIELETNEICHAVDLSVSNLNVLLYRARLRLRECLE 197
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 5-187 5.08e-22

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 88.71  E-value: 5.08e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    5 TDAELLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIGRSH-TEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKS 83
Cdd:PRK11923   6 EDQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAeAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKN 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   84 RL-RQVRREvflddlPGPHGTVDDQRFAADGHwsqpphAWHE-DSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQ 161
Cdd:PRK11923  86 HLvSRGRRP------PDSDVSSEDAEFYDGDH------ALKDiESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFD 153

                        170       180
                 ....*....|....*....|....*.
gi 15598481  162 GLELEEIRDLLDITLSNVRVLLHRAR 187
Cdd:PRK11923 154 GLSYEDIASVMQCPVGTVRSRIFRAR 179
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
1-196 9.30e-21

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 88.07  E-value: 9.30e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    1 MAAPTDAELLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIGRSH-TEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITAN 79
Cdd:PRK08241   1 DPATAAAALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHdAEDAVQETLLRAWRGYDRFEGRSSLRTWLYRIATN 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   80 TAKSRLRQVRREVFLDDLPGPHGTVDDQRFA-ADGHWSQP-PHAWHEDS---PEALLTEGE-LRDCLDKTLNGLSELQRS 153
Cdd:PRK08241  81 VCLDALEGRARRPLPTDLGAPAADPVDELVErPEVPWLEPyPDALLDPAaadPAARVVAREsVRLAFVAALQHLPPRQRA 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 15598481  154 VLTLRERQGLELEEIRDLLDITLSNVRVLLHRARlkvfATLEH 196
Cdd:PRK08241 161 VLILRDVLGWSAAEVAELLDTSVAAVNSALQRAR----ATLAE 199
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 46-194 2.31e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 81.35  E-value: 2.31e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   46 EEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSRLRQVRREVFLDDLpgPHGTVDDQRFAADGHWSQ---PPHAW 122
Cdd:PRK12530  35 EDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIRYRKRFVNESEL--IEEDSPNSFFDEKGHWKPeyyEPSEW 112

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15598481  123 HEdsPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRARLKVFATL 194
Cdd:PRK12530 113 QE--VENTVYKEEFWLIFEACLNHLPAQQARVFMMREYLELSSEQICQECDISTSNLHVLLYRARLQLQACL 182
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 1-180 6.10e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 77.81  E-value: 6.10e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    1 MAAPTDAELLPRLLAGEQRAFRELVGAY-QGAMRAVAWAIIGRSHTEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITAN 79
Cdd:PRK12513   8 TAAASDEALMLRYRAGDAAAFEALYARHrTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARN 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   80 TAKSRLRQVRREVFLDDLPGPHGTVDdqrfAADGHwsqpphawhedSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRE 159
Cdd:PRK12513  88 LLIDHWRRHGARQAPSLDADEQLHAL----ADDGA-----------APEQQLSLFRDRRRLQAALETLPDEQREVFLLRE 152

                        170       180
                 ....*....|....*....|.
gi 15598481  160 RQGLELEEIRDLLDITLSNVR 180
Cdd:PRK12513 153 HGDLELEEIAELTGVPEETVK 173
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 5-186 2.75e-16

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 73.43  E-value: 2.75e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    5 TDAELLPRL---LAGEQRAFRELVGAYQGAMRAVAWAIIG-RSHTEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANT 80
Cdd:PRK09640   9 NDEELVARVhveLFHVTRAYEELMRRYQRTLFNVCARYLGnDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNE 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   81 AKSRLRQVRREVFL-DDLpgphgTVDDQRFAAdghwsqpphawHEDSPEAlltegELRDCLDKTLNGLSELQRSVLTLRE 159
Cdd:PRK09640  89 CITQYRKERRKRRLmDAL-----SLDPLEEAS-----------EEKAPKP-----EERGGLDRWLVHVNPIDREILVLRF 147

                        170       180
                 ....*....|....*....|....*..
gi 15598481  160 RQGLELEEIRDLLDITLSNVRVLLHRA 186
Cdd:PRK09640 148 VAELEFQEIADIMHMGLSATKMRYKRA 174
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 1-189 2.61e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 70.53  E-value: 2.61e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    1 MAAPTDAELLPRLLAGEQRAFREL-----VGAYQGAMRAVAWAIIGRSHTEEVVQDAWlaavRGLDGFQGRSSLKTWLLT 75
Cdd:PRK12515   4 AQATTDEMLLARIAQGDRTAMQTLygrhhVRVYRFGLRLVRDEQTAEDLVSEVFLDVW----RQAGQFEGRSQVSTWLLS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   76 ITANTAKSRLRQvRREVFLDDlpgphgtvDDQRFAADGhwsqpphawhEDSPEALLTEGELRDCLDKTLNGLSELQRSVL 155
Cdd:PRK12515  80 IARFKALSALRR-RKHEEIDD--------EAAAAIEDG----------ADTPEVALQKSDTSAALRACLAKLSPAHREII 140

                        170       180       190
                 ....*....|....*....|....*....|....
gi 15598481  156 TLRERQGLELEEIRDLLDITLSNVRVLLHRARLK 189
Cdd:PRK12515 141 DLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKK 174
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 1-195 3.79e-15

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 70.07  E-value: 3.79e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    1 MAAPTDAELLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIG-RSHTEEVVQDAWLAAVRGLDGFQ-GRSSLKTWLLTITA 78
Cdd:PRK05602   2 MDADPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGdPAEAEDVAQETFLRIWKQAPSWRpGEARFDTWLHRVVL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   79 NTAKSRLRQvRREVFLDDLPGPhgtVDDQRfaadghwsqpphawhedSPEALLTEGELRDCLDKTLNGLSELQRSVLTLR 158
Cdd:PRK05602  82 NLCYDRLRR-RREVPVEDAPDV---PDPAP-----------------GPDAGLEARQRARRVEQALAALPERQREAIVLQ 140

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 15598481  159 ERQGLELEEIRDLLDITLSNVRVLLHRARLKVFATLE 195
Cdd:PRK05602 141 YYQGLSNIEAAAVMDISVDALESLLARGRRALRAQLA 177
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 4-202 3.91e-14

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 67.81  E-value: 3.91e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    4 PTDAELLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIG-RSHTEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAK 82
Cdd:PRK09643  12 RSDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGtREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACL 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   83 SRLRQ--VRREVFLDDlpgphgTVDDQRFAADghwsqpphawhedspeaLLTEGELRDCLDKTLNGLSELQRSVLTLRER 160
Cdd:PRK09643  92 DRLRRakARPTVPLDD------VYPVAQLERD-----------------PTARVETALAVQRALMRLPVEQRAALVAVDM 148

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 15598481  161 QGLELEEIRDLLDITLSNVRVLLHRARLKVFATLEHFEETGQ 202
Cdd:PRK09643 149 QGYSVADAARMLGVAEGTVKSRCARGRARLAELLGYLRAGGN 190
PRK12545 PRK12545
RNA polymerase factor sigma-70;
46-190 1.26e-13

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 66.52  E-value: 1.26e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   46 EEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSRLRQVRREVFLDDLPGP---HGTVDDQRFAADGHWSQ--PPH 120
Cdd:PRK12545  36 EDAVQEALAAAWSQAGRFAGQSAHKTWVFGILRNKLIDTLRARQRTVNLSALDAEldgEALLDRELFKDNGHWAAhaKPR 115

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481  121 AWheDSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRARLKV 190
Cdd:PRK12545 116 PW--PKPETILQQQQFWTLFETCLDHLPEQIGRVFMMREFLDFEIDDICTELTLTANHCSVLLYRARTRL 183
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 9-187 1.33e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 65.89  E-value: 1.33e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    9 LLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIGRSHTEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSRLRQV 88
Cdd:PRK12518   1 LILRCQRGDRQSFRQLYRRYQQKVRSTLYQLCGRELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRQF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   89 RREvflddlpgphgtvdDQRFAADGHWSQPPHAwhEDSPEalLTEGELRDCLDKTLNGLSELQRSVLTLRERQGLELEEI 168
Cdd:PRK12518  81 AQR--------------PSRIQDDSLNDQPSRP--SDTPD--LMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEI 142

                        170
                 ....*....|....*....
gi 15598481  169 RDLLDITLSNVRVLLHRAR 187
Cdd:PRK12518 143 AEILNIPVGTVKSRLFYAR 161
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 28-199 1.05e-12

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 63.04  E-value: 1.05e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   28 YQGAMRAVAWAIIGRSHTEEVVQDAWLAAVRglDGFQGRSSLKTWLLTITANTA-----KSRLRQVRREVFLDdlpgphg 102
Cdd:PRK09639  13 YPDVVQQIFYIVKDRTQAEDLAQEVFLRLYR--SDFKGIENEKGWLIKSARNVAynylrSEKRRRARILGEFQ------- 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481  103 tvddqrfaadghwsqpphaWHEDSPEALLTEG--------ELRDCLDKtlngLSELQRSVLTLRErQGLELEEIRDLLDI 174
Cdd:PRK09639  84 -------------------WQEVDNEPSPEEIwirkeeitKVQEVLAK----MTERDRTVLLLRF-SGYSYKEIAEALGI 139

                        170       180
                 ....*....|....*....|....*
gi 15598481  175 TLSNVRVLLHRARlKVFAtlEHFEE 199
Cdd:PRK09639 140 KESSVGTTLARAK-KKFR--KIYEQ 161
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 1-195 4.29e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 59.52  E-value: 4.29e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    1 MAAPTDAELLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIG-RSHTEEVVQDAWLAAVR-GLDGFQGRSSLKTWLLTITA 78
Cdd:PRK12524   8 LSDVSDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGdRAEAEDVTQEAMLRLWRiAPDWRQGEARVSTWLYRVVC 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   79 NTAKSRLRQVRR-EVFLDDLPGPhgtvddqrfaADGhwsqpphawhEDSPEALLTEGELRDCLDKTLNGLSELQRSVLTL 157
Cdd:PRK12524  88 NLCTDRLRRRRRaSVDLDDAPEP----------ADA----------APGAEEALIEGDRMRALDAALAALPERQRQAVVL 147

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 15598481  158 RERQGLELEEIRDLLDITLSNVRVLLHRARLKVFATLE 195
Cdd:PRK12524 148 RHIEGLSNPEIAEVMEIGVEAVESLTARGKRALAALLA 185
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 6-186 1.49e-10

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 57.72  E-value: 1.49e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    6 DAELLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIGRSH-TEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSR 84
Cdd:PRK09638   5 EKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDlAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDH 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   85 LRQVRREVFLDDlpgpHGTVDDQRfAADGHWSQPPHAWHEdspealltegelrdcldkTLNGLSELQ---RSVLTLRERQ 161
Cdd:PRK09638  85 LRKQKREKLRLQ----RAKEETLR-KEKWEAAIKGAEWSE------------------MLDALSKLDpefRAPVILKHYY 141

                        170       180
                 ....*....|....*....|....*
gi 15598481  162 GLELEEIRDLLDITLSNVRVLLHRA 186
Cdd:PRK09638 142 GYTYEEIAKMLNIPEGTVKSRVHHG 166
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 137-190 7.42e-10

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: 52.49  E-value: 7.42e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15598481 137 RDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRARLKV 190
Cdd:cd06171   1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 20-194 9.66e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 55.36  E-value: 9.66e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   20 AFRELVGAYQGAMRAVAWAIIGRS-HTEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSRLRQVRREVflDDLP 98
Cdd:PRK12540   6 SLRDDILAAVPSLRAFAISLSGNGdRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRSDYRKRRREV--EDAD 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   99 GPHgtvddqrfaADGHWSQPPHAWHedspealLTEGELRDCLDKtlngLSELQRSVLTLRERQGLELEEIRDLLDITLSN 178
Cdd:PRK12540  84 GSY---------AKTLKSQPGQNAH-------LEFEEFRAALDK----LPQDQREALILVGASGFSYEDAAAICGCAVGT 143

                        170
                 ....*....|....*.
gi 15598481  179 VRVLLHRARLKVFATL 194
Cdd:PRK12540 144 IKSRVNRARSKLSALL 159
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 1-194 1.04e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 55.45  E-value: 1.04e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    1 MAAPTDAELLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIGRSH-TEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITAN 79
Cdd:PRK12519  11 LSSRSDAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQeAEDLTQEIFLSLWRKSSYDPKRGSLSSYLLTLTRS 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   80 TAKSRLRQVRREvflddlpgphgtvddQRFAAdgHWSQ-----PPhawhEDSPEALLTEGELRDCLDKTLNGLSELQRSV 154
Cdd:PRK12519  91 RAIDRLRSRRSR---------------QRLLE--RWQQellgeAS----EDTPLEQASLAERSQRVQTALAQLPESQRQV 149

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 15598481  155 LTLRERQGLELEEIRDLLDITLSNVRVLLHRARLKVFATL 194
Cdd:PRK12519 150 LELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 6-198 1.78e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 55.63  E-value: 1.78e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    6 DAELLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIG-RSHTEEVVQDAWLAAVRGLDGFQ-GRSSLKTWLLTITANTAKS 83
Cdd:PRK12538  50 DEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGnRADAEDVVQDTMLKVWTHRGRWQhGRAKFSTWLYRVVSNRCID 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   84 RLRQVRREVfLDDLPGPhgtvddqrfaADGHwsqpphawhedsPEALLT--EGELRDCLDKTLNGLSELQRSVLTLRERQ 161
Cdd:PRK12538 130 LRRKPRTEN-VDAVPEV----------ADGK------------PDAVSVieRNELSDLLEAAMQRLPEQQRIAVILSYHE 186

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 15598481  162 GLELEEIRDLLDITLSNVRVLLHRARLKVFATLEHFE 198
Cdd:PRK12538 187 NMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLRRHE 223
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 46-198 2.40e-09

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 54.22  E-value: 2.40e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   46 EEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSRLRQVRREVFLDDLpgphgtvddqrfaadghwsqpphAWHED 125
Cdd:PRK09637  29 DDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKNRSEELPDD-----------------------LLFED 85

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15598481  126 SPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLSNV--RVLLHRARLK-VFATLEHFE 198
Cdd:PRK09637  86 EEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAksRVQRGRVKLKeLLEGCCDFE 161
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 137-190 2.60e-09

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: 51.30  E-value: 2.60e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 15598481   137 RDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRARLKV 190
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 46-195 4.30e-09

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 53.60  E-value: 4.30e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   46 EEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSRLRQ--VRREVFLDDLpgphgtvddqrfaADGHWSQPPHAwh 123
Cdd:PRK09415  44 EDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSwhNKKVIVTEDI-------------FTYMESQKESV-- 108

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15598481  124 edsPEALLTEGELRDCLDKTLNgLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRARLKVFATLE 195
Cdd:PRK09415 109 ---EEEVIQNAEDERLASAVMS-LPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLE 176
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 15-194 4.60e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 53.97  E-value: 4.60e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   15 AGEQRAFRELVGAYQGAMRAVAWAIIGRSH-TEEVVQDAWLAAVRGLDGFQGRSSlKTWLLTITANTAKS--RLRQVRRE 91
Cdd:PRK12533  14 AARGERFRQLVLPHLDAAYNLARWLCGNASdADDVVQEACMRALRFFDSFRGDNA-RPWLLAIVRHTWYSewRRRANAHE 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   92 VFLDDlpgphgTVDDQrfaadghwsQPPHAWHEDS--PEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQGLELEEIR 169
Cdd:PRK12533  93 VAAPD------TLDDA---------DSLDDWQPAGedPLALLLRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIA 157

                        170       180
                 ....*....|....*....|....*
gi 15598481  170 DLLDITLSNVRVLLHRARLKVFATL 194
Cdd:PRK12533 158 AIADVPVGTVMSRLARARRRLAALL 182
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 24-91 5.53e-09

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: 50.66  E-value: 5.53e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15598481    24 LVGAYQGAMRAVAWAIIGRSHT-EEVVQDAWLAAVRGLDGFQGR--SSLKTWLLTITANTAKSRLRQVRRE 91
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADaEDLVQEGFLGLWRAIERFDPErgVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 31-195 6.14e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 53.30  E-value: 6.14e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   31 AMRAVAWAIIGRSHT-EEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSRLRQVRREVflDDLPGPHGTVDDQRF 109
Cdd:PRK12546  19 ALRAFAISLTRNVAVaDDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKREV--PDPEGVHAASLAVKP 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481  110 AADGHwsqpphawhedspealLTEGELRDCLDKtlngLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRARLK 189
Cdd:PRK12546  97 AHDGR----------------LAMSDFRAAFAQ----LPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARAR 156


                 ....*.
gi 15598481  190 VFATLE 195
Cdd:PRK12546 157 LAELLQ 162
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 17-111 6.91e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 50.35  E-value: 6.91e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   17 EQRAF-RELVGAYQgAMRAVAWAIIGRSH-TEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSRLRQVRREV-- 92
Cdd:PRK12516   8 GTPPFkRELLAALP-SLRAFAVSLIGRHDrADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRGREVqd 86

                         90       100
                 ....*....|....*....|....*.
gi 15598481   93 ----FLDDL---PGPHGTVDDQRFAA 111
Cdd:PRK12516  87 tdgmFTEQLavhPSQYGTLDLQDFRA 112
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 38-187 1.12e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 49.55  E-value: 1.12e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   38 AIIGRSH-TEEVVQDAWLAAVRGLDGFQGRSsLKTWLLTITANTAKSRLRQVRRevflddlpgpHGTVDDQRFaadgHWS 116
Cdd:PRK12541  24 SLTGDSHfAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWYRKEKK----------YKTTTIEEF----HLP 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15598481  117 QPPHAWHEdspeaLLTEGELRDCLDkTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRAR 187
Cdd:PRK12541  89 NVPSTEHE-----YFIKHEIASWLD-SLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGR 153
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
3-180 2.73e-07

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 48.90  E-value: 2.73e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    3 APTDAELLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIgRSH--TEEVVQDAWLAAVRGLDGFQ-GRSSLKTWLLTITAN 79
Cdd:PRK09646  14 SPDLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVL-RDPgySEETTQEVYLEVWRTASRFDpARGSALAWLLTLAHR 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   80 TAKSRLRQVRRevflddlpgphGTVDDQRFAADGHwsQPPHAWHEDSPEALLTEGELRDCLDKtlngLSELQRSVLTLRE 159
Cdd:PRK09646  93 RAVDRVRSEQA-----------ASQREVRYGARNV--DPAFDQVAEEVEARLERERVRDCLDA----LTDTQRESVTLAY 155

                        170       180
                 ....*....|....*....|.
gi 15598481  160 RQGLELEEIRDLLDITLSNVR 180
Cdd:PRK09646 156 YGGLTYREVAERLAVPLGTVK 176
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 23-196 3.25e-07

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 48.63  E-value: 3.25e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   23 ELVGAYQGAMRAVAWAIIGRSH-TEEVVQDAWLAAVRGLDGFQGrSSLKTWLLTITANTAKSRLRQvRREVFLDDLPGph 101
Cdd:PRK09647  32 ELVRQHADRVYRLAYRLSGNQHdAEDLTQETFIRVFRSLQNYQP-GTFEGWLHRITTNLFLDMVRR-RARIRMEALPE-- 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481  102 gtvDDQRFAADghwsqpphawhEDSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRV 181
Cdd:PRK09647 108 ---DYDRVPGD-----------EPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRS 173

                        170
                 ....*....|....*
gi 15598481  182 LLHRARLKVFATLEH 196
Cdd:PRK09647 174 RIHRGRQQLRAALAA 188
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 22-190 4.26e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 47.95  E-value: 4.26e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   22 RELVGAYQgAMRAVAWAIIG-RSHTEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSRLRQVRREV------FL 94
Cdd:PRK12547  10 QELLLALP-ALRAFAVSLSSkHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKRGREVqdsdgvFT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   95 DDL---PGPHGTVDDQRFAadghwsqpphawhedspealltegelrdcldKTLNGLSELQRSVLTLRERQGLELEEIRDL 171
Cdd:PRK12547  89 ARVavhPAQYGSLDLQDFK-------------------------------KALNLLSADQREAIILIGASGFSYEDAAAI 137

                        170
                 ....*....|....*....
gi 15598481  172 LDITLSNVRVLLHRARLKV 190
Cdd:PRK12547 138 CGCAVGTIKSRVSRARNRL 156
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 27-190 4.32e-07

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 49.15  E-value: 4.32e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   27 AYQGAMRAVAWAIIG-RSHTEEVVQDAWLAAvRGLDGFQGRSsLKTWLLTITANTAKSRLR--QVRREVFLddlpgphgt 103
Cdd:PRK09636  12 PLRPHLLSVAYRMLGsVADAEDIVQEAWLRW-NNADRAQIRD-PRAWLTRVVTRLCLDRLRsaRHRRETYV--------- 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481  104 vddqrfaadGHWSQPPHAWHEDSPEALLTEGE-LRDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRVL 182
Cdd:PRK09636  81 ---------GPWLPEPVVEELDDPLEAVVAAEdLSLALMLALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQL 151


                 ....*...
gi 15598481  183 LHRARLKV 190
Cdd:PRK09636 152 ASRARKHV 159
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 1-201 5.58e-07

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 47.73  E-value: 5.58e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    1 MAAPTDAELLPRLLA---GEQRAFRELVGA-YQGAMRAVAWaIIGRSHTEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTI 76
Cdd:PRK09649   3 ATASDDEAVTALALSaakGNGRALEAFIKAtQQDVWRFVAY-LSDVGSADDLTQETFLRAIGAIPRFSARSSARTWLLAI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   77 TANTAKSRLRqvrrevflddlpgphgtvddqrfaadgHWSQPPHAWHEDSPEALLTEGE----LRDCLDKT--LNGLSEL 150
Cdd:PRK09649  82 ARHVVADHIR---------------------------HVRSRPRTTRGARPEHLIDGDRhargFEDLVEVTtmIADLTTD 134

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 15598481  151 QRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRARLKVFATLEHFEETG 201
Cdd:PRK09649 135 QREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDALLADAEPDDLTG 185
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 4-190 1.02e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 47.12  E-value: 1.02e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    4 PTDAE-LLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIG-RSHTEEVVQDAWLAAVRGLDGFQ-GRSSLKTWLLTITANT 80
Cdd:PRK12514   3 PDDIEkLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKdRSEAEEALQDVYVKIWTKADRFAvSGLSPMTWLITIARNH 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   81 AKSRLRQvrREVFLDDLPGPHGTVDDQRfaadghwsqpphawhedSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRER 160
Cdd:PRK12514  83 AIDRLRA--RKAVAVDIDEAHDLADPSP-----------------GPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYL 143

                        170       180       190
                 ....*....|....*....|....*....|
gi 15598481  161 QGLELEEIRDLLDITLSNVRVLLHRARLKV 190
Cdd:PRK12514 144 EGLSYKELAERHDVPLNTMRTWLRRSLLKL 173
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 144-190 1.70e-06

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


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 43.57  E-value: 1.70e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 15598481   144 LNGLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRARLKV 190
Cdd:pfam04545   2 LASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKL 48
PRK06930 PRK06930
positive control sigma-like factor; Validated
 116-190 4.99e-06

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 45.11  E-value: 4.99e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15598481  116 SQPPHAWHEDSPEALLTEGElRDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRARLKV 190
Cdd:PRK06930  85 SMEDLEWDIEEPESVISEWD-KIRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKI 158
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 42-202 8.33e-06

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 44.10  E-value: 8.33e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   42 RSH--TEEVVQDAWLAAVRGLDGFQgRSSLKTWLLTITANTAKSRLRQVRREVFL-DDLPGphgtvddqrfaadghwsqp 118
Cdd:PRK09644  23 KSHhaAEDLLQETFYRAYIYLEDYD-NQKVKPWLFKVAYHTFIDFVRKEKKVSFVgTDEIE------------------- 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481  119 phAWHEDSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRARLKVFATLEhfE 198
Cdd:PRK09644  83 --AIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK--E 158


                 ....
gi 15598481  199 ETGQ 202
Cdd:PRK09644 159 EKSQ 162
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 23-190 1.76e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 43.50  E-value: 1.76e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   23 ELVGAYQGAMRAVAWAIIGR-SHTEEVVQDAWLAAVRGLDGFQGRSS--LKTWLLTITANTAKSRLRQVRR-EVFLDDLP 98
Cdd:PRK12542  13 ELYELYEQKVYYVAYSILNNiQQAEDAVQETFITLYKNLEKLHSLNTqeLKRYILRVAKNKAIDSYRKNKRhETFLEEYE 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   99 GPHGTVDDQRFaadghwsqpphawhEDSPEALLTEGELrdclDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLSN 178
Cdd:PRK12542  93 RESIEAVDENI--------------EEWEKRKMSEVQI----DTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEAN 154

                        170
                 ....*....|..
gi 15598481  179 VRVLLHRARLKV 190
Cdd:PRK12542 155 VRKQFERARKRV 166
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 16-186 7.32e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 41.69  E-value: 7.32e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   16 GEQRAFRELVGAYQGAMRAVAWAIIGRSHT-EEVVQDAWLAAVRGLDGFQ-GRSSLKTWLLTITANTAKSRLRQVRREVF 93
Cdd:PRK12537  20 GDRRALQALYQQESARLLGVARRIVRDRALaEDIVHDAFIKIWTGAASFDpARGSARGWIYSVTRHLALNVLRDTRREVV 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   94 LDDlpgphgtvDDQRFAADGHWSQPPHAWHEDSpeallteGELRDCLDKtlngLSELQRSVLTLRERQGLELEEIRDLLD 173
Cdd:PRK12537 100 LDD--------DAEETAQTLHEIIDDFDLWANS-------GKIHRCLEQ----LEPARRNCILHAYVDGCSHAEIAQRLG 160

                        170
                 ....*....|...
gi 15598481  174 ITLSNVRVLLHRA 186
Cdd:PRK12537 161 APLGTVKAWIKRS 173
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 7-186 2.22e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 40.45  E-value: 2.22e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    7 AELLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIGR-----SHTEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTA 81
Cdd:PRK12512  10 TDLMRSANAGDAAAYRRLLKAVTPVLRAAARRGLARagqpaDQAEDIVQEILLAVHLKRHTWDPGAPFAPWLFAIARNKL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   82 KSRLRQVRREVFLDdlpgphgtVDDqrFAadghwsqpphawhEDSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQ 161
Cdd:PRK12512  90 IDALRRRGRRVFVD--------IDD--FA-------------ETLPAEPATETLPAGDVGRHLETLPPRQRDVVQSISVE 146

                        170       180
                 ....*....|....*....|....*
gi 15598481  162 GLELEEIRDLLDITLSNVRVLLHRA 186
Cdd:PRK12512 147 GASIKETAAKLSMSEGAVRVALHRG 171
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 7-190 2.73e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 40.30  E-value: 2.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    7 AELLPRLLAGEQRAFRELVGAYQGAMRAVAWAIIGRSHTE-EVVQDAWLAAVRGLDGFQG-RSSLKTWLLTITANTAKSR 84
Cdd:PRK12531  15 LECMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAmEMVQETMSTVWQKAHLFDGqKSALSTWIYTIIRNLCFDL 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   85 LRQVRREvflddlpgphgtvdDQRFAADGHWSQ---PPHAWHEDSPEALLtegeLRDCLDKTLNGLSELQRSVLTLRERQ 161
Cdd:PRK12531  95 LRKQKGK--------------DLHIHADDIWPSdyyPPDLVDHYSPEQDM----LKEQVMKFLDRLPKAQRDVLQAVYLE 156

                        170       180
                 ....*....|....*....|....*....
gi 15598481  162 GLELEEIRDLLDITLSNVRvllHRARLKV 190
Cdd:PRK12531 157 ELPHQQVAEMFDIPLGTVK---SRLRLAV 182
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 18-195 6.08e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 39.28  E-value: 6.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   18 QRAFRELVGAYQGAMRAVAWAIIGRSH-TEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTItanTAKSRLRQVRREVFldD 96
Cdd:PRK12517  22 QRRYEALVKALHADIYRYAYWLCKDKHiAEDLVQETFLRAWRSLDSLKDEKAAKAWLITI---LRRENARRFERKQF--D 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   97 LpgphgtVD-DQRFAADghwsqppHAWHEDSPEallTEGELrdcLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDIT 175
Cdd:PRK12517  97 L------VDiEDDSIED-------DASHSSEEE---MEQEW---LRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLN 157

                        170       180
                 ....*....|....*....|
gi 15598481  176 LSNVRVLLHRARLKVFATLE 195
Cdd:PRK12517 158 KNTVMTRLFRARNQLKEALE 177
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 13-186 9.55e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 38.56  E-value: 9.55e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   13 LLAGEQRAFRELVGA-YQGAMRAVAWAIIGRSHTEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSRLRQVRRE 91
Cdd:PRK12543   1 MLSGDQEAFSEIYDVtIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSWRRKRWRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   92 VFLddlpgphgtvddqrFAADGHWSQPPHawHEDSPEALltEGELRDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDL 171
Cdd:PRK12543  81 FRI--------------FEKAEEQRKPVS--IDFSEDVL--SKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQL 142

                        170
                 ....*....|....*
gi 15598481  172 LDITLSNVRVLLHRA 186
Cdd:PRK12543 143 LQIPIGTVKSRIHAA 157
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 123-186 1.14e-03

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 39.06  E-value: 1.14e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15598481  123 HEDSPEALLTEGELRDCLDKTLNGLSELQRSVLTLR----ERQGLELEEIRDLLDITLSNVRVLLHRA 186
Cdd:PRK05949 243 EGPSPDQYITQELLRQDLNNLLAELTPQQREVLTLRfgleDGKELSLAKVGERLNLSRERVRQLEHQA 310
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
1-196 1.23e-03

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 38.41  E-value: 1.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    1 MAAPTDAEL---LPRLLAGEQRAFRELVGAYQGAMRAVAWAIIG---RSHT--EEVVQDAWLAAVRGLDGF--QGRSSLk 70
Cdd:PRK09648   3 AMTDTGEELdalVAEAVAGDRRALREVLEIIRPLVVRYCRARLGgveRPGLsaDDVAQEVCLAVITALPRYrdQGRPFL- 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   71 TWLLTITAN--TAKSRLRQVRREVFLDDLPGphgTVDDqrfaadghwsqpphawhEDSPEALLTEGELRDCLDKTLNGLS 148
Cdd:PRK09648  82 AFVYGIAAHkvADAHRAAGRDKAVPTEEVPE---RPSD-----------------DAGPEERALRSESSNRMRELLDTLP 141

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 15598481  149 ELQRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRARLKVFATLEH 196
Cdd:PRK09648 142 EKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALARLRAEIEA 189
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 122-189 2.27e-03

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: 37.88  E-value: 2.27e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481 122 WHEDSPEALLTEGELRDCLDKTLNGLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRA--RLK 189
Cdd:COG1191 162 LESGDPEEELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKAlaRLR 231
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 5-189 2.93e-03

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 37.20  E-value: 2.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481    5 TDAELLPRLLAGEQRAFRELVGAYQGAMRAVAWAI-IGRSHTEEVVQDAWLAAVRGLDGFQ-GRSSLKTWLLTITANTAK 82
Cdd:PRK13919   9 SDEALLALVARGEEEALRALFRRYAGAFLALARRMgLDGAAAEDVVQEVFIRVWKKAKEFDpRRGSARAWLLALAHHAAV 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   83 SRLRqvRREVflddlpGPHGTVDDQRfaadghwsqPPHAWHEDSPeALLTEGEL-RDCLDKTLNGLSELQRSVLTLRERQ 161
Cdd:PRK13919  89 DHVR--RRAA------RPQPLEPDER---------EPEAFDLPGP-GLDEEGHLdRTRLGRALKALSPEERRVIEVLYYQ 150

                        170       180       190
                 ....*....|....*....|....*....|
gi 15598481  162 GLELEEIRDLLDITLSNVRVLLHRA--RLK 189
Cdd:PRK13919 151 GYTHREAAQLLGLPLGTLKTRARRAlsRLK 180
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 30-201 3.08e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 37.07  E-value: 3.08e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481   30 GAMRAVAWAIIGRSH-TEEVVQDAWLAAVRGLDGFQGRSSLKTWLLTITANTAKSRLRQVRrevflddlpgphgtVDDQR 108
Cdd:PRK12511  15 VPLRRYARSLTRDSAeAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRR--------------VEARR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15598481  109 FAADGHWSQPPHAWHEDSPEALlteGELRDCLDKtlngLSELQRSVLTLRERQGLELEEIRDLLDITLSNVRVLLHRARl 188
Cdd:PRK12511  81 ADELAVLADASLPAAQEHAVRL---AQIRDAFFD----LPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRAR- 152

                        170
                 ....*....|...
gi 15598481  189 kvfATLEHFEETG 201
Cdd:PRK12511 153 ---AALRAFEEGT 162
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 126-175 4.27e-03

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 36.96  E-value: 4.27e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15598481 126 SPEALLTEGELRDCLDKTLNGLSELQRSVltLRERQGLE------LEEIRDLLDIT 175
Cdd:COG0568 186 SPEEALEEELLREELREALDTLTEREREI--LRLRFGLDdgephtLEEIGKEFGVS 239
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH