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Conserved domains on  [gi|1830457784|ref|WP_168205284|]
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RNA polymerase sigma factor [Bythopirellula goksoeyrii]

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]; ...
 56-218 1.54e-23

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: 92.75  E-value: 1.54e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  56 FLSFFGNLGPELMAFASKQLGknHADAAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVADYFRRLKGKQLMLSK 135
Cdd:COG1595    19 FEELYERYRPRLYRYARRLLG--DRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDE 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784 136 LNEKCPPPLPSAEELCSLDEQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNTERHRYFQDLKRLRKYLD 215
Cdd:COG1595    97 LAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALE 176


                  ...
gi 1830457784 216 AQL 218
Cdd:COG1595   177 EEG 179
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 56-218 1.54e-23

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: 92.75  E-value: 1.54e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  56 FLSFFGNLGPELMAFASKQLGknHADAAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVADYFRRLKGKQLMLSK 135
Cdd:COG1595    19 FEELYERYRPRLYRYARRLLG--DRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDE 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784 136 LNEKCPPPLPSAEELCSLDEQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNTERHRYFQDLKRLRKYLD 215
Cdd:COG1595    97 LAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALE 176


                  ...
gi 1830457784 216 AQL 218
Cdd:COG1595   177 EEG 179
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 41-217 1.98e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 79.24  E-value: 1.98e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  41 SYYQFIATLGDSsDPFLSFFGNLGPELMAFASKQLGknHADAAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVA 120
Cdd:PRK11924    1 GQLMPVDATGDK-EAFSELFRPHAPDLLRYARRQLG--DRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCY 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784 121 DYFRRLKGKQLMLSKLNEK--CPPPLPSAEELCSLDEQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNT 198
Cdd:PRK11924   78 DLLRRRRREKAVLSDDALEpeFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGT 157

                         170
                  ....*....|....*....
gi 1830457784 199 ERHRYFQDLKRLRKYLDAQ 217
Cdd:PRK11924  158 VKSRLRRARQLLRECLEAQ 176
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 65-214 2.13e-16

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: 73.15  E-value: 2.13e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  65 PELMAFASKQLGKNHAdaAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVADYFRRLKGKQLMLSKLnEKCPPPL 144
Cdd:TIGR02937  12 PLVYRYARRYLGDDAD--AEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLL-EELLDSD 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784 145 PSAEELCSLDEQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNTERHRYFQDLKRLRKYL 214
Cdd:TIGR02937  89 PSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 59-127 1.05e-06

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: 44.89  E-value: 1.05e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1830457784  59 FFGNLGPELMAFASKQLGKNHAdaAEDILQETFQRASL---KFDLKRSNAEkRSFLYSIVRNLVADYFRRLK 127
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGAD--AEDLVQEGFLGLWRaieRFDPERGVSF-STWLYTIIRNAIIDYLRKQR 69
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 56-218 1.54e-23

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: 92.75  E-value: 1.54e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  56 FLSFFGNLGPELMAFASKQLGknHADAAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVADYFRRLKGKQLMLSK 135
Cdd:COG1595    19 FEELYERYRPRLYRYARRLLG--DRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDE 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784 136 LNEKCPPPLPSAEELCSLDEQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNTERHRYFQDLKRLRKYLD 215
Cdd:COG1595    97 LAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALE 176


                  ...
gi 1830457784 216 AQL 218
Cdd:COG1595   177 EEG 179
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 41-217 1.98e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 79.24  E-value: 1.98e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  41 SYYQFIATLGDSsDPFLSFFGNLGPELMAFASKQLGknHADAAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVA 120
Cdd:PRK11924    1 GQLMPVDATGDK-EAFSELFRPHAPDLLRYARRQLG--DRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCY 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784 121 DYFRRLKGKQLMLSKLNEK--CPPPLPSAEELCSLDEQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNT 198
Cdd:PRK11924   78 DLLRRRRREKAVLSDDALEpeFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGT 157

                         170
                  ....*....|....*....
gi 1830457784 199 ERHRYFQDLKRLRKYLDAQ 217
Cdd:PRK11924  158 VKSRLRRARQLLRECLEAQ 176
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 65-214 2.13e-16

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: 73.15  E-value: 2.13e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  65 PELMAFASKQLGKNHAdaAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVADYFRRLKGKQLMLSKLnEKCPPPL 144
Cdd:TIGR02937  12 PLVYRYARRYLGDDAD--AEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLL-EELLDSD 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784 145 PSAEELCSLDEQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNTERHRYFQDLKRLRKYL 214
Cdd:TIGR02937  89 PSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 65-214 8.13e-15

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: 69.13  E-value: 8.13e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  65 PELMAFASKQLGknHADAAEDILQETF-----QRASLKFDlkrsnAEKRSFLYSIVRNLVADYFRRLKGKQLMLSKLNEK 139
Cdd:TIGR02985  12 PKLCAFARRYVK--DEEDAEDIVQDVFlklweNRETLEIS-----ESIKAYLFTIVKNRCLNYLRHKQVEEKYQEELAEI 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1830457784 140 CPPPLPSAEELCSL--DEQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELG-SPRNTERHrYFQDLKRLRKYL 214
Cdd:TIGR02985  85 EERELSEADPEEELeaKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGiSVKTVEYH-ITKALKFLRKEL 161
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 65-218 1.85e-10

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 57.89  E-value: 1.85e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  65 PELMAFASKqLGKNHADAaEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVADYFRRLKGKQLMLSKLNEKC---- 140
Cdd:PRK09652   21 PRVKRLLSR-LTRDPADA-EDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQGRRPPASDVDAEEAedfd 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784 141 ----PPPLPSAEELCSLDEQIALLDKAIEQL--DQQSArrIRLHIFDGKNWREIEEELGSPRNTERHRYFqdlkRLRKYL 214
Cdd:PRK09652   99 ladaLRDISTPENELLSAELEQRVRAAIESLpeELRTA--ITLREIEGLSYEEIAEIMGCPIGTVRSRIF----RAREAL 172


                  ....
gi 1830457784 215 DAQL 218
Cdd:PRK09652  173 RAKL 176
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 66-201 2.89e-10

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 56.71  E-value: 2.89e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  66 ELMAFASKQLGKNHAdaAEDILQETFQRAslkfdLKRSNAEK----RSFLYSIVRNLVADYFRRLKGKQLM-LSKLNEKC 140
Cdd:PRK12527    7 ELVRFLSARLGNRQA--AEDVAHDAYLRV-----LERSSSAQiehpRAFLYRTALNLVVDRHRRHRVRQAEpLEVLDEEE 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1830457784 141 PPPLPSAEELCSLDEQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRN-TERH 201
Cdd:PRK12527   80 RLHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSlVEKH 141
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 78-216 2.92e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 54.70  E-value: 2.92e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  78 NHADAAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVADYFRRLKGKQ-LMLSKLNEKCPPPLPSA--EELCSLD 154
Cdd:PRK12513   48 RDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWRRHGARQaPSLDADEQLHALADDGAapEQQLSLF 127

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1830457784 155 EQIALLDKAIEQL--DQQSARRIRLHifDGKNWREIEEELGSPRNTERHRYFQDLKRLRKYLDA 216
Cdd:PRK12513  128 RDRRRLQAALETLpdEQREVFLLREH--GDLELEEIAELTGVPEETVKSRLRYALQKLRELLAE 189
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 66-193 1.13e-08

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 52.68  E-value: 1.13e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  66 ELMAFASKQLgkNHADAAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVADYFRrlkgkqlmlSKLNEKCPPPLP 145
Cdd:PRK09637   13 QLKAFLHSRV--SNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYR---------KKNRSEELPDDL 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1830457784 146 SAEEL----CSLDEQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELG 193
Cdd:PRK09637   82 LFEDEereeNAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLG 133
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 79-215 2.47e-08

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 51.56  E-value: 2.47e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  79 HADAAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVADYFRRLKGKQLMLSKLNEKCPPPLPSAEELCSLDEQIA 158
Cdd:PRK09638   41 DPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHLRKQKREKLRLQRAKEETLRKEKWEAAIKGAEWSEM 120

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1830457784 159 LldKAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNTERHRYFQDLKRLRKYLD 215
Cdd:PRK09638  121 L--DALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEWG 175
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 67-193 4.30e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 51.10  E-value: 4.30e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  67 LMAFASKQLGKNHAdaAEDILQETFQRASLKFDlKRSNAEKRSFLYSIVRNLVADYFRRLKGKQLMLSKLNEKCPPPLPS 146
Cdd:PRK12525   22 LCKKLSRQLGCPHS--AEDIASETFLQVLALPD-PASIREPRALLTTIARRLMYEGWRRQDLERAYLQSLAEAPEAVQPS 98

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1830457784 147 AEELCSLDEQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELG 193
Cdd:PRK12525   99 PEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLG 145
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 83-214 1.12e-07

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 49.85  E-value: 1.12e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  83 AEDILQETFQRASLKFDLkRSNAEKRSFLYSIVRNLVADYFRRLKGKQLMLSKLNEKCPPPLPSAEELCSLDEQIALLDK 162
Cdd:PRK12523   37 AEDLSQDTFVRLLGRPEL-PTPREPRAFLAAVAKGLMFDHFRRAALEQAYLAELALVPEAEQPSPEEQHLILEDLKAIDR 115

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1830457784 163 AIEQLDQQSARRIRLHIFDGKNWREIEEELGSprnterhryfqDLKRLRKYL 214
Cdd:PRK12523  116 LLGKLSSKARAAFLYNRLDGMGHAEIAERLGV-----------SVSRVRQYL 156
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 83-212 1.91e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 49.16  E-value: 1.91e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  83 AEDILQETFQRASLKFDLKRSNaEKRSFLYSIVRNLVADYFRrlKGKQLMLSKLNEKCPPPLPSAEELCSLDEQIALLDK 162
Cdd:PRK12541   32 AEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFIDWYR--KEKKYKTTTIEEFHLPNVPSTEHEYFIKHEIASWLD 108

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1830457784 163 AIEQLDQQSARRIRLHIFDGKNWREIEEELG---SPRNTERHRYFQDLKRLRK 212
Cdd:PRK12541  109 SLSSLPLERRNVLLLRDYYGFSYKEIAEMTGlslAKVKIELHRGRKETKSIKE 161
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 83-210 1.94e-07

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


Pssm-ID: 274361 [Multi-domain]  Cd Length: 154  Bit Score: 48.99  E-value: 1.94e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  83 AEDILQETFQRASLKFDLKRsNAEKRSFLYSIVRNLVADYFRRLKGKQLMLSK-LNEKCPPPLPSAEELCSLDEQIALLD 161
Cdd:TIGR02950  22 AEDLLQETFLKAYIHLHSFK-DSSIKPWLFRIARNAFIDWYRKDKKIQTIDDDaIGDLEQHPVESPEHHLLIKIEQEEIT 100

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1830457784 162 KAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRN---TERHRYFQDLKRL 210
Cdd:TIGR02950 101 HHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAkvkSNLFRARKELKKL 152
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 71-216 2.02e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 49.29  E-value: 2.02e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  71 ASKQLGknHADAAEDILQETF----QRASlkFDLKRSNAekRSFLYSIVRNLVADYFRRLKGKQLMLSKL------NEKC 140
Cdd:PRK12519   46 ALKILG--NSQEAEDLTQEIFlslwRKSS--YDPKRGSL--SSYLLTLTRSRAIDRLRSRRSRQRLLERWqqellgEASE 119

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1830457784 141 PPPLPSAeelcSLDEQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNTERHRYFQDLKRLRKYLDA 216
Cdd:PRK12519  120 DTPLEQA----SLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQD 191
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 65-214 2.46e-07

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


Pssm-ID: 274379 [Multi-domain]  Cd Length: 159  Bit Score: 48.47  E-value: 2.46e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  65 PELMAFASKQLGknHADAAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVADYFRRLKGKQLMLSKLNEKCPPPL 144
Cdd:TIGR02989  12 RALRAFVRSLVA--DRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLGRDRLVFDDDLLEALAAE 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784 145 PSAEELCSLDEQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNterhRYFQDLKRLRKYL 214
Cdd:TIGR02989  90 AEPTEAERLSDDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVN----AVYKALQRIRVSL 155
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 59-127 1.05e-06

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: 44.89  E-value: 1.05e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1830457784  59 FFGNLGPELMAFASKQLGKNHAdaAEDILQETFQRASL---KFDLKRSNAEkRSFLYSIVRNLVADYFRRLK 127
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGAD--AEDLVQEGFLGLWRaieRFDPERGVSF-STWLYTIIRNAIIDYLRKQR 69
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
83-214 2.31e-06

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 46.23  E-value: 2.31e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  83 AEDILQETFQRA-SLKFDLKRSNAEKRSFLYSIVRNLVADYFRRLKgkqlmlSKLNEKCPPPLPSAEELCSlDEQIALLD 161
Cdd:PRK09645   36 AEDVVQETLLRAwQHPEVLADTGRSARAWLFTVARNLVIDERRSAR------ARPVEGGDDVLGVPEQSAP-DEVDRALD 108

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1830457784 162 K-----AIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNTERHRYFQDLKRLRKYL 214
Cdd:PRK09645  109 RllvadALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALRLAL 166
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 52-193 4.36e-06

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 45.19  E-value: 4.36e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  52 SSDPFLSFFGNLGPELMAFASKQLGKnhADAAEDILQETFQRAsLKFDLKRSNAEKRSFLYSIVRNLVADYFRRLKGKQL 131
Cdd:PRK09651    8 ASLTFESLYGTHHGWLKSWLTRKLQS--AFDADDIAQDTFLRV-MVSETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKA 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1830457784 132 MLSKLNEKCPPPLPSAEELCSLDEQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELG 193
Cdd:PRK09651   85 YLEMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLG 146
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 54-217 5.19e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 45.31  E-value: 5.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  54 DPFLSFFGNLGPELMAFASKQLGKNHAdaAEDILQET----FQRASLkFDLKRSNAEkrSFLYSIVRNLVADYFRRLKGK 129
Cdd:PRK12531   27 QAFALVFSYYAPKLKQFAMKHVGNEQV--AMEMVQETmstvWQKAHL-FDGQKSALS--TWIYTIIRNLCFDLLRKQKGK 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784 130 QLMLSKLN----EKCPPPLPS--AEELCSLDEQIAlldKAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNTERHRY 203
Cdd:PRK12531  102 DLHIHADDiwpsDYYPPDLVDhySPEQDMLKEQVM---KFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRL 178

                         170
                  ....*....|....
gi 1830457784 204 FQDLKRLRKYLDAQ 217
Cdd:PRK12531  179 RLAVEKLRHSMDAE 192
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 83-217 6.46e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 45.06  E-value: 6.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  83 AEDILQETFQRASLKFD-LKRSNAEKrSFLYSIVRNLVAdyfRRLKGKQLMLSKLNEKcpppLPSAEELCSLDEQIA--L 159
Cdd:PRK12517   50 AEDLVQETFLRAWRSLDsLKDEKAAK-AWLITILRRENA---RRFERKQFDLVDIEDD----SIEDDASHSSEEEMEqeW 121

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1830457784 160 LDKAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNTERHRYFQDLKRLRKYLDAQ 217
Cdd:PRK12517  122 LRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKP 179
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 71-214 1.01e-05

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 44.30  E-value: 1.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  71 ASKQLGKNHAdaAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVADYFRR----------LKGKQ--LMLSKLNE 138
Cdd:PRK09641   35 CYRMLGNRHE--AEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRKrkpdyyldaeVAGTEglTMYSQLAA 112

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1830457784 139 KCPPPlpsAEELCSLdEQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNTERHRYFQDLKRLRKYL 214
Cdd:PRK09641  113 DDALP---EEQVVSL-ELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREALRKQL 184
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 83-211 1.21e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 44.38  E-value: 1.21e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  83 AEDILQETF---QRASLKFDLKRSNAekRSFLYSIVRNLVADYFRRlKGKQLMLSKLNEKCPPPLPSAEELCSLDEQIAL 159
Cdd:PRK12537   50 AEDIVHDAFikiWTGAASFDPARGSA--RGWIYSVTRHLALNVLRD-TRREVVLDDDAEETAQTLHEIIDDFDLWANSGK 126

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1830457784 160 LDKAIEQLDQQSARRIrLHIF-DGKNWREIEEELGSPRNTERHRYFQDLKRLR 211
Cdd:PRK12537  127 IHRCLEQLEPARRNCI-LHAYvDGCSHAEIAQRLGAPLGTVKAWIKRSLKALR 178
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 45-215 2.28e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 43.51  E-value: 2.28e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  45 FIATLGDSSDPFLSFFGNLGPELMAFASKQLGKNhaDAAEDILQETFQ---RASLKFDLKRsnAEKRSFLYSIVRNLVAD 121
Cdd:PRK12534   16 LTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQR--AEAEEVLQDVFTliwHKAGQFDPSR--ARGLTWLAMIARNKAID 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784 122 YFRRlKGKQLMLSKLNEKCPPPLPSAEELCSLDEQIA--LLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNTE 199
Cdd:PRK12534   92 HLRA-NAPQRRNVALDDAGELRAADASPLERTERASTrrRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTV 170

                         170
                  ....*....|....*.
gi 1830457784 200 RHRYFQDLKRLRKYLD 215
Cdd:PRK12534  171 KSWIRRGLAKLKACLE 186
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 78-214 3.05e-05

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 43.20  E-value: 3.05e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  78 NHADAAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVADYFRRLKGKQLMLSKLN-EKCPPPLPSAEELCSLDEQ 156
Cdd:PRK09415   38 KNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSWHNKKVIVTEDIfTYMESQKESVEEEVIQNAE 117

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1830457784 157 IALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNTERHRYFQDLKRLRKYL 214
Cdd:PRK09415  118 DERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 84-217 4.93e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 42.40  E-value: 4.93e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  84 EDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVADYFRRL-KGKQLMLSKLNEKCPPPLPSAEELCSLDEQiALLDK 162
Cdd:PRK12518   38 DDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRQFaQRPSRIQDDSLNDQPSRPSDTPDLMQLHYQ-DLVQQ 116

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1830457784 163 AIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNTERHRYFQDLKRLRKYLDAQ 217
Cdd:PRK12518  117 GLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQ 171
Sig70_famx1 TIGR02943
RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of ...
 63-140 9.91e-05

RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.


Pssm-ID: 274359 [Multi-domain]  Cd Length: 188  Bit Score: 41.67  E-value: 9.91e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1830457784  63 LGPELMAFASKQLgkNHADAAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVADYFRRlKGKQLMLSKLNEKC 140
Cdd:TIGR02943  11 LRRDLLRFARLQL--RDRDLAEDAVQETLLAALSHRDSFAGRSALKTWLFAILKNKIIDALRA-KGREVKVSDLDDEL 85
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 83-201 1.39e-04

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 40.82  E-value: 1.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  83 AEDILQETFQR---ASLKFDLKrsnaEKRSFLYSIVRNLVADYFRRlkgkQLMLSKLNE------KCPPPLPSAEELCSL 153
Cdd:PRK07037   25 AEDVVQDAFVKlveAPNQDAVK----QPVAYLFRIVRNLAIDHYRR----QALENKYHGdeedglDVPSPEASPEAALIN 96

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1830457784 154 DEQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELG-SP-------RNTERH 201
Cdd:PRK07037   97 RDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGvSPtlvnfmiRDALVH 152
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 81-214 3.61e-04

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 39.55  E-value: 3.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  81 DAAEDILQETFQRAsLKFDLKRSNAEKrSFLYSIVRNLVADYFR---RLKGKQLMLSKLNEKcpPPLPSAEELCSLDEQI 157
Cdd:PRK09639   28 TQAEDLAQEVFLRL-YRSDFKGIENEK-GWLIKSARNVAYNYLRsekRRRARILGEFQWQEV--DNEPSPEEIWIRKEEI 103

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784 158 ALLDKAIEQLDQQSaRRIRLHIFDGKNWREIEEELG---SPRNTERHRyfqDLKRLRKYL 214
Cdd:PRK09639  104 TKVQEVLAKMTERD-RTVLLLRFSGYSYKEIAEALGikeSSVGTTLAR---AKKKFRKIY 159
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 81-201 6.87e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 39.06  E-value: 6.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  81 DAAEDILQETFQRASLKFDLKRSnAEKRSFLYSIVRNLVADYFRRLKGKQLMLSKLNEKCPPPLPSAEELCSLDEQIALL 160
Cdd:PRK12528   29 QSAADLAQDTFVKVLVARETAQI-IEPRAFLTTIAKRVLCNHYRRQDLERAYLEALAQLPERVAPSEEERAIILETLVEL 107

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1830457784 161 DKAIEQLDQQSARRIRLHIFDGKNWREIEEELG-SPRNTERH 201
Cdd:PRK12528  108 DQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGiSLATVKRY 149
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 80-129 7.42e-04

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 39.25  E-value: 7.42e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1830457784  80 ADAAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVADYFRRLKGK 129
Cdd:PRK09649   47 VGSADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVADHIRHVRSR 96
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 65-214 1.87e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 37.99  E-value: 1.87e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  65 PELMAFASKQLgKNHADAAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVADYFRRlKGKQLMLSKL-------- 136
Cdd:PRK12532   16 KLLLHFARLQL-PDHPDLAEDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQ-IGRQRKVFTLlddellde 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784 137 -------------NEKCPPPLPSAEELCSLDEQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELG-SPRNterhr 202
Cdd:PRK12532   94 afeshfsqnghwtPEGQPQHWNTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGiSTSN----- 168

                         170
                  ....*....|..
gi 1830457784 203 YFQDLKRLRKYL 214
Cdd:PRK12532  169 YHTIMHRARESL 180
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 74-217 2.79e-03

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 37.46  E-value: 2.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  74 QLGKNHADAaEDILQETFQRA--SLKfdlkrsNAEKRSF---LYSIVRNLVADYFRRlKGKQLM--LSKLNEKCPPPLPS 146
Cdd:PRK09647   47 RLSGNQHDA-EDLTQETFIRVfrSLQ------NYQPGTFegwLHRITTNLFLDMVRR-RARIRMeaLPEDYDRVPGDEPN 118

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1830457784 147 AEELCSLDEQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNTERHRYFQDLKRLRKYLDAQ 217
Cdd:PRK09647  119 PEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAH 189
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 65-125 2.92e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 37.25  E-value: 2.92e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1830457784  65 PELMAFASKQLGKnhADAAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLV-ADYFRR 125
Cdd:PRK12540   16 PSLRAFAISLSGN--GDRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFrSDYRKR 75
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 75-214 2.97e-03

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 37.17  E-value: 2.97e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  75 LGKNHAdAAEDILQETFQRASLKFdLKRSNAEKRSFLYSIVRNLVADYFRRLKGKQLMLSKLNEKCppPLPSAEELCSLD 154
Cdd:PRK09644   21 LTKSHH-AAEDLLQETFYRAYIYL-EDYDNQKVKPWLFKVAYHTFIDFVRKEKKVSFVGTDEIEAI--QAESTEEYVVAK 96

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784 155 EQIALLDKAIEQLDQQSARRIRLHIFDGKNWREIEEELGSPRNTERHRYFQDLKRLRKYL 214
Cdd:PRK09644   97 NSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 43-133 3.48e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 37.09  E-value: 3.48e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  43 YQFIATLGDSSD--PFLSFFGNLGPELMAFASKQLGKNhaDAAEDILQETFQRASLKFDLkrSNAEK---RSFLYSIVRN 117
Cdd:PRK12526   25 SQWLILVAISRDkqAFTHLFQFFAPKIKRFGIKQLGNE--AQANELVQETMSNVWRKAHL--YNGDKgaaTTWVYTVMRN 100

                          90
                  ....*....|....*.
gi 1830457784 118 LVADYFRRLKGKQLML 133
Cdd:PRK12526  101 AAFDMLRKIKAKKEQN 116
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 65-217 4.44e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 36.87  E-value: 4.44e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  65 PELMAFASKQLGKNhaDAAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVADYFRRlKGKQLMlsklnekcPPPL 144
Cdd:PRK12516   21 PSLRAFAVSLIGRH--DRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRK-RGREVQ--------DTDG 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784 145 PSAEELCSLDEQIALLD-----KAIEQL--DQQSArrIRLHIFDGKNWREIEEELGSPRNTERHRYFQDLKRLRKYLDAQ 217
Cdd:PRK12516   90 MFTEQLAVHPSQYGTLDlqdfrAALDQLpdDQREA--IILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIE 167
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 83-193 5.13e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 36.45  E-value: 5.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1830457784  83 AEDILQETFQRASLKFDLKRSNA--EKRSFLYSIVRNLVADYFRRLKGKQLMLSKLNEKCPPPLPSAEELCSLDEQIALL 160
Cdd:PRK12529   42 ADDLAHDIFLRILASRDGGQREAirQPRAYLARIANCVLVSWRRRQSLELAWLEALATLPEPLHPSPEQQSVILETLHEI 121

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1830457784 161 DKAIEQLDQQSARRIRLHIFDGKNWREIEEELG 193
Cdd:PRK12529  122 DALLDTLRPRVKQAFLMATLDGMKQKDIAQALD 154
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 66-142 8.96e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 35.90  E-value: 8.96e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1830457784  66 ELMAFASKQLgkNHADAAEDILQETFQRASLKFDLKRSNAEKRSFLYSIVRNLVADYFRRlKGKQLMLSKLNEKCPP 142
Cdd:PRK12530   19 QMLKFATLQL--KDADLAEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIRY-RKRFVNESELIEEDSP 92
 
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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