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Conserved domains on  [gi|544955230|ref|WP_021360617|]
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RNA polymerase sigma factor [Clostridioides difficile]

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]; ...
 2-168 5.52e-45

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: 146.29  E-value: 5.52e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   2 NDARIISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKD 81
Cdd:COG1595    3 SDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAID 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  82 FWKKKQ--PIYLESLDKEISN------QELSDIENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKY 153
Cdd:COG1595   83 HLRKRRrrRELLDELAEELPDeaadpeEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKS 162

                        170
                 ....*....|....*
gi 544955230 154 RMSRALKKLELYLEG 168
Cdd:COG1595  163 RLSRARKKLREALEE 177
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 2-168 5.52e-45

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: 146.29  E-value: 5.52e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   2 NDARIISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKD 81
Cdd:COG1595    3 SDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAID 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  82 FWKKKQ--PIYLESLDKEISN------QELSDIENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKY 153
Cdd:COG1595   83 HLRKRRrrRELLDELAEELPDeaadpeEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKS 162

                        170
                 ....*....|....*
gi 544955230 154 RMSRALKKLELYLEG 168
Cdd:COG1595  163 RLSRARKKLREALEE 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 16-166 6.51e-33

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 114.75  E-value: 6.51e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   16 ELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDFWKKKQ--PIYLES 93
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRrlRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 544955230   94 LDKEISN-----QELSDIENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKLELYL 166
Cdd:TIGR02937  81 LEELLDSdpspeEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 3-161 7.84e-26

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 97.07  E-value: 7.84e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   3 DARIISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDF 82
Cdd:PRK09641   5 IKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDR 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  83 WKKKQPIYleSLDKEIS------------------NQELSDIENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIM 144
Cdd:PRK09641  85 LRKRKPDY--YLDAEVAgtegltmysqlaaddalpEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEIL 162

                        170       180
                 ....*....|....*....|
gi 544955230 145 ESSVSVTKYRMSR---ALKK 161
Cdd:PRK09641 163 DLPVGTVKTRIHRgreALRK 182
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 21-87 5.32e-13

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: 60.68  E-value: 5.32e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   21 LIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENY---KHYgKFENYLYVIAKNKCKDFWKKKQ 87
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFdpeRGV-SFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 112-162 8.39e-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: 51.72  E-value: 8.39e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 544955230 112 IKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKL 162
Cdd:cd06171    4 LEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 2-168 5.52e-45

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: 146.29  E-value: 5.52e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   2 NDARIISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKD 81
Cdd:COG1595    3 SDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAID 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  82 FWKKKQ--PIYLESLDKEISN------QELSDIENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKY 153
Cdd:COG1595   83 HLRKRRrrRELLDELAEELPDeaadpeEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKS 162

                        170
                 ....*....|....*
gi 544955230 154 RMSRALKKLELYLEG 168
Cdd:COG1595  163 RLSRARKKLREALEE 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 16-166 6.51e-33

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 114.75  E-value: 6.51e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   16 ELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDFWKKKQ--PIYLES 93
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRrlRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 544955230   94 LDKEISN-----QELSDIENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKLELYL 166
Cdd:TIGR02937  81 LEELLDSdpspeEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 3-161 7.84e-26

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 97.07  E-value: 7.84e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   3 DARIISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDF 82
Cdd:PRK09641   5 IKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDR 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  83 WKKKQPIYleSLDKEIS------------------NQELSDIENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIM 144
Cdd:PRK09641  85 LRKRKPDY--YLDAEVAgtegltmysqlaaddalpEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEIL 162

                        170       180
                 ....*....|....*....|
gi 544955230 145 ESSVSVTKYRMSR---ALKK 161
Cdd:PRK09641 163 DLPVGTVKTRIHRgreALRK 182
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 16-162 9.49e-25

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: 93.78  E-value: 9.49e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   16 ELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDFWKKKQPI--YLES 93
Cdd:TIGR02985   1 EAFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEekYQEE 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 544955230   94 L-DKEISNQELSDIENKMFIKE-------ALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKL 162
Cdd:TIGR02985  81 LaEIEERELSEADPEEELEAKEleeiieeAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFL 157
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 3-162 2.55e-24

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 93.60  E-value: 2.55e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   3 DARIISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDF 82
Cdd:PRK12513  13 DEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDH 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  83 WKK------KQPIYLESL-----DKEISNQELSDIENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVT 151
Cdd:PRK12513  93 WRRhgarqaPSLDADEQLhaladDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETV 172

                        170
                 ....*....|.
gi 544955230 152 KYRMSRALKKL 162
Cdd:PRK12513 173 KSRLRYALQKL 183
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 13-168 4.25e-22

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 87.33  E-value: 4.25e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  13 GKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDFWKKKQP--IY 90
Cdd:PRK11924  10 GDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRRekAV 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  91 LES-LDKEISNQELSDIENKMF-------IKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKL 162
Cdd:PRK11924  90 LSDdALEPEFAETAETPEAALLakddlarIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLL 169


                 ....*.
gi 544955230 163 ELYLEG 168
Cdd:PRK11924 170 RECLEA 175
Sig70_famx3 TIGR02954
RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of ...
 1-168 6.76e-21

RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.


Pssm-ID: 213752 [Multi-domain]  Cd Length: 169  Bit Score: 83.99  E-value: 6.76e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230    1 MNDARIISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCK 80
Cdd:TIGR02954   1 MNDEELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPKYFNTWLTRILINECI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   81 DFWKKKQPIYLESLDKEISNQELS-DIENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRAL 159
Cdd:TIGR02954  81 DLLKKKKKVIPFDPNTSIEKGECEtHADSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRAL 160


                  ....*....
gi 544955230  160 KKLELYLEG 168
Cdd:TIGR02954 161 KKLKKRLEE 169
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 14-169 3.38e-20

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 82.49  E-value: 3.38e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  14 KKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDF-----WKKKQP 88
Cdd:PRK09415  14 KEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYlkswhNKKVIV 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  89 -----IYLESlDKEISNQELSDIENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKLE 163
Cdd:PRK09415  94 tedifTYMES-QKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLK 172


                 ....*.
gi 544955230 164 LYLEGG 169
Cdd:PRK09415 173 KGLEEE 178
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 7-168 7.87e-20

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 81.39  E-value: 7.87e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   7 ISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDFW--K 84
Cdd:PRK09652   1 VERVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLrkQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  85 KKQPIYLESLDKEISNQELSDI-------ENKMF-------IKEALTKLPElEF-EVIILRYYHDLKFKDIAKIMESSVS 149
Cdd:PRK09652  81 GRRPPASDVDAEEAEDFDLADAlrdistpENELLsaeleqrVRAAIESLPE-ELrTAITLREIEGLSYEEIAEIMGCPIG 159

                        170
                 ....*....|....*....
gi 544955230 150 VTKYRMSRALKKLELYLEG 168
Cdd:PRK09652 160 TVRSRIFRAREALRAKLQP 178
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 1-162 9.69e-20

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 81.22  E-value: 9.69e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   1 MNDARIISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCK 80
Cdd:PRK09638   3 MDEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYK 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  81 DFWKKKQPIylESLDKEISNQELSDIENKMFIK--------EALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTK 152
Cdd:PRK09638  83 DHLRKQKRE--KLRLQRAKEETLRKEKWEAAIKgaewsemlDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVK 160

                        170
                 ....*....|
gi 544955230 153 YRMSRALKKL 162
Cdd:PRK09638 161 SRVHHGIKQL 170
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 17-162 3.87e-19

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 79.98  E-value: 3.87e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  17 LFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKC-----KDFWKKKQ--PI 89
Cdd:PRK09640  27 AYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECitqyrKERRKRRLmdAL 106

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 544955230  90 YLESLDkEISNQELSDIENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKL 162
Cdd:PRK09640 107 SLDPLE-EASEEKAPKPEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKL 178
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 15-168 6.25e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 71.05  E-value: 6.25e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  15 KELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDFWKKKQ---PIYL 91
Cdd:PRK12522   2 EEKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKKKrwkDRIL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  92 ESLDKE------------ISNQELSDIENKMfIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRAL 159
Cdd:PRK12522  82 DLFHKEdggeiefaddvnISEEFIQKVEAEM-IREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAK 160


                 ....*....
gi 544955230 160 KKLELYLEG 168
Cdd:PRK12522 161 KQMREHLEG 169
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 16-169 3.58e-14

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 66.13  E-value: 3.58e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  16 ELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINN----IENYKhygkfeNYLYVIAKNKCKDFWKKKQPIYL 91
Cdd:PRK09639   3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRSdfkgIENEK------GWLIKSARNVAYNYLRSEKRRRA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  92 ESLDK----EISNQELSD-----IENKMFIKEALTKLPELEFEVIILRyYHDLKFKDIAKIM---ESSVSVTKYRMSRAL 159
Cdd:PRK09639  77 RILGEfqwqEVDNEPSPEeiwirKEEITKVQEVLAKMTERDRTVLLLR-FSGYSYKEIAEALgikESSVGTTLARAKKKF 155

                        170
                 ....*....|
gi 544955230 160 KKLELYLEGG 169
Cdd:PRK09639 156 RKIYEQMEEE 165
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 3-158 8.88e-14

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 65.98  E-value: 8.88e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   3 DARIISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDF 82
Cdd:PRK11923   7 DQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNH 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  83 W----KKKQPIYLESLDKEI--SNQELSDIEN----------KMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMES 146
Cdd:PRK11923  87 LvsrgRRPPDSDVSSEDAEFydGDHALKDIESperallrdeiEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQC 166

                        170
                 ....*....|..
gi 544955230 147 SVSVTKYRMSRA 158
Cdd:PRK11923 167 PVGTVRSRIFRA 178
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 10-162 4.76e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 63.60  E-value: 4.76e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  10 IKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDF----WK- 84
Cdd:PRK12543   1 MLSGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSWrrkrWRr 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  85 ----KKQPIYLESLDKEISNQELSDIENKMFIkEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALK 160
Cdd:PRK12543  81 frifEKAEEQRKPVSIDFSEDVLSKESNQELI-ELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALK 159


                 ..
gi 544955230 161 KL 162
Cdd:PRK12543 160 KL 161
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 21-87 5.32e-13

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: 60.68  E-value: 5.32e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   21 LIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENY---KHYgKFENYLYVIAKNKCKDFWKKKQ 87
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFdpeRGV-SFSTWLYTIIRNAIIDYLRKQR 69
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 3-162 6.72e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 64.11  E-value: 6.72e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   3 DARIISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKH-YGKFENYLYVIAKNKCKD 81
Cdd:PRK12538  50 DEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHgRAKFSTWLYRVVSNRCID 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  82 FWKKKQPiylESLD-------------KEISNQELSDIenkmfIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSV 148
Cdd:PRK12538 130 LRRKPRT---ENVDavpevadgkpdavSVIERNELSDL-----LEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTV 201

                        170
                 ....*....|....
gi 544955230 149 SVTKYRMSRALKKL 162
Cdd:PRK12538 202 AAVESLLKRGRQQL 215
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 18-170 4.71e-12

RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.


Pssm-ID: 132028 [Multi-domain]  Cd Length: 162  Bit Score: 60.48  E-value: 4.71e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   18 FDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDFWKKKQPiyLESLDKE 97
Cdd:TIGR02983   8 FTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRRRRL--LELPTRE 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 544955230   98 ISNQELSD----IENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKLELYLEGGK 170
Cdd:TIGR02983  86 LPDAAAPDpapdVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELLEEPT 162
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 3-168 2.78e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 59.30  E-value: 2.78e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   3 DARIISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNienyKHY----GKFENYLYVIAKNK 78
Cdd:PRK12519  16 DAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK----SSYdpkrGSLSSYLLTLTRSR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  79 CKD---FWKKKQPIyLESLDKEISN--------QELSDIENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESS 147
Cdd:PRK12519  92 AIDrlrSRRSRQRL-LERWQQELLGeasedtplEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIP 170

                        170       180
                 ....*....|....*....|.
gi 544955230 148 VSVTKYRMSRALKKLELYLEG 168
Cdd:PRK12519 171 LGTVKARARQGLLKLRELLQD 191
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 112-162 2.96e-11

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 55.54  E-value: 2.96e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 544955230  112 IKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKL 162
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 3-168 1.23e-10

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 57.35  E-value: 1.23e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   3 DARIISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYG-KFENYLYVIAKNKCKD 81
Cdd:PRK05602   7 DEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGEaRFDTWLHRVVLNLCYD 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  82 FWKKKQPIYLESLDKEISNQELSD-----IENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMS 156
Cdd:PRK05602  87 RLRRRREVPVEDAPDVPDPAPGPDagleaRQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLA 166

                        170
                 ....*....|..
gi 544955230 157 RALKKLELYLEG 168
Cdd:PRK05602 167 RGRRALRAQLAD 178
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 6-167 2.18e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 56.26  E-value: 2.18e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   6 IISQIKAGKKELFDTLIKKYYDSI----YCYCYRHVdnkmtAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKD 81
Cdd:PRK12518   1 LILRCQRGDRQSFRQLYRRYQQKVrstlYQLCGREL-----LDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATD 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  82 FWKK--KQPIYLESLDKEISNQELSDIENKM------FIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKY 153
Cdd:PRK12518  76 ARRQfaQRPSRIQDDSLNDQPSRPSDTPDLMqlhyqdLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKS 155

                        170
                 ....*....|....
gi 544955230 154 RMSRALKKLELYLE 167
Cdd:PRK12518 156 RLFYARRQLRKFLQ 169
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 19-167 2.27e-10

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 56.72  E-value: 2.27e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  19 DTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHyGKFENYLYVIAKNKCKDFWKKKQPIYLESL---- 94
Cdd:PRK09647  31 EELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP-GTFEGWLHRITTNLFLDMVRRRARIRMEALpedy 109

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 544955230  95 ----DKEISNQELSDIEN-KMFIKEALTKLPElEFEV-IILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKLELYLE 167
Cdd:PRK09647 110 drvpGDEPNPEQIYHDARlDPDLQAALDSLPP-EFRAaVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 112-162 8.39e-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: 51.72  E-value: 8.39e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 544955230 112 IKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKL 162
Cdd:cd06171    4 LEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 32-168 1.01e-09

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 54.61  E-value: 1.01e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  32 YCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDFWKKKQP--------IYLESLDKEISNQEL 103
Cdd:PRK09637  17 FLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRKKNRseelpddlLFEDEEREENAKKEL 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 544955230 104 SDIenkmfIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKLELYLEG 168
Cdd:PRK09637  97 APC-----LRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 3-162 1.19e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 54.74  E-value: 1.19e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   3 DARIISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVinnienYKHYGKFE------NYLYVIAK 76
Cdd:PRK12515   9 DEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDV------WRQAGQFEgrsqvsTWLLSIAR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  77 NKCKDFWKKKQPiylESLDKEISNQ--------ELS-DIENKMFI-KEALTKLPELEFEVIILRYYHDLKFKDIAKIMES 146
Cdd:PRK12515  83 FKALSALRRRKH---EEIDDEAAAAiedgadtpEVAlQKSDTSAAlRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGI 159

                        170
                 ....*....|....*.
gi 544955230 147 SVSVTKYRMSRALKKL 162
Cdd:PRK12515 160 PESTVKTRMFYARKKL 175
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 19-163 3.96e-09

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 52.96  E-value: 3.96e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  19 DTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHyGKFENYLYVIAKNKCKDFWKKKQPIY------LE 92
Cdd:PRK09644   4 EEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDN-QKVKPWLFKVAYHTFIDFVRKEKKVSfvgtdeIE 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 544955230  93 SLDKEISNQELSDIENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKLE 163
Cdd:PRK09644  83 AIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLK 153
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 90-168 1.72e-08

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: 51.75  E-value: 1.72e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  90 YLESLDKEISNQELSDIENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIM---ESSVSvtkyRM-SRALKKLELY 165
Cdd:COG1191  158 LLDLLESGDPEEELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLgvsESRVS----RLhKKALARLREY 233


                 ...
gi 544955230 166 LEG 168
Cdd:COG1191  234 LKE 236
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 1-162 3.31e-08

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 50.71  E-value: 3.31e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   1 MNDARIISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQ---DVFVTVINNIENYK-HYGKFENYLYVIAK 76
Cdd:PRK06811   3 INEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEEcvnDIFLSIWNNIDKFDeEKGSFKKWIAAISK 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  77 NKCKDFWKKKQPIY-LESLDKEISN------QELSDIENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVS 149
Cdd:PRK06811  83 YKAIDYKRKLTKNNeIDSIDEFILIseesieNEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRS 162

                        170
                 ....*....|...
gi 544955230 150 VTKYRMSRALKKL 162
Cdd:PRK06811 163 AIDNRLSRGRKKL 175
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 115-162 5.58e-08

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: 47.04  E-value: 5.58e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 544955230  115 ALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKL 162
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKL 48
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 7-171 9.12e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 49.54  E-value: 9.12e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   7 ISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYK-HYGKFENYLYVIAKNKCKDFWKK 85
Cdd:PRK12531  18 MEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDgQKSALSTWIYTIIRNLCFDLLRK 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  86 KQ--PIYLESLDKEISNQELSDI------ENKMfIKEALTK----LPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKY 153
Cdd:PRK12531  98 QKgkDLHIHADDIWPSDYYPPDLvdhyspEQDM-LKEQVMKfldrLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKS 176

                        170
                 ....*....|....*...
gi 544955230 154 RMSRALKKLELYLEGGKL 171
Cdd:PRK12531 177 RLRLAVEKLRHSMDAESL 194
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 43-168 1.58e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 48.81  E-value: 1.58e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  43 AQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCK-DFWKKKQPI------YLESLDKEISNQELSDIENkmfIKEA 115
Cdd:PRK12540  32 ADDLVQETLLRALANIDSFQPGSNLPAWLFTILRNLFRsDYRKRRREVedadgsYAKTLKSQPGQNAHLEFEE---FRAA 108

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 544955230 116 LTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKLE--LYLEG 168
Cdd:PRK12540 109 LDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSalLYVDG 163
PRK12530 PRK12530
RNA polymerase sigma factor; Provisional
 43-154 1.87e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237128 [Multi-domain]  Cd Length: 189  Bit Score: 48.61  E-value: 1.87e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  43 AQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDFWKKKQPIYLES-LDKEISN-----------------QELS 104
Cdd:PRK12530  34 AEDVVQEALVSAYKNADSFKGQSALKTWIFAILKNKIIDLIRYRKRFVNESeLIEEDSPnsffdekghwkpeyyepSEWQ 113

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230 105 DIENKMFIKE-------ALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVS---VTKYR 154
Cdd:PRK12530 114 EVENTVYKEEfwlifeaCLNHLPAQQARVFMMREYLELSSEQICQECDISTSnlhVLLYR 173
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 18-162 7.95e-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: 46.55  E-value: 7.95e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   18 FDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDFWKKKQ-------PIY 90
Cdd:TIGR02989   3 FVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLGrdrlvfdDDL 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 544955230   91 LESLDKEISNQELSDIENKM-FIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKL 162
Cdd:TIGR02989  83 LEALAAEAEPTEAERLSDDRqALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSL 155
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 91-156 4.39e-06

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 45.45  E-value: 4.39e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 544955230  91 LESLDKEISNQELSDIENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMEssvsVTKYRMS 156
Cdd:PRK06288 185 LESPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYYYEDLTLKEIGKVLG----VTESRIS 246
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 5-167 5.12e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 44.66  E-value: 5.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   5 RIISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVinnienYKHYGKFE-------NYLYVIAKN 77
Cdd:PRK12534  14 RLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLI------WHKAGQFDpsrarglTWLAMIARN 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  78 KCKDFWKKKQPIYLE-SLD-----KEISNQELSDIENKMFIKEALTKLPELE---FEVIILRYYHDLKFKDIAKIMESSV 148
Cdd:PRK12534  88 KAIDHLRANAPQRRNvALDdagelRAADASPLERTERASTRRRIDHCLAELEpprSELIRTAFFEGITYEELAARTDTPI 167

                        170
                 ....*....|....*....
gi 544955230 149 SVTKYRMSRALKKLELYLE 167
Cdd:PRK12534 168 GTVKSWIRRGLAKLKACLE 186
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 14-163 5.90e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 44.16  E-value: 5.90e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  14 KKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYgKFENYLYVIAKNKCKDfWKKKQPIYLES 93
Cdd:PRK12541   3 RKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE-EIRPWLFTIAYNAFID-WYRKEKKYKTT 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 544955230  94 LDKEISNQELSDIENKMFIK-------EALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKLE 163
Cdd:PRK12541  81 TIEEFHLPNVPSTEHEYFIKheiaswlDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETK 157
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 16-168 1.57e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 43.12  E-value: 1.57e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  16 ELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYG--KFENYLYVIAKNKCKDFWK--KKQPIYL 91
Cdd:PRK12542   9 EKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNtqELKRYILRVAKNKAIDSYRknKRHETFL 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  92 ESLDKEISNQELSDIE-------NKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKLEL 164
Cdd:PRK12542  89 EEYERESIEAVDENIEewekrkmSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRVQN 168


                 ....
gi 544955230 165 YLEG 168
Cdd:PRK12542 169 MIGG 172
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
42-162 2.34e-05

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 42.65  E-value: 2.34e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  42 TAQDLTQDVFVTVINNIENYKHYGK-FENYLYVIAKNKCKDFWK-----KKQPIylESLDKEISNQE-------LSDIEN 108
Cdd:PRK09648  54 SADDVAQEVCLAVITALPRYRDQGRpFLAFVYGIAAHKVADAHRaagrdKAVPT--EEVPERPSDDAgpeeralRSESSN 131

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 544955230 109 KMfiKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKL 162
Cdd:PRK09648 132 RM--RELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALARL 183
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
88-168 5.46e-05

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 41.88  E-value: 5.46e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  88 PIYLesLDKeISNQELSDIENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIME-SSVSVTKYRmSRALKKLELYL 166
Cdd:PRK05572 175 PITL--LDQ-IADQSEEDWFDKIALKEAIRELDERERLIVYLRYFKDKTQSEVAKRLGiSQVQVSRLE-KKILKQMKEKL 250


                 ..
gi 544955230 167 EG 168
Cdd:PRK05572 251 DE 252
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 91-162 1.03e-04

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 40.99  E-value: 1.03e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 544955230  91 LESLDKEISNQELSDIENKMF---IKEALTKLPELEFEVIILRYYHDLKFKDIAKIMEssvsVTKYRMS----RALKKL 162
Cdd:PRK06986 154 ILVTEDHQDEDPLQQLEDEELreaLVEAIESLPEREQLVLSLYYQEELNLKEIGAVLG----VSESRVSqihsQAIKRL 228
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 107-162 1.34e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 40.87  E-value: 1.34e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 544955230 107 ENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKL 162
Cdd:PRK12533 123 EDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRRL 178
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 1-163 5.18e-04

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 38.74  E-value: 5.18e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   1 MNDARIISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENY-KHYGKFENYLYVIAKNKC 79
Cdd:PRK13919   8 LSDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFdPRRGSARAWLLALAHHAA 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  80 KDFWKKK--QPIYLESLDKEISNQELS----DIE---NKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSV 150
Cdd:PRK13919  88 VDHVRRRaaRPQPLEPDEREPEAFDLPgpglDEEghlDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGT 167

                        170
                 ....*....|...
gi 544955230 151 TKYRMSRALKKLE 163
Cdd:PRK13919 168 LKTRARRALSRLK 180
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 13-162 1.21e-03

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 37.71  E-value: 1.21e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  13 GKKELFDTLIKKYYDSIYCYCyRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDFWKKKQ--PIY 90
Cdd:PRK09649  21 GNGRALEAFIKATQQDVWRFV-AYLSDVGSADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHVVADHIRHVRsrPRT 99

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 544955230  91 LESLDKEI---SNQELSDIENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKL 162
Cdd:PRK09649 100 TRGARPEHlidGDRHARGFEDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDAL 174
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 112-167 1.30e-03

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 37.26  E-value: 1.30e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 544955230 112 IKEALTKLPELEFEVIILRYYHDLKFKDIAKIM---ESSVsvtKYRMSRALKKLELYLE 167
Cdd:PRK09047 100 IEEAIQKLPARQREAFLLRYWEDMDVAETAAAMgcsEGSV---KTHCSRATHALAKALE 155
PRK09642 PRK09642
RNA polymerase sigma factor;
22-160 1.39e-03

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 37.39  E-value: 1.39e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  22 IKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGkFENYLYVIAKNKCKDFWKKKQPIYLE-SLDKEI-- 98
Cdd:PRK09642   1 MQTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFRG-LKTWMARIATNHAIDYKRKKARENEElSLCKETee 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 544955230  99 ---SNQELSDI----ENKMFIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALK 160
Cdd:PRK09642  80 nikSSHNIEDLlltkEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARK 148
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 43-163 2.02e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 36.78  E-value: 2.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  43 AQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDFWKKK-------QPIYLESLDKEISNQELSDIENkmfIKEA 115
Cdd:PRK12547  33 AEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMRKRgrevqdsDGVFTARVAVHPAQYGSLDLQD---FKKA 109

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 544955230 116 LTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKLE 163
Cdd:PRK12547 110 LNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQ 157
PRK06704 PRK06704
RNA polymerase subunit sigma-70;
24-169 2.40e-03

RNA polymerase subunit sigma-70;


Pssm-ID: 180663 [Multi-domain]  Cd Length: 228  Bit Score: 37.31  E-value: 2.40e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  24 KYYDSIYCYCYRHVDNKMTAQDLTQDvfvTVINNIENYKHYGKFENYLYVIAKNKCKDFWKKKQpiYLESLDKEISNQEL 103
Cdd:PRK06704  25 EQYGELKRYCTFLTKNKWDGEDLAQE---TVCKVLQKYSNKDICMTLVYKIARNRWLDQIKSKS--VHEKIRDQITFEEP 99

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 544955230 104 SDIENKM--FIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKLELYLEGG 169
Cdd:PRK06704 100 HEKIADLheMVGKVLSSLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEEG 167
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 22-160 3.55e-03

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 36.29  E-value: 3.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  22 IKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVI--NNIENYKHYGKFenyLYVIAKNKCKDFWKK---KQPIYLESLDK 96
Cdd:PRK12527   1 MENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLerSSSAQIEHPRAF---LYRTALNLVVDRHRRhrvRQAEPLEVLDE 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  97 EI-----SNQELSDIENKM-FIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALK 160
Cdd:PRK12527  78 EErlhspSPQTRLDLGQRLaLLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMK 147
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 14-167 4.42e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 36.20  E-value: 4.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230  14 KKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYGKFENYLYVIAKNKCKDFWKKKQPIYLES 93
Cdd:PRK12517  21 KQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLITILRRENARRFERKQFDLVDI 100

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 544955230  94 LDKEISNQELSDIENKM---FIKEALTKLPELEFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKLELYLE 167
Cdd:PRK12517 101 EDDSIEDDASHSSEEEMeqeWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALE 177
DUF134 pfam02001
Protein of unknown function DUF134; This family of archaeal proteins has no known function. A ...
 123-171 4.80e-03

Protein of unknown function DUF134; This family of archaeal proteins has no known function. A study suggests that some members may be G-quadruplex binding proteins.


Pssm-ID: 280223  Cd Length: 98  Bit Score: 34.90  E-value: 4.80e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 544955230  123 EFEVIILRYYHDLKFKDIAKIMESSVSVTKYRMSRALKKLE--------LYLEGGKL 171
Cdd:pfam02001  39 EAEAIRLVDYEDMSQDDAAAKMGISKATLWRLLTAARKKIAdalfegraIIIKGGEY 95
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 4-88 8.87e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 35.18  E-value: 8.87e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544955230   4 ARIISQIKAGKKELFDTLIKKYYDSIYCYCYRHVDNKMTAQDLTQDVFVTVINNIENYKHYG-KFENYLYVIAKNKCKDF 82
Cdd:PRK12514   7 EKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGlSPMTWLITIARNHAIDR 86


                 ....*.
gi 544955230  83 WKKKQP 88
Cdd:PRK12514  87 LRARKA 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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