NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1586794385|gb|TCB63267|]
View 

sigma-70 family RNA polymerase sigma factor [Rhizobium leguminosarum bv. viciae]

Protein Classification

sigma-70 family RNA polymerase sigma factor family protein( domain architecture ID 1002136)

sigma-70 family RNA polymerase sigma factor family protein, similar to Streptomyces sp. AgN23 RNA polymerase sigma-70 factor; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK08241 super family cl30683
RNA polymerase subunit sigma-70;
7-282 5.95e-82

RNA polymerase subunit sigma-70;


The actual alignment was detected with superfamily member PRK09636:

Pssm-ID: 357559 [Multi-domain]  Cd Length: 293  Bit Score: 248.68  E-value: 5.95e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385   7 LADEFEANRAHLRAAAYRMLGSRSEAEDAVQEAWLRLSRTDTTGVGNLGGWLTTVVARICLDMLRTRKTRRE----EPLE 82
Cdd:PRK09636    6 AAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLRWNNADRAQIRDPRAWLTRVVTRLCLDRLRSARHRREtyvgPWLP 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  83 APVHGGIADPANDPEReaafADSVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQG 162
Cdd:PRK09636   86 EPVVEELDDPLEAVVA----AEDLSLALMLALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKHVRA 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385 163 VDEAPDVDFGRKRTIAEAFLTASRNGDLEGLLAVLAPDVVFRPDATAARFGTIGETRGAAHVAEAFKGRAQ--------A 234
Cdd:PRK09636  162 ARPRFPVSDEEGAELVEAFFAALASGDLDALVALLAPDVVLHADGGGKVPTALRPIYGADKVARFFLGLARrygpggstL 241

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1586794385 235 AEIAIVDGELGFVVQIKGQLRVVVALTIADGRIAAIDAIADPDHLERL 282
Cdd:PRK09636  242 VRLALVNGLPGFVTAEADGEPQTTALEVEDGKIVAIYDVRNPDKLTHL 289
 
Name Accession Description Interval E-value
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 7-282 5.95e-82

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 248.68  E-value: 5.95e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385   7 LADEFEANRAHLRAAAYRMLGSRSEAEDAVQEAWLRLSRTDTTGVGNLGGWLTTVVARICLDMLRTRKTRRE----EPLE 82
Cdd:PRK09636    6 AAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLRWNNADRAQIRDPRAWLTRVVTRLCLDRLRSARHRREtyvgPWLP 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  83 APVHGGIADPANDPEReaafADSVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQG 162
Cdd:PRK09636   86 EPVVEELDDPLEAVVA----AEDLSLALMLALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKHVRA 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385 163 VDEAPDVDFGRKRTIAEAFLTASRNGDLEGLLAVLAPDVVFRPDATAARFGTIGETRGAAHVAEAFKGRAQ--------A 234
Cdd:PRK09636  162 ARPRFPVSDEEGAELVEAFFAALASGDLDALVALLAPDVVLHADGGGKVPTALRPIYGADKVARFFLGLARrygpggstL 241

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1586794385 235 AEIAIVDGELGFVVQIKGQLRVVVALTIADGRIAAIDAIADPDHLERL 282
Cdd:PRK09636  242 VRLALVNGLPGFVTAEADGEPQTTALEVEDGKIVAIYDVRNPDKLTHL 289
SigX4 TIGR02957
RNA polymerase sigma-70 factor, TIGR02957 family; This group of sigma factors are members of ...
 10-282 2.04e-64

RNA polymerase sigma-70 factor, TIGR02957 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.


Pssm-ID: 132002 [Multi-domain]  Cd Length: 281  Bit Score: 203.74  E-value: 2.04e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  10 EFEANRAHLRAAAYRMLGSRSEAEDAVQEAWLRLSRTDTTGVGNLGGWLTTVVARICLDMLRTRKTRREEP----LEAPV 85
Cdd:TIGR02957   2 EFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEADRAQIENPKAYLTKVVTRRCIDVLRSARARREVYvgpwLPEPL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  86 HGGIADPANDPEReaafADSVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQGVDE 165
Cdd:TIGR02957  82 LTTSADPAESVEL----AESLSMAYLLLLERLSPLERAVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARRHLDARRP 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385 166 APDVDFGRKRTIAEAFLTASRNGDLEGLLAVLAPDVVFRPDATAARFGTIGETRGAAHVAEAFKGRAQ------AAEIAI 239
Cdd:TIGR02957 158 RFEVSREESRQLLERFVEAAQTGDLDGLLELLAEDVVLYGDGGGKVRAALRPIYGADRVARFFFGLVRrlgpggRVDPVD 237

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1586794385 240 VDGELGFVVQIKGQLRVVVALTIADGRIAAIDAIADPDHLERL 282
Cdd:TIGR02957 238 VNGQPAVLVRIDGKLAYVVTFAIEGGGIQNIYIVRNPEKLAHI 280
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 7-161 2.20e-31

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: 115.09  E-value: 2.20e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385   7 LADEFEANRAHLRAAAYRMLGSRSEAEDAVQEAWLRL--SRTDTTGVGNLGGWLTTVVARICLDMLRTRKTRREEPLEAP 84
Cdd:COG1595    19 FEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLwrKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELA 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1586794385  85 VHggIADPANDPErEAAFADSVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQ 161
Cdd:COG1595    99 EE--LPDEAADPE-EALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLR 172
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 11-74 6.77e-10

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: 54.13  E-value: 6.77e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1586794385  11 FEANRAHLRAAAYRMLGSRSEAEDAVQEAWLRL----SRTDTTGVGNLGGWLTTVVARICLDMLRTRK 74
Cdd:pfam04542   2 VERYLPLVYSLARRYLGDGADAEDLVQEGFLGLwraiERFDPERGVSFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 113-161 3.16e-03

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: 35.16  E-value: 3.16e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1586794385 113 VLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQ 161
Cdd:cd06171     7 ALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 7-282 5.95e-82

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 248.68  E-value: 5.95e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385   7 LADEFEANRAHLRAAAYRMLGSRSEAEDAVQEAWLRLSRTDTTGVGNLGGWLTTVVARICLDMLRTRKTRRE----EPLE 82
Cdd:PRK09636    6 AAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLRWNNADRAQIRDPRAWLTRVVTRLCLDRLRSARHRREtyvgPWLP 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  83 APVHGGIADPANDPEReaafADSVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQG 162
Cdd:PRK09636   86 EPVVEELDDPLEAVVA----AEDLSLALMLALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKHVRA 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385 163 VDEAPDVDFGRKRTIAEAFLTASRNGDLEGLLAVLAPDVVFRPDATAARFGTIGETRGAAHVAEAFKGRAQ--------A 234
Cdd:PRK09636  162 ARPRFPVSDEEGAELVEAFFAALASGDLDALVALLAPDVVLHADGGGKVPTALRPIYGADKVARFFLGLARrygpggstL 241

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*...
gi 1586794385 235 AEIAIVDGELGFVVQIKGQLRVVVALTIADGRIAAIDAIADPDHLERL 282
Cdd:PRK09636  242 VRLALVNGLPGFVTAEADGEPQTTALEVEDGKIVAIYDVRNPDKLTHL 289
SigX4 TIGR02957
RNA polymerase sigma-70 factor, TIGR02957 family; This group of sigma factors are members of ...
 10-282 2.04e-64

RNA polymerase sigma-70 factor, TIGR02957 family; This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.


Pssm-ID: 132002 [Multi-domain]  Cd Length: 281  Bit Score: 203.74  E-value: 2.04e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  10 EFEANRAHLRAAAYRMLGSRSEAEDAVQEAWLRLSRTDTTGVGNLGGWLTTVVARICLDMLRTRKTRREEP----LEAPV 85
Cdd:TIGR02957   2 EFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEADRAQIENPKAYLTKVVTRRCIDVLRSARARREVYvgpwLPEPL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  86 HGGIADPANDPEReaafADSVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQGVDE 165
Cdd:TIGR02957  82 LTTSADPAESVEL----AESLSMAYLLLLERLSPLERAVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARRHLDARRP 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385 166 APDVDFGRKRTIAEAFLTASRNGDLEGLLAVLAPDVVFRPDATAARFGTIGETRGAAHVAEAFKGRAQ------AAEIAI 239
Cdd:TIGR02957 158 RFEVSREESRQLLERFVEAAQTGDLDGLLELLAEDVVLYGDGGGKVRAALRPIYGADRVARFFFGLVRrlgpggRVDPVD 237

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1586794385 240 VDGELGFVVQIKGQLRVVVALTIADGRIAAIDAIADPDHLERL 282
Cdd:TIGR02957 238 VNGQPAVLVRIDGKLAYVVTFAIEGGGIQNIYIVRNPEKLAHI 280
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 7-280 9.12e-57

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 184.40  E-value: 9.12e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385   7 LADEFEANRAHLRAAAYRMLGSRSEAEDAVQEAWLRLSRTDTTGVGNLGGWLTTVVARICLDMLRTRKTRREEPLE-APV 85
Cdd:PRK09635    7 VSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGDIDDERGWLIVVTSRLCLDHIKSASTRRERPQDiAAW 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  86 HGGIADPAN-DPEREAAFADSVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQGVD 164
Cdd:PRK09635   87 HDGDASVSSvDPADRVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKINESR 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385 165 EAPDVDFGRKRTIAEAFLTASRNGDLEGLLAVLAPDVVFRPDATAARFgTIGETRGAAHVAEAFKGRAQAAEIAIVDGEL 244
Cdd:PRK09635  167 IAASVEPAQHRVVTRAFIEACSNGDLDTLLEVLDPGVAGEIDARKGVV-VVGADRVGPTILRHWSHPATVLVAQPVCGQP 245

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1586794385 245 GFVVQIKGQLRVVVALTIADGRIAAIDAIADPDHLE 280
Cdd:PRK09635  246 AVLAFVNRALAGVLALSIEAGKITKIHVLVQPSTLD 281
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 7-161 2.20e-31

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: 115.09  E-value: 2.20e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385   7 LADEFEANRAHLRAAAYRMLGSRSEAEDAVQEAWLRL--SRTDTTGVGNLGGWLTTVVARICLDMLRTRKTRREEPLEAP 84
Cdd:COG1595    19 FEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLwrKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELA 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1586794385  85 VHggIADPANDPErEAAFADSVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQ 161
Cdd:COG1595    99 EE--LPDEAADPE-EALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLR 172
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
7-281 1.09e-22

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 95.77  E-value: 1.09e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385   7 LADEFEANRAHLRAAAYRMLGSRSEAEDAVQE----AWLRLSRTDttGVGNLGGWLTTVVARICLDMLRTRKtRREEPLE 82
Cdd:PRK08241   21 FAALVEPHRRELLAHCYRMLGSVHDAEDAVQEtllrAWRGYDRFE--GRSSLRTWLYRIATNVCLDALEGRA-RRPLPTD 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  83 ------APVHGGIADP----------------ANDPEREAAFADSVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAP 140
Cdd:PRK08241   98 lgapaaDPVDELVERPevpwlepypdalldpaAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRDVLGWSAAEVAE 177

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385 141 IIGRSSGATRQLASRARRRVQGVDEAPDVDFG-----RKRTIAEAFLTASRNGDLEGLLAVLAPDVVFR----------P 205
Cdd:PRK08241  178 LLDTSVAAVNSALQRARATLAERGPSAADTLRepddpEERALLARYVAAFEAYDVDALVALLTEDATWSmppfplwyrgR 257

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1586794385 206 DATAARFGTIGETRGAA---HVAEAFKGRAQAAEIAIVDGELGFVVQikgqlrVVVALTIADGRIAAIDAIADPDHLER 281
Cdd:PRK08241  258 DAIAAFLAGQCPGAGCGgsrLVPTRANGQPAFAQYMRDPDGGGHRPW------ALHVLELRGGRIAHVTSFLDTTLFPR 330
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 7-161 8.34e-22

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: 89.33  E-value: 8.34e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385   7 LADEFEANRAHLRAAAYRMLGSRSEAEDAVQEAWLRL--SRTDTTGVGNLGGWLTTVVARICLDMLRTRKTRREEPLEAP 84
Cdd:TIGR02937   3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLleALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLE 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1586794385  85 VhggIADPANDPEREAAFADSVgLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQ 161
Cdd:TIGR02937  83 E---LLDSDPSPEEELEQEEER-EALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLR 155
SigX5 TIGR02960
RNA polymerase sigma-70 factor, TIGR02960 family; This group of sigma factors are members of ...
 12-279 7.63e-20

RNA polymerase sigma-70 factor, TIGR02960 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: 132005 [Multi-domain]  Cd Length: 324  Bit Score: 87.61  E-value: 7.63e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  12 EANRAHLRAAAYRMLGSRSEAEDAVQEAWLRL--SRTDTTGVGNLGGWLTTVVARICLDMLRTRKTR------------- 76
Cdd:TIGR02960  12 EPHRRELLAHCYRMLGSLHEAEDLVQETLLRAwrARDRFEGRSSVRTWLYRIATNACLDALEARQRRprpvglgapsadg 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  77 -------RE----EPLEAPVHGGIADPANDPEREAAFADSVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRS 145
Cdd:TIGR02960  92 taaaseaAEvtwlEPLPDLTLDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRDVLGWRAAETAELLGTS 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385 146 SGATRQLASRARRRVQGV------DEAPDVDFGRKRTIAEAFLTASRNGDLEGLLAVLAPDVVF-----------RPDAT 208
Cdd:TIGR02960 172 TASVNSALQRARATLDEVgpsardDQLAQPPSPEEQDLLERYIAAFESYDLDALTALLHEDAIWemppytlwyqgRPAIV 251

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1586794385 209 AArFGTIGETRGAA---HVAEAFKGRAQAAEIAIVDGELGFVVQikgQLRVvvaLTIADGRIAAIDAIADPDHL 279
Cdd:TIGR02960 252 GF-IHTVCPGEGAAgmrLLPTIANGQPAAAMYMRRPDAERHTAF---QLHV---LEIRGGRITHVTAFLDGPSL 318
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 22-157 3.56e-15

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 72.51  E-value: 3.56e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  22 AYRMLGSRSEAEDAVQEAWLRLSRT-DTTGVGNLGGWLTTVVARICLDMLRTRKTRREEPLeapvhGGIAD--PANDPER 98
Cdd:PRK09647   45 AYRLSGNQHDAEDLTQETFIRVFRSlQNYQPGTFEGWLHRITTNLFLDMVRRRARIRMEAL-----PEDYDrvPGDEPNP 119

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  99 EAAFADS-VGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRAR 157
Cdd:PRK09647  120 EQIYHDArLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGR 179
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 15-161 8.88e-15

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 71.28  E-value: 8.88e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  15 RAHLRAAAYRMLGSRSEAEDAVQEAWLRLSRTDTT--GVGNLGGWLTTVVARICLDMLRTRKTRREEPLEapvhggiaDP 92
Cdd:PRK09643   37 HRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSfrGDAAVSSWLHRIVVNACLDRLRRAKARPTVPLD--------DV 108

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1586794385  93 ANDPEREAAFADSVGLALLV--VLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQ 161
Cdd:PRK09643  109 YPVAQLERDPTARVETALAVqrALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRARLA 179
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 11-159 1.42e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 70.38  E-value: 1.42e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  11 FEANRAHLRAAAYRMLGSRSEAEDAVQEAWLRLSRTDTT--GVGNLGGWLTTVVARICLDMLRTRKTRREEPLEAPVHGG 88
Cdd:PRK11924   19 FRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLfnGKGSARTWLLTIARNVCYDLLRRRRREKAVLSDDALEPE 98

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1586794385  89 IADPANDPErEAAFADSVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRR 159
Cdd:PRK11924   99 FAETAETPE-AALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQL 168
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 23-159 1.32e-11

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 61.50  E-value: 1.32e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  23 YRMLGSRSEAEDAVQEAWLRLSRTDTTGVGNLGGWLTTVVARICLDMLRTRKTRREEPLEAPVHGGIaDPANDPEREAAF 102
Cdd:PRK09639   21 FYIVKDRTQAEDLAQEVFLRLYRSDFKGIENEKGWLIKSARNVAYNYLRSEKRRRARILGEFQWQEV-DNEPSPEEIWIR 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1586794385 103 ADSVGLaLLVVLQTLAPAERVAFVLHdmF-DLPFDEIAPIIGRSSGATRQLASRARRR 159
Cdd:PRK09639  100 KEEITK-VQEVLAKMTERDRTVLLLR--FsGYSYKEIAEALGIKESSVGTTLARAKKK 154
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 20-158 3.98e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 61.06  E-value: 3.98e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  20 AAAYRMLGSRSEAEDAVQEAWLRLSRTDT---TGVGNLGGWLTTVVARICLDMLRTRKTRREEPLEAPVHGGIADPANDP 96
Cdd:PRK12524   41 AVATRVLGDRAEAEDVTQEAMLRLWRIAPdwrQGEARVSTWLYRVVCNLCTDRLRRRRRASVDLDDAPEPADAAPGAEEA 120

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1586794385  97 EREAAFADSVGLALLvvlqTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARR 158
Cdd:PRK12524  121 LIEGDRMRALDAALA----ALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKR 178
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 11-161 1.11e-10

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: 58.94  E-value: 1.11e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  11 FEANRAHLRAAAYRMLGSRSEAEDAVQEA-------WLRLSRTDttgvgNLGGWLTTVVARICLDMLRTRKtRREEPLEA 83
Cdd:TIGR02983  12 VAARYPRLLRTAYLLTGDPHEAEDLVQEAlvrtyvrWDRIRDPD-----APDAYVRRVLVNLARSRWRRRR-LLELPTRE 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1586794385  84 PVHGGIADPANDPEREAAFADSvglallvvLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQ 161
Cdd:TIGR02983  86 LPDAAAPDPAPDVALRAALARA--------LRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLR 155
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 20-162 2.54e-10

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 58.51  E-value: 2.54e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  20 AAAYRMLGSRSEAEDAVQEAWLRLSRTDTT---GVGNLGGWLTTVVARICLDmlRTRKtRREEPLEAPVHggIADPANDP 96
Cdd:PRK05602   35 ALATRMLGDPAEAEDVAQETFLRIWKQAPSwrpGEARFDTWLHRVVLNLCYD--RLRR-RREVPVEDAPD--VPDPAPGP 109

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1586794385  97 EREAAfADSVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQG 162
Cdd:PRK05602  110 DAGLE-ARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRA 174
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 11-74 6.77e-10

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: 54.13  E-value: 6.77e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1586794385  11 FEANRAHLRAAAYRMLGSRSEAEDAVQEAWLRL----SRTDTTGVGNLGGWLTTVVARICLDMLRTRK 74
Cdd:pfam04542   2 VERYLPLVYSLARRYLGDGADAEDLVQEGFLGLwraiERFDPERGVSFSTWLYTIIRNAIIDYLRKQR 69
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 8-143 1.01e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 57.01  E-value: 1.01e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385   8 ADEFEANRAHLRAAAYRML----GSRSEAEDAVQEAWLRL--SRTDTTGVGNLGGWLTTVVARICLDMLRTRKTRREEPL 81
Cdd:PRK12513   25 AAAFEALYARHRTGLYRFLlrlaRDRALAEDIFQETWLRVirARAQYQPRARFRTWLYQIARNLLIDHWRRHGARQAPSL 104

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1586794385  82 EA-PVHGGIADPANDPEREAAFADsVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIG 143
Cdd:PRK12513  105 DAdEQLHALADDGAAPEQQLSLFR-DRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTG 166
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 22-143 6.95e-09

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 54.32  E-value: 6.95e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  22 AYRMLGSRSEAEDAVQEAWLR----LSRTDTTgvGNLGGWLTTVVARICLDMLRTRKTrrEEPLEAPVHGG--------I 89
Cdd:PRK09641   35 CYRMLGNRHEAEDAAQEAFIRayvnIDSYDIN--RKFSTWLYRIATNLTIDRLRKRKP--DYYLDAEVAGTegltmysqL 110

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1586794385  90 ADPANDPERE---AAFADSVGLALLvvlqTLAPAERVAFVLHDMFDLPFDEIAPIIG 143
Cdd:PRK09641  111 AADDALPEEQvvsLELQETIQEAIL----QLPEKYRTVIVLKYIEDLSLKEISEILD 163
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 1-104 2.73e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 52.52  E-value: 2.73e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385   1 MDEKKWLADEFEANRAHLRAAAYRMLGSRSEAEDAVQEAWLRL-SRTDTTGVGNLG--GWLTTVVARICLDMLRTRKTRR 77
Cdd:PRK12514   15 LGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIwTKADRFAVSGLSpmTWLITIARNHAIDRLRARKAVA 94

                          90       100
                  ....*....|....*....|....*..
gi 1586794385  78 EEPLEApvhGGIADPANDPEREAAFAD 104
Cdd:PRK12514   95 VDIDEA---HDLADPSPGPEAEVIAGD 118
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 108-160 1.07e-07

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: 47.84  E-value: 1.07e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1586794385 108 LALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRV 160
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
YesE COG3631
Ketosteroid isomerase-related protein [General function prediction only];
175-281 1.11e-07

Ketosteroid isomerase-related protein [General function prediction only];


Pssm-ID: 442849  Cd Length: 126  Bit Score: 49.54  E-value: 1.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385 175 RTIAEAFLTASRNGDLEGLLAVLAPDVVFrpdaTAARFGTIGETRGAAHVAEAFKGRAQAAEIA-------IVDGELGFV 247
Cdd:COG3631     3 RELVRRFYAAFNAGDVDALLALLAEDVVW----EDPGGPGAGTYRGKEAVRAFFARLAAAFEDLrfevrrvVADGDRVVV 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1586794385 248 V-QIKG---------QLRVVVALTIADGRIAAIDAIADPDHLER 281
Cdd:COG3631    79 EgTVRGtvlatgkpyENRYADVFTVRDGKIVRVREYFDTAALAA 122
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 11-139 4.51e-07

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: 48.71  E-value: 4.51e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  11 FEANRAHLRAAAYRMLGSRSEAEDAVQEAWLRL--SRTDTTGVGNLGGWLTTVVARICLDMLRtRKTRREEPLEAPV-HG 87
Cdd:TIGR02985   7 YRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLweNRETLEISESIKAYLFTIVKNRCLNYLR-HKQVEEKYQEELAeIE 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1586794385  88 GIADPANDPEREaAFADSVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIA 139
Cdd:TIGR02985  86 ERELSEADPEEE-LEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIA 136
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 30-158 6.52e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 49.19  E-value: 6.52e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  30 SEAEDAVQEAWLRLSRT--DTTGVGNLGGWLTTVVARICLDMLRTRKtRREEPLEAPVHGGIA--------DPANDPERE 99
Cdd:PRK11922   55 AEAEDVVQEAYLRAFRAlgTFRGDASLSTWLSRIVLNEALGRLRRRR-RLVNLAEMVMASTIAggertplaDPAEDPERA 133

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385 100 AAFADSvgLALL-VVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARR 158
Cdd:PRK11922  134 AARREI--RALLeRAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARR 191
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 24-162 6.72e-07

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 48.78  E-value: 6.72e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  24 RMLGSRSEAEDAVQEAWLRLsrtdTTGVGNLGG------WLTTVVARICLDMLRT-RKTRRE------EPLEAPVHggia 90
Cdd:PRK09640   45 RYLGNDRDADDVCQEVMLKV----LYGLKNFEGkskfktWLYSITYNECITQYRKeRRKRRLmdalslDPLEEASE---- 116

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1586794385  91 dpandpEREAAFADSVGLALLVVlqTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQG 162
Cdd:PRK09640  117 ------EKAPKPEERGGLDRWLV--HVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLRE 180
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 17-162 2.93e-06

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 46.72  E-value: 2.93e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  17 HLRAAAYRMLGSRSEAEDAVQEAWLRLSR------TDTtgvgNLGGWLTT--VVARIclDMLRTRKtRREEPLEAPV--- 85
Cdd:PRK09652   22 RVKRLLSRLTRDPADAEDLVQETFIKAYRalhsfrGGA----AFYTWLYRiaRNTAI--NYLRKQG-RRPPASDVDAeea 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  86 ----HGGIADPANDPEREaAFADSVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQ 161
Cdd:PRK09652   95 edfdLADALRDISTPENE-LLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALR 173


                  .
gi 1586794385 162 G 162
Cdd:PRK09652  174 A 174
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 17-159 3.15e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 47.03  E-value: 3.15e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  17 HLRAA---AYRMLGSRSEAEDAVQEAWLRLSR-TDTTGVGNLGGWLTTVVARICLDMLRTRKTRREEPLE-----APVHG 87
Cdd:PRK12533   27 HLDAAynlARWLCGNASDADDVVQEACMRALRfFDSFRGDNARPWLLAIVRHTWYSEWRRRANAHEVAAPdtlddADSLD 106

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1586794385  88 GIADPANDPEREAAFADSVGLaLLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRR 159
Cdd:PRK12533  107 DWQPAGEDPLALLLRAEDVRL-VNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRR 177
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 24-145 7.14e-06

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 45.15  E-value: 7.14e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  24 RMLGSRSEAEDAVQEAWLR-LSRTDTTGVGNLGGWLTTVVARICLDMLRTRKTRREEPLEApvhggiadpANDPEREAAF 102
Cdd:PRK12527   14 ARLGNRQAAEDVAHDAYLRvLERSSSAQIEHPRAFLYRTALNLVVDRHRRHRVRQAEPLEV---------LDEEERLHSP 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1586794385 103 ADSVG------LALL-VVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRS 145
Cdd:PRK12527   85 SPQTRldlgqrLALLqRALAELPPACRDSFLLRKLEGLSHQQIAEHLGIS 134
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 22-163 7.59e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 45.43  E-value: 7.59e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  22 AYRMLGSRSEAEDAVQEAWL----RLSRTDTTGVGNLGGWLTTVVARICLDMLRTRKtRREEPLEAPVHGGI-ADPANDP 96
Cdd:PRK12542   26 AYSILNNIQQAEDAVQETFItlykNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNK-RHETFLEEYERESIeAVDENIE 104

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1586794385  97 EREAAFADSVGLALLvvLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQGV 163
Cdd:PRK12542  105 EWEKRKMSEVQIDTL--LKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRVQNM 169
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 22-158 7.80e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 45.44  E-value: 7.80e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  22 AYRMLGSRSEAEDAVQEAWLRLSRTDT--TGVGNLGGWLTTVVARICLDMLRTRkTRREEPLEAPVHGGIADPANDPERE 99
Cdd:PRK12519   46 ALKILGNSQEAEDLTQEIFLSLWRKSSydPKRGSLSSYLLTLTRSRAIDRLRSR-RSRQRLLERWQQELLGEASEDTPLE 124

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1586794385 100 AAFADSVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRqlaSRARR 158
Cdd:PRK12519  125 QASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVK---ARARQ 180
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 7-155 8.14e-06

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 45.40  E-value: 8.14e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385   7 LADEFEANRAHLRAAAYRMLGSRSEAEDAVQEAWLR--LSRTDTTGVGNLGGWLTTVVARICLDMLRTRKtrREEPLEap 84
Cdd:PRK09638   20 LTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKaiENLSSFQGRSKFSTWLISIASRLYKDHLRKQK--REKLRL-- 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1586794385  85 vhGGIADPANDPER-EAAFADSVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRqlaSR 155
Cdd:PRK09638   96 --QRAKEETLRKEKwEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVK---SR 162
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 7-187 1.64e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 44.57  E-value: 1.64e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385   7 LADEFEANRAHLRAAAYRMLGSRSEAEDAVQEAWLR-LSRTDTTGVG-NLGGWLTTVVAriclDMLRT--RKTRREEPLE 82
Cdd:PRK12540    7 LRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRaLANIDSFQPGsNLPAWLFTILR----NLFRSdyRKRRREVEDA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  83 APVHGGIADPANDPEREAAFADsvglaLLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQG 162
Cdd:PRK12540   83 DGSYAKTLKSQPGQNAHLEFEE-----FRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSA 157

                         170       180
                  ....*....|....*....|....*.
gi 1586794385 163 VDEAPDV-DFGRKRTIaEAFLTASRN 187
Cdd:PRK12540  158 LLYVDGAeDFGPDDTV-RAVIGGSGG 182
COG4941 COG4941
Predicted RNA polymerase sigma factor, contains C-terminal TPR domain [Transcription];
6-139 1.81e-05

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


Pssm-ID: 443968 [Multi-domain]  Cd Length: 412  Bit Score: 45.47  E-value: 1.81e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385   6 WLADEFEANRAHLRAAAYRMLGSRSEAEDAVQEAWLR-LSRTDTTGV-GNLGGWLTTVVARICLDMLRtRKTRREEPLEA 83
Cdd:COG4941     7 AIEALFREESGRLVAALARRFGDLDLAEDAVQDAFLAaLEQWPRDGVpDNPAAWLYTVARRRAIDRLR-REARRRRKEAE 85

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1586794385  84 PVHGGIADPANDPEREAAFADSVgLALLVVL--QTLAPAERVAFVLHDMFDLPFDEIA 139
Cdd:COG4941    86 LAADLEAEAPAEDADDDDIPDDR-LRLLFTCchPALSPEAQVALTLRLVGGLTTAEIA 142
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 11-159 6.75e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 42.63  E-value: 6.75e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  11 FEANRAHLRAAAYRMLGSRSEAEDAVQEAWLR-LSRTDTTGVGNLGGWLTTVVARICLDMLRTRKTRRE-----EPLEAP 84
Cdd:PRK12525   15 FQQDYDWLCKKLSRQLGCPHSAEDIASETFLQvLALPDPASIREPRALLTTIARRLMYEGWRRQDLERAylqslAEAPEA 94

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1586794385  85 VHggiadPAndPEREAAFADSVgLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRR 159
Cdd:PRK12525   95 VQ-----PS--PEEQWMVIETL-LAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKC 161
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 16-158 8.17e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 42.40  E-value: 8.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  16 AHLRAAAYRMLGsRSEAEDAVQEAWLRLSRtdttGVGNLGG------WLTTVVARICLDMLRTRKTRREE-PLEAPVHGG 88
Cdd:PRK12518   22 QKVRSTLYQLCG-RELLDDLVQEVFLRVWK----GLPKLRNpayfstWLYRITWNVATDARRQFAQRPSRiQDDSLNDQP 96

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  89 IADPANDPEREAAFADSVGLALlvvlQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARR 158
Cdd:PRK12518   97 SRPSDTPDLMQLHYQDLVQQGL----QTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARR 162
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 9-145 1.40e-04

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 41.59  E-value: 1.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385   9 DEFEANRAHLRAAAYRMLGSRSEAEDAVQEAWLRLSRT-DTTGVGNLGGWLTTVVARICLDMLrtrktrREEPLEAPVHG 87
Cdd:PRK07037    2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEApNQDAVKQPVAYLFRIVRNLAIDHY------RRQALENKYHG 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1586794385  88 GIAD----PANDPEREAAFADSVGLALLV-VLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRS 145
Cdd:PRK07037   76 DEEDgldvPSPEASPEAALINRDTLRHVAdALSELPARTRYAFEMYRLHGETQKDIARELGVS 138
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 23-161 5.79e-04

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 39.86  E-value: 5.79e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  23 YRMLGSRSEAEDAVQE----AWLRLSRTDTTGVGNlggWLTTVVARICLDMlrTRKTRREEPLEAPVHGGIAdpANDPEr 98
Cdd:PRK09644   19 FSLTKSHHAAEDLLQEtfyrAYIYLEDYDNQKVKP---WLFKVAYHTFIDF--VRKEKKVSFVGTDEIEAIQ--AESTE- 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1586794385  99 EAAFADSVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQ 161
Cdd:PRK09644   91 EYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLK 153
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 20-161 7.64e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 40.22  E-value: 7.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  20 AAAYRMLGSRSEAEDAVQEAWLRLSRTD---TTGVGNLGGWLTTVVARICLDMLRTRKTRREEPLEAPVHGGiADPANDP 96
Cdd:PRK12538   78 AIALRIVGNRADAEDVVQDTMLKVWTHRgrwQHGRAKFSTWLYRVVSNRCIDLRRKPRTENVDAVPEVADGK-PDAVSVI 156

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1586794385  97 EReaafaDSVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQ 161
Cdd:PRK12538  157 ER-----NELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLR 216
PRK09191 PRK09191
two-component response regulator; Provisional
 92-162 8.11e-04

two-component response regulator; Provisional


Pssm-ID: 236402 [Multi-domain]  Cd Length: 261  Bit Score: 40.22  E-value: 8.11e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1586794385  92 PANDPEREAAFADSVGLALlvvlQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQG 162
Cdd:PRK09191   68 GANDPEPGSPFEARAERRL----AGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAEIAR 134
SnoaL_2 pfam12680
SnoaL-like domain; This family contains a large number of proteins that share the SnoaL fold.
 178-268 8.54e-04

SnoaL-like domain; This family contains a large number of proteins that share the SnoaL fold.


Pssm-ID: 432716 [Multi-domain]  Cd Length: 100  Bit Score: 38.04  E-value: 8.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385 178 AEAFLTASRNGDLEGLLAVLAPDVVFRpdataarfGTIGETRGAAHVAEAFKGRAQAAEIA-------IVDGELGFV-VQ 249
Cdd:pfam12680   1 VRRFYEALNAGDLDALAALFAPDAVFH--------DPGGPLRGRDAIRAFFAALFAAFPDLrfeihdvIADGDRVAVrWT 72

                          90       100
                  ....*....|....*....|....*...
gi 1586794385 250 IKG---------QLRVVVALTIADGRIA 268
Cdd:pfam12680  73 VTGtipptgrgvRVRGVDVFRFRDGKIV 100
PRK06704 PRK06704
RNA polymerase subunit sigma-70;
67-203 1.17e-03

RNA polymerase subunit sigma-70;


Pssm-ID: 180663 [Multi-domain]  Cd Length: 228  Bit Score: 39.62  E-value: 1.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  67 LDMLRTR----KTRREEPLEAPvHGGIADPANDPEReaafadsvglallvVLQTLAPAERVAFVLHDMFDLPFDEIAPII 142
Cdd:PRK06704   78 LDQIKSKsvheKIRDQITFEEP-HEKIADLHEMVGK--------------VLSSLNVQQSAILLLKDVFQYSIADIAKVC 142

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1586794385 143 GRSSGATRQLASRARRRVQGVDEApDVDFGRKRTIAEAFLTASRNGDLEgLLAVLAPDVVF 203
Cdd:PRK06704  143 SVSEGAVKASLFRSRNRLKTVSEE-GIEIVEFTDDMEVVVTSIREERPE-LLTKLLPTIDF 201
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 19-157 1.43e-03

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 38.87  E-value: 1.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  19 RAAAYrmLGSRSEAEDAVQEAWLRLSRTDTTGVGNLGG--WLTTVVARICLDMLRTRKTRREEpleapVHGGIADPANDP 96
Cdd:PRK09649   39 RFVAY--LSDVGSADDLTQETFLRAIGAIPRFSARSSArtWLLAIARHVVADHIRHVRSRPRT-----TRGARPEHLIDG 111

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1586794385  97 EREA-AFADSVGLALLVVlqTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRAR 157
Cdd:PRK09649  112 DRHArGFEDLVEVTTMIA--DLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARAR 171
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 11-161 1.59e-03

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: 38.46  E-value: 1.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  11 FEANRAHLRAAAYRMLGSRSEAEDAVQEAWLRLSR--TDTTGVGNLGGWLTTVVARICLDMLRTRKTRREEpLEAPVHGG 88
Cdd:TIGR02989   7 LTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRkfDQFDPGTNFVAWARGIARNKVLNYRRKLGRDRLV-FDDDLLEA 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1586794385  89 IADPANDPEREAAFADSVglALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQ 161
Cdd:TIGR02989  86 LAAEAEPTEAERLSDDRQ--ALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSLR 156
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 113-161 3.16e-03

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: 35.16  E-value: 3.16e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1586794385 113 VLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQ 161
Cdd:cd06171     7 ALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 113-161 5.21e-03

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: 34.33  E-value: 5.21e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1586794385 113 VLQTLAPAERVAFVLHDMFDLPFDEIAPIIGRSSGATRQLASRARRRVQ 161
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLR 49
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 15-143 6.11e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 37.02  E-value: 6.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  15 RAHLRAAAY--RMLGSRSEAEDAVQEAWLRLSRT--DTTGVGNLGGWLTTVVARICLDMLRTRKtrrEEPLEAPVHGGIA 90
Cdd:PRK12515   30 RHHVRVYRFglRLVRDEQTAEDLVSEVFLDVWRQagQFEGRSQVSTWLLSIARFKALSALRRRK---HEEIDDEAAAAIE 106

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1586794385  91 DPANDPEREAAFADsVGLALLVVLQTLAPAERVAFVLHDMFDLPFDEIAPIIG 143
Cdd:PRK12515  107 DGADTPEVALQKSD-TSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVG 158
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
18-122 7.48e-03

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 36.60  E-value: 7.48e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1586794385  18 LRAAAYRMLGSRSEAEDAVQE----AWLRLSRTDTTGvGNLGGWLTTVVARICLDMLRTRKTRREEPLEAPVhgGIADPA 93
Cdd:PRK09645   22 LWRYALRLTGDRARAEDVVQEtllrAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARPVEGGDDVL--GVPEQS 98

                          90       100
                  ....*....|....*....|....*....
gi 1586794385  94 NDPEREAAFAdsvGLALLVVLQTLAPAER 122
Cdd:PRK09645   99 APDEVDRALD---RLLVADALAQLSPEHR 124
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH