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Conserved domains on  [gi|742394841|ref|WP_038873966|]
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MULTISPECIES: ferric citrate uptake sigma factor FecI [Serratia]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK09651 super family cl32400
RNA polymerase sigma factor FecI; Provisional
 2-174 3.14e-91

RNA polymerase sigma factor FecI; Provisional


The actual alignment was detected with superfamily member PRK09651:

Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 263.21  E-value: 3.14e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841   2 SATATASAPHTaLSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKSDAAATLREPKDFLVTVAKRVMVDLFRRR 81
Cdd:PRK09651   1 SDRATTTASLT-FESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVDLFRRN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  82 TLERAYLEMLALIPDGYAPSPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKA 161
Cdd:PRK09651  80 ALEKAYLEMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 159

                        170
                 ....*....|...
gi 742394841 162 TEHCLLFSLENDV 174
Cdd:PRK09651 160 TEHCLLFRLEYGL 172
 
Name Accession Description Interval E-value
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 2-174 3.14e-91

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 263.21  E-value: 3.14e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841   2 SATATASAPHTaLSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKSDAAATLREPKDFLVTVAKRVMVDLFRRR 81
Cdd:PRK09651   1 SDRATTTASLT-FESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVDLFRRN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  82 TLERAYLEMLALIPDGYAPSPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKA 161
Cdd:PRK09651  80 ALEKAYLEMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 159

                        170
                 ....*....|...
gi 742394841 162 TEHCLLFSLENDV 174
Cdd:PRK09651 160 TEHCLLFRLEYGL 172
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 11-165 3.70e-35

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


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 121.25  E-value: 3.70e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  11 HTALSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKsdAAATLREPKDF---LVTVAKRVMVDLFRRRTLERAY 87
Cdd:COG1595   16 EAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWR--KLDSFRGRGSFrawLYRIARNLAIDHLRKRRRRREL 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 742394841  88 LEMLALIPDGYAPSPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKATEHC 165
Cdd:COG1595   94 LDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 13-165 4.48e-28

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


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 102.43  E-value: 4.48e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841   13 ALSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKsdAAATLREPKDF---LVTVAKRVMVDLFRRRTLERAYLE 89
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLE--ALDRFDPEGSFkawLFRIARNLILDYLRRKRRLRRELD 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 742394841   90 MLALIPDgYAPSPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKATEHC 165
Cdd:TIGR02937  80 LLEELLD-SDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 17-81 6.91e-12

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: 57.98  E-value: 6.91e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841   17 LYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKsdAAATLREPKD-----FLVTVAKRVMVDLFRRR 81
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWR--AIERFDPERGvsfstWLYTIIRNAIIDYLRKQ 68
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 112-161 1.27e-06

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: 43.63  E-value: 1.27e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 742394841 112 LQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKA 161
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRA 50
 
Name Accession Description Interval E-value
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 2-174 3.14e-91

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 263.21  E-value: 3.14e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841   2 SATATASAPHTaLSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKSDAAATLREPKDFLVTVAKRVMVDLFRRR 81
Cdd:PRK09651   1 SDRATTTASLT-FESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVDLFRRN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  82 TLERAYLEMLALIPDGYAPSPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKA 161
Cdd:PRK09651  80 ALEKAYLEMLALMPEGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 159

                        170
                 ....*....|...
gi 742394841 162 TEHCLLFSLENDV 174
Cdd:PRK09651 160 TEHCLLFRLEYGL 172
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 9-165 3.10e-62

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 189.67  E-value: 3.10e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841   9 APHTALSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKSDAAATLREPKDFLVTVAKRVMVDLFRRRTLERAYL 88
Cdd:PRK12528   1 AHSATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQIIEPRAFLTTIAKRVLCNHYRRQDLERAYL 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 742394841  89 EMLALIPDGYAPSPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKATEHC 165
Cdd:PRK12528  81 EALAQLPERVAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRC 157
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 5-165 9.17e-55

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 170.80  E-value: 9.17e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841   5 ATASAPHTAL-SRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKSDAAATLREPKDFLVTVAKRVMVDLFRRRTL 83
Cdd:PRK12523   2 SSAQSPHSELvGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGRPELPTPREPRAFLAAVAKGLMFDHFRRAAL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  84 ERAYLEMLALIPDGYAPSPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKATE 163
Cdd:PRK12523  82 EQAYLAELALVPEAEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLR 161


                 ..
gi 742394841 164 HC 165
Cdd:PRK12523 162 QC 163
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 11-165 2.30e-50

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 159.73  E-value: 2.30e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  11 HTALSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKSDAAATLREPKDFLVTVAKRVMVDLFRRRTLERAYLEM 90
Cdd:PRK12525   8 NTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASIREPRALLTTIARRLMYEGWRRQDLERAYLQS 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 742394841  91 LALIPDGYAPSPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKATEHC 165
Cdd:PRK12525  88 LAEAPEAVQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKCC 162
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 4-166 6.62e-44

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 143.54  E-value: 6.62e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841   4 TATASAPHTALSRLYATHHAWLQGWLRRRLG----CAfdADDVAQDTFMRLLKSDAAA---TLREPKDFLVTVAKRVMVD 76
Cdd:PRK12529   5 SSCLSADRDKVATLYRENHAWLRNWLAYRLRswgrGV--ADDLAHDIFLRILASRDGGqreAIRQPRAYLARIANCVLVS 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  77 LFRRRTLERAYLEMLALIPDGYAPSPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKK 156
Cdd:PRK12529  83 WRRRQSLELAWLEALATLPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKK 162

                        170
                 ....*....|
gi 742394841 157 YMAKATEHCL 166
Cdd:PRK12529 163 YIHQAYVTCL 172
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 11-165 3.70e-35

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


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 121.25  E-value: 3.70e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  11 HTALSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKsdAAATLREPKDF---LVTVAKRVMVDLFRRRTLERAY 87
Cdd:COG1595   16 EAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWR--KLDSFRGRGSFrawLYRIARNLAIDHLRKRRRRREL 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 742394841  88 LEMLALIPDGYAPSPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKATEHC 165
Cdd:COG1595   94 LDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 5-161 4.83e-33

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 115.84  E-value: 4.83e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841   5 ATASAPHTALSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLK-SDAAATLREPKDFLVTVAKRVMVDLFRRRTL 83
Cdd:PRK11924   6 VDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRkADLFNGKGSARTWLLTIARNVCYDLLRRRRR 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  84 ERAYLEMLALIPDG--YAPSPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKA 161
Cdd:PRK11924  86 EKAVLSDDALEPEFaeTAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRA 165
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 13-165 4.48e-28

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


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 102.43  E-value: 4.48e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841   13 ALSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKsdAAATLREPKDF---LVTVAKRVMVDLFRRRTLERAYLE 89
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLE--ALDRFDPEGSFkawLFRIARNLILDYLRRKRRLRRELD 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 742394841   90 MLALIPDgYAPSPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKATEHC 165
Cdd:TIGR02937  80 LLEELLD-SDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 21-165 1.50e-24

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 93.30  E-value: 1.50e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  21 HHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKSDAAATLREPKDFLVTVAKRVMVDLFRRRTLERAY-LEMLALIPDGYA 99
Cdd:PRK12527   4 YYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALNLVVDRHRRHRVRQAEpLEVLDEEERLHS 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 742394841 100 PSPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKATEHC 165
Cdd:PRK12527  84 PSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHC 149
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 30-165 8.32e-15

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 68.17  E-value: 8.32e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  30 RRRLGCAFDADDVAQDTFMRLLKSDAAATLREPKDFLVTVAKRVMVDLFRRRTLERAYLE-----MLALIPDgyaPSPEQ 104
Cdd:PRK07037  16 ARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKQPVAYLFRIVRNLAIDHYRRQALENKYHGdeedgLDVPSPE---ASPEA 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 742394841 105 RQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKATEHC 165
Cdd:PRK07037  93 ALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHC 153
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 13-163 2.27e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 62.40  E-value: 2.27e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  13 ALSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKSdaAATLREPKDF---LVTVAKRVMVDLFRRRTLERA--- 86
Cdd:PRK12513  27 AFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRA--RAQYQPRARFrtwLYQIARNLLIDHWRRHGARQApsl 104

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 742394841  87 -YLEMLALIPDGyAPSPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKATE 163
Cdd:PRK12513 105 dADEQLHALADD-GAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQ 181
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 17-81 6.91e-12

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: 57.98  E-value: 6.91e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841   17 LYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKsdAAATLREPKD-----FLVTVAKRVMVDLFRRR 81
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWR--AIERFDPERGvsfstWLYTIIRNAIIDYLRKQ 68
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 112-165 1.98e-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: 56.31  E-value: 1.98e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 742394841  112 LQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKATEHC 165
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 12-155 8.89e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 57.76  E-value: 8.89e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  12 TALSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLL-KSDAAATLREPKDFLVTVAKRVMVDLFRRRT-----LER 85
Cdd:PRK12519  29 AALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWrKSSYDPKRGSLSSYLLTLTRSRAIDRLRSRRsrqrlLER 108

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  86 AYLEMLAlipDGYAPSPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVK 155
Cdd:PRK12519 109 WQQELLG---EASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVK 175
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 28-155 3.23e-10

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 56.72  E-value: 3.23e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  28 WLRRRL-GCAFDADDVAQDTFMRLLKSDAAATLREPKDFLVTVAKRVMVDLFRRRtlerAYLEMLALiPDGY------AP 100
Cdd:PRK09647  43 RLAYRLsGNQHDAEDLTQETFIRVFRSLQNYQPGTFEGWLHRITTNLFLDMVRRR----ARIRMEAL-PEDYdrvpgdEP 117

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 742394841 101 SPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVK 155
Cdd:PRK09647 118 NPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVR 172
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 8-161 1.19e-09

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 55.74  E-value: 1.19e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841   8 SAPHTALSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKSdAAATLREPKDFLVTVAKRVMVDLFRRRTLERAY 87
Cdd:PRK09635   1 MSQHDPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRA-PVGDIDDERGWLIVVTSRLCLDHIKSASTRRER 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  88 LEMLALIPDGyAPSP-------------EQRQSLLEslqqidaMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSV 154
Cdd:PRK09635  80 PQDIAAWHDG-DASVssvdpadrvtlddEVRLALLI-------MLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTC 151


                 ....*..
gi 742394841 155 KKYMAKA 161
Cdd:PRK09635 152 RQLAHRA 158
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 38-174 1.36e-09

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 54.66  E-value: 1.36e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  38 DADDVAQDTFMRLLKSDAAATLREP-KDFLVTVAKRVMVDLFRR-----RTLERAYLEMLAlipdgyapSPEQRQSLLES 111
Cdd:PRK09649  49 SADDLTQETFLRAIGAIPRFSARSSaRTWLLAIARHVVADHIRHvrsrpRTTRGARPEHLI--------DGDRHARGFED 120

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 742394841 112 LQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKATEHCLLFSLENDV 174
Cdd:PRK09649 121 LVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDALLADAEPDDL 183
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 16-164 2.65e-09

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 53.41  E-value: 2.65e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  16 RLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKSDAAAtlRE-PKDFLVTVAKRVMVDLFRRRTLERAYLEMLALI 94
Cdd:PRK09639   7 DLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRSDFKG--IEnEKGWLIKSARNVAYNYLRSEKRRRARILGEFQW 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 742394841  95 PDG-YAPSPEQRQSLLESLQQIDAMLDGLGPKvKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKATEH 164
Cdd:PRK09639  85 QEVdNEPSPEEIWIRKEEITKVQEVLAKMTER-DRTVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKKK 154
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 38-163 4.07e-09

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 52.66  E-value: 4.07e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  38 DADDVAQDTFMRLLKSDAAATLREPKDFLVTVAKRVMVDLFRRRTLERAYLEML-----------------ALIPDGYAP 100
Cdd:PRK09047   6 AALDIVQDAMIKLAEKYGDRPAAEWPPLFQRILQNRIHDWFRRQKVRNTWVSLFssfsdddddddfdpletLDSADEGAE 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 742394841 101 SPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKATE 163
Cdd:PRK09047  86 SPADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATH 148
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 21-155 4.44e-09

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 53.06  E-value: 4.44e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  21 HHAWLQGWLRRRLGCAFDADDVAQDTFMRllksdAAATLREPKD------FLVTVAKRVMVDLFRRRTLERAYLEMLAli 94
Cdd:PRK09637  10 YKAQLKAFLHSRVSNEADVDDLLQEVLIK-----THSNLHSLKDgssiksWLYQIANNTIIDFYRKKNRSEELPDDLL-- 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 742394841  95 pdgyAPSPEQRQSLLESLQQ-IDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVK 155
Cdd:PRK09637  83 ----FEDEEREENAKKELAPcLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAK 140
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 13-158 9.12e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 52.13  E-value: 9.12e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  13 ALSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLL-KSDA-AATLREPKDFLVTVAKRVMVDLFRRRTLERAYLEM 90
Cdd:PRK12514  20 AFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWtKADRfAVSGLSPMTWLITIARNHAIDRLRARKAVAVDIDE 99

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 742394841  91 LALIPDGyAPSPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYM 158
Cdd:PRK12514 100 AHDLADP-SPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWL 166
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 38-155 9.24e-09

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 52.12  E-value: 9.24e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  38 DADDVAQDTFMRLLKsdAAATLREPKDF---LVTVAKRVMVDLFRRRTLERAYLEMLALIPDGYAPSPEQRQS------L 108
Cdd:PRK09652  36 DAEDLVQETFIKAYR--ALHSFRGGAAFytwLYRIARNTAINYLRKQGRRPPASDVDAEEAEDFDLADALRDIstpeneL 113

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 742394841 109 LESL--QQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVK 155
Cdd:PRK09652 114 LSAEleQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVR 162
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 9-164 1.10e-07

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 49.92  E-value: 1.10e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841   9 APHTALSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKSDAAAtLREPKDFLVTVAKRVMVDLFR--RRTLERA 86
Cdd:PRK09636   1 MTMADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLRWNNADRAQ-IRDPRAWLTRVVTRLCLDRLRsaRHRRETY 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  87 YLEMLaliPDgyaPSPEQRQSLLES-LQQIDA------MLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMA 159
Cdd:PRK09636  80 VGPWL---PE---PVVEELDDPLEAvVAAEDLslalmlALERLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLAS 153


                 ....*
gi 742394841 160 KATEH 164
Cdd:PRK09636 154 RARKH 158
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 34-161 5.71e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 47.80  E-value: 5.71e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  34 GCAFDADDVAQDTFMRLLKSDAAATLREPKDFLVTVAKRVMVDLFRRRTLERAYLE----MLALIPDGYAPSPEQRQSLL 109
Cdd:PRK12533  40 GNASDADDVVQEACMRALRFFDSFRGDNARPWLLAIVRHTWYSEWRRRANAHEVAApdtlDDADSLDDWQPAGEDPLALL 119

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 742394841 110 ---ESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKA 161
Cdd:PRK12533 120 lraEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARA 174
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 31-160 1.13e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 46.81  E-value: 1.13e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  31 RRLGCAFDADDVAQDTFMRLLKsdAAATLRE----PKDFLVTVAKRVMVDLFRRRTLERAYLEMLALIPDGYAPSPEQRQ 106
Cdd:PRK12524  45 RVLGDRAEAEDVTQEAMLRLWR--IAPDWRQgearVSTWLYRVVCNLCTDRLRRRRRASVDLDDAPEPADAAPGAEEALI 122

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 742394841 107 SLlESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAK 160
Cdd:PRK12524 123 EG-DRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTAR 175
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 112-161 1.27e-06

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: 43.63  E-value: 1.27e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 742394841 112 LQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKA 161
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRA 50
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 39-175 2.21e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 45.81  E-value: 2.21e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  39 ADDVAQDTFMRLLKSDA---AATLREPKDFLVTVAKRVMVDLFRRRTLERAYLEMLALIP-DGYAPSPEQRQSLLESLQQ 114
Cdd:PRK12542  36 AEDAVQETFITLYKNLEklhSLNTQELKRYILRVAKNKAIDSYRKNKRHETFLEEYERESiEAVDENIEEWEKRKMSEVQ 115

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 742394841 115 IDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKATE--HCLLFSLENDVF 175
Cdd:PRK12542 116 IDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKrvQNMIGGIQHDEF 178
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 38-161 2.48e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 45.55  E-value: 2.48e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  38 DADDVAQDTFMRLLKSDAaaTLREPKD---FLVTVAKRVMVDLFRRRTLERAYLEMLALIPDGYAPSPEQRQSlleSLQQ 114
Cdd:PRK12511  30 EAEDLVHDALVRALERRA--SFRSGGNlrtWLMSILHNAFIDELRRRRVEARRADELAVLADASLPAAQEHAV---RLAQ 104

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 742394841 115 IDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKA 161
Cdd:PRK12511 105 IRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRA 151
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 4-161 3.40e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 45.05  E-value: 3.40e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841   4 TATASAPHTALSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKSdaaATLREPK-----DFLVTVAKRVMVDLF 78
Cdd:PRK12534  17 TATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHK---AGQFDPSrarglTWLAMIARNKAIDHL 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  79 RRRTLERaylEMLALIPDGYAP----SPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSV 154
Cdd:PRK12534  94 RANAPQR---RNVALDDAGELRaadaSPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTV 170


                 ....*..
gi 742394841 155 KKYMAKA 161
Cdd:PRK12534 171 KSWIRRG 177
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
5-155 4.24e-06

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 44.68  E-value: 4.24e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841   5 ATASAPHTALSR-LYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLK--SDAAATLREPKDFLVTVAKRVMVDLFRRR 81
Cdd:PRK09645   1 SGMATAEAALMRaLYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQhpEVLADTGRSARAWLFTVARNLVIDERRSA 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 742394841  82 tleRAYLEMLALIPDGYA--PSPEQRQSLLESLQQIDAmLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVK 155
Cdd:PRK09645  81 ---RARPVEGGDDVLGVPeqSAPDEVDRALDRLLVADA-LAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVK 152
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 13-155 1.31e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 43.39  E-value: 1.31e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  13 ALSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKSDAAATLREPKDFLVTVAKRVMVDLFRRrtlERAY----L 88
Cdd:PRK12541   6 SLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRK---EKKYktttI 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  89 EMLALIPdgyAPSPEQrQSLLESlqQIDAMLD---GLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVK 155
Cdd:PRK12541  83 EEFHLPN---VPSTEH-EYFIKH--EIASWLDslsSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVK 146
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 45-165 1.42e-05

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


Pssm-ID: 254323 [Multi-domain]  Cd Length: 185  Bit Score: 43.56  E-value: 1.42e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841   45 DTFMRLLKSDAAATLREPKDF---LVTVAKRVMVDLFRRRTLER-----AYLEMLALIPDGYAPSPEQRQSLLESLQQid 116
Cdd:pfam07638  55 EAFVRLVDTEDFPDWSGRGHFfaaAAEAMRRILIDHARRRQRQKrggdvQRRELDEVVDNGDSPNPDLLLDLDEALEQ-- 132

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 742394841  117 amLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKATEHC 165
Cdd:pfam07638 133 --LFSLSPRQARLVELRFFAGLSNDEIAERLGVSERTVERNWALARAWL 179
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 13-161 1.55e-05

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 43.10  E-value: 1.55e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  13 ALSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKSdaAATLREPKDFLVTVAKRVMVDL----FRRRTLerAYL 88
Cdd:PRK05602  21 AFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQ--APSWRPGEARFDTWLHRVVLNLcydrLRRRRE--VPV 96

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 742394841  89 EMLALIPDGyAPSPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKA 161
Cdd:PRK05602  97 EDAPDVPDP-APGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARG 168
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 31-155 1.86e-05

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 43.15  E-value: 1.86e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  31 RRLGCAFDADDVAQDTFMRLLKS-DAAATLREPKDFLVTVAKRVMVDLFRRRTLErAYLE----------MLALIPDGyA 99
Cdd:PRK09641  37 RMLGNRHEAEDAAQEAFIRAYVNiDSYDINRKFSTWLYRIATNLTIDRLRKRKPD-YYLDaevagtegltMYSQLAAD-D 114

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 742394841 100 PSPEQRQSLLESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVK 155
Cdd:PRK09641 115 ALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVK 170
SigM_subfam TIGR02950
RNA polymerase sigma factor, SigM family; This family of RNA polymerase sigma factors is a ...
 39-155 2.56e-05

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


Pssm-ID: 274361 [Multi-domain]  Cd Length: 154  Bit Score: 42.44  E-value: 2.56e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841   39 ADDVAQDTFMRLLKSDAAATLREPKDFLVTVAKRVMVDLFR----RRTLERAYLEMLALIPdgyAPSPEQRQSLLESLQQ 114
Cdd:TIGR02950  22 AEDLLQETFLKAYIHLHSFKDSSIKPWLFRIARNAFIDWYRkdkkIQTIDDDAIGDLEQHP---VESPEHHLLIKIEQEE 98

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 742394841  115 IDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVK 155
Cdd:TIGR02950  99 ITHHLSRLPENYRTVLILREFKEFSYKEIAELLNLSLAKVK 139
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 13-161 9.46e-05

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 40.77  E-value: 9.46e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  13 ALSRLYATHHAWLQGWLrrrLGCAFD---ADDVAQDTFMR-LLKSDAAATLREPKDFLVTVAKRVMVDLFRRRTLERAYL 88
Cdd:PRK09638  19 ALTTLFQQHYSFLYKYL---LKLTLDpdlAEDLVQETMLKaIENLSSFQGRSKFSTWLISIASRLYKDHLRKQKREKLRL 95

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 742394841  89 EMLAlipdGYAPSPEQRQSLLESLQQIDAM--LDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKA 161
Cdd:PRK09638  96 QRAK----EETLRKEKWEAAIKGAEWSEMLdaLSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHG 166
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 39-161 1.14e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 41.04  E-value: 1.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  39 ADDVAQDTFMRLLKSDAAATLRE-PKDFLVTVAKRVMVDLFR----RRTLERAYLEMLAlipdGYAPSPEQRQSLLESLQ 113
Cdd:PRK12535  51 ADDLTQETYLRVMSALPRFAARSsARTWLLSLARRVWVDNIRhdmaRPRKSATEYEDAA----ATTASNETTGSWSEWID 126

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 742394841 114 qIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKA 161
Cdd:PRK12535 127 -VRTLIDALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARA 173
PRK06930 PRK06930
positive control sigma-like factor; Validated
 113-161 1.33e-04

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 40.48  E-value: 1.33e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 742394841 113 QQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKA 161
Cdd:PRK06930 106 IRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERA 154
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 39-161 1.39e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 40.72  E-value: 1.39e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  39 ADDVAQDTFMRL-LKSDAAATLREPKDFLVTVAKRVMVDLFRRRTleRAYLEMLALIPDGYAPSPEQRQSLleSLQQIDA 117
Cdd:PRK12516  37 ADDLVQDTIMKAwAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRG--REVQDTDGMFTEQLAVHPSQYGTL--DLQDFRA 112

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 742394841 118 MLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKA 161
Cdd:PRK12516 113 ALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRA 156
PRK08241 PRK08241
RNA polymerase subunit sigma-70;
1-49 5.17e-04

RNA polymerase subunit sigma-70;


Pssm-ID: 236196 [Multi-domain]  Cd Length: 339  Bit Score: 39.53  E-value: 5.17e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 742394841   1 MSATATASAPHTALSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMR 49
Cdd:PRK08241   8 ALLARAAAGDRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLR 56
PRK09191 PRK09191
two-component response regulator; Provisional
 76-163 8.15e-04

two-component response regulator; Provisional


Pssm-ID: 236402 [Multi-domain]  Cd Length: 261  Bit Score: 38.68  E-value: 8.15e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  76 DLFRRRTLErAYLEMLALIPDGYAPspeqRQSLLESLQQI-------------------DAMLDGLGPKVKQAFLLSQLE 136
Cdd:PRK09191  29 DAYVAATLE-ALLADPSIFPEASSP----RVGLYRLFHRLwssagandpepgspfearaERRLAGLTPLPRQAFLLTALE 103

                         90       100
                 ....*....|....*....|....*..
gi 742394841 137 GLGYADIAVRLGVSISSVKKYMAKATE 163
Cdd:PRK09191 104 GFSVEEAAEILGVDPAEAEALLDDARA 130
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 13-156 8.69e-04

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: 38.07  E-value: 8.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841   13 ALSRLYATHHAWLQGWLRRRLGCAFDADDVAQDTFMRLLKSdaAATLREPKDF---LVTVAKRVMVDLFRRRTLERAYL- 88
Cdd:TIGR02989   2 AFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRK--FDQFDPGTNFvawARGIARNKVLNYRRKLGRDRLVFd 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 742394841   89 -EMLALIPDGYAPSPEQRQSllESLQQIDAMLDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKK 156
Cdd:TIGR02989  80 dDLLEALAAEAEPTEAERLS--DDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYK 146
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 39-161 1.82e-03

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 37.17  E-value: 1.82e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742394841  39 ADDVAQDTFMRLLKSDAAATLREPKDFLVTVAKRVMVDLFRRRtlERAYLEMLALIPDGYAPSPEQRQSLLESLQQIDAM 118
Cdd:PRK09644  28 AEDLLQETFYRAYIYLEDYDNQKVKPWLFKVAYHTFIDFVRKE--KKVSFVGTDEIEAIQAESTEEYVVAKNSYEKLIQI 105

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 742394841 119 LDGLGPKVKQAFLLSQLEGLGYADIAVRLGVSISSVKKYMAKA 161
Cdd:PRK09644 106 IHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRG 148
TnsD pfam15978
Tn7-like transposition protein D; TnsD is a family of putative Tn7-like transposition proteins ...
 122-157 7.38e-03

Tn7-like transposition protein D; TnsD is a family of putative Tn7-like transposition proteins type D.


Pssm-ID: 379756  Cd Length: 360  Bit Score: 36.24  E-value: 7.38e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 742394841  122 LGPKVKQAF-LLSQLEGLGYADIAVRLGVSISSVKKY 157
Cdd:pfam15978 183 FGPVWEERLkILVEDEGLSLREIAKELGVDIKTVKRY 219
 
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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