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RNA polymerase sporulation sigma factor SigH [Caldibacillus debilis]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 11483241)

sigma-70 family RNA polymerase sigma factor such as RNA polymerase sporulation sigma factor SigH, which is involved in the transition to post-exponential phase in the beginning of sporulation and is also required for the transcription of several stationary phase genes

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
8-213 2.92e-126

RNA polymerase sporulation sigma factor SigH;


:

Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 354.98  E-value: 2.92e-126
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498   8 NKAQKYKDLDDELIVELVHQGESDALDYLVHKYRLFVRAKARSYFLIGADREDIIQEGMIGLFKAIRDYKDDKFTSFKAF 87
Cdd:PRK08295   1 LRMKDYDELEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  88 AELCITRQMITAIKTATRQKHIPLNSYISLDKPIYDEESDRTLMDTLSGSKLSDPEELIINKEEYDHIEVKMSELLSDLE 167
Cdd:PRK08295  81 AELCITRQIITAIKTANRQKHIPLNSYVSLDKPIYDEESDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 518999498 168 RKVLALYLDGQSYQEISEELNRHVKSIDNALQRVKRKLEKYLETRE 213
Cdd:PRK08295 161 KEVLELYLDGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYLENRE 206
 
Name Accession Description Interval E-value
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
8-213 2.92e-126

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 354.98  E-value: 2.92e-126
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498   8 NKAQKYKDLDDELIVELVHQGESDALDYLVHKYRLFVRAKARSYFLIGADREDIIQEGMIGLFKAIRDYKDDKFTSFKAF 87
Cdd:PRK08295   1 LRMKDYDELEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  88 AELCITRQMITAIKTATRQKHIPLNSYISLDKPIYDEESDRTLMDTLSGSKLSDPEELIINKEEYDHIEVKMSELLSDLE 167
Cdd:PRK08295  81 AELCITRQIITAIKTANRQKHIPLNSYVSLDKPIYDEESDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 518999498 168 RKVLALYLDGQSYQEISEELNRHVKSIDNALQRVKRKLEKYLETRE 213
Cdd:PRK08295 161 KEVLELYLDGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYLENRE 206
spore_sigH TIGR02859
RNA polymerase sigma-H factor; Members of this protein family are RNA polymerase sigma-H ...
 13-210 5.71e-119

RNA polymerase sigma-H factor; Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs in Listeria score well against this model, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt. [Transcription, Transcription factors, Cellular processes, Sporulation and germination]


Pssm-ID: 131906 [Multi-domain]  Cd Length: 198  Bit Score: 336.00  E-value: 5.71e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498   13 YKDLDDELIVELVHQGESDALDYLVHKYRLFVRAKARSYFLIGADREDIIQEGMIGLFKAIRDYKDDKFTSFKAFAELCI 92
Cdd:TIGR02859   1 FKQLEDEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498   93 TRQMITAIKTATRQKHIPLNSYISLDKPIYDEESDRTLMDTLSGSKLSDPEELIINKEEYDHIEVKMSELLSDLERKVLA 172
Cdd:TIGR02859  81 TRQIITAIKTATRQKHIPLNSYVSLNKPIYDEESDRTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQ 160

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 518999498  173 LYLDGQSYQEISEELNRHVKSIDNALQRVKRKLEKYLE 210
Cdd:TIGR02859 161 SYLDGKSYQEIACDLNRHVKSIDNALQRVKRKLEKYLE 198
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 17-215 8.95e-23

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


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 90.44  E-value: 8.95e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  17 DDELIVELVHQGESDALDYLVHKYRLFVRAKARSYFLIGADREDIIQEGMIGLFKAIRDYKDDkfTSFKAFAELCITRQM 96
Cdd:COG1595    3 SDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGR--GSFRAWLYRIARNLA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  97 ITAIKTATRQKHIplnsyisLDKPIYDEESDRtlmdtlsgsklSDPEELIINKEEYDHIEVKMSElLSDLERKVLAL-YL 175
Cdd:COG1595   81 IDHLRKRRRRREL-------LDELAEELPDEA-----------ADPEEALEAEELLEALLAALER-LPPRQREVLVLrYL 141

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 518999498 176 DGQSYQEISEELNRHVKSIDNALQRVKRKLEKYLETRETS 215
Cdd:COG1595  142 EGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGAL 181
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 36-105 1.46e-13

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 63.38  E-value: 1.46e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498   36 LVHKYRLFVRAKARSYFLIGADREDIIQEGMIGLFKAIRDYKDDKFTSFKAFAELCITRQMITAIKTATR 105
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 161-205 2.64e-06

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 43.28  E-value: 2.64e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 518999498   161 ELLSDLERKVLALYLDGQSYQEISEELNRHVKSIDNALQRVKRKL 205
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 163-205 8.56e-05

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 39.05  E-value: 8.56e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 518999498 163 LSDLERKVLALYLDGQSYQEISEELNRHVKSIDNALQRVKRKL 205
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKL 43
 
Name Accession Description Interval E-value
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
8-213 2.92e-126

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 354.98  E-value: 2.92e-126
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498   8 NKAQKYKDLDDELIVELVHQGESDALDYLVHKYRLFVRAKARSYFLIGADREDIIQEGMIGLFKAIRDYKDDKFTSFKAF 87
Cdd:PRK08295   1 LRMKDYDELEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  88 AELCITRQMITAIKTATRQKHIPLNSYISLDKPIYDEESDRTLMDTLSGSKLSDPEELIINKEEYDHIEVKMSELLSDLE 167
Cdd:PRK08295  81 AELCITRQIITAIKTANRQKHIPLNSYVSLDKPIYDEESDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 518999498 168 RKVLALYLDGQSYQEISEELNRHVKSIDNALQRVKRKLEKYLETRE 213
Cdd:PRK08295 161 KEVLELYLDGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYLENRE 206
spore_sigH TIGR02859
RNA polymerase sigma-H factor; Members of this protein family are RNA polymerase sigma-H ...
 13-210 5.71e-119

RNA polymerase sigma-H factor; Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs in Listeria score well against this model, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt. [Transcription, Transcription factors, Cellular processes, Sporulation and germination]


Pssm-ID: 131906 [Multi-domain]  Cd Length: 198  Bit Score: 336.00  E-value: 5.71e-119
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498   13 YKDLDDELIVELVHQGESDALDYLVHKYRLFVRAKARSYFLIGADREDIIQEGMIGLFKAIRDYKDDKFTSFKAFAELCI 92
Cdd:TIGR02859   1 FKQLEDEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498   93 TRQMITAIKTATRQKHIPLNSYISLDKPIYDEESDRTLMDTLSGSKLSDPEELIINKEEYDHIEVKMSELLSDLERKVLA 172
Cdd:TIGR02859  81 TRQIITAIKTATRQKHIPLNSYVSLNKPIYDEESDRTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQ 160

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 518999498  173 LYLDGQSYQEISEELNRHVKSIDNALQRVKRKLEKYLE 210
Cdd:TIGR02859 161 SYLDGKSYQEIACDLNRHVKSIDNALQRVKRKLEKYLE 198
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 17-215 8.95e-23

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


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 90.44  E-value: 8.95e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  17 DDELIVELVHQGESDALDYLVHKYRLFVRAKARSYFLIGADREDIIQEGMIGLFKAIRDYKDDkfTSFKAFAELCITRQM 96
Cdd:COG1595    3 SDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGR--GSFRAWLYRIARNLA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  97 ITAIKTATRQKHIplnsyisLDKPIYDEESDRtlmdtlsgsklSDPEELIINKEEYDHIEVKMSElLSDLERKVLAL-YL 175
Cdd:COG1595   81 IDHLRKRRRRREL-------LDELAEELPDEA-----------ADPEEALEAEELLEALLAALER-LPPRQREVLVLrYL 141

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 518999498 176 DGQSYQEISEELNRHVKSIDNALQRVKRKLEKYLETRETS 215
Cdd:COG1595  142 EGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGAL 181
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 31-209 1.11e-20

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: 84.32  E-value: 1.11e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498   31 DALDYLVHKYRLFVRAKARSYFLIGADREDIIQEGMIGLFKAIRDYKDDKftSFKAFAELCITRQMITAIKtatRQKHIP 110
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDYLR---RKRRLR 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  111 LNSYISLDKPIYDEesdrtlmdtlsgsklsDPEELIINKEEYDHIEVKMSElLSDLERKVLAL-YLDGQSYQEISEELNR 189
Cdd:TIGR02937  76 RELDLLEELLDSDP----------------SPEEELEQEEEREALREALEK-LPEREREVLVLrYLEGLSYKEIAEILGI 138

                         170       180
                  ....*....|....*....|
gi 518999498  190 HVKSIDNALQRVKRKLEKYL 209
Cdd:TIGR02937 139 SVGTVKRRLKRARKKLRELL 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 36-105 1.46e-13

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 63.38  E-value: 1.46e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498   36 LVHKYRLFVRAKARSYFLIGADREDIIQEGMIGLFKAIRDYKDDKFTSFKAFAELCITRQMITAIKTATR 105
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 22-211 8.92e-13

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 64.06  E-value: 8.92e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  22 VELVHQGESDALDYLVHKY-----RLFVRakarsyfLIG--ADREDIIQEGMIGLFKAIRDYKDDkfTSFKAFaelcITR 94
Cdd:PRK09652   1 VERVQRGDRAAFALLVRRYqprvkRLLSR-------LTRdpADAEDLVQETFIKAYRALHSFRGG--AAFYTW----LYR 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  95 QMI-TAIKTATRQKHIPLNSYISLDKPIYDEESDrTLMDTlsgsklSDPEELIINKEEYDHIEVKMSELLSDLeRKVLAL 173
Cdd:PRK09652  68 IARnTAINYLRKQGRRPPASDVDAEEAEDFDLAD-ALRDI------STPENELLSAELEQRVRAAIESLPEEL-RTAITL 139

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 518999498 174 -YLDGQSYQEISEELN---RHVKS-IDNALQRVKRKLEKYLET 211
Cdd:PRK09652 140 rEIEGLSYEEIAEIMGcpiGTVRSrIFRAREALRAKLQPLLDE 182
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 17-207 1.73e-10

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


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 58.68  E-value: 1.73e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  17 DDELIVELVHQGESDALDYLVHKYRLFVRAKARSYFL-IGADREDIIQEGMIGLFKAIRDYKDDKFTSFKAFAELCITRQ 95
Cdd:COG1191    1 DLEELLRRYQEGDEEAREELIEEYLPLVKKIASRLAGrLPAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  96 MI-----------------TAIKTATR---QKH--------------IPLNSY------------ISLDKPIYDEESdrt 129
Cdd:COG1191   81 ILdylrdedwvprsvrelaRKIEEAIEeleQELgreptdeeiaeelgISLEEVqealeaanayqlLSLDEPLEDGDD--- 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498 130 LMDTLSGsklSDPEELIINKEEYDHIeVKMSELLSDLERKVLAL-YLDGQSYQEISEELNRHVKSI----DNALQRVKRK 204
Cdd:COG1191  158 LLDLLES---GDPEEELEHEELREAL-AEAIEQLPERERLVLSLyYFEELTLKEIAEVLGVSESRVsrlhKKALARLREY 233


                 ...
gi 518999498 205 LEK 207
Cdd:COG1191  234 LKE 236
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
23-173 2.93e-08

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 52.26  E-value: 2.93e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  23 ELVHQGESDALDYLV-HKYRLfVRAKARSYFLIGADREDIIQEGMIGLFKAIRDYKDDKFTSFKAFAELCITRQMITAIK 101
Cdd:PRK05803  41 ELMKEGDEEARNILIeRNLRL-VAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLR 119

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 518999498 102 TATRQKhiplnSYISLDKPI-YDEE-SDRTLMDTLSgsklSDPE---ELIINKEEYDHIEVKMSeLLSDLERKVLAL 173
Cdd:PRK05803 120 NLKKTK-----KEVSLQDPIgVDKEgNEISLIDILG----SEEDdviEQVELKMEVEKLYKKID-ILDEREKEVIEM 186
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 14-110 7.66e-08

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 51.23  E-value: 7.66e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  14 KDLDDELIVELVHQGESDALDYLVHKYRLFVRAKARSYFLIGADREDIIQEGMIGLFKAIRDYKDDKFTSFKAFAELCIt 93
Cdd:PRK08583  12 KEEVNKWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTI- 90

                         90       100
                 ....*....|....*....|.
gi 518999498  94 rqmITAIKTATRQK----HIP 110
Cdd:PRK08583  91 ---IGEIKRYLRDKtwsvHVP 108
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 26-188 1.49e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 46.89  E-value: 1.49e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  26 HQGESDALDYLVHKYRLFVRAKARSYFLIGADREDIIQEGMIGLFKairdykddKFTSFKAFAELcitRQMITAIktaTR 105
Cdd:PRK11924   8 ATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWR--------KADLFNGKGSA---RTWLLTI---AR 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498 106 QKHIPLNSYISLDKpiYDEESDrtLMDTLSGSKLSDPEELIINKEEYDHIEvKMSELLSDLERKVLAL-YLDGQSYQEIS 184
Cdd:PRK11924  74 NVCYDLLRRRRREK--AVLSDD--ALEPEFAETAETPEAALLAKDDLARID-RCLDALPVKQREVFLLrYVEGLSYREIA 148


                 ....
gi 518999498 185 EELN 188
Cdd:PRK11924 149 EILG 152
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 147-206 1.68e-06

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 45.65  E-value: 1.68e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498 147 INKEEYDHIEVkMSELLSDLERKVLALYLDGQSYQEISEELNRHVKSIDNALQRVKRKLE 206
Cdd:COG2197   55 IRMPGMDGLEA-LRRLLTPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLG 113
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 16-210 1.75e-06

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 46.83  E-value: 1.75e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  16 LDDELIVELVHQGESDALDYLVHKYRLFVRAKARSYFLIGADREDIIQEGMIGLFKAIRDYkDDKFTSFKAFAeLCITRQ 95
Cdd:PRK13919   8 LSDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEF-DPRRGSARAWL-LALAHH 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  96 miTAIKTATRQKHIPLnsyisldkPIYDEESDRTLMDtLSGSKLSDPEELiinkeeyDHIEVKMS-ELLSDLERKVL-AL 173
Cdd:PRK13919  86 --AAVDHVRRRAARPQ--------PLEPDEREPEAFD-LPGPGLDEEGHL-------DRTRLGRAlKALSPEERRVIeVL 147

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 518999498 174 YLDGQSYQEISEELNRHVKSIDNalqRVKRKLEKYLE 210
Cdd:PRK13919 148 YYQGYTHREAAQLLGLPLGTLKT---RARRALSRLKE 181
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 161-205 2.58e-06

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 43.21  E-value: 2.58e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 518999498  161 ELLSDLERKVLAL-YLDGQSYQEISEELNRHVKSIDNALQRVKRKL 205
Cdd:pfam08281   9 EELPPRQREVFLLrYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 161-205 2.64e-06

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 43.28  E-value: 2.64e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 518999498   161 ELLSDLERKVLALYLDGQSYQEISEELNRHVKSIDNALQRVKRKL 205
Cdd:smart00421   2 ASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 115-188 3.98e-06

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


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 46.20  E-value: 3.98e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 518999498 115 ISLDKPIyDEESDRTLMDTLSGSKLSDPEELIINKEEYDHIEVKMSElLSDLERKVLALY---LDGQSY--QEISEELN 188
Cdd:COG0568  161 VSLDAPV-GDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDT-LTEREREILRLRfglDDGEPHtlEEIGKEFG 237
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
163-205 6.98e-06

DNA-binding transcriptional regulator, CsgD family [Transcription];


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 45.13  E-value: 6.98e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 518999498 163 LSDLERKVLALYLDGQSYQEISEELNRHVKSIDNALQRVKRKL 205
Cdd:COG2771  128 LTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKL 170
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 17-210 2.65e-05

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 43.25  E-value: 2.65e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  17 DDELIVELVHQGESDALDYLVHKYRLFVRAKARSYFLIGADREDIIQEGMIGLFKAIRDYKDDKftsfkAFaelcITRQM 96
Cdd:PRK11923   6 EDQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS-----AF----YTWLY 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  97 ITAIKTA-----TRQKHIPLNSYISLDKPIYDEESDRTLMDTlsgsklsdPEELIINKEEYDHIEVKMSELLSDLERKVL 171
Cdd:PRK11923  77 RIAINTAknhlvSRGRRPPDSDVSSEDAEFYDGDHALKDIES--------PERALLRDEIEGTVHRTIQQLPEDLRTALT 148

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 518999498 172 ALYLDGQSYQEISEELNRHVKSIDNALQRVKRKLEKYLE 210
Cdd:PRK11923 149 LREFDGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
1-81 3.88e-05

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 43.42  E-value: 3.88e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498   1 MRVEPSRNKAQ-KYKDLDDELIVELVHQGESDALDYLVHKYRLFVRAKARSYFLIGADREDIIQEGMIGLFKAIrdykdD 79
Cdd:PRK05572   1 MDIEVKNKKKKpQLKDEENKELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAV-----D 75


                 ..
gi 518999498  80 KF 81
Cdd:PRK05572  76 KF 77
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 15-212 5.36e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 42.57  E-value: 5.36e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  15 DLDDELIVELVHQGESDALDYLVHkyRLFVRAKARSYFLIG--ADREDIIQEGMIGLFKAIRDYKDDKFTS----FKAFA 88
Cdd:PRK12524  10 DVSDEALLVLYANGDPAAARALTL--RLAPRALAVATRVLGdrAEAEDVTQEAMLRLWRIAPDWRQGEARVstwlYRVVC 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  89 ELCITRqmitaiKTATRQKHIplnsyisldkpiyDEESDRTLMDTLSGSklsdpEELIINKEEYDHIEVKMSELLSDLER 168
Cdd:PRK12524  88 NLCTDR------LRRRRRASV-------------DLDDAPEPADAAPGA-----EEALIEGDRMRALDAALAALPERQRQ 143

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 518999498 169 KVLALYLDGQSYQEISEELNRHVKSIDNALQRVKRKLEKYLETR 212
Cdd:PRK12524 144 AVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRALAALLAGQ 187
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 163-205 8.56e-05

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 39.05  E-value: 8.56e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 518999498 163 LSDLERKVLALYLDGQSYQEISEELNRHVKSIDNALQRVKRKL 205
Cdd:cd06170    1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKL 43
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 135-213 4.59e-04

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 39.55  E-value: 4.59e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498 135 SGSKLSDPEELIINKEEYDhievKMSELLSDL---ERKVLALYLDGQSYQEISEELNRHVKSIDNALQRVKRKLEKYLET 211
Cdd:PRK09639  86 EVDNEPSPEEIWIRKEEIT----KVQEVLAKMterDRTVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQ 161


                 ..
gi 518999498 212 RE 213
Cdd:PRK09639 162 ME 163
PRK08311 PRK08311
RNA polymerase sigma factor SigI;
14-199 1.19e-03

RNA polymerase sigma factor SigI;


Pssm-ID: 236233 [Multi-domain]  Cd Length: 237  Bit Score: 38.70  E-value: 1.19e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  14 KDLDDELIVELVHQGESDALDYLVHKYRLFVrAKARSYFL---IGADREDIIQEGMIGLFKAIRDYKDDKFTSFKAFAEL 90
Cdd:PRK08311   1 RKKSLEDILEKIKNGDEELREELIEEYKPFI-AKVVSSVCgryIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAEL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  91 CITRQMITAIKTATRQKHIPLNSYisldkpiYDEESDRTLMDTLSGSKLSDPEELIINKEEYDHIEvkmsellsdlerKV 170
Cdd:PRK08311  80 VIKRRLIDYFRKESKHNLVLSNSD-------EEDEEENDIEIELSLEEYQEEEENEERREEIEEFK------------KE 140

                        170       180
                 ....*....|....*....|....*....
gi 518999498 171 LALYldGQSYQEISEELNRHVKSIDNALQ 199
Cdd:PRK08311 141 LKEF--GITFEDLVKESPKHRDTRENAIK 167
PRK09642 PRK09642
RNA polymerase sigma factor;
143-213 1.80e-03

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 37.77  E-value: 1.80e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 518999498 143 EELIINKEEYDHIEVKMSELLSDLERKVLALYLDGQSYQEISEELNRHVKSIDNALQRVKRKLEKYLETRE 213
Cdd:PRK09642  88 EDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEEE 158
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 57-88 2.06e-03

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 37.90  E-value: 2.06e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 518999498  57 DREDIIQEGMIGLFKAIRDYKDDKFTSFKAFA 88
Cdd:PRK06986  37 DLDDLIQAGMIGLLEAARRYDGEQGASFETYA 68
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 109-187 2.49e-03

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 37.74  E-value: 2.49e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498 109 IPLNSYISLDKPIY-DEESDR-TLMDTLSGSKLSDPEElIINKEEYDHIEVKMSELLSDLERKVLAL-YLDGQSYQEISE 185
Cdd:PRK06288 158 LSGTSVVSLNDLWFgGDEGDEvSLMDTLESPAALNPDE-IAEREEIKRVIVEAIKTLPEREKKVLILyYYEDLTLKEIGK 236


                 ..
gi 518999498 186 EL 187
Cdd:PRK06288 237 VL 238
PRK11475 PRK11475
DNA-binding transcriptional activator BglJ; Provisional
 88-194 3.45e-03

DNA-binding transcriptional activator BglJ; Provisional


Pssm-ID: 236915 [Multi-domain]  Cd Length: 207  Bit Score: 37.03  E-value: 3.45e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498  88 AELCITRQMITAIKTATRQKHIPLNSYIS---LDKPIYDEESDRTLMDTLSGSkLSDPEEliINKEEYDHIEVKMSELLS 164
Cdd:PRK11475  60 TELAIKFPRMRRLVIADDDIEARLIGSLSpspLDGVLSKASTLEILQQELFLS-LNGVRQ--ATDRLNNQWYINQSRMLS 136

                         90       100       110
                 ....*....|....*....|....*....|
gi 518999498 165 DLERKVLALYLDGQSYQEISEELNRHVKSI 194
Cdd:PRK11475 137 PTEREILRFMSRGYSMPQIAEQLERNIKTI 166
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 111-207 4.81e-03

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 37.24  E-value: 4.81e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518999498 111 LNSYI-SLDKPIyDEESDRTLMDTLSGSKLSDPEELIINKEEYDHIEVKMSElLSDLERKVLA-----LYLDGQSYQEIS 184
Cdd:PRK05657 212 LNERItSLDTPL-GGDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFE-LNDKQREVLArrfglLGYEAATLEDVA 289

                         90       100
                 ....*....|....*....|....*..
gi 518999498 185 EELN---RHVKSID-NALQRVKRKLEK 207
Cdd:PRK05657 290 REIGltrERVRQIQvEALRRLREILQT 316
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 143-207 6.64e-03

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 36.07  E-value: 6.64e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 518999498 143 EELIINKEEYDHIeVKMSELLSDLERKVLAL-YLDGQSYQEISEELNRHVKSIDNALQRVKRKLEK 207
Cdd:PRK06811 113 ENEIILKENKEEI-LKLINDLEKLDREIFIRrYLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177
 
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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