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Conserved domains on  [gi|1490909940|gb|RLE41330|]
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DNA-binding response regulator [Candidatus Acetothermia bacterium]

Protein Classification

response regulator transcription factor( domain architecture ID 11450879)

response regulator transcription factor with a signal receiver (REC) domain and a LuxR family helix-turn-helix (HTH) domain that may be part of a two-component regulatory system; similar to Staphylococcus aureus response regulator VraR

CATH:  1.10.10.10
Gene Ontology:  GO:0000160|GO:0006355|GO:0003677
PubMed:  10966457
SCOP:  3001179

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 4-189 8.20e-26

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: 96.11  E-value: 8.20e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   4 IRIAIVDDHALVRAGLVRLLSA--RYDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLiaaspntrilvl 81
Cdd:COG2197     2 IRVLIVDDHPLVREGLRALLEAepDIEVVGEAADGEEALELLEELRPDVVLLDIRMPGMDGLEALRRL------------ 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940  82 tmydepeyaaaavaagacglvsksasadtlyaaidaavkgtlerpsfgLTEREQDVLSLLGEGKEDAEIAALLGISPRTV 161
Cdd:COG2197    70 ------------------------------------------------LTPREREVLRLLAEGLSNKEIAERLGISERTV 101

                         170       180
                  ....*....|....*....|....*...
gi 1490909940 162 ANHCARLMEKLGIHTRAGLIAHARRIRL 189
Cdd:COG2197   102 KTHVSNILRKLGVRNRTELVLLALRLGL 129
 
Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 4-189 8.20e-26

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: 96.11  E-value: 8.20e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   4 IRIAIVDDHALVRAGLVRLLSA--RYDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLiaaspntrilvl 81
Cdd:COG2197     2 IRVLIVDDHPLVREGLRALLEAepDIEVVGEAADGEEALELLEELRPDVVLLDIRMPGMDGLEALRRL------------ 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940  82 tmydepeyaaaavaagacglvsksasadtlyaaidaavkgtlerpsfgLTEREQDVLSLLGEGKEDAEIAALLGISPRTV 161
Cdd:COG2197    70 ------------------------------------------------LTPREREVLRLLAEGLSNKEIAERLGISERTV 101

                         170       180
                  ....*....|....*....|....*...
gi 1490909940 162 ANHCARLMEKLGIHTRAGLIAHARRIRL 189
Cdd:COG2197   102 KTHVSNILRKLGVRNRTELVLLALRLGL 129
PRK15369 PRK15369
two component system response regulator;
1-189 1.15e-23

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 92.83  E-value: 1.15e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   1 MPGIRIAIVDDHALVRAGLVRLLSA--RYDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPNTRI 78
Cdd:PRK15369    1 MKNYKILLVDDHELIINGIKNMLAPypRYKIVGQVDNGLEVYNACRQLEPDIVILDLGLPGMNGLDVIPQLHQRWPAMNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940  79 LVLTMYDEPEYAAAAVAAGACGLVSKSASADTLYAAIDAAVKG------TLER------------PSFGLTEREQDVLSL 140
Cdd:PRK15369   81 LVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGkryidpALNReailallnaddtNPPLLTPRERQILKL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1490909940 141 LGEGKEDAEIAALLGISPRTVANHCARLMEKLGIHTRAGLIAHARRIRL 189
Cdd:PRK15369  161 ITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWARRLGL 209
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 6-118 3.68e-19

phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family response regulators; The NarL family is one of the more abundant families of DNA-binding response regulators (RRs). Members of the NarL family contain a REC domain and a helix-turn-helix (HTH) DNA-binding output domain, with a majority of members containing a LuxR-type HTH domain. They function as transcriptional regulators. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381090 [Multi-domain]  Cd Length: 117  Bit Score: 78.71  E-value: 3.68e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   6 IAIVDDHALVRAGLVRLLSAR--YDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPNTRILVLTM 83
Cdd:cd17535     1 VLIVDDHPLVREGLRRLLESEpdIEVVGEAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRRYPDLKVIVLTA 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1490909940  84 YDEPEYAAAAVAAGACGLVSKSASADTLYAAIDAA 118
Cdd:cd17535    81 HDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAV 115
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 129-184 5.10e-18

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 74.10  E-value: 5.10e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1490909940  129 GLTEREQDVLSLLGEGKEDAEIAALLGISPRTVANHCARLMEKLGIHTRAGLIAHA 184
Cdd:smart00421   3 SLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
GerE pfam00196
Bacterial regulatory proteins, luxR family;
130-184 1.29e-14

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 64.91  E-value: 1.29e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1490909940 130 LTEREQDVLSLLGEGKEDAEIAALLGISPRTVANHCARLMEKLGIHTRAGLIAHA 184
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 130-172 1.31e-03

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: 37.71  E-value: 1.31e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1490909940 130 LTEREQDVLSL-LGEGKEDAEIAALLGISPRTVANHCARLMEKL 172
Cdd:TIGR02937 111 LPEREREVLVLrYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 4-189 8.20e-26

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: 96.11  E-value: 8.20e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   4 IRIAIVDDHALVRAGLVRLLSA--RYDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLiaaspntrilvl 81
Cdd:COG2197     2 IRVLIVDDHPLVREGLRALLEAepDIEVVGEAADGEEALELLEELRPDVVLLDIRMPGMDGLEALRRL------------ 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940  82 tmydepeyaaaavaagacglvsksasadtlyaaidaavkgtlerpsfgLTEREQDVLSLLGEGKEDAEIAALLGISPRTV 161
Cdd:COG2197    70 ------------------------------------------------LTPREREVLRLLAEGLSNKEIAERLGISERTV 101

                         170       180
                  ....*....|....*....|....*...
gi 1490909940 162 ANHCARLMEKLGIHTRAGLIAHARRIRL 189
Cdd:COG2197   102 KTHVSNILRKLGVRNRTELVLLALRLGL 129
PRK15369 PRK15369
two component system response regulator;
1-189 1.15e-23

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 92.83  E-value: 1.15e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   1 MPGIRIAIVDDHALVRAGLVRLLSA--RYDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPNTRI 78
Cdd:PRK15369    1 MKNYKILLVDDHELIINGIKNMLAPypRYKIVGQVDNGLEVYNACRQLEPDIVILDLGLPGMNGLDVIPQLHQRWPAMNI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940  79 LVLTMYDEPEYAAAAVAAGACGLVSKSASADTLYAAIDAAVKG------TLER------------PSFGLTEREQDVLSL 140
Cdd:PRK15369   81 LVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGkryidpALNReailallnaddtNPPLLTPRERQILKL 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1490909940 141 LGEGKEDAEIAALLGISPRTVANHCARLMEKLGIHTRAGLIAHARRIRL 189
Cdd:PRK15369  161 ITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELLNWARRLGL 209
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 6-118 3.68e-19

phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family response regulators; The NarL family is one of the more abundant families of DNA-binding response regulators (RRs). Members of the NarL family contain a REC domain and a helix-turn-helix (HTH) DNA-binding output domain, with a majority of members containing a LuxR-type HTH domain. They function as transcriptional regulators. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381090 [Multi-domain]  Cd Length: 117  Bit Score: 78.71  E-value: 3.68e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   6 IAIVDDHALVRAGLVRLLSAR--YDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPNTRILVLTM 83
Cdd:cd17535     1 VLIVDDHPLVREGLRRLLESEpdIEVVGEAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRRYPDLKVIVLTA 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1490909940  84 YDEPEYAAAAVAAGACGLVSKSASADTLYAAIDAA 118
Cdd:cd17535    81 HDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAV 115
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 129-184 5.10e-18

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 74.10  E-value: 5.10e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1490909940  129 GLTEREQDVLSLLGEGKEDAEIAALLGISPRTVANHCARLMEKLGIHTRAGLIAHA 184
Cdd:smart00421   3 SLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
5-177 9.34e-18

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 77.59  E-value: 9.34e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   5 RIAIVDDHALVRAGLVRLLS--ARYDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPNTRILVLT 82
Cdd:PRK10403    8 QVLIVDDHPLMRRGVRQLLEldPGFEVVAEAGDGASAIDLANRLDPDVILLDLNMKGMSGLDTLNALRRDGVTAQIIILT 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940  83 MYDEPEYAAAAVAAGACGLVSKSASADTLYAAIDAAVKGT-----------LERPSFG--------LTEREQDVLSLLGE 143
Cdd:PRK10403   88 VSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSkvfservnqylREREMFGaeedpfsvLTERELDVLHELAQ 167

                         170       180       190
                  ....*....|....*....|....*....|....
gi 1490909940 144 GKEDAEIAALLGISPRTVANHCARLMEKLGIHTR 177
Cdd:PRK10403  168 GLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSR 201
PRK10360 PRK10360
transcriptional regulator UhpA;
4-187 4.15e-17

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 75.40  E-value: 4.15e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   4 IRIAIVDDHALVRAGLVRLLSARYD--VIGEAADTASALALVRRASPDLLLLDLSLPDRDGLsaipDLIAASPN-TRILV 80
Cdd:PRK10360    2 ITVALIDDHLIVRSGFAQLLGLEPDlqVVAEFGSGREALAGLPGRGVQVCICDISMPDISGL----ELLSQLPKgMATIM 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940  81 LTMYDEPEYAAAAVAAGACGLVSKSASADTLYAAI-DAAVKGTLERPSFG----------LTEREQDVLSLLGEGKEDAE 149
Cdd:PRK10360   78 LSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVhTVATGGCYLTPDIAiklasgrqdpLTKRERQVAEKLAQGMAVKE 157

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1490909940 150 IAALLGISPRTVANHCARLMEKLGIHTRAGLiahARRI 187
Cdd:PRK10360  158 IAAELGLSPKTVHVHRANLMEKLGVSNDVEL---ARRM 192
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 130-193 5.12e-17

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 71.91  E-value: 5.12e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1490909940 130 LTEREQDVLSLLGEGKEDAEIAALLGISPRTVANHCARLMEKLGIHTRAGLIAHARRIRLEARD 193
Cdd:COG5905    13 LTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWALRLGLLSLD 76
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 130-186 3.10e-16

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: 69.49  E-value: 3.10e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1490909940 130 LTEREQDVLSLLGEGKEDAEIAALLGISPRTVANHCARLMEKLGIHTRAGLIAHARR 186
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
PRK09483 PRK09483
response regulator; Provisional
 4-175 1.02e-14

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 69.36  E-value: 1.02e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   4 IRIAIVDDHALVRAGLVRLLS--ARYDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPNTRILVL 81
Cdd:PRK09483    2 INVLLVDDHELVRAGIRRILEdiKGIKVVGEACCGEDAVKWCRTNAVDVVLMDMNMPGIGGLEATRKILRYTPDVKIIML 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940  82 TMYDEPEYAAAAVAAGACGLVSKSASADTLYAAIDAAVKG-------------------TLERPSFGLTEREQDVLSLLG 142
Cdd:PRK09483   82 TVHTENPLPAKVMQAGAAGYLSKGAAPQEVVSAIRSVHSGqryiasdiaqqmalsqiepATENPFASLSERELQIMLMIT 161

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1490909940 143 EGKEDAEIAALLGISPRTVANHCARLMEKLGIH 175
Cdd:PRK09483  162 KGQKVNEISEQLNLSPKTVNSYRYRMFSKLNIS 194
GerE pfam00196
Bacterial regulatory proteins, luxR family;
130-184 1.29e-14

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 64.91  E-value: 1.29e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1490909940 130 LTEREQDVLSLLGEGKEDAEIAALLGISPRTVANHCARLMEKLGIHTRAGLIAHA 184
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 130-188 1.51e-13

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 65.89  E-value: 1.51e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1490909940 130 LTEREQDVLSLLGEGKEDAEIAALLGISPRTVANHCARLMEKLGIHTRAGLIAHARRIR 188
Cdd:COG4566   138 LTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARSLAELVRLALALG 196
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 5-187 1.73e-13

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 66.21  E-value: 1.73e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   5 RIAIVDDHALVRAGLVRLLSA--RYDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPNTRILVLT 82
Cdd:PRK10651    8 TILLIDDHPMLRTGVKQLISMapDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLSGRIVVFS 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940  83 MYDEPEYAAAAVAAGACGLVSKSASADTLYAAIDAAVKG---------------------TLERPSFGLTEREQDVLSLL 141
Cdd:PRK10651   88 VSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQAAAGemvlsealtpvlaaslranraTTERDVNQLTPRERDILKLI 167

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1490909940 142 GEGKEDAEIAALLGISPRTVANHCARLMEKLGIHTR--AGLIAHARRI 187
Cdd:PRK10651  168 AQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRveAAVWVHQERI 215
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
8-189 2.69e-13

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 65.30  E-value: 2.69e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   8 IVDDHALVRAGLVRLL-SARYDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPNTRILVLTMYDE 86
Cdd:PRK09958    5 IIDDHPLAIAAIRNLLiKNDIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSAKND 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940  87 PEYAAAAVAAGACGLVSKSASADTLYAAIDAAVKG------TLERPSFGLTEREQDVLSLLGE----------GKEDAEI 150
Cdd:PRK09958   85 HFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGycyfpfSLNRFVGSLTSDQQKLDSLSKQeisvmryildGKDNNDI 164

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1490909940 151 AALLGISPRTVANHCARLMEKLGIHTRAGLIAHARRIRL 189
Cdd:PRK09958  165 AEKMFISNKTVSTYKSRLMEKLECKSLMDLYTFAQRNKI 203
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
4-189 3.28e-13

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 64.78  E-value: 3.28e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   4 IRIAIVDDHALVRAGLVRLLSARYDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPNTRILVLTM 83
Cdd:COG2771     2 LLLALALLLLALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940  84 YDEPEYAAAAVAAGACGLVSKSASADTLYAAIDAAVKGTLERPSFGLTEREQDVLSLLGEGKEDAEIAALLGISPRTVAN 163
Cdd:COG2771    82 LALLLLLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRT 161

                         170       180
                  ....*....|....*....|....*.
gi 1490909940 164 HCARLMEKLGIHTRAGLIAHARRIRL 189
Cdd:COG2771   162 HLKRIYRKLGVSSRAELVALALRLGL 187
AmiR COG3707
Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding ...
 1-119 1.21e-08

Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding antiterminator (ANTAR) domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 442921 [Multi-domain]  Cd Length: 194  Bit Score: 52.27  E-value: 1.21e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   1 MPGIRIAIVDDHALVRAGLVRLLS-ARYDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPnTRIL 79
Cdd:COG3707     1 MRGLRVLVVDDEPLRRADLREGLReAGYEVVAEAADGEDAVELVRELKPDLVIVDIDMPDRDGLEAARQISEERP-APVI 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1490909940  80 VLTMYDEPEYAAAAVAAGACGLVSKSASADTLYAAIDAAV 119
Cdd:COG3707    80 LLTAYSDPELIERALEAGVSAYLVKPLDPEDLLPALELAL 119
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
1-189 7.68e-08

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 50.26  E-value: 7.68e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   1 MPGIRIAIVDDHALVRAGLVRLL--SARYDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPNTRI 78
Cdd:PRK09935    1 MKPASVIIMDTHPIIRMSIEVLLqkNSELQIVLKTDDYRITIDYLRTRPVDLIIMDIDLPGTDGFTFLKRIKQIQSTVKV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940  79 LVLTMYDEPEYAAAAVAAGACGLVSKSASADTLYAAIDAAVKG-------TLE-----RPSFG------LTEREQDVLSL 140
Cdd:PRK09935   81 LFLSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMILSGytffpseTLNyiksnKCSTNsstdtvLSNREVTILRY 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1490909940 141 LGEGKEDAEIAALLGISPRTVANHCARLMEKLGIHTRAGLIAHARRIRL 189
Cdd:PRK09935  161 LVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELIDYAKLHEL 209
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
140-189 4.50e-07

ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 47.78  E-value: 4.50e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1490909940 140 LLGEGKEDAEIAALLGISPRTVANHCARLMEKLGIHTRAGLIAHARRIRL 189
Cdd:COG2909   133 LLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARARELGL 182
REC_PdtaR-like cd19932
phosphoacceptor receiver (REC) domain of PdtaR and similar proteins; This subfamily includes ...
 4-119 7.89e-07

phosphoacceptor receiver (REC) domain of PdtaR and similar proteins; This subfamily includes Mycobacterium tuberculosis PdtaR, also called Rv1626, and similar proteins containing a REC domain and an ANTAR (AmiR and NasR transcription antitermination regulators) RNA-binding output domain. PdtaR is a response regulator that acts at the level of transcriptional antitermination and is a member of the PdtaR/PdtaS two-component regulatory system. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381159 [Multi-domain]  Cd Length: 118  Bit Score: 45.87  E-value: 7.89e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   4 IRIAIVDDHALVRAGLVRLL-SARYDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAiPDLIAASPNTRILVLT 82
Cdd:cd19932     1 VRVLIAEDEALIRMDLREMLeEAGYEVVGEASDGEEAVELAKKHKPDLVIMDVKMPRLDGIEA-AKIITSENIAPIVLLT 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1490909940  83 MYDEPEYAAAAVAAGACGLVSKSASADTLYAAIDAAV 119
Cdd:cd19932    80 AYSQQDLVERAKEAGAMAYLVKPFSESDLIPAIEMAI 116
REC_DesR-like cd19930
phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of ...
 6-115 2.87e-06

phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of Bacillus subtilis DesR, Streptococcus pneumoniae response regulator spr1814, and similar proteins, all containing an N-terminal REC domain and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. DesR is a response regulator that, together with its cognate sensor kinase DesK, comprises a two-component regulatory system that controls membrane fluidity. Phosphorylation of the REC domain of DesR is allosterically coupled to two distinct exposed surfaces of the protein, controlling noncanonical dimerization/tetramerization, cooperative activation, and DesK binding. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381157 [Multi-domain]  Cd Length: 117  Bit Score: 44.57  E-value: 2.87e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   6 IAIVDDHALVRAGLVRLLSARYD--VIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPNTRILVLTM 83
Cdd:cd19930     1 VLIAEDQEMVRGALAALLELEDDleVVAQASNGQEALRLVLKHSPDVAILDIEMPGRTGLEVAAELREELPDTKVLIVTT 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1490909940  84 YDEPEYAAAAVAAGACGLVSKSASADTLYAAI 115
Cdd:cd19930    81 FGRPGYFRRALAAGVDGYVLKDRPIEELADAI 112
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 6-116 3.09e-06

Response regulator receiver domain; This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.


Pssm-ID: 395025 [Multi-domain]  Cd Length: 111  Bit Score: 44.06  E-value: 3.09e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   6 IAIVDDHALVRAGLVRLLSARYDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPNTRILVLTMYD 85
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEKEGYVVAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTAHG 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1490909940  86 EPEYAAAAVAAGACGLVSKSASADTLYAAID 116
Cdd:pfam00072  81 DEDDAVEALEAGADDFLSKPFDPDELLAAIR 111
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 1-193 8.80e-06

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 44.44  E-value: 8.80e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   1 MPGIRIAIVDDHALVRAGLVRLLSAR--YDVIGEAADTAS---ALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPN 75
Cdd:PRK10840    1 MNNMNVIIADDHPIVLFGIRKSLEQIewVNVVGEFEDSTAlinNLPKLDAHVLITDLSMPGDKYGDGITLIKYIKRHFPS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940  76 TRILVLTMYDEPEYAAAAVAAGACGLVSKSASADTLYAAIDAAVKGT----------LERPSFG------LTEREQDVLS 139
Cdd:PRK10840   81 LSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKkftpesvsrlLEKISAGgygdkrLSPKESEVLR 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1490909940 140 LLGEGKEDAEIAALLGISPRTVANHCARLMEKLGIHTRAGLIAHARRIRLEARD 193
Cdd:PRK10840  161 LFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSSVTLSPAD 214
COG4567 COG4567
DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains ...
 5-160 1.74e-05

DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443624 [Multi-domain]  Cd Length: 177  Bit Score: 43.37  E-value: 1.74e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   5 RIAIVDDHALVRAGLVRLLSAR-YDVIGeAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPNTRILVLTM 83
Cdd:COG4567     6 SLLLVDDDEAFARVLARALERRgFEVTT-AASVEEALALLEQAPPDYAVLDLRLGDGSGLDLIEALRERDPDARIVVLTG 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940  84 YDEPEYAAAAVAAGACGLVSKSASADTLYAAIDAAVKGTLERPSFGLT----EREQDVLSLLGEGKEDAEIAALLGISPR 159
Cdd:COG4567    85 YASIATAVEAIKLGADDYLAKPADADDLLAALERAEGDAPAPPENPMSldrlEWEHIQRVLAECDGNISATARALGMHRR 164


                  .
gi 1490909940 160 T 160
Cdd:COG4567   165 T 165
YesN COG4753
Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding ...
 5-89 3.19e-05

Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443786 [Multi-domain]  Cd Length: 103  Bit Score: 41.30  E-value: 3.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   5 RIAIVDDHALVRAGLVRLLSAR--YDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPNTRILVLT 82
Cdd:COG4753     1 KVLIVDDEPLIREGLKRILEWEagFEVVGEAENGEEALELLEEHKPDLVITDINMPGMDGLELLEAIRELDPDTKIIILS 80


                  ....*..
gi 1490909940  83 MYDEPEY 89
Cdd:COG4753    81 GYSDFEY 87
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
130-187 3.91e-05

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 43.39  E-value: 3.91e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1490909940 130 LTEREQDVLSLLGEGKEDAEIAALLGISPRTVANHCARLMEKLGIHTRAGLIAHARRI 187
Cdd:PRK04841  839 LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEAVQHAQDL 896
REC_YesN-like cd17536
phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response ...
 8-89 1.34e-04

phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response regulators; This family is composed of uncharacterized response regulators that contain a REC domain and a AraC family helix-turn-helix (HTH) DNA-binding output domain, including Bacillus subtilis uncharacterized transcriptional regulatory protein YesN and Staphylococcus aureus uncharacterized response regulatory protein SAR0214. YesN is a member of the two-component regulatory system YesM/YesN and SAR0214 is a member of the probable two-component regulatory system SAR0215/SAR0214. Also included in this family is the AlgR-like group of LytTR/AlgR family response, which includes Pseudomonas aeruginosa positive alginate biosynthesis regulatory protein AlgR and Bacillus subtilis sensory transduction protein LytT, among others. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381091 [Multi-domain]  Cd Length: 121  Bit Score: 40.01  E-value: 1.34e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   8 IVDDHALVRAGLVRLL---SARYDVIGEAADTASALALVRRaspdlllldlslpDR-------------DGLSAIPDLIA 71
Cdd:cd17536     3 IVDDEPLIREGLKKLIdweELGFEVVGEAENGEEALELIEE-------------HKpdivitdirmpgmDGLELIEKIRE 69

                          90
                  ....*....|....*...
gi 1490909940  72 ASPNTRILVLTMYDEPEY 89
Cdd:cd17536    70 LYPDIKIIILSGYDDFEY 87
CitB COG4565
DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ...
 1-120 1.35e-04

DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal transduction mechanisms];


Pssm-ID: 443622 [Multi-domain]  Cd Length: 138  Bit Score: 40.34  E-value: 1.35e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   1 MPGIRIAIVDDHALVRAGLVRLLS--ARYDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPNTRI 78
Cdd:COG4565     1 MKMIRVLIVEDDPMVAELLRRYLErlPGFEVVGVASSGEEALALLAEHRPDLILLDIYLPDGDGLELLRELRARGPDVDV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1490909940  79 LVLTMYDEPEYAAAAVAAGACGLVSKSASADTLYAAIDAAVK 120
Cdd:COG4565    81 IVITAARDPETVREALRAGVVDYLIKPFTFERLREALERYLE 122
fixJ PRK09390
response regulator FixJ; Provisional
 130-188 1.80e-04

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 40.76  E-value: 1.80e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1490909940 130 LTEREQDVLSLLGEGKEDAEIAALLGISPRTVANHCARLMEKLGIHTRAGLIAHARRIR 188
Cdd:PRK09390  142 LSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLSELVRMALRAG 200
REC_CheY cd17542
phosphoacceptor receiver (REC) domain of chemotaxis protein CheY; The chemotaxis response ...
 4-119 3.30e-04

phosphoacceptor receiver (REC) domain of chemotaxis protein CheY; The chemotaxis response regulator CheY contains a stand-alone REC domain. Chemotaxis is a behavior known for motile bacteria that directs their movement in response to chemical gradients. CheY is involved in transmitting sensory signals from chemoreceptors to the flagellar motors. Phosphorylated CheY interacts with the flagella switch components FliM and FliY, which causes counterclockwise rotation of the flagella, resulting in smooth swimming. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381097 [Multi-domain]  Cd Length: 117  Bit Score: 38.80  E-value: 3.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   4 IRIAIVDDHALVRAGLVRLLS-ARYDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPNTRILVLT 82
Cdd:cd17542     1 KKVLIVDDAAFMRMMLKDILTkAGYEVVGEAANGEEAVEKYKELKPDLVTMDITMPEMDGIEALKEIKKIDPNAKVIMCS 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1490909940  83 MYDEPEYAAAAVAAGACGLVSKSASADTLYAAIDAAV 119
Cdd:cd17542    81 AMGQEEMVKEAIKAGAKDFIVKPFQPERVLEAVEKVL 117
REC_RegA-like cd17563
phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA; ...
 5-84 8.91e-04

phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA; Rhodobacter sphaeroides RegA, also called response regulator PrrA, is the DNA binding regulatory protein of a redox-responsive two-component regulatory system RegB/RegA that is involved in transactivating anaerobic expression of the photosynthetic apparatus. It contains a REC domain and a DNA-binding helix-turn-helix output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381111 [Multi-domain]  Cd Length: 112  Bit Score: 37.42  E-value: 8.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   5 RIAIVDDHALVRAGLVRLLSARYDVIGEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPNTRILVLTMY 84
Cdd:cd17563     2 SLLLVDDDEVFAERLARALERRGFEVETAHSVEEALALAREEKPDYAVLDLRLGGDSGLDLIPPLRALQPDARIVVLTGY 81
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 130-172 1.29e-03

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: 38.05  E-value: 1.29e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1490909940 130 LTEREQDVLSL-LGEGKEDAEIAALLGISPRTVANHCARLMEKL 172
Cdd:COG1595   128 LPPRQREVLVLrYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 130-172 1.31e-03

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: 37.71  E-value: 1.31e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1490909940 130 LTEREQDVLSL-LGEGKEDAEIAALLGISPRTVANHCARLMEKL 172
Cdd:TIGR02937 111 LPEREREVLVLrYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 5-120 1.60e-03

DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, and a Fis-type DNA-binding domains [Signal transduction mechanisms];


Pssm-ID: 441806 [Multi-domain]  Cd Length: 418  Bit Score: 38.41  E-value: 1.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940   5 RIAIVDDHALVRAGLVRLLSAR-YDVIgEAADTASALALVRRASPDLLLLDLSLPDRDGLSAIPDLIAASPNTRILVLTM 83
Cdd:COG2204     4 RILVVDDDPDIRRLLKELLERAgYEVE-TAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALDPDLPVILLTG 82

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1490909940  84 YDEPEYAAAAVAAGACGLVSKSASADTLYAAIDAAVK 120
Cdd:COG2204    83 YGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERALE 119
PRK10100 PRK10100
transcriptional regulator CsgD;
130-177 2.22e-03

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 37.54  E-value: 2.22e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1490909940 130 LTEREQDVLSLLGEGKEDAEIAALLGISPRTVANHCARLMEKLGIHTR 177
Cdd:PRK10100  156 LTHREKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVKNR 203
PRK10188 PRK10188
transcriptional regulator SdiA;
126-164 2.47e-03

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 37.46  E-value: 2.47e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1490909940 126 PSFGLTEREQDVLSLLGEGKEDAEIAALLGISPRTVANH 164
Cdd:PRK10188  176 PEMNFSKREKEILKWTAEGKTSAEIAMILSISENTVNFH 214
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 143-172 2.97e-03

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: 36.77  E-value: 2.97e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 1490909940 143 EGKEDAEIAALLGISPRTVANHCARLMEKL 172
Cdd:TIGR02985 128 EGLSNKEIAEELGISVKTVEYHITKALKFL 157
PRK11475 PRK11475
DNA-binding transcriptional activator BglJ; Provisional
 60-184 4.58e-03

DNA-binding transcriptional activator BglJ; Provisional


Pssm-ID: 236915 [Multi-domain]  Cd Length: 207  Bit Score: 36.65  E-value: 4.58e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1490909940  60 RDGLSAIPDLIAASPNTRILVLTMyDEPEYAAAAVAAGAC--GLVSKSASADTLYAAIDAAVKGTL---ERP-------- 126
Cdd:PRK11475   53 REGLSCLTELAIKFPRMRRLVIAD-DDIEARLIGSLSPSPldGVLSKASTLEILQQELFLSLNGVRqatDRLnnqwyinq 131

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1490909940 127 SFGLTEREQDVLSLLGEGKEDAEIAALLGISPRTVANHCARLMEKLGIHTRAGLIAHA 184
Cdd:PRK11475  132 SRMLSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVSSDAGLLDAA 189
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 130-172 9.04e-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.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 33.20  E-value: 9.04e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1490909940 130 LTEREQDVLSLL-GEGKEDAEIAALLGISPRTVANHCARLMEKL 172
Cdd:pfam08281  11 LPPRQREVFLLRyLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
 
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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