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Conserved domains on  [gi|1732753220|gb|TYR21642|]
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response regulator transcription factor [Enterobacter cloacae]

Protein Classification

response regulator transcription factor( domain architecture ID 1013612)

two-component system response regulator transcription factor binds DNA upon phosphorylation and functions as transcriptional regulator

CATH:  3.40.50.2300
Gene Ontology:  GO:0000156|GO:0000160|GO:0003677|GO:0006355
PubMed:  31100988|10966457
SCOP:  4003632

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK15369 super family cl33127
two component system response regulator;
1-212 3.39e-30

two component system response regulator;


The actual alignment was detected with superfamily member PRK15369:

Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 110.94  E-value: 3.39e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   1 MDIKIVIAEESSLIRRGLSSMMQSLSlpavgmdqRCVLIGEAAASAELQSLLGQHNPDIAILGYSLTtslsrpplgGMDG 80
Cdd:PRK15369    2 KNYKILLVDDHELIINGIKNMLAPYP--------RYKIVGQVDNGLEVYNACRQLEPDIVILDLGLP---------GMNG 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  81 LKLLRWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVLKGEIYIE----NQLVNMLFRHEK 156
Cdd:PRK15369   65 LDVIPQLHQRWPAMNILVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKRYIDpalnREAILALLNADD 144

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1732753220 157 TDVEKLSPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQNDCQL 212
Cdd:PRK15369  145 TNPPLLTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAEL 200
 
Name Accession Description Interval E-value
PRK15369 PRK15369
two component system response regulator;
1-212 3.39e-30

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 110.94  E-value: 3.39e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   1 MDIKIVIAEESSLIRRGLSSMMQSLSlpavgmdqRCVLIGEAAASAELQSLLGQHNPDIAILGYSLTtslsrpplgGMDG 80
Cdd:PRK15369    2 KNYKILLVDDHELIINGIKNMLAPYP--------RYKIVGQVDNGLEVYNACRQLEPDIVILDLGLP---------GMNG 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  81 LKLLRWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVLKGEIYIE----NQLVNMLFRHEK 156
Cdd:PRK15369   65 LDVIPQLHQRWPAMNILVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKRYIDpalnREAILALLNADD 144

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1732753220 157 TDVEKLSPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQNDCQL 212
Cdd:PRK15369  145 TNPPLLTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAEL 200
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 5-137 1.49e-20

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: 83.33  E-value: 1.49e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   5 IVIAEESSLIRRGLSSMMQSLSlpavGMDqrcvLIGEAAASAELQSLLGQHNPDIAILGYSLttslsrpplGGMDGLKLL 84
Cdd:cd17535     1 VLIVDDHPLVREGLRRLLESEP----DIE----VVGEAADGEEALALLRELRPDVVLMDLSM---------PGMDGIEAL 63

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1732753220  85 RWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVL 137
Cdd:cd17535    64 RRLRRRYPDLKVIVLTAHDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAVA 116
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 3-223 2.27e-19

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: 80.32  E-value: 2.27e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   3 IKIVIAEESSLIRRGLSSMMQSlslpavgmDQRCVLIGEAAASAELQSLLGQHNPDIAILGYSLTtslsrpplgGMDGLK 82
Cdd:COG2197     2 IRVLIVDDHPLVREGLRALLEA--------EPDIEVVGEAADGEEALELLEELRPDVVLLDIRMP---------GMDGLE 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  83 LLRWLkqtypalniillspyanatlirqalkegvraylsrdinektlsqaittvlkgeiyienqlvnmlfrhektdvekL 162
Cdd:COG2197    65 ALRRL--------------------------------------------------------------------------L 70

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1732753220 163 SPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQNDCQLYSLIIKNQMFE 223
Cdd:COG2197    71 TPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLLD 131
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 162-215 1.92e-16

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 70.63  E-value: 1.92e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1732753220  162 LSPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQNDCQLYSL 215
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
GerE pfam00196
Bacterial regulatory proteins, luxR family;
162-215 3.51e-13

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 61.83  E-value: 3.51e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1732753220 162 LSPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQNDCQLYSL 215
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRM 56
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 99-204 1.17e-05

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: 43.88  E-value: 1.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  99 LSPYANATLIRQALKEgVRAYLSRDINEKTLSQAITTVLKGEIYIENQLVNMLFRhekTDVEKLSPREIDVLRLI-CKGL 177
Cdd:TIGR02937  52 FKAWLFRIARNLILDY-LRRKRRLRRELDLLEELLDSDPSPEEELEQEEEREALR---EALEKLPEREREVLVLRyLEGL 127

                          90       100
                  ....*....|....*....|....*..
gi 1732753220 178 NLKEIAQFMHLSIKTVSAHKVRAMEKL 204
Cdd:TIGR02937 128 SYKEIAEILGISVGTVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
PRK15369 PRK15369
two component system response regulator;
1-212 3.39e-30

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 110.94  E-value: 3.39e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   1 MDIKIVIAEESSLIRRGLSSMMQSLSlpavgmdqRCVLIGEAAASAELQSLLGQHNPDIAILGYSLTtslsrpplgGMDG 80
Cdd:PRK15369    2 KNYKILLVDDHELIINGIKNMLAPYP--------RYKIVGQVDNGLEVYNACRQLEPDIVILDLGLP---------GMNG 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  81 LKLLRWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVLKGEIYIE----NQLVNMLFRHEK 156
Cdd:PRK15369   65 LDVIPQLHQRWPAMNILVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKRYIDpalnREAILALLNADD 144

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1732753220 157 TDVEKLSPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQNDCQL 212
Cdd:PRK15369  145 TNPPLLTPRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVAEL 200
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 5-137 1.49e-20

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: 83.33  E-value: 1.49e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   5 IVIAEESSLIRRGLSSMMQSLSlpavGMDqrcvLIGEAAASAELQSLLGQHNPDIAILGYSLttslsrpplGGMDGLKLL 84
Cdd:cd17535     1 VLIVDDHPLVREGLRRLLESEP----DIE----VVGEAADGEEALALLRELRPDVVLMDLSM---------PGMDGIEAL 63

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1732753220  85 RWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVL 137
Cdd:cd17535    64 RRLRRRYPDLKVIVLTAHDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAVA 116
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 3-223 2.27e-19

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: 80.32  E-value: 2.27e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   3 IKIVIAEESSLIRRGLSSMMQSlslpavgmDQRCVLIGEAAASAELQSLLGQHNPDIAILGYSLTtslsrpplgGMDGLK 82
Cdd:COG2197     2 IRVLIVDDHPLVREGLRALLEA--------EPDIEVVGEAADGEEALELLEELRPDVVLLDIRMP---------GMDGLE 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  83 LLRWLkqtypalniillspyanatlirqalkegvraylsrdinektlsqaittvlkgeiyienqlvnmlfrhektdvekL 162
Cdd:COG2197    65 ALRRL--------------------------------------------------------------------------L 70

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1732753220 163 SPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQNDCQLYSLIIKNQMFE 223
Cdd:COG2197    71 TPREREVLRLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGLLD 131
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 75-208 9.31e-19

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: 80.53  E-value: 9.31e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  75 LGGMDGLKLLRWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVLkgEIYIENQLVNMLFRH 154
Cdd:COG4566    53 MPGMSGLELQEELAARGSPLPVIFLTGHGDVPMAVRAMKAGAVDFLEKPFDDQALLDAVRRAL--ARDRARRAERARRAE 130

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1732753220 155 EKTDVEKLSPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQN 208
Cdd:COG4566   131 LRARLASLTPREREVLDLVVAGLSNKQIARELGISPRTVEVHRANVMEKLGARS 184
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 2-212 8.39e-18

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 78.72  E-value: 8.39e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   2 DIKIVIAEESSLIRRGLSSMMQSLSLPAVgmdqrcvlIGEAAASAELQSLLGQHNPDIAIlgysltTSLSRPPLGGMDGL 81
Cdd:PRK10840    3 NMNVIIADDHPIVLFGIRKSLEQIEWVNV--------VGEFEDSTALINNLPKLDAHVLI------TDLSMPGDKYGDGI 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  82 KLLRWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVLKGEIYIENQLVNMLFRHEKTDV-- 159
Cdd:PRK10840   69 TLIKYIKRHFPSLSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKISAGGYgd 148

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1732753220 160 EKLSPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQNDCQL 212
Cdd:PRK10840  149 KRLSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIAL 201
PRK10360 PRK10360
transcriptional regulator UhpA;
3-212 9.36e-18

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 78.10  E-value: 9.36e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   3 IKIVIAEESSLIRRGLSSMMqslslpavGMDQRCVLIGEAAASAELQSLLGQHNPDIAIlgysltTSLSRPPLGGMDglk 82
Cdd:PRK10360    2 ITVALIDDHLIVRSGFAQLL--------GLEPDLQVVAEFGSGREALAGLPGRGVQVCI------CDISMPDISGLE--- 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  83 llrWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVLKGEIYIENQLVNMLFRHEKtdvEKL 162
Cdd:PRK10360   65 ---LLSQLPKGMATIMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASGRQ---DPL 138

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1732753220 163 SPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQNDCQL 212
Cdd:PRK10360  139 TKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVEL 188
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 5-204 2.66e-17

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 77.38  E-value: 2.66e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   5 IVIAEESSLIRRGLSSMmqslslpaVGMDQRCVLIGEAAASAELQSLLGQHNPDIAILgyslttSLSRPplgGMDGLKLL 84
Cdd:PRK10651    9 ILLIDDHPMLRTGVKQL--------ISMAPDITVVGEASNGEQGIELAESLDPDLILL------DLNMP---GMNGLETL 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  85 RWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVLKGEIYIENQLVNML---FRHEKT---- 157
Cdd:PRK10651   72 DKLREKSLSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQAAAGEMVLSEALTPVLaasLRANRAtter 151

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1732753220 158 DVEKLSPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKL 204
Cdd:PRK10651  152 DVNQLTPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKM 198
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 162-218 1.75e-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: 70.64  E-value: 1.75e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1732753220 162 LSPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQNDCQLYSLIIK 218
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 162-215 1.92e-16

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 70.63  E-value: 1.92e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1732753220  162 LSPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQNDCQLYSL 215
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRL 57
YesN COG4753
Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding ...
 4-120 3.83e-15

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: 68.65  E-value: 3.83e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   4 KIVIAEESSLIRRGLSSMMQSLSlpavgmdqRCVLIGEAAASAELQSLLGQHNPDIAILGYSLttslsrpPlgGMDGLKL 83
Cdd:COG4753     1 KVLIVDDEPLIREGLKRILEWEA--------GFEVVGEAENGEEALELLEEHKPDLVITDINM-------P--GMDGLEL 63

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1732753220  84 LRWLKQTYPALNIILLSPYANATLIRQALKEGVRAYL 120
Cdd:COG4753    64 LEAIRELDPDTKIIILSGYSDFEYAQEAIKLGADDYL 100
REC_DesR-like cd19930
phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of ...
 5-138 1.99e-14

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: 66.91  E-value: 1.99e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   5 IVIAEESSLIRRGLSSMMqslslpavGMDQRCVLIGEAAASAELQSLLGQHNPDIAILGYSLTtslsrpplgGMDGLKLL 84
Cdd:cd19930     1 VLIAEDQEMVRGALAALL--------ELEDDLEVVAQASNGQEALRLVLKHSPDVAILDIEMP---------GRTGLEVA 63

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1732753220  85 RWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVLK 138
Cdd:cd19930    64 AELREELPDTKVLIVTTFGRPGYFRRALAAGVDGYVLKDRPIEELADAIRTVHA 117
PRK09483 PRK09483
response regulator; Provisional
 3-225 3.04e-14

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 68.98  E-value: 3.04e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   3 IKIVIAEESSLIRRGLSSMMQSLSlpavGMDqrcvLIGEAAASAELQSLLGQHNPDIAILgyslttSLSRPPLGGMDGL- 81
Cdd:PRK09483    2 INVLLVDDHELVRAGIRRILEDIK----GIK----VVGEACCGEDAVKWCRTNAVDVVLM------DMNMPGIGGLEATr 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  82 KLLRWlkqtYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVLKGEIYIENQL-----VNMLFRHEK 156
Cdd:PRK09483   68 KILRY----TPDVKIIMLTVHTENPLPAKVMQAGAAGYLSKGAAPQEVVSAIRSVHSGQRYIASDIaqqmaLSQIEPATE 143

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1732753220 157 TDVEKLSPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQNDCQLYSLIIKNQMFEIG 225
Cdd:PRK09483  144 NPFASLSERELQIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHGLLNAE 212
REC_YesN-like cd17536
phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response ...
 5-138 7.43e-14

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: 65.44  E-value: 7.43e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   5 IVIAEESSLIRRGLSSMMQSLSLPavgmdqrCVLIGEAAASAELQSLLGQHNPDIAIlgysltTSLSRPplgGMDGLKLL 84
Cdd:cd17536     1 VLIVDDEPLIREGLKKLIDWEELG-------FEVVGEAENGEEALELIEEHKPDIVI------TDIRMP---GMDGLELI 64

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1732753220  85 RWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVLK 138
Cdd:cd17536    65 EKIRELYPDIKIIILSGYDDFEYAQKAIRLGVVDYLLKPVDEEELEEALEKAKE 118
GerE pfam00196
Bacterial regulatory proteins, luxR family;
162-215 3.51e-13

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 61.83  E-value: 3.51e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1732753220 162 LSPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQNDCQLYSL 215
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRM 56
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
38-222 3.96e-13

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 65.55  E-value: 3.96e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  38 LIGEAAASAELQSLLGQHNPDIAILGYSLTTSLSRPPLGGMDGLKLLRWLKQTYPALNIILLSPYANATLIRQALKEGVR 117
Cdd:COG2771     3 LLALALLLLALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220 118 AYLSRDINEKTLSQAITTVLKGEIYIENQLVNMLFRHE-KTDVEKLSPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAH 196
Cdd:COG2771    83 ALLLLLALLALLAALLARLAALLLALALAALLLAALARlLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTH 162

                         170       180
                  ....*....|....*....|....*.
gi 1732753220 197 KVRAMEKLDVQNDCQLYSLIIKNQMF 222
Cdd:COG2771   163 LKRIYRKLGVSSRAELVALALRLGLI 188
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
4-208 6.25e-13

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 65.26  E-value: 6.25e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   4 KIVIAEESSLIRRGLSSMMQslslpavgMDQRCVLIGEAAASAELQSLLGQHNPDIAILGYSLTtslsrpplgGMDGLKL 83
Cdd:PRK10403    8 QVLIVDDHPLMRRGVRQLLE--------LDPGFEVVAEAGDGASAIDLANRLDPDVILLDLNMK---------GMSGLDT 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  84 LRWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVLKGEIYIENQlVNMLFRHEKTDVEKLS 163
Cdd:PRK10403   71 LNALRRDGVTAQIIILTVSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSKVFSER-VNQYLREREMFGAEED 149

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1732753220 164 P------REIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQN 208
Cdd:PRK10403  150 PfsvlteRELDVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRS 200
CitB COG4565
DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ...
 1-138 6.26e-13

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


Pssm-ID: 443622 [Multi-domain]  Cd Length: 138  Bit Score: 63.45  E-value: 6.26e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   1 MDIKIVIAEESSLIRRGLSSMMQSLSLpavgmdqrCVLIGEAAASAELQSLLGQHNPDIAILGYSLttslsrpplGGMDG 80
Cdd:COG4565     2 KMIRVLIVEDDPMVAELLRRYLERLPG--------FEVVGVASSGEEALALLAEHRPDLILLDIYL---------PDGDG 64

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1732753220  81 LKLLRWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVLK 138
Cdd:COG4565    65 LELLRELRARGPDVDVIVITAARDPETVREALRAGVVDYLIKPFTFERLREALERYLE 122
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
75-212 1.93e-12

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 63.74  E-value: 1.93e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  75 LGGMDGLKLLRWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVLKGEIYIENQLVNMLFRH 154
Cdd:PRK09935   59 LPGTDGFTFLKRIKQIQSTVKVLFLSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMILSGYTFFPSETLNYIKSN 138

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1732753220 155 E----KTDVEKLSPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQNDCQL 212
Cdd:PRK09935  139 KcstnSSTDTVLSNREVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVEL 200
AmiR COG3707
Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding ...
 1-137 2.89e-12

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: 63.05  E-value: 2.89e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   1 MDIKIVIAEESSLIRRGLSSMMQSLslpavgmdqRCVLIGEAAASAELQSLLGQHNPDIAILGYslttslsrpPLGGMDG 80
Cdd:COG3707     2 RGLRVLVVDDEPLRRADLREGLREA---------GYEVVAEAADGEDAVELVRELKPDLVIVDI---------DMPDRDG 63

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1732753220  81 LKLLRWLKQTYPAlNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVL 137
Cdd:COG3707    64 LEAARQISEERPA-PVILLTAYSDPELIERALEAGVSAYLVKPLDPEDLLPALELAL 119
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 5-133 5.13e-12

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: 60.63  E-value: 5.13e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   5 IVIAEESSLIRRGLSSMMQSLslpavGMDqrcvlIGEAAASAELQSLLGQHNPDIAILGYSLttslsrpplGGMDGLKLL 84
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEKE-----GYV-----VAEADDGKEALELLKEERPDLILLDINM---------PGMDGLELL 61

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1732753220  85 RWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAI 133
Cdd:pfam00072  62 KRIRRRDPTTPVIILTAHGDEDDAVEALEAGADDFLSKPFDPDELLAAI 110
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 1-170 6.85e-12

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: 63.83  E-value: 6.85e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   1 MDIKIVIAEESSLIRRGLSSMMQSLslpavGMDqrcvlIGEAAASAELQSLLGQHNPDIAILGYSLttslsrpplGGMDG 80
Cdd:COG2204     1 SMARILVVDDDPDIRRLLKELLERA-----GYE-----VETAASGEEALALLREEPPDLVLLDLRM---------PGMDG 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  81 LKLLRWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVL-KGEIYIENQLVNML------FR 153
Cdd:COG2204    62 LELLRELRALDPDLPVILLTGYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERALeRRRLRRENAEDSGLigrspaMQ 141

                         170
                  ....*....|....*..
gi 1732753220 154 HEKTDVEKLSPREIDVL 170
Cdd:COG2204   142 EVRRLIEKVAPSDATVL 158
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 150-212 2.58e-10

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: 54.97  E-value: 2.58e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1732753220 150 MLFRHEKTDVEKLSPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQNDCQL 212
Cdd:COG5905     1 MMPSSSTSHPSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQA 63
CheY COG0784
CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator ...
 1-140 2.90e-10

CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator Spo0F [Signal transduction mechanisms];


Pssm-ID: 440547 [Multi-domain]  Cd Length: 128  Bit Score: 56.01  E-value: 2.90e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   1 MDIKIVIAEESSLIRRGLSSMMQSLslpavGMDqrcVLigEAAASAELQSLLGQHNPDIAILGYSLttslsrpPlgGMDG 80
Cdd:COG0784     4 GGKRILVVDDNPDNRELLRRLLERL-----GYE---VT--TAEDGAEALELLRAGPPDLILLDINM-------P--GMDG 64

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1732753220  81 LKLLRWLKQ--TYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVLKGE 140
Cdd:COG0784    65 LELLRRIRAlpRLPDIPIIALTAYADEEDRERALEAGADDYLTKPVDPEELLEALRRLLARA 126
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
57-221 5.08e-10

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 57.21  E-value: 5.08e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  57 PDIAILGYSLttslsrPPLGGMDGLKLLRwlKQTYPALnIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTV 136
Cdd:PRK09958   46 PDIVIIDVDI------PGVNGIQVLETLR--KRQYSGI-IIIVSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAA 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220 137 LKGEIYIENQLvNMLFRHEKTD---VEKLSPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQNDCQLY 213
Cdd:PRK09958  117 KNGYCYFPFSL-NRFVGSLTSDqqkLDSLSKQEISVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLY 195


                  ....*...
gi 1732753220 214 SLIIKNQM 221
Cdd:PRK09958  196 TFAQRNKI 203
PleD COG3706
Two-component response regulator, PleD family, consists of two REC domains and a diguanylate ...
 4-136 1.59e-09

Two-component response regulator, PleD family, consists of two REC domains and a diguanylate cyclase (GGDEF) domain [Signal transduction mechanisms, Transcription];


Pssm-ID: 442920 [Multi-domain]  Cd Length: 179  Bit Score: 55.30  E-value: 1.59e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   4 KIVIAEESSLIRRGLSSMMQSLslpavGMDQRCVLIGEAAasaeLQsLLGQHNPDIAILGYSLttslsrpplGGMDGLKL 83
Cdd:COG3706     3 RILVVDDDPTNRKLLRRLLEAA-----GYEVVEAADGEEA----LE-LLQEHRPDLILLDLEM---------PDMDGLEL 63

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1732753220  84 LRWLKQTyPALN---IILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTV 136
Cdd:COG3706    64 CRRLRAD-PRTAdipIIFLTALDDEEDRARALEAGADDYLTKPFDPEELLARVDLV 118
REC cd00156
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...
 7-121 2.32e-08

phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response regulators (PRRs); Two-component systems (TCSs) involving a sensor and a response regulator are used by bacteria to adapt to changing environments. Processes regulated by two-component systems in bacteria include sporulation, pathogenicity, virulence, chemotaxis, and membrane transport. Response regulators (RRs) share the common phosphoacceptor REC domain and different effector/output domains such as DNA, RNA, ligand-binding, protein-binding, or enzymatic domains. Response regulators regulate transcription, post-transcription or post-translation, or have functions such as methylesterases, adenylate or diguanylate cyclase, c-di-GMP-specific phosphodiesterases, histidine kinases, serine/threonine protein kinases, and protein phosphatases, depending on their output domains. The function of some output domains are still unknown. TCSs are found in all three domains of life - bacteria, archaea, and eukaryotes, however, the presence and abundance of particular RRs vary between the lineages. Archaea encode very few RRs with DNA-binding output domains; most are stand-alone REC domains. Among eukaryotes, TCSs are found primarily in protozoa, fungi, algae, and green plants. REC domains function as phosphorylation-mediated switches within RRs, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381085 [Multi-domain]  Cd Length: 99  Bit Score: 50.30  E-value: 2.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   7 IAEESSLIRRGLSSMMQSLSlpavgmdqrcVLIGEAAASAELQSLLGQHNPDIAILGYSLttslsrpplGGMDGLKLLRW 86
Cdd:cd00156     2 IVDDDPAIRELLKSLLEREG----------YEVDTAADGEEALELLREERPDLVLLDLMM---------PGMDGLELLRK 62

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1732753220  87 LKQTYPALNIILLSPYANATLIRQALKEGVRAYLS 121
Cdd:cd00156    63 LRELPPDIPVIVLTAKADEEDAVRALELGADDYLV 97
PRK11475 PRK11475
DNA-binding transcriptional activator BglJ; Provisional
 79-212 4.99e-08

DNA-binding transcriptional activator BglJ; Provisional


Pssm-ID: 236915 [Multi-domain]  Cd Length: 207  Bit Score: 51.28  E-value: 4.99e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  79 DGLKLLRWLKQTYPALN-IILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVLKGEIYIENQLVNMLFRHEKt 157
Cdd:PRK11475   54 EGLSCLTELAIKFPRMRrLVIADDDIEARLIGSLSPSPLDGVLSKASTLEILQQELFLSLNGVRQATDRLNNQWYINQS- 132

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1732753220 158 dvEKLSPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQNDCQL 212
Cdd:PRK11475  133 --RMLSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVSSDAGL 185
COG4567 COG4567
DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains ...
 42-134 3.00e-07

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: 48.76  E-value: 3.00e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  42 AAASAELQSLLGQHNPDIAILGYslttslsrpPLGGMDGLKLLRWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLS 121
Cdd:COG4567    34 AASVEEALALLEQAPPDYAVLDL---------RLGDGSGLDLIEALRERDPDARIVVLTGYASIATAVEAIKLGADDYLA 104

                          90
                  ....*....|...
gi 1732753220 122 RDINEKTLSQAIT 134
Cdd:COG4567   105 KPADADDLLAALE 117
fixJ PRK09390
response regulator FixJ; Provisional
 77-204 6.48e-07

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 48.07  E-value: 6.48e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  77 GMDGLKLLRWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVLKgeiyienqlvnMLFRHEK 156
Cdd:PRK09390   59 GIDGIELLRRLKARGSPLPVIVMTGHGDVPLAVEAMKLGAVDFIEKPFEDERLIGAIERALA-----------QAPEAAK 127

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1732753220 157 TD---------VEKLSPREIDVLRLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKL 204
Cdd:PRK09390  128 SEavaadirarIASLSERERQVMDGLVAGLSNKVIARDLDISPRTVEVYRANVMTKM 184
REC_PdtaR-like cd19932
phosphoacceptor receiver (REC) domain of PdtaR and similar proteins; This subfamily includes ...
 3-137 1.88e-06

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: 45.48  E-value: 1.88e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   3 IKIVIAEESSLIRRGLSSMMQSlslpavgmdQRCVLIGEAAASAELQSLLGQHNPDIAILGYSLTTslsrpplggMDGLK 82
Cdd:cd19932     1 VRVLIAEDEALIRMDLREMLEE---------AGYEVVGEASDGEEAVELAKKHKPDLVIMDVKMPR---------LDGIE 62

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1732753220  83 LLRWLKQTYPAlNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVL 137
Cdd:cd19932    63 AAKIITSENIA-PIVLLTAYSQQDLVERAKEAGAMAYLVKPFSESDLIPAIEMAI 116
OmpR COG0745
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 4-172 4.17e-06

DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain [Signal transduction mechanisms, Transcription];


Pssm-ID: 440508 [Multi-domain]  Cd Length: 204  Bit Score: 45.72  E-value: 4.17e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   4 KIVIAEESSLIRRGLSSMMQSLslpavGMDQRCVLIGEAAasaelQSLLGQHNPDIAILGYSLttslsrpPlgGMDGLKL 83
Cdd:COG0745     3 RILVVEDDPDIRELLADALERE-----GYEVDTAADGEEA-----LELLEEERPDLILLDLML-------P--GMDGLEV 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  84 LRWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVLK---GEIYIENQLVNMLFRHEKTDVE 160
Cdd:COG0745    64 CRRLRARPSDIPIIMLTARDDEEDRVRGLEAGADDYLTKPFDPEELLARIRALLRrraAEVLRVGDLLDLAAREVTRDGE 143

                         170
                  ....*....|....
gi 1732753220 161 --KLSPREIDVLRL 172
Cdd:COG0745   144 pvELTPKEFRLLEL 157
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 99-204 1.17e-05

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: 43.88  E-value: 1.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  99 LSPYANATLIRQALKEgVRAYLSRDINEKTLSQAITTVLKGEIYIENQLVNMLFRhekTDVEKLSPREIDVLRLI-CKGL 177
Cdd:TIGR02937  52 FKAWLFRIARNLILDY-LRRKRRLRRELDLLEELLDSDPSPEEELEQEEEREALR---EALEKLPEREREVLVLRyLEGL 127

                          90       100
                  ....*....|....*....|....*..
gi 1732753220 178 NLKEIAQFMHLSIKTVSAHKVRAMEKL 204
Cdd:TIGR02937 128 SYKEIAEILGISVGTVKRRLKRARKKL 154
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 160-204 3.86e-05

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 40.10  E-value: 3.86e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1732753220 160 EKLSPREIDVLRLI-CKGLNLKEIAQFMHLSIKTVSAHKVRAMEKL 204
Cdd:pfam04545   3 ASLPPRERQVLVLRyGEGLTLEEIGERLGISRERVRQIEKRALRKL 48
LytT COG3279
DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction ...
 3-138 5.39e-05

DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction mechanisms];


Pssm-ID: 442510 [Multi-domain]  Cd Length: 235  Bit Score: 42.88  E-value: 5.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   3 IKIVIAEESSLIRRGLSSMMQSLSlpavgmdqRCVLIGEAAASAELQSLLGQHNPDIAILGYSlttslsrppLGGMDGLK 82
Cdd:COG3279     2 MKILIVDDEPLARERLERLLEKYP--------DLEVVGEASNGEEALELLEEHKPDLVFLDIQ---------MPGLDGFE 64

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1732753220  83 LLRWLKQTYPALNIILLSPYANATLirQALKEGVRAYLSRDINEKTLSQAITTVLK 138
Cdd:COG3279    65 LARQLRELDPPPPIIFTTAYDEYAL--EAFEVNAVDYLLKPIDEERLAKALEKAKE 118
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 119-204 1.14e-04

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: 41.01  E-value: 1.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220 119 YLSRDINEKTLSQAITTVLKGEIYIENQLVNM----LFRHEKTDVEKLSP--REIDVLRLIcKGLNLKEIAQFMHLSIKT 192
Cdd:TIGR02985  67 YLRHKQVEEKYQEELAEIEERELSEADPEEELeakeLEEIIEEAIEKLPEqcREIFILSRF-EGLSNKEIAEELGISVKT 145

                          90
                  ....*....|..
gi 1732753220 193 VSAHKVRAMEKL 204
Cdd:TIGR02985 146 VEYHITKALKFL 157
REC_NtrX-like cd17550
phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and ...
 75-130 1.39e-04

phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and similar proteins; NtrX is part of the two-component regulatory system NtrY/NtrX that is involved in the activation of nitrogen assimilatory genes such as Gln. It is phosphorylated by the histidine kinase NtrY and interacts with sigma-54. NtrX is a member of the NtrC family, characterized by a domain architecture containing an N-terminal REC domain, followed by a central sigma-54 interaction/ATPase domain, and a C-terminal DNA binding domain. NtrC family response regulators are sigma54-dependent transcriptional activators. Also included in this subfamily is Aquifex aeolicus NtrC4. The ability of the central domain to hydrolyze ATP and thus to interact effectively with a complex of RNA polymerase, sigma54, and promoter, is controlled by the phosphorylation status of the REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381102 [Multi-domain]  Cd Length: 115  Bit Score: 40.17  E-value: 1.39e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1732753220  75 LGGMDGLKLLRWLKQTYPALNIILLSPYANATLIRQALKEGvrAYlsrDINEKTLS 130
Cdd:cd17550    52 LPDMDGLELLKEIKEKYPDLPVIMISGHGTIETAVKATKLG--AY---DFIEKPLS 102
REC_HupR-like cd17569
phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR) and similar ...
 77-133 2.02e-04

phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR) and similar domains; This family is composed of mostly uncharacterized response regulators with similarity to the REC domains of response regulator components of two-component systems that regulates hydrogenase activity, including HupR and HoxA. HupR is part of the HupT/HupR system that controls the synthesis of the membrane-bound [NiFe]hydrogenase, HupSL, of the photosynthetic bacterium Rhodobacter capsulatus. It contains an N-terminal REC domain, a central sigma-54 interaction domain that lacks ATPase activity, and a C-terminal DNA-binding domain. Members of this family contain a REC domain and various output domains including the cyclase homology domain (CHD) and the c-di-GMP phosphodiesterase domains, HD-GYP and EAL. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381113 [Multi-domain]  Cd Length: 118  Bit Score: 39.69  E-value: 2.02e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1732753220  77 GMDGLKLLRWLKQTYPALNIILLSPYANATLIRQALKEG-VRAYLSRDINEKTLSQAI 133
Cdd:cd17569    56 GMDGAELLKRVRERYPDTVRILLTGYADLDAAIEAINEGeIYRFLTKPWDDEELKETI 113
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 159-204 2.39e-04

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: 40.36  E-value: 2.39e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1732753220 159 VEKLSPREIDVLRLIC-KGLNLKEIAQFMHLSIKTVSAHKVRAMEKL 204
Cdd:COG1595   125 LERLPPRQREVLVLRYlEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
RpfG COG3437
Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ...
 1-137 3.12e-04

Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains [Signal transduction mechanisms];


Pssm-ID: 442663 [Multi-domain]  Cd Length: 224  Bit Score: 40.53  E-value: 3.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   1 MDIKIVIAEESSLIRRGLSSMMQSLslpavGMDQRCVLIGEAAASaelqsLLGQHNPDIAILGYSLTtslsrpplgGMDG 80
Cdd:COG3437     5 QAPTVLIVDDDPENLELLRQLLRTL-----GYDVVTAESGEEALE-----LLLEAPPDLILLDVRMP---------GMDG 65

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1732753220  81 LKLLRWLKQTYPALNI--ILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVL 137
Cdd:COG3437    66 FELLRLLRADPSTRDIpvIFLTALADPEDRERALEAGADDYLTKPFDPEELLARVRNAL 124
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
171-208 3.69e-04

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 40.07  E-value: 3.69e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1732753220 171 RLICKGLNLKEIAQFMHLSIKTVSAHKVRAMEKLDVQN 208
Cdd:COG2909   132 RLLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRS 169
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 160-204 3.96e-04

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: 37.47  E-value: 3.96e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1732753220 160 EKLSPREIDVLRLI-CKGLNLKEIAQFMHLSIKTVSAHKVRAMEKL 204
Cdd:cd06171     9 DKLPEREREVILLRfGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
REC_NarL cd19931
phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate ...
 5-133 4.45e-04

phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate/nitrite response regulator protein NarL contains an N-terminal REC domain and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. Escherichia coli NarL activates the expression of the nitrate reductase (narGHJI) and formate dehydrogenase-N (fdnGHI) operons, and represses the transcription of the fumarate reductase (frdABCD) operon in response to a nitrate/nitrite induction signal. Phosphorylation of the NarL REC domain releases the C-terminal HTH output domain that subsequently binds specific DNA promoter sites to repress or activate gene expression. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381158 [Multi-domain]  Cd Length: 117  Bit Score: 38.87  E-value: 4.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   5 IVIAEESSLIRRGLSSMMQslslpavgMDQRCVLIGEAAASAELQSLLGQHNPDIAILgyslttSLSRPplgGMDGLKLL 84
Cdd:cd19931     1 VLLIDDHPLLRKGIKQLIE--------LDPDFTVVGEASSGEEGIELAERLDPDLILL------DLNMK---GMSGLDTL 63

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1732753220  85 RWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAI 133
Cdd:cd19931    64 KALREEGVSARIVILTVSDAEDDVVTALRAGADGYLLKDMEPEDLLEAL 112
REC_RegA-like cd17563
phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA; ...
 42-121 4.90e-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: 38.58  E-value: 4.90e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  42 AAASAELQSLLGQHNPDIAILgyslttSLSrppLGGMDGLKLLRWLKQTYPALNIILLSPYAN-ATLIrQALKEGVRAYL 120
Cdd:cd17563    30 AHSVEEALALAREEKPDYAVL------DLR---LGGDSGLDLIPPLRALQPDARIVVLTGYASiATAV-EAIKLGADDYL 99


                  .
gi 1732753220 121 S 121
Cdd:cd17563   100 A 100
REC_citrate_TCS cd19925
phosphoacceptor receiver (REC) domain of citrate family two-component system response ...
 38-134 7.84e-04

phosphoacceptor receiver (REC) domain of citrate family two-component system response regulators; This family includes Lactobacillus paracasei MaeR, Escherichia coli DcuR and DpiA, Klebsiella pneumoniae CitB, as well as Bacillus DctR, MalR, and CitT. These are all response regulators of two-component systems (TCSs) from the citrate family, and are involved in the transcriptional regulation of genes associated with L-malate catabolism (MaeRK), citrate-specific fermentation (DpiAB, CitAB), plasmid inheritance (DpiAB), anaerobic fumarate respiratory system (DcuRS), and malate transport/utilization (MalKR). REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381152 [Multi-domain]  Cd Length: 118  Bit Score: 37.99  E-value: 7.84e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  38 LIGEAAASAELQSLLGQHNPDIAILGYSLttslsrpPLGgmDGLKLLRWLKQTYPALNIILLSPYANATLIRQALKEGVR 117
Cdd:cd19925    28 VIGTAGTGEEALKLLKERQPDLILLDIYL-------PDG--NGLDLLRELRAAGHDVDVIVVTAANDVETVREALRLGVV 98

                          90
                  ....*....|....*..
gi 1732753220 118 AYLSRDINEKTLSQAIT 134
Cdd:cd19925    99 DYLIKPFTFERLRQRLE 115
glnG PRK10923
nitrogen regulation protein NR(I); Provisional
 4-173 8.63e-04

nitrogen regulation protein NR(I); Provisional


Pssm-ID: 182842 [Multi-domain]  Cd Length: 469  Bit Score: 39.85  E-value: 8.63e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   4 KIVIAEESSLIRRGLSSmmqslSLPAVGMDQRCVLIGEAAASAelqslLGQHNPDIAIlgyslttSLSRPPlgGMDGLKL 83
Cdd:PRK10923    5 IVWVVDDDSSIRWVLER-----ALAGAGLTCTTFENGNEVLEA-----LASKTPDVLL-------SDIRMP--GMDGLAL 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  84 LRWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSR--DINEKT--LSQAITTVLKgeiyiENQLVNMLFRHEKTDV 159
Cdd:PRK10923   66 LKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKpfDIDEAValVERAISHYQE-----QQQPRNIQVNGPTTDI 140

                         170
                  ....*....|....
gi 1732753220 160 EKLSPREIDVLRLI 173
Cdd:PRK10923  141 IGEAPAMQDVFRII 154
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 159-204 1.09e-03

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: 39.04  E-value: 1.09e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1732753220 159 VEKLSPREIDVLRLI-CKGLNLKEIAQFMHLSIKTVS-AHKvRAMEKL 204
Cdd:COG1191   184 IEQLPERERLVLSLYyFEELTLKEIAEVLGVSESRVSrLHK-KALARL 230
REC_CheY_CheY3 cd19923
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY ...
 3-137 1.96e-03

phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY family proteins; CheY family chemotaxis response regulators (RRs) comprise about 17% of bacterial RRs and almost half of all RRs in archaea. This subfamily contains Vibrio cholerae CheY3, Escherichia coli CheY, and similar CheY family RRs. CheY proteins control bacterial motility and participate in signaling phosphorelays and in protein-protein interactions. CheY RRs contain only the REC domain with no output/effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381150 [Multi-domain]  Cd Length: 119  Bit Score: 36.93  E-value: 1.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   3 IKIVIAEESSLIRRGLSSMMQSLSLpavgmdqrcVLIGEAAASAELQSLLGQHNPDIAILGYSLttslsrPPlggMDGLK 82
Cdd:cd19923     1 MKVLVVDDFSTMRRIIKNLLKELGF---------NNVEEAEDGVDALEKLKAGGFDFVITDWNM------PN---MDGLE 62

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1732753220  83 LLRWLK--QTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAITTVL 137
Cdd:cd19923    63 LLKTIRadGALSHLPVLMVTAEAKKENVIAAAQAGVNNYIVKPFTAATLKEKLEKIF 119
PRK10100 PRK10100
transcriptional regulator CsgD;
125-214 2.01e-03

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 37.93  E-value: 2.01e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220 125 NEKTLSQAITTVLKGEIYIENQLVNML------FRHEKTDVEKLSPREIDVL-RLICKGLNLkEIAQFMHLSIKTVSAHK 197
Cdd:PRK10100  113 DQERVVNGLQGVLRGECYFTQKLASYLithsgnYRYNSTESALLTHREKEILnKLRIGASNN-EIARSLFISENTVKTHL 191

                          90
                  ....*....|....*..
gi 1732753220 198 VRAMEKLDVQNDCQLYS 214
Cdd:PRK10100  192 YNLFKKIAVKNRTQAVS 208
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 159-204 2.29e-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: 35.12  E-value: 2.29e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1732753220 159 VEKLSPREIDVLRLIC-KGLNLKEIAQFMHLSIKTVSAHKVRAMEKL 204
Cdd:pfam08281   8 LEELPPRQREVFLLRYlEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
REC_NtrC cd19919
phosphoacceptor receiver (REC) domain of DNA-binding transcriptional regulator NtrC; ...
 77-126 2.42e-03

phosphoacceptor receiver (REC) domain of DNA-binding transcriptional regulator NtrC; DNA-binding transcriptional regulator NtrC is also called nitrogen regulation protein NR(I) or nitrogen regulator I (NRI). It contains an N-terminal receiver (REC) domain, followed by a sigma-54 interaction domain, and a C-terminal helix-turn-helix DNA-binding domain. It is part of the two-component regulatory system NtrB/NtrC, which controls expression of the nitrogen-regulated (ntr) genes in response to nitrogen limitation. DNA-binding response regulator NtrC is phosphorylated by NtrB; phosphorylation of the N-terminal REC domain activates the central sigma-54 interaction domain and leads to the transcriptional activation from promoters that require sigma(54)-containing RNA polymerase. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381146 [Multi-domain]  Cd Length: 116  Bit Score: 36.48  E-value: 2.42e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1732753220  77 GMDGLKLLRWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSR--DINE 126
Cdd:cd19919    56 GMDGLALLAQIKQRHPDLPVIIMTAHSDLDSAVSAYQGGAFEYLPKpfDIDE 107
REC_CpdR_CckA-like cd18160
phosphoacceptor receiver (REC) domain of Brucella abortus CpdR and CckA, and similar domains; ...
 4-122 2.78e-03

phosphoacceptor receiver (REC) domain of Brucella abortus CpdR and CckA, and similar domains; Two-component systems (TCSs), consisting of a sensor and a response regulator, are used by bacteria to adapt to changing environments. Processes regulated by TCSs in bacteria include sporulation, pathogenicity, virulence, chemotaxis and membrane transport. Response regulators share the common phosphoacceptor REC domain and differ output domains such as DNA, RNA, ligand, and protein-binding, or enzymatic domain. CpdR is a stand-alone REC protein. CckA is a sensor histidine kinase containing N-terminal PAS domains and a C-terminal REC domain. CpdR and CckA are components of a regulatory phosphorelay system (composed of CckA, ChpT, CtrA and CpdR) that controls Brucella abortus cell growth, division, and intracellular survival inside mammalian host cells. CckA autophosphorylates in the presence of ATP and transfers a phosphoryl group to the conserved aspartic acid residue on its C-terminal REC domain, which is relayed to the ChpT phosphotransferase. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381144 [Multi-domain]  Cd Length: 103  Bit Score: 36.33  E-value: 2.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   4 KIVIAEESSLIRRGLSSMMQSlslpavgmdqRCVLIGEAAASAELQSLLGQHNP-DIAIlgysltTSLSRPPlggMDGLK 82
Cdd:cd18160     1 TILLADDEPSVRKFIVTTLKK----------AGYAVTEAESGAEALEKLQQGKDiDIVV------TDIVMPE---MDGIE 61

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1732753220  83 LLRWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSR 122
Cdd:cd18160    62 LAREARKIDPDVKILFISGGAAAAPELLSDAVGDNATLKK 101
REC_FixJ cd17537
phosphoacceptor receiver (REC) domain of FixJ family response regulators; FixJ family response ...
 77-134 3.48e-03

phosphoacceptor receiver (REC) domain of FixJ family response regulators; FixJ family response regulators contain an N-terminal receiver domain (REC) and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. The Sinorhizobium meliloti two-component system FixL/FixJ regulates nitrogen fixation in response to oxygen during symbiosis. Under microaerobic conditions, the kinase FixL phosphorylates the response regulator FixJ resulting in the regulation of nitrogen fixation genes such as nifA and fixK. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381092 [Multi-domain]  Cd Length: 116  Bit Score: 36.03  E-value: 3.48e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1732753220  77 GMDGLKLLRWLKQTYPALNIILLSPYANATLIRQALKEGVRAYLSRDINEKTLSQAIT 134
Cdd:cd17537    56 GMSGLELQDELLARGSNIPIIFITGHGDVPMAVEAMKAGAVDFLEKPFRDQVLLDAIE 113
REC_CheB-like cd17541
phosphoacceptor receiver (REC) domain of chemotaxis response regulator protein-glutamate ...
 3-115 4.50e-03

phosphoacceptor receiver (REC) domain of chemotaxis response regulator protein-glutamate methylesterase CheB and similar chemotaxis proteins; Methylesterase CheB is a chemotaxis response regulator with an N-terminal REC domain and a C-terminal methylesterase domain. Chemotaxis is a behavior known in motile bacteria that directs their movement in response to chemical gradients. CheB is a phosphorylation-activated response regulator involved in the reversible modification of bacterial chemotaxis receptors. It catalyzes the demethylation of specific methylglutamate residues introduced into the chemoreceptors (methyl-accepting chemotaxis proteins) by CheR. The CheB REC domain packs against the active site of the C-terminal domain and inhibits methylesterase activity by directly restricting access to the active site. Also included in this family is chemotaxis response regulator CheY, which contains a stand-alone REC domain, and an uncharacterized subfamily composed of proteins containing an N-terminal REC domain and a C-terminal CheY-P phosphatase (CheC) domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381096 [Multi-domain]  Cd Length: 125  Bit Score: 35.83  E-value: 4.50e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   3 IKIVIAEESSLIRRGLSSMMQSlslpavgmDQRCVLIGEAAASAELQSLLGQHNPDIailgysLTTSLSRPplgGMDGLK 82
Cdd:cd17541     1 IRVLIVDDSAVMRKLLSRILES--------DPDIEVVGTARDGEEALEKIKELKPDV------ITLDIEMP---VMDGLE 63

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1732753220  83 LLRWLKQTYPALnIILLS--PYANATLIRQALKEG 115
Cdd:cd17541    64 ALRRIMAERPTP-VVMVSslTEEGAEITLEALELG 97
PRK11361 PRK11361
acetoacetate metabolism transcriptional regulator AtoC;
4-175 5.69e-03

acetoacetate metabolism transcriptional regulator AtoC;


Pssm-ID: 183099 [Multi-domain]  Cd Length: 457  Bit Score: 37.14  E-value: 5.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220   4 KIVIAEESSLIRRglssmMQSLSLPAVGMDQRCvligeAAASAELQSLLGQHNPDIAILgyslttSLSRPPLGGMDGLKL 83
Cdd:PRK11361    6 RILIVDDEDNVRR-----MLSTAFALQGFETHC-----ANNGRTALHLFADIHPDVVLM------DIRMPEMDGIKALKE 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732753220  84 LRWLKQTYPalnIILLSPYANATLIRQALKEGVRAYLSR--DINEKTL--SQAIT-TVLKGEIYIENQLVNMLFR--HEK 156
Cdd:PRK11361   70 MRSHETRTP---VILMTAYAEVETAVEALRCGAFDYVIKpfDLDELNLivQRALQlQSMKKEIRHLHQALSTSWQwgHIL 146

                         170
                  ....*....|....*....
gi 1732753220 157 TDveklSPREIDVLRLICK 175
Cdd:PRK11361  147 TN----SPAMMDICKDTAK 161
 
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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