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Conserved domains on  [gi|2446202491|ref|WP_274077122|]
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response regulator transcription factor [Pseudomonas putida]

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
PRK10840 super family cl32589
transcriptional regulator RcsB; Provisional
 5-208 1.48e-47

transcriptional regulator RcsB; Provisional


The actual alignment was detected with superfamily member PRK10840:

Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 155.38  E-value: 1.48e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   5 IILADDHPVVLIGARTALTASpgSPFSVVAEALNADELIYHLDVTPCDILISDYSMPYGRFPDGLALMGYLNRHFGHIPL 84
Cdd:PRK10840    6 VIIADDHPIVLFGIRKSLEQI--EWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKYGDGITLIKYIKRHFPSLSI 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491  85 IVMTMLRNPSLLQALLNHGACGLFDKRSPLSELKQAVNSVTKGRRYLSPSFARILEARSlphCRSDATANLSEREMEVVR 164
Cdd:PRK10840   84 IVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKIS---AGGYGDKRLSPKESEVLR 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2446202491 165 LFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKLGLGHDGGLVEF 208
Cdd:PRK10840  161 LFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNY 204
 
Name Accession Description Interval E-value
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 5-208 1.48e-47

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 155.38  E-value: 1.48e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   5 IILADDHPVVLIGARTALTASpgSPFSVVAEALNADELIYHLDVTPCDILISDYSMPYGRFPDGLALMGYLNRHFGHIPL 84
Cdd:PRK10840    6 VIIADDHPIVLFGIRKSLEQI--EWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKYGDGITLIKYIKRHFPSLSI 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491  85 IVMTMLRNPSLLQALLNHGACGLFDKRSPLSELKQAVNSVTKGRRYLSPSFARILEARSlphCRSDATANLSEREMEVVR 164
Cdd:PRK10840   84 IVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKIS---AGGYGDKRLSPKESEVLR 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2446202491 165 LFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKLGLGHDGGLVEF 208
Cdd:PRK10840  161 LFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNY 204
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 5-124 1.34e-25

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: 96.04  E-value: 1.34e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   5 IILADDHPVVLIGARTALTASPGspFSVVAEALNADELIYHLDVTPCDILISDYSMPYGrfpDGLALMGYLNRHFGHIPL 84
Cdd:cd17535     1 VLIVDDHPLVREGLRRLLESEPD--IEVVGEAADGEEALALLRELRPDVVLMDLSMPGM---DGIEALRRLRRRYPDLKV 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2446202491  85 IVMTMLRNPSLLQALLNHGACGLFDKRSPLSELKQAVNSV 124
Cdd:cd17535    76 IVLTAHDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAV 115
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 4-214 7.54e-20

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: 81.48  E-value: 7.54e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   4 RIILADDHPVVLIGARTALTASPGspFSVVAEALNADELIYHLDVTPCDILISDYSMPYGrfpDGLALMGYLnrhfghip 83
Cdd:COG2197     3 RVLIVDDHPLVREGLRALLEAEPD--IEVVGEAADGEEALELLEELRPDVVLLDIRMPGM---DGLEALRRL-------- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491  84 livmtmlrnpsllqallnhgacglfdkrsplselkqavnsvtkgrrylspsfarilearslphcrsdatanLSEREMEVV 163
Cdd:COG2197    70 -----------------------------------------------------------------------LTPREREVL 78

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2446202491 164 RLFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKLGLGHDGGLVEFARVSGL 214
Cdd:COG2197    79 RLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGL 129
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 5-122 1.13e-14

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: 67.18  E-value: 1.13e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   5 IILADDHPVVLIGARTALTaSPGSpfsVVAEALNADELIYHLDVTPCDILISDYSMPyGRfpDGLALMGYLNRHFGHIPL 84
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLE-KEGY---VVAEADDGKEALELLKEERPDLILLDINMP-GM--DGLELLKRIRRRDPTTPV 73

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2446202491  85 IVMTMLRNPSLLQALLNHGACGLFDKRSPLSELKQAVN 122
Cdd:pfam00072  74 IILTAHGDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 155-209 1.14e-13

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 62.93  E-value: 1.14e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2446202491  155 LSEREMEVVRLFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKLGLGHDGGLVEFA 209
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 150-197 6.51e-06

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: 44.65  E-value: 6.51e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2446202491 150 DATANLSEREMEVVRL-FVQGLSGRQIAAQLNRSEKTISRQKRTAMDKL 197
Cdd:TIGR02937 106 EALEKLPEREREVLVLrYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
 
Name Accession Description Interval E-value
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 5-208 1.48e-47

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 155.38  E-value: 1.48e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   5 IILADDHPVVLIGARTALTASpgSPFSVVAEALNADELIYHLDVTPCDILISDYSMPYGRFPDGLALMGYLNRHFGHIPL 84
Cdd:PRK10840    6 VIIADDHPIVLFGIRKSLEQI--EWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKYGDGITLIKYIKRHFPSLSI 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491  85 IVMTMLRNPSLLQALLNHGACGLFDKRSPLSELKQAVNSVTKGRRYLSPSFARILEARSlphCRSDATANLSEREMEVVR 164
Cdd:PRK10840   84 IVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKIS---AGGYGDKRLSPKESEVLR 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2446202491 165 LFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKLGLGHDGGLVEF 208
Cdd:PRK10840  161 LFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNY 204
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 5-124 1.34e-25

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: 96.04  E-value: 1.34e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   5 IILADDHPVVLIGARTALTASPGspFSVVAEALNADELIYHLDVTPCDILISDYSMPYGrfpDGLALMGYLNRHFGHIPL 84
Cdd:cd17535     1 VLIVDDHPLVREGLRRLLESEPD--IEVVGEAADGEEALALLRELRPDVVLMDLSMPGM---DGIEALRRLRRRYPDLKV 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2446202491  85 IVMTMLRNPSLLQALLNHGACGLFDKRSPLSELKQAVNSV 124
Cdd:cd17535    76 IVLTAHDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAV 115
PRK10360 PRK10360
transcriptional regulator UhpA;
5-210 4.17e-22

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 89.27  E-value: 4.17e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   5 IILADDHPVVLIGARTALTASPGspFSVVAEALNADELIYHLDVTPCDILISDYSMP-------YGRFPDGLALmgylnr 77
Cdd:PRK10360    4 VALIDDHLIVRSGFAQLLGLEPD--LQVVAEFGSGREALAGLPGRGVQVCICDISMPdisglelLSQLPKGMAT------ 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491  78 hfghiplIVMTMLRNPSLLQALLNHGACGLFDKRSPLSELKQAVNSVTKGRRYLSPSFARILEARslphcRSDAtanLSE 157
Cdd:PRK10360   76 -------IMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASG-----RQDP---LTK 140

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2446202491 158 REMEVVRLFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKLGLGHDgglVEFAR 210
Cdd:PRK10360  141 RERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSND---VELAR 190
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 4-214 7.54e-20

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: 81.48  E-value: 7.54e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   4 RIILADDHPVVLIGARTALTASPGspFSVVAEALNADELIYHLDVTPCDILISDYSMPYGrfpDGLALMGYLnrhfghip 83
Cdd:COG2197     3 RVLIVDDHPLVREGLRALLEAEPD--IEVVGEAADGEEALELLEELRPDVVLLDIRMPGM---DGLEALRRL-------- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491  84 livmtmlrnpsllqallnhgacglfdkrsplselkqavnsvtkgrrylspsfarilearslphcrsdatanLSEREMEVV 163
Cdd:COG2197    70 -----------------------------------------------------------------------LTPREREVL 78

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2446202491 164 RLFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKLGLGHDGGLVEFARVSGL 214
Cdd:COG2197    79 RLLAEGLSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRLGL 129
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
1-197 1.34e-18

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 80.28  E-value: 1.34e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   1 MSQRIILADDHPVVLIGARTALTASPGspFSVVAEALNADELIYHLDVTPCDILISDYSMpygRFPDGLALMGYLNRHFG 80
Cdd:PRK10403    5 TPFQVLIVDDHPLMRRGVRQLLELDPG--FEVVAEAGDGASAIDLANRLDPDVILLDLNM---KGMSGLDTLNALRRDGV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491  81 HIPLIVMTMLRNPSLLQALLNHGACGLFDKRSPLSELKQAVNSVTKGRRYLSPSFARILEARSLPHCRSDATANLSEREM 160
Cdd:PRK10403   80 TAQIIILTVSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSKVFSERVNQYLREREMFGAEEDPFSVLTEREL 159

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2446202491 161 EVVRLFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKL 197
Cdd:PRK10403  160 DVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKL 196
PRK09483 PRK09483
response regulator; Provisional
 5-209 9.88e-17

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 75.53  E-value: 9.88e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   5 IILADDHPVVLIGARTALTASPGspFSVVAEALNADELIYHLDVTPCDILISDYSMP-YGrfpdGLALMGYLNRHFGHIP 83
Cdd:PRK09483    4 VLLVDDHELVRAGIRRILEDIKG--IKVVGEACCGEDAVKWCRTNAVDVVLMDMNMPgIG----GLEATRKILRYTPDVK 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491  84 LIVMTM-LRNP---SLLQAllnhGACGLFDKRSPLSELKQAVNSVTKGRRYLSPSFARILEARSLPHCRSDATANLSERE 159
Cdd:PRK09483   78 IIMLTVhTENPlpaKVMQA----GAAGYLSKGAAPQEVVSAIRSVHSGQRYIASDIAQQMALSQIEPATENPFASLSERE 153

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2446202491 160 MEVVRLFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKLGLGHDGGLVEFA 209
Cdd:PRK09483  154 LQIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLA 203
PRK15369 PRK15369
two component system response regulator;
1-197 3.61e-16

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 73.96  E-value: 3.61e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   1 MSQRIILADDHPVVLIGARTALTASPgsPFSVVAEALNADElIYHL--DVTPcDILISDYSMPyGRfpDGLALMGYLNRH 78
Cdd:PRK15369    2 KNYKILLVDDHELIINGIKNMLAPYP--RYKIVGQVDNGLE-VYNAcrQLEP-DIVILDLGLP-GM--NGLDVIPQLHQR 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491  79 FGHIPLIVMTMLRNPSLLQALLNHGACGLFDKRSPLSELKQAVNSVTKGRRYLSPSFARILEARSLPHCRSDATAnLSER 158
Cdd:PRK15369   75 WPAMNILVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKRYIDPALNREAILALLNADDTNPPL-LTPR 153

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2446202491 159 EMEVVRLFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKL 197
Cdd:PRK15369  154 ERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKL 192
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 5-122 1.13e-14

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: 67.18  E-value: 1.13e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   5 IILADDHPVVLIGARTALTaSPGSpfsVVAEALNADELIYHLDVTPCDILISDYSMPyGRfpDGLALMGYLNRHFGHIPL 84
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLE-KEGY---VVAEADDGKEALELLKEERPDLILLDINMP-GM--DGLELLKRIRRRDPTTPV 73

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2446202491  85 IVMTMLRNPSLLQALLNHGACGLFDKRSPLSELKQAVN 122
Cdd:pfam00072  74 IILTAHGDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 2-199 4.89e-14

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 68.13  E-value: 4.89e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   2 SQRIILADDHPVVLIGARTALTASPGspFSVVAEALNADE---LIYHLDvtPcDILISDYSMPYGrfpDGLALMGYLnRH 78
Cdd:PRK10651    6 PATILLIDDHPMLRTGVKQLISMAPD--ITVVGEASNGEQgieLAESLD--P-DLILLDLNMPGM---NGLETLDKL-RE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491  79 FGHIPLIVM-TMLRNPSLLQALLNHGACGLFDKRSPLSELKQAVNSVTKGRRYLSPSFARILEA--RSLPHCRSDATANL 155
Cdd:PRK10651   77 KSLSGRIVVfSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQAAAGEMVLSEALTPVLAAslRANRATTERDVNQL 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2446202491 156 SEREMEVVRLFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKLGL 199
Cdd:PRK10651  157 TPRERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKL 200
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 155-210 5.71e-14

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: 63.71  E-value: 5.71e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2446202491 155 LSEREMEVVRLFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKLGLGHDGGLVEFAR 210
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAI 56
CitB COG4565
DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ...
 1-132 1.13e-13

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


Pssm-ID: 443622 [Multi-domain]  Cd Length: 138  Bit Score: 65.38  E-value: 1.13e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   1 MSQRIILADDHPVVLIGARTALTASPGspFSVVAEALNADELIYHLDVTPCDILISDYSMPYGrfpDGLALMGYLNRHFG 80
Cdd:COG4565     2 KMIRVLIVEDDPMVAELLRRYLERLPG--FEVVGVASSGEEALALLAEHRPDLILLDIYLPDG---DGLELLRELRARGP 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2446202491  81 HIPLIVMTMLRNPSLLQALLNHGACGLFDKrsPLS--ELKQAVNSVTKGRRYLS 132
Cdd:COG4565    77 DVDVIVITAARDPETVREALRAGVVDYLIK--PFTfeRLREALERYLEYRRLLR 128
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 155-209 1.14e-13

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 62.93  E-value: 1.14e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2446202491  155 LSEREMEVVRLFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKLGLGHDGGLVEFA 209
Cdd:smart00421   4 LTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
5-214 2.42e-13

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 66.05  E-value: 2.42e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   5 IILADDHPVVLIGARTALTASpgSPFSVVAEALNADELIYHLDVTPCDILISDYSMPYgrfPDGLALMGYLNRHFGHIPL 84
Cdd:PRK09935    6 VIIMDTHPIIRMSIEVLLQKN--SELQIVLKTDDYRITIDYLRTRPVDLIIMDIDLPG---TDGFTFLKRIKQIQSTVKV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491  85 IVMTMLRNPSLLQALLNHGACGLFDKRSPLSELKQAVNSVTKGRRYLsPSFARILEARSLPHCRSDATANLSEREMEVVR 164
Cdd:PRK09935   81 LFLSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMILSGYTFF-PSETLNYIKSNKCSTNSSTDTVLSNREVTILR 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2446202491 165 LFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKLGLGHDGGLVEFARVSGL 214
Cdd:PRK09935  160 YLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIVELIDYAKLHEL 209
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 38-210 7.84e-12

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: 61.65  E-value: 7.84e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491  38 NADELIYHLDVTPCDILISDYSMPyGRfpDGLALMGYLNRHFGHIPLIVMT------MLRnpsllQALLnHGACGLFDKr 111
Cdd:COG4566    31 SAEAFLAALDPDRPGCLLLDVRMP-GM--SGLELQEELAARGSPLPVIFLTghgdvpMAV-----RAMK-AGAVDFLEK- 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491 112 sPLSE--LKQAVNSVTKGRRYLSPSFARILEARSLphcrsdaTANLSEREMEVVRLFVQGLSGRQIAAQLNRSEKTISRQ 189
Cdd:COG4566   101 -PFDDqaLLDAVRRALARDRARRAERARRAELRAR-------LASLTPREREVLDLVVAGLSNKQIARELGISPRTVEVH 172

                         170       180
                  ....*....|....*....|.
gi 2446202491 190 KRTAMDKLGLGHdggLVEFAR 210
Cdd:COG4566   173 RANVMEKLGARS---LAELVR 190
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
6-215 1.04e-11

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 61.45  E-value: 1.04e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   6 ILADDHPVVLIGARTALTASPgspFSVVAEALNADELIYHLDVTPCDILISDYSMPYgrfPDGLALMGYLN-RHFGHIpL 84
Cdd:PRK09958    4 IIIDDHPLAIAAIRNLLIKND---IEILAELTEGGSAVQRVETLKPDIVIIDVDIPG---VNGIQVLETLRkRQYSGI-I 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491  85 IVMTMLRNPSLLQALLNHGACGLFDKRSPLSELKQAVNSVTKGRRYLSPSFARILEARSLPHCRSDAtanLSEREMEVVR 164
Cdd:PRK09958   77 IIVSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYCYFPFSLNRFVGSLTSDQQKLDS---LSKQEISVMR 153

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2446202491 165 LFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKLGLGHDGGLVEFARVSGLG 215
Cdd:PRK09958  154 YILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSLMDLYTFAQRNKIG 204
YesN COG4753
Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding ...
 4-104 1.08e-11

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: 59.02  E-value: 1.08e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   4 RIILADDHPVVLIGARTALTASPGspFSVVAEALNADELIYHLDVTPCDILISDYSMPygrFPDGLALMGYLNRHFGHIP 83
Cdd:COG4753     1 KVLIVDDEPLIREGLKRILEWEAG--FEVVGEAENGEEALELLEEHKPDLVITDINMP---GMDGLELLEAIRELDPDTK 75

                          90       100
                  ....*....|....*....|.
gi 2446202491  84 LIVMTMLRNPSLLQALLNHGA 104
Cdd:COG4753    76 IIILSGYSDFEYAQEAIKLGA 96
GerE pfam00196
Bacterial regulatory proteins, luxR family;
153-209 2.58e-11

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 56.82  E-value: 2.58e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2446202491 153 ANLSEREMEVVRLFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKLGLGHDGGLVEFA 209
Cdd:pfam00196   1 DSLSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
PRK11475 PRK11475
DNA-binding transcriptional activator BglJ; Provisional
 67-209 1.38e-10

DNA-binding transcriptional activator BglJ; Provisional


Pssm-ID: 236915 [Multi-domain]  Cd Length: 207  Bit Score: 58.60  E-value: 1.38e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491  67 DGLALMGYLNRHFGHIPLIVMTMLRNPS-LLQALLNHGACGLFDKRSPLSELKQAVNSVTKGRRYLSPSFARILEArslp 145
Cdd:PRK11475   54 EGLSCLTELAIKFPRMRRLVIADDDIEArLIGSLSPSPLDGVLSKASTLEILQQELFLSLNGVRQATDRLNNQWYI---- 129

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2446202491 146 hCRSDAtanLSEREMEVVRLFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKLGLGHDGGLVEFA 209
Cdd:PRK11475  130 -NQSRM---LSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVSSDAGLLDAA 189
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 144-198 1.83e-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: 1.83e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2446202491 144 LPHCRSDATANLSEREMEVVRLFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKLG 198
Cdd:COG5905     2 MPSSSTSHPSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLG 56
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
32-214 2.11e-10

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 57.84  E-value: 2.11e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491  32 VVAEALNADELIYHLDVTPCDILISDYSMPYGRFPDGLALMGYLNRHFGHIPLIVMTMLRNPSLLQALLNHGACGLFDKR 111
Cdd:COG2771     5 ALALLLLALLLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLAL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491 112 SPLSELKQAVNSVTKGRRYLSPSFARILEARSLPHCRSDATANLSEREMEVVRLFVQGLSGRQIAAQLNRSEKTISRQKR 191
Cdd:COG2771    85 LLLLALLALLAALLARLAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLK 164

                         170       180
                  ....*....|....*....|...
gi 2446202491 192 TAMDKLGLGHDGGLVEFARVSGL 214
Cdd:COG2771   165 RIYRKLGVSSRAELVALALRLGL 187
RpfG COG3437
Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ...
 4-130 1.87e-09

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: 55.56  E-value: 1.87e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   4 RIILADDHPVVLIGARTALTASPgspFSVVaEALNADELIYHLDVTPCDILISDYSMPYGrfpDGLALMGYLNRH--FGH 81
Cdd:COG3437     8 TVLIVDDDPENLELLRQLLRTLG---YDVV-TAESGEEALELLLEAPPDLILLDVRMPGM---DGFELLRLLRADpsTRD 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2446202491  82 IPLIVMTMLRNPSLLQALLNHGACGLFDKRSPLSELKQAVNSVTKGRRY 130
Cdd:COG3437    81 IPVIFLTALADPEDRERALEAGADDYLTKPFDPEELLARVRNALELRRL 129
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 1-129 2.74e-09

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: 56.13  E-value: 2.74e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   1 MSQRIILADDHPVVLIGARTALTASPgspFSVVaEALNADELIYHLDVTPCDILISDYSMPYGrfpDGLALMGYLNRHFG 80
Cdd:COG2204     1 SMARILVVDDDPDIRRLLKELLERAG---YEVE-TAASGEEALALLREEPPDLVLLDLRMPGM---DGLELLRELRALDP 73

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2446202491  81 HIPLIVMTMLRNPSLLQALLNHGACGLFDKRSPLSELKQAVNSVTKGRR 129
Cdd:COG2204    74 DLPVILLTGYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERALERRR 122
CheY COG0784
CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator ...
 1-129 5.66e-09

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: 52.55  E-value: 5.66e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   1 MSQRIILADDHPVVLIGARTALTASpGspFSVVaEALNADELIYHLDVTPCDILISDYSMPYGrfpDGLALMGYLNRH-- 78
Cdd:COG0784     4 GGKRILVVDDNPDNRELLRRLLERL-G--YEVT-TAEDGAEALELLRAGPPDLILLDINMPGM---DGLELLRRIRALpr 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2446202491  79 FGHIPLIVMTMLRNPSLLQALLNHGACGLFDKRSPLSELKQAVNSVTKGRR 129
Cdd:COG0784    77 LPDIPIIALTAYADEEDRERALEAGADDYLTKPVDPEELLEALRRLLARAS 127
PleD COG3706
Two-component response regulator, PleD family, consists of two REC domains and a diguanylate ...
 4-164 2.59e-08

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: 51.83  E-value: 2.59e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   4 RIILADDHPVVLIGARTALTASPgspFSVVaEALNADELIYHLDVTPCDILISDYSMPYGrfpDGLALMGYL--NRHFGH 81
Cdd:COG3706     3 RILVVDDDPTNRKLLRRLLEAAG---YEVV-EAADGEEALELLQEHRPDLILLDLEMPDM---DGLELCRRLraDPRTAD 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491  82 IPLIVMTMLRNPSLLQALLNHGACGLFDKrsPLS--ELKQAVNSVTkgrRYLSPSFARIlearsLPHCRSDATANLSERE 159
Cdd:COG3706    76 IPIIFLTALDDEEDRARALEAGADDYLTK--PFDpeELLARVDLVA---RYGGEEFAIL-----LPGTDLEGALAVAERI 145


                  ....*
gi 2446202491 160 MEVVR 164
Cdd:COG3706   146 REAVA 150
REC cd00156
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...
 7-110 7.72e-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: 48.76  E-value: 7.72e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   7 LADDHPVVLIGARTALTASpgspFSVVAEALNADELIYHLDVTPCDILISDYSMPYGrfpDGLALMGYLNRHFGHIPLIV 86
Cdd:cd00156     2 IVDDDPAIRELLKSLLERE----GYEVDTAADGEEALELLREERPDLVLLDLMMPGM---DGLELLRKLRELPPDIPVIV 74

                          90       100
                  ....*....|....*....|....
gi 2446202491  87 MTMLRNPSLLQALLNHGACGLFDK 110
Cdd:cd00156    75 LTAKADEEDAVRALELGADDYLVK 98
OmpR COG0745
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 2-168 1.45e-07

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: 49.95  E-value: 1.45e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   2 SQRIILADDHPVVLIGARTALTASpGspFSVVaEALNADELIYHLDVTPCDILISDYSMPYGrfpDGLALMGYLNRHFGH 81
Cdd:COG0745     1 MPRILVVEDDPDIRELLADALERE-G--YEVD-TAADGEEALELLEEERPDLILLDLMLPGM---DGLEVCRRLRARPSD 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491  82 IPLIVMTMLRNPSLLQALLNHGACGLFDKrsPLS--ELKQAVNSVTKGRRYLSPSFARILEARSLPHCRSDATANLSERE 159
Cdd:COG0745    74 IPIIMLTARDDEEDRVRGLEAGADDYLTK--PFDpeELLARIRALLRRRAAEVLRVGDLLDLAAREVTRDGEPVELTPKE 151


                  ....*....
gi 2446202491 160 MEVVRLFVQ 168
Cdd:COG0745   152 FRLLELLMR 160
AmiR COG3707
Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding ...
 1-116 1.02e-06

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: 47.26  E-value: 1.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   1 MSQRIILADDHPVVLIGARTALTASPgspFSVVAEALNADELIYHLDVTPCDILISDYSMPygrFPDGLALMGYLNRHfG 80
Cdd:COG3707     2 RGLRVLVVDDEPLRRADLREGLREAG---YEVVAEAADGEDAVELVRELKPDLVIVDIDMP---DRDGLEAARQISEE-R 74

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2446202491  81 HIPLIVMTMLRNPSLLQALLNHGACGLFDKrsPLSE 116
Cdd:COG3707    75 PAPVILLTAYSDPELIERALEAGVSAYLVK--PLDP 108
REC_NtrC cd19919
phosphoacceptor receiver (REC) domain of DNA-binding transcriptional regulator NtrC; ...
 38-88 6.01e-06

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: 43.80  E-value: 6.01e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2446202491  38 NADELIYHLDVTPCDILISDYSMPYGrfpDGLALMGYLNRHFGHIPLIVMT 88
Cdd:cd19919    32 NAQEALAALASSQPDVLISDIRMPGM---DGLALLAQIKQRHPDLPVIIMT 79
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 150-197 6.51e-06

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: 44.65  E-value: 6.51e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2446202491 150 DATANLSEREMEVVRL-FVQGLSGRQIAAQLNRSEKTISRQKRTAMDKL 197
Cdd:TIGR02937 106 EALEKLPEREREVLVLrYLEGLSYKEIAEILGISVGTVKRRLKRARKKL 154
REC_YesN-like cd17536
phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response ...
 5-88 7.29e-06

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: 43.87  E-value: 7.29e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   5 IILADDHPVVLIGARTAL-TASPGspFSVVAEALNADE---LIYHLDVtpcDILISDYSMPygrFPDGLALMGYLNRHFG 80
Cdd:cd17536     1 VLIVDDEPLIREGLKKLIdWEELG--FEVVGEAENGEEaleLIEEHKP---DIVITDIRMP---GMDGLELIEKIRELYP 72


                  ....*...
gi 2446202491  81 HIPLIVMT 88
Cdd:cd17536    73 DIKIIILS 80
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 151-197 8.84e-06

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. 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: 41.64  E-value: 8.84e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2446202491 151 ATANLSEREMEVVRL-FVQGLSGRQIAAQLNRSEKTISRQKRTAMDKL 197
Cdd:pfam04545   1 ALASLPPRERQVLVLrYGEGLTLEEIGERLGISRERVRQIEKRALRKL 48
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
137-214 2.35e-05

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 43.54  E-value: 2.35e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2446202491 137 RILEARSLPHCRSDATAnlseREMEVVRLFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKLGLGHDGGLVEFARVSGL 214
Cdd:COG2909   109 LLLRALALRALGDREEA----LAALRRRLLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEAVARARELGL 182
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 150-197 2.92e-05

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: 40.55  E-value: 2.92e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2446202491 150 DATANLSEREMEVVRL-FVQGLSGRQIAAQLNRSEKTISRQKRTAMDKL 197
Cdd:cd06171     6 EALDKLPEREREVILLrFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 132-197 2.99e-05

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: 43.06  E-value: 2.99e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2446202491 132 SPSFARILEARSLPHCRSDATANLSEREMEVVRL-FVQGLSGRQIAAQLNRSEKTISRQKRTAMDKL 197
Cdd:COG1595   105 AADPEEALEAEELLEALLAALERLPPRQREVLVLrYLEGLSYAEIAEILGISEGTVKSRLSRARKKL 171
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 150-197 3.05e-05

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: 43.27  E-value: 3.05e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2446202491 150 DATANLSEREMEVVRL-FVQGLSGRQIAAQLNRSEKTISRQKRTAMDKL 197
Cdd:COG1191   182 EAIEQLPERERLVLSLyYFEELTLKEIAEVLGVSESRVSRLHKKALARL 230
Tra8 COG2826
Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];
154-188 5.18e-05

Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons];


Pssm-ID: 442074 [Multi-domain]  Cd Length: 325  Bit Score: 42.95  E-value: 5.18e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2446202491 154 NLSEREmEVVRLFVQGLSGRQIAAQLNRSEKTISR 188
Cdd:COG2826     8 TLEERE-EIEALLKAGLSVREIARRLGRSPSTISR 41
HTH_38 pfam13936
Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is ...
 154-188 2.57e-04

Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.


Pssm-ID: 433591 [Multi-domain]  Cd Length: 44  Bit Score: 37.49  E-value: 2.57e-04
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2446202491 154 NLSEREmEVVRLFVQGLSGRQIAAQLNRSEKTISR 188
Cdd:pfam13936   6 SLEERE-EIARLLAEGLSLREIARRLGRSPSTISR 39
REC_Ycf29 cd19927
phosphoacceptor receiver (REC) domain of probable transcriptional regulator Ycf29; Ycf29 is a ...
 5-88 2.85e-04

phosphoacceptor receiver (REC) domain of probable transcriptional regulator Ycf29; Ycf29 is a probable response regulator of a two-component system (TCS), typically consisting a sensor and a response regulator, that functions in adaptation to changing environments. Processes regulated by TCSs in bacteria include sporulation, pathogenicity, virulence, chemotaxis, and membrane transport. Ycf29 contains an N-terminal REC domain and a LuxR-type helix-turn-helix DNA-binding output domain. REC domains function as phosphorylation-mediated switches within RRs, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381154 [Multi-domain]  Cd Length: 102  Bit Score: 38.90  E-value: 2.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   5 IILADDHPVVLIGARTALTaSPGspFSVVAeALNADELIYHLDVTPCDILISDYSMPYGrfpDGLALMGYL--NRHFGHI 82
Cdd:cd19927     1 ILLVDDDPGIRLAVKDYLE-DQG--FTVIA-ASNGLEALDLLNQYIPDLIISDIIMPGV---DGYSLLGKLrkNADFDTI 73


                  ....*.
gi 2446202491  83 PLIVMT 88
Cdd:cd19927    74 PVIFLT 79
LytT COG3279
DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction ...
 4-88 3.42e-04

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


Pssm-ID: 442510 [Multi-domain]  Cd Length: 235  Bit Score: 40.18  E-value: 3.42e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2446202491   4 RIILADDHPVVLIGARTALTASPGspFSVVAEALNADELIYHLDVTPCDILISDYSMPYGrfpDGLALMGYLnRHFGHIP 83
Cdd:COG3279     3 KILIVDDEPLARERLERLLEKYPD--LEVVGEASNGEEALELLEEHKPDLVFLDIQMPGL---DGFELARQL-RELDPPP 76


                  ....*
gi 2446202491  84 LIVMT 88
Cdd:COG3279    77 PIIFT 81
COG4584 COG4584
Transposase [Mobilome: prophages, transposons];
157-188 7.25e-04

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 443641 [Multi-domain]  Cd Length: 484  Bit Score: 39.82  E-value: 7.25e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2446202491 157 EREMEVVRLFVQGLSGRQIAAQLNRSEKTISR 188
Cdd:COG4584     5 EQIREIRRLLREGLSIREIARELGISRNTVRK 36
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
154-191 8.01e-04

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 39.12  E-value: 8.01e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2446202491 154 NLSEREMEVVRLFVQGLSGRQIAAQLNRSEK----TISRQKR 191
Cdd:PRK08295  155 LLSELEKEVLELYLDGKSYQEIAEELNRHVKsidnALQRVKR 196
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 150-197 2.91e-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: 34.74  E-value: 2.91e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2446202491 150 DATANLSEREMEVVRL-FVQGLSGRQIAAQLNRSEKTISRQKRTAMDKL 197
Cdd:pfam08281   6 RALEELPPRQREVFLLrYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
COG1356 COG1356
Transcriptional regulator [Transcription];
155-197 3.86e-03

Transcriptional regulator [Transcription];


Pssm-ID: 440967 [Multi-domain]  Cd Length: 139  Bit Score: 36.37  E-value: 3.86e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2446202491 155 LSEREMEVVRLFVQGLSGRQIAAQLNRSEKTISRQKRTAMDKL 197
Cdd:COG1356     9 LTRRQAEVLALRERGLTQQEIADILGTSRANVSSIEKSARENI 51
HTH_23 pfam13384
Homeodomain-like domain;
157-188 4.01e-03

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 34.17  E-value: 4.01e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2446202491 157 EREMEVVRLFVQGLSGRQIAAQLNRSEKTISR 188
Cdd:pfam13384   5 RRRARALLLLAEGLSVKEIAELLGVSRRTVYR 36
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 139-197 5.42e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 36.58  E-value: 5.42e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2446202491 139 LEARSLPHCRS---DATANLSEREMEVVRL-FVQGLSGRQIAAQLNRSEKTISRQKRTAMDKL 197
Cdd:PRK12519  123 LEQASLAERSQrvqTALAQLPESQRQVLELaYYEGLSQSEIAKRLGIPLGTVKARARQGLLKL 185
YerC COG4496
Predicted DNA-binding transcriptional regulator YerC, contains ArsR-like HTH domain [General ...
 155-203 7.62e-03

Predicted DNA-binding transcriptional regulator YerC, contains ArsR-like HTH domain [General function prediction only];


Pssm-ID: 443584  Cd Length: 92  Bit Score: 34.74  E-value: 7.62e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2446202491 155 LSEReMEVVRLFVQGLSGRQIAAQLNRSEKTISRQKRTamdkLGLGHDG 203
Cdd:COG4496    42 LAQR-LEVARLLREGKTYREIAEETGASTATISRVKRC----LNYGAGG 85
 
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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