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Conserved domains on  [gi|1332281222|gb|PNM78388|]
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DNA-binding response regulator [Vibrio vulnificus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10403 super family cl32510
nitrate/nitrite response regulator protein NarP;
3-205 2.19e-84

nitrate/nitrite response regulator protein NarP;


The actual alignment was detected with superfamily member PRK10403:

Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 249.00  E-value: 2.19e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:PRK10403    8 QVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANRLDPDVILLDLNMKGMSGLDTLNALRRDGVTAQIIILT 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  83 VSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKAHLGDKAYSSVVAKYLLQRE---ENTDVFDELTERERQILQEVAR 159
Cdd:PRK10403   88 VSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSKVFSERVNQYLREREmfgAEEDPFSVLTERELDVLHELAQ 167

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1332281222 160 GFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLFLERYG 205
Cdd:PRK10403  168 GLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILFLQQRG 213
 
Name Accession Description Interval E-value
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
3-205 2.19e-84

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 249.00  E-value: 2.19e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:PRK10403    8 QVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANRLDPDVILLDLNMKGMSGLDTLNALRRDGVTAQIIILT 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  83 VSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKAHLGDKAYSSVVAKYLLQRE---ENTDVFDELTERERQILQEVAR 159
Cdd:PRK10403   88 VSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSKVFSERVNQYLREREmfgAEEDPFSVLTERELDVLHELAQ 167

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1332281222 160 GFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLFLERYG 205
Cdd:PRK10403  168 GLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILFLQQRG 213
REC_NarL cd19931
phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate ...
 4-118 1.72e-51

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: 161.75  E-value: 1.72e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTV 83
Cdd:cd19931     1 VLLIDDHPLLRKGIKQLIELDPDFTVVGEASSGEEGIELAERLDPDLILLDLNMKGMSGLDTLKALREEGVSARIVILTV 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1332281222  84 SDSPADIEAIVKAGADGYLLKDTEPDELVELLEKA 118
Cdd:cd19931    81 SDAEDDVVTALRAGADGYLLKDMEPEDLLEALKQA 115
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 1-203 1.02e-39

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: 132.32  E-value: 1.02e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   1 MCRVMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALradgceasivi 80
Cdd:COG2197     1 MIRVLIVDDHPLVREGLRALLEAEPDIEVVGEAADGEEALELLEELRPDVVLLDIRMPGMDGLEALRRL----------- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  81 ltvsdspadieaivkagadgyllkdtepdelvellekahlgdkayssvvakyllqreentdvfdeLTERERQILQEVARG 160
Cdd:COG2197    70 -----------------------------------------------------------------LTPREREVLRLLAEG 84

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1332281222 161 FRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLFLER 203
Cdd:COG2197    85 LSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRL 127
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 4-116 2.94e-30

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: 107.62  E-value: 2.94e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfEEQFeVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTV 83
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLE-KEGY-VVAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTA 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1332281222  84 SDSPADIEAIVKAGADGYLLKDTEPDELVELLE 116
Cdd:pfam00072  79 HGDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 143-200 2.08e-20

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 80.65  E-value: 2.08e-20
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1332281222  143 FDELTERERQILQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLF 200
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 105-189 5.10e-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: 5.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222 105 DTEPDELVELLEKAHLGDKAYSSVVAKYLLQreentDVFDELTERERQILQEVA-RGFRNKQIADRLFISESTVKVHMKS 183
Cdd:TIGR02937  75 RRELDLLEELLDSDPSPEEELEQEEEREALR-----EALEKLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKR 149


                  ....*.
gi 1332281222 184 LLKKLK 189
Cdd:TIGR02937 150 ARKKLR 155
 
Name Accession Description Interval E-value
PRK10403 PRK10403
nitrate/nitrite response regulator protein NarP;
3-205 2.19e-84

nitrate/nitrite response regulator protein NarP;


Pssm-ID: 182431 [Multi-domain]  Cd Length: 215  Bit Score: 249.00  E-value: 2.19e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:PRK10403    8 QVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLANRLDPDVILLDLNMKGMSGLDTLNALRRDGVTAQIIILT 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  83 VSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKAHLGDKAYSSVVAKYLLQRE---ENTDVFDELTERERQILQEVAR 159
Cdd:PRK10403   88 VSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAGAKGSKVFSERVNQYLREREmfgAEEDPFSVLTERELDVLHELAQ 167

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1332281222 160 GFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLFLERYG 205
Cdd:PRK10403  168 GLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATILFLQQRG 213
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 2-203 1.52e-76

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 229.15  E-value: 1.52e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   2 CRVMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVIL 81
Cdd:PRK10651    7 ATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLSGRIVVF 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  82 TVSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKAHLGDKAYSS----VVAKYLLQREENTDV-FDELTERERQILQE 156
Cdd:PRK10651   87 SVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQAAAGEMVLSEaltpVLAASLRANRATTERdVNQLTPRERDILKL 166

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1332281222 157 VARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLFLER 203
Cdd:PRK10651  167 IAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQE 213
REC_NarL cd19931
phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate ...
 4-118 1.72e-51

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: 161.75  E-value: 1.72e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTV 83
Cdd:cd19931     1 VLLIDDHPLLRKGIKQLIELDPDFTVVGEASSGEEGIELAERLDPDLILLDLNMKGMSGLDTLKALREEGVSARIVILTV 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1332281222  84 SDSPADIEAIVKAGADGYLLKDTEPDELVELLEKA 118
Cdd:cd19931    81 SDAEDDVVTALRAGADGYLLKDMEPEDLLEALKQA 115
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 4-119 7.73e-43

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: 139.95  E-value: 7.73e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTV 83
Cdd:cd17535     1 VLIVDDHPLVREGLRRLLESEPDIEVVGEAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRRYPDLKVIVLTA 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1332281222  84 SDSPADIEAIVKAGADGYLLKDTEPDELVELLEKAH 119
Cdd:cd17535    81 HDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAVA 116
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 1-203 1.02e-39

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: 132.32  E-value: 1.02e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   1 MCRVMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALradgceasivi 80
Cdd:COG2197     1 MIRVLIVDDHPLVREGLRALLEAEPDIEVVGEAADGEEALELLEELRPDVVLLDIRMPGMDGLEALRRL----------- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  81 ltvsdspadieaivkagadgyllkdtepdelvellekahlgdkayssvvakyllqreentdvfdeLTERERQILQEVARG 160
Cdd:COG2197    70 -----------------------------------------------------------------LTPREREVLRLLAEG 84

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1332281222 161 FRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLFLER 203
Cdd:COG2197    85 LSNKEIAERLGISERTVKTHVSNILRKLGVRNRTELVLLALRL 127
PRK10360 PRK10360
transcriptional regulator UhpA;
1-190 7.72e-36

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 124.70  E-value: 7.72e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   1 MCRVMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADgceASIVI 80
Cdd:PRK10360    1 MITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKG---MATIM 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKAHLGDKAYSSVVAKYLLQREEntdvfDELTERERQILQEVARG 160
Cdd:PRK10360   78 LSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVATGGCYLTPDIAIKLASGRQ-----DPLTKRERQVAEKLAQG 152

                         170       180       190
                  ....*....|....*....|....*....|
gi 1332281222 161 FRNKQIADRLFISESTVKVHMKSLLKKLKV 190
Cdd:PRK10360  153 MAVKEIAAELGLSPKTVHVHRANLMEKLGV 182
OmpR COG0745
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 1-189 1.66e-35

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: 123.91  E-value: 1.66e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   1 MCRVMLVDDHPLMRRGINQLLSfEEQFEVVaEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVI 80
Cdd:COG0745     1 MPRILVVEDDPDIRELLADALE-REGYEVD-TAADGEEALELLEEERPDLILLDLMLPGMDGLEVCRRLRARPSDIPIIM 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLKDTEPDELVELLeKAHLGDKAYSSVVAKYLLQREENTDVFD----ELTERERQILQE 156
Cdd:COG0745    79 LTARDDEEDRVRGLEAGADDYLTKPFDPEELLARI-RALLRRRAAEVLRVGDLLDLAAREVTRDgepvELTPKEFRLLEL 157

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 1332281222 157 VA----RGFRNKQIADRL----FISESTVKVHMKSLLKKLK 189
Cdd:COG0745   158 LMrnpgRVVSREQLLEEVwgydYGDDRTVDVHISRLRKKLE 198
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 4-192 9.47e-35

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: 121.75  E-value: 9.47e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfEEQFEVVAEASnGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTv 83
Cdd:COG4566     2 VYIVDDDEAVRDSLAFLLE-SAGLRVETFAS-AEAFLAALDPDRPGCLLLDVRMPGMSGLELQEELAARGSPLPVIFLT- 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  84 sdSPADIEAIV---KAGADGYLLKDTEPDELVELLEKAHLGDKAYSSVVAkyllQREENTDVFDELTERERQILQEVARG 160
Cdd:COG4566    79 --GHGDVPMAVramKAGAVDFLEKPFDDQALLDAVRRALARDRARRAERA----RRAELRARLASLTPREREVLDLVVAG 152

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1332281222 161 FRNKQIADRLFISESTVKVHMKSLLKKLKVPS 192
Cdd:COG4566   153 LSNKQIARELGISPRTVEVHRANVMEKLGARS 184
PRK09483 PRK09483
response regulator; Provisional
 1-208 2.87e-32

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 115.97  E-value: 2.87e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   1 MCRVMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLD-TLKALRADGcEASIV 79
Cdd:PRK09483    1 MINVLLVDDHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWCRTNAVDVVLMDMNMPGIGGLEaTRKILRYTP-DVKII 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  80 ILTV-SDSPADIEaIVKAGADGYLLKDTEPDELVELLEKAHLGDKAYSSVVAKY--LLQREENTDV-FDELTERERQILQ 155
Cdd:PRK09483   80 MLTVhTENPLPAK-VMQAGAAGYLSKGAAPQEVVSAIRSVHSGQRYIASDIAQQmaLSQIEPATENpFASLSERELQIML 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1332281222 156 EVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLFLeRYGELK 208
Cdd:PRK09483  159 MITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAI-RHGLLN 210
PRK15369 PRK15369
two component system response regulator;
3-190 5.10e-32

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 115.18  E-value: 5.10e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:PRK15369    5 KILLVDDHELIINGIKNMLAPYPRYKIVGQVDNGLEVYNACRQLEPDIVILDLGLPGMNGLDVIPQLHQRWPAMNILVLT 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  83 VSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKAHLG----DKAYSSVVAKYLLQREENTDVFdeLTERERQILQEVA 158
Cdd:PRK15369   85 ARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGkryiDPALNREAILALLNADDTNPPL--LTPRERQILKLIT 162

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1332281222 159 RGFRNKQIADRLFISESTVKVHMKSLLKKLKV 190
Cdd:PRK15369  163 EGYTNRDIAEQLSISIKTVETHRLNMMRKLDV 194
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 4-116 2.94e-30

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: 107.62  E-value: 2.94e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfEEQFeVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTV 83
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLE-KEGY-VVAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTA 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1332281222  84 SDSPADIEAIVKAGADGYLLKDTEPDELVELLE 116
Cdd:pfam00072  79 HGDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111
YesN COG4753
Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding ...
 3-104 9.99e-30

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: 106.01  E-value: 9.99e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:COG4753     1 KVLIVDDEPLIREGLKRILEWEAGFEVVGEAENGEEALELLEEHKPDLVITDINMPGMDGLELLEAIRELDPDTKIIILS 80

                          90       100
                  ....*....|....*....|..
gi 1332281222  83 VSDSPADIEAIVKAGADGYLLK 104
Cdd:COG4753    81 GYSDFEYAQEAIKLGADDYLLK 102
CitB COG4565
DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ...
 1-118 1.06e-28

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


Pssm-ID: 443622 [Multi-domain]  Cd Length: 138  Bit Score: 104.28  E-value: 1.06e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   1 MCRVMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVI 80
Cdd:COG4565     3 MIRVLIVEDDPMVAELLRRYLERLPGFEVVGVASSGEEALALLAEHRPDLILLDIYLPDGDGLELLRELRARGPDVDVIV 82

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKA 118
Cdd:COG4565    83 ITAARDPETVREALRAGVVDYLIKPFTFERLREALERY 120
CheY COG0784
CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator ...
 3-118 1.68e-27

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: 101.08  E-value: 1.68e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEVVaEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEAS--IVI 80
Cdd:COG0784     7 RILVVDDNPDNRELLRRLLE-RLGYEVT-TAEDGAEALELLRAGPPDLILLDINMPGMDGLELLRRIRALPRLPDipIIA 84

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKA 118
Cdd:COG0784    85 LTAYADEEDRERALEAGADDYLTKPVDPEELLEALRRL 122
REC_DesR-like cd19930
phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of ...
 4-119 2.70e-27

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: 100.04  E-value: 2.70e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTV 83
Cdd:cd19930     1 VLIAEDQEMVRGALAALLELEDDLEVVAQASNGQEALRLVLKHSPDVAILDIEMPGRTGLEVAAELREELPDTKVLIVTT 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1332281222  84 SDSPADIEAIVKAGADGYLLKDTEPDELVELLEKAH 119
Cdd:cd19930    81 FGRPGYFRRALAAGVDGYVLKDRPIEELADAIRTVH 116
REC_YesN-like cd17536
phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response ...
 4-118 1.01e-26

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: 98.56  E-value: 1.01e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSFEE-QFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:cd17536     1 VLIVDDEPLIREGLKKLIDWEElGFEVVGEAENGEEALELIEEHKPDIVITDIRMPGMDGLELIEKIRELYPDIKIIILS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1332281222  83 vsdSPADIE----AIvKAGADGYLLKDTEPDELVELLEKA 118
Cdd:cd17536    81 ---GYDDFEyaqkAI-RLGVVDYLLKPVDEEELEEALEKA 116
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 1-118 1.50e-26

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: 105.05  E-value: 1.50e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   1 MCRVMLVDDHPLMRRGINQLLSfEEQFEVVaEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVI 80
Cdd:COG2204     2 MARILVVDDDPDIRRLLKELLE-RAGYEVE-TAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALDPDLPVIL 79

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKA 118
Cdd:COG2204    80 LTGYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERA 117
PleD COG3706
Two-component response regulator, PleD family, consists of two REC domains and a diguanylate ...
 1-122 1.18e-25

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: 97.67  E-value: 1.18e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   1 MCRVMLVDDHPLMRRGINQLLSfEEQFEVVaEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEAS--I 78
Cdd:COG3706     1 PARILVVDDDPTNRKLLRRLLE-AAGYEVV-EAADGEEALELLQEHRPDLILLDLEMPDMDGLELCRRLRADPRTADipI 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1332281222  79 VILTVSDSPADIEAIVKAGADGYLLKDTEPDELVELLEK-AHLGD 122
Cdd:COG3706    79 IFLTALDDEEDRARALEAGADDYLTKPFDPEELLARVDLvARYGG 123
REC cd00156
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...
 5-104 1.34e-25

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: 95.37  E-value: 1.34e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   5 MLVDDHPLMRRGINQLLsfEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTVS 84
Cdd:cd00156     1 LIVDDDPAIRELLKSLL--EREGYEVDTAADGEEALELLREERPDLVLLDLMMPGMDGLELLRKLRELPPDIPVIVLTAK 78

                          90       100
                  ....*....|....*....|
gi 1332281222  85 DSPADIEAIVKAGADGYLLK 104
Cdd:cd00156    79 ADEEDAVRALELGADDYLVK 98
LytT COG3279
DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction ...
 1-118 1.46e-24

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


Pssm-ID: 442510 [Multi-domain]  Cd Length: 235  Bit Score: 96.42  E-value: 1.46e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   1 MCRVMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVI 80
Cdd:COG3279     1 MMKILIVDDEPLARERLERLLEKYPDLEVVGEASNGEEALELLEEHKPDLVFLDIQMPGLDGFELARQLRELDPPPPIIF 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1332281222  81 LTVSDSPAdIEAIvKAGADGYLLKDTEPDELVELLEKA 118
Cdd:COG3279    81 TTAYDEYA-LEAF-EVNAVDYLLKPIDEERLAKALEKA 116
RpfG COG3437
Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ...
 3-118 2.75e-23

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: 92.92  E-value: 2.75e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLsFEEQFEVVaEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRAD--GCEASIVI 80
Cdd:COG3437     8 TVLIVDDDPENLELLRQLL-RTLGYDVV-TAESGEEALELLLEAPPDLILLDVRMPGMDGFELLRLLRADpsTRDIPVIF 85

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKA 118
Cdd:COG3437    86 LTALADPEDRERALEAGADDYLTKPFDPEELLARVRNA 123
REC_CheY cd17542
phosphoacceptor receiver (REC) domain of chemotaxis protein CheY; The chemotaxis response ...
 3-118 5.27e-23

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


Pssm-ID: 381097 [Multi-domain]  Cd Length: 117  Bit Score: 89.26  E-value: 5.27e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:cd17542     2 KVLIVDDAAFMRMMLKDILT-KAGYEVVGEAANGEEAVEKYKELKPDLVTMDITMPEMDGIEALKEIKKIDPNAKVIMCS 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1332281222  83 -VSDSPADIEAIvKAGADGYLLKDTEPDELVELLEKA 118
Cdd:cd17542    81 aMGQEEMVKEAI-KAGAKDFIVKPFQPERVLEAVEKV 116
REC_CheY_CheY3 cd19923
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY ...
 3-118 7.85e-23

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: 88.55  E-value: 7.85e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:cd19923     2 KVLVVDDFSTMRRIIKNLLK-ELGFNNVEEAEDGVDALEKLKAGGFDFVITDWNMPNMDGLELLKTIRADGALSHLPVLM 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1332281222  83 VSdSPADIEAIV---KAGADGYLLKDTEPDELVELLEKA 118
Cdd:cd19923    81 VT-AEAKKENVIaaaQAGVNNYIVKPFTAATLKEKLEKI 118
REC_hyHK_CKI1_RcsC-like cd17546
phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinases/response regulators ...
 4-115 6.41e-22

phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinases/response regulators similar to Arabidopsis thaliana CKI1 and Escherichia coli RcsC; This family is composed of hybrid sensor histidine kinases/response regulators that are sensor histidine kinases (HKs) fused with a REC domain, similar to the sensor histidine kinase CKI1 from Arabidopsis thaliana, which is involved in multi-step phosphorelay (MSP) signaling that mediates responses to a variety of important stimuli in plants. MSP involves a signal being transferred from HKs via histidine phosphotransfer proteins (AHP1-AHP5) to nuclear response regulators. The CKI1 REC domain specifically interacts with the downstream signaling protein AHP2, AHP3 and AHP5. The plant MSP system has evolved from the prokaryotic two-component system (TCS), which allows organisms to sense and respond to changes in environmental conditions. This family also includes bacterial hybrid sensor HKs such as Escherichia coli RcsC, which is a component of the Rcs signalling pathway that controls a variety of physiological functions like capsule synthesis, cell division, and motility. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381099 [Multi-domain]  Cd Length: 113  Bit Score: 85.98  E-value: 6.41e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLsfEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEAS---IVI 80
Cdd:cd17546     1 VLVVDDNPVNRKVLKKLL--EKLGYEVDVAENGQEALELLKEEPFDLVLMDLQMPVMDGLEATRRIRELEGGGRrtpIIA 78

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLKDTEPDELVELL 115
Cdd:cd17546    79 LTANALEEDREKCLEAGMDDYLSKPVKLDQLKEVL 113
REC_CheB-like cd17541
phosphoacceptor receiver (REC) domain of chemotaxis response regulator protein-glutamate ...
 3-117 2.69e-21

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: 84.75  E-value: 2.69e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADgCEASIVI-- 80
Cdd:cd17541     2 RVLIVDDSAVMRKLLSRILESDPDIEVVGTARDGEEALEKIKELKPDVITLDIEMPVMDGLEALRRIMAE-RPTPVVMvs 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1332281222  81 -LTVSDSPADIEAIvKAGADGYLLKDTEPDELV------ELLEK 117
Cdd:cd17541    81 sLTEEGAEITLEAL-ELGAVDFIAKPSGGISLDleeiaeELIEK 123
fixJ PRK09390
response regulator FixJ; Provisional
 4-192 9.86e-21

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 85.44  E-value: 9.86e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfEEQFEVVAEASnGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT- 82
Cdd:PRK09390    6 VHVVDDDEAMRDSLAFLLD-SAGFEVRLFES-AQAFLDALPGLRFGCVVTDVRMPGIDGIELLRRLKARGSPLPVIVMTg 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  83 VSDSPADIEAIvKAGADGYLLKDTEPDELVELLEKA--HLGDKAYSSVVAKYLLQREEntdvfdELTERERQILQEVARG 160
Cdd:PRK09390   84 HGDVPLAVEAM-KLGAVDFIEKPFEDERLIGAIERAlaQAPEAAKSEAVAADIRARIA------SLSERERQVMDGLVAG 156

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1332281222 161 FRNKQIADRLFISESTVKVHMKSLLKKLKVPS 192
Cdd:PRK09390  157 LSNKVIARDLDISPRTVEVYRANVMTKMQAGS 188
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 136-208 1.19e-20

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: 81.54  E-value: 1.19e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1332281222 136 REENTDVFDELTERERQILQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLFLeRYGELK 208
Cdd:COG5905     3 PSSSTSHPSLLTKREREVLELLAEGLTNKEIARQLFISEKTVKNHVSNILRKLGVRNRVQAVVWAL-RLGLLS 74
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 143-200 2.08e-20

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 80.65  E-value: 2.08e-20
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1332281222  143 FDELTERERQILQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLF 200
Cdd:smart00421   1 LASLTPREREVLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQAVRLA 58
COG4567 COG4567
DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains ...
 3-118 9.78e-20

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: 82.27  E-value: 9.78e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRginqLL--SFEEQ-FEVVAeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIV 79
Cdd:COG4567     6 SLLLVDDDEAFAR----VLarALERRgFEVTT-AASVEEALALLEQAPPDYAVLDLRLGDGSGLDLIEALRERDPDARIV 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1332281222  80 ILTVSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKA 118
Cdd:COG4567    81 VLTGYASIATAVEAIKLGADDYLAKPADADDLLAALERA 119
REC_OmpR cd17574
phosphoacceptor receiver (REC) domain of OmpR family response regulators; OmpR-like proteins ...
 5-104 1.47e-19

phosphoacceptor receiver (REC) domain of OmpR family response regulators; OmpR-like proteins are one of the most widespread transcriptional regulators. OmpR family members contain REC and winged helix-turn-helix (wHTH) DNA-binding output effector domain. They are involved in the control of environmental stress tolerance (such as the oxidative, osmotic and acid stress response), motility, virulence, outer membrane biogenesis and other processes. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381116 [Multi-domain]  Cd Length: 99  Bit Score: 79.37  E-value: 1.47e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   5 MLVDDHPLMRRGINQLLSfEEQFEVVaEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTVS 84
Cdd:cd17574     1 LVVEDDEEIAELLSDYLE-KEGYEVD-TAADGEEALELAREEQPDLIILDVMLPGMDGFEVCRRLREKGSDIPIIMLTAK 78

                          90       100
                  ....*....|....*....|
gi 1332281222  85 DSPADIEAIVKAGADGYLLK 104
Cdd:cd17574    79 DEEEDKVLGLELGADDYITK 98
GerE pfam00196
Bacterial regulatory proteins, luxR family;
146-200 1.80e-19

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 78.01  E-value: 1.80e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1332281222 146 LTERERQILQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLF 200
Cdd:pfam00196   3 LSPREREVLRWLAAGKSNKEIADELGISEKTVKVHRSNIMRKLNVHSRVELVRMA 57
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
5-192 8.72e-19

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 80.32  E-value: 8.72e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   5 MLVDDHPLMRRGINQLLSfEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTVS 84
Cdd:PRK09958    4 IIIDDHPLAIAAIRNLLI-KNDIEILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSAK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  85 DSPADIEAIVKAGADGYLLKDTEPDELVELLEKAHLGDKAYSSVVAKYLLQREENTDVFDELTERERQILQEVARGFRNK 164
Cdd:PRK09958   83 NDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAKNGYCYFPFSLNRFVGSLTSDQQKLDSLSKQEISVMRYILDGKDNN 162

                         170       180
                  ....*....|....*....|....*...
gi 1332281222 165 QIADRLFISESTVKVHMKSLLKKLKVPS 192
Cdd:PRK09958  163 DIAEKMFISNKTVSTYKSRLMEKLECKS 190
REC_Rcp-like cd17557
phosphoacceptor receiver (REC) domain of cyanobacterial phytochrome response regulator Rcp and ...
 3-116 1.00e-18

phosphoacceptor receiver (REC) domain of cyanobacterial phytochrome response regulator Rcp and similar domains; This family is composed of response regulators (RRs) that are members of phytochrome-associated, light-sensing two-component signal transduction pathways such as Synechocystis sp. Rcp1, Tolypothrix sp. RcpA, and Agrobacterium tumefaciens bacteriophytochrome response regulator AtBRR. They are stand-alone RRs containing only a REC domain with no output/effector domain. The REC domain itself functions as an effector domain. Also included in this family us Methanosaeta harundinacea methanogenesis regulatory protein FilR2, also a stand-alone RR. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381108 [Multi-domain]  Cd Length: 129  Bit Score: 78.23  E-value: 1.00e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHP----LMRRGInqllsfeEQFEVVAE---ASNGTEAVA------KAHENEL-DLILLDLNMKGMSGLDTLKA 68
Cdd:cd17557     1 TILLVEDNPgdaeLIQEAF-------KEAGVPNElhvVRDGEEALDflrgegEYADAPRpDLILLDLNMPRMDGFEVLRE 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1332281222  69 LRAD--GCEASIVILTVSDSPADIEAIVKAGADGYLLKDTEPDELVELLE 116
Cdd:cd17557    74 IKADpdLRRIPVVVLTTSDAEEDIERAYELGANSYIVKPVDFEEFVEAIR 123
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 146-202 1.20e-18

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: 76.03  E-value: 1.20e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1332281222 146 LTERERQILQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATVLFLE 202
Cdd:cd06170     1 LTPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRTQLVAYAIR 57
AmiR COG3707
Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding ...
 3-118 4.37e-18

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: 78.46  E-value: 4.37e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGcEASIVILT 82
Cdd:COG3707     5 RVLVVDDEPLRRADLREGLR-EAGYEVVAEAADGEDAVELVRELKPDLVIVDIDMPDRDGLEAARQISEER-PAPVILLT 82

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1332281222  83 VSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKA 118
Cdd:COG3707    83 AYSDPELIERALEAGVSAYLVKPLDPEDLLPALELA 118
REC_OmpR_PrrA-like cd17627
phosphoacceptor receiver (REC) domain of PrrA-like OmpR family response regulators; The ...
 4-112 5.86e-18

phosphoacceptor receiver (REC) domain of PrrA-like OmpR family response regulators; The Mycobacterium tuberculosis PrrA is part of the PrrA/PrrB two-component system (TCS) that has been implicated in early intracellular multiplication and is essential for viability. Also included in this subfamily is Mycobacterium tuberculosis MprA, part of the MprAB TCS that regulates EspR, a key regulator of the ESX-1 secretion system, and is required for establishment and maintenance of persistent infection in a tissue- and stage-specific fashion. PrrA and MprA belong to the OmpR family of DNA-binding response regulators, which contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381142 [Multi-domain]  Cd Length: 116  Bit Score: 75.88  E-value: 5.86e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSFEeQFEVvAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTV 83
Cdd:cd17627     1 ILVVDDDRAVRESLRRSLRFE-GYEV-ETAVDGAEALRVISGNRPDAVVLDVMMPRLDGLEVCRRLRAAGNDLPILVLTA 78

                          90       100
                  ....*....|....*....|....*....
gi 1332281222  84 SDSPADIEAIVKAGADGYLLKDTEPDELV 112
Cdd:cd17627    79 RDSVSDRVAGLDAGADDYLVKPFALEELL 107
REC_CheY4-like cd17562
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY4 and similar CheY ...
 3-117 6.40e-18

phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY4 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 CheY4 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: 381110 [Multi-domain]  Cd Length: 118  Bit Score: 75.80  E-value: 6.40e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRrginQLLSF---EEQFEVVaEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEAS-- 77
Cdd:cd17562     2 KILAVDDSASIR----QMVSFtlrGAGYEVV-EAADGRDALSKAQSKKFDLIITDQNMPNMDGIELIKELRKLPAYKFtp 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1332281222  78 IVILTVSDSPADIEAIVKAGADGYLLKDTEPDELVELLEK 117
Cdd:cd17562    77 ILMLTTESSDEKKQEGKAAGATGWLVKPFDPEQLLEVVKK 116
REC_LytTR_AlgR-like cd17532
phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR; ...
 4-119 7.16e-18

phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR; Members of the LytTR/AlgR family of response regulators contain a REC domain and a unique LytTR DNA-binding output domain that lacks the helix-turn-helix motif and consists mostly of beta-strands. Transcriptional regulators with the LytTR-type output domains are involved in biosynthesis of extracellular polysaccharides, fimbriation, expression of exoproteins, including toxins, and quorum sensing. Included in this AlgR-like group of LytTR/AlgR family response regulators are Streptococcus agalactiae sensory transduction protein LytR, Pseudomonas aeruginosa positive alginate biosynthesis regulatory protein AlgR, Bacillus subtilis sensory transduction protein LytT, and Escherichia coli transcriptional regulatory protein BtsR, which are members of two-component regulatory systems. LytR and LytT are components of regulatory systems that regulate genes involved in cell wall metabolism. AlgR positively regulates the algD gene, which codes for a GDP-mannose dehydrogenase, a key enzyme in the alginate biosynthesis pathway. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381087 [Multi-domain]  Cd Length: 118  Bit Score: 75.65  E-value: 7.16e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTV 83
Cdd:cd17532     1 ALIVDDEPLAREELRYLLEEHPDIEIVGEAENGEEALEAIEELKPDVVFLDIQMPGLDGLELAKKLSKLAKPPLIVFVTA 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1332281222  84 SDSPAdieaiVKA---GADGYLLKDTEPDELVELLEKAH 119
Cdd:cd17532    81 YDEYA-----VEAfelNAVDYLLKPFSEERLAEALAKLR 114
REC_D1_PleD-like cd17538
first (D1) phosphoacceptor receiver (REC) domain of response regulator PleD and similar ...
 3-104 1.74e-17

first (D1) phosphoacceptor receiver (REC) domain of response regulator PleD and similar domains; PleD contains a REC domain (D1) with the phosphorylatable aspartate, a REC-like adaptor domain (D2), and the enzymatic diguanylate cyclase (DGC) domain, also called the GGDEF domain according to a conserved sequence motif, as its output domain. The GGDEF-containing PleD response regulators are global regulators of cell metabolism in some important human pathogens. This model describes D1 of PleD and similar domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381093 [Multi-domain]  Cd Length: 104  Bit Score: 74.46  E-value: 1.74e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEVVaEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASI--VI 80
Cdd:cd17538     1 KILVVDDEPANRELLEALLS-AEGYEVL-TADSGQEALALAEEELPDLILLDVMMPGMDGFEVCRRLKEDPETRHIpvIM 78

                          90       100
                  ....*....|....*....|....
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLK 104
Cdd:cd17538    79 ITALDDREDRIRGLEAGADDFLSK 102
PRK10840 PRK10840
transcriptional regulator RcsB; Provisional
 4-190 1.12e-16

transcriptional regulator RcsB; Provisional


Pssm-ID: 182771 [Multi-domain]  Cd Length: 216  Bit Score: 75.26  E-value: 1.12e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKG---MSGLDTLKALRADGCEASIVI 80
Cdd:PRK10840    6 VIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGdkyGDGITLIKYIKRHFPSLSIIV 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKAHLGDKAYSSVVAKYLLQREENTDVFDELTERERQILQEVARG 160
Cdd:PRK10840   86 LTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAALQKGKKFTPESVSRLLEKISAGGYGDKRLSPKESEVLRLFAEG 165

                         170       180       190
                  ....*....|....*....|....*....|
gi 1332281222 161 FRNKQIADRLFISESTVKVHMKSLLKKLKV 190
Cdd:PRK10840  166 FLVTEIAKKLNRSIKTISSQKKSAMMKLGV 195
PRK10610 PRK10610
chemotaxis protein CheY;
3-117 1.94e-16

chemotaxis protein CheY;


Pssm-ID: 170568 [Multi-domain]  Cd Length: 129  Bit Score: 72.31  E-value: 1.94e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:PRK10610    7 KFLVVDDFSTMRRIVRNLLK-ELGFNNVEEAEDGVDALNKLQAGGFGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 85

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1332281222  83 VSDSPA--DIEAIVKAGADGYLLKDTEPDELVELLEK 117
Cdd:PRK10610   86 VTAEAKkeNIIAAAQAGASGYVVKPFTAATLEEKLNK 122
REC_OmpR_PmrA-like cd17624
phosphoacceptor receiver (REC) domain of PmrA-like OmpR family response regulators; This ...
 4-112 3.17e-16

phosphoacceptor receiver (REC) domain of PmrA-like OmpR family response regulators; This subfamily contains various OmpR family response regulators including PmrA, BasR, QseB, tctD, and RssB, which are components of two-component regulatory systems (TCSs). The PmrA/PmrB TCS controls transcription of genes that are involved in lipopolysaccharide modification in the outer membrane of bacteria, increasing bacterial resistance to host-derived antimicrobial peptides. The BasS/BasR TCS functions as an iron- and zinc-sensing transcription regulator. The QseB/QseC TCS activates the flagella regulon by activating transcription of FlhDC. The RssA/RssB TCS regulates swarming behavior in Serratia marcescens. OmpR family DNA-binding response regulators contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381139 [Multi-domain]  Cd Length: 115  Bit Score: 71.36  E-value: 3.17e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfEEQFEVvAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTV 83
Cdd:cd17624     1 ILLVEDDALLGDGLKTGLR-KAGYAV-DWVRTGAEAEAALASGPYDLVILDLGLPDGDGLDLLRRWRRQGQSLPVLILTA 78

                          90       100
                  ....*....|....*....|....*....
gi 1332281222  84 SDSPADIEAIVKAGADGYLLKDTEPDELV 112
Cdd:cd17624    79 RDGVDDRVAGLDAGADDYLVKPFALEELL 107
REC_RpfG-like cd17551
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator ...
 3-112 3.92e-16

phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator RpfG and similar proteins; Cyclic di-GMP phosphodiesterase response regulator RpfG, together with sensory/regulatory protein RpfC, constitute a two-component system implicated in sensing and responding to the diffusible signal factor (DSF) that is essential for cell-cell signaling. RpfC is a hybrid sensor/histidine kinase that phosphorylates and activates RpfG, which degrades cyclic di-GMP to GMP, leading to the activation of Clp, a global transcriptional regulator that regulates a large set of genes in the DSF pathway. RpfG contains a CheY-like receiver domain attached to a histidine-aspartic acid-glycine-tyrosine-proline (HD-GYP) cyclic di-GMP phosphodiesterase domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381103 [Multi-domain]  Cd Length: 118  Bit Score: 71.32  E-value: 3.92e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEEQFEVVAeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEAS--IVI 80
Cdd:cd17551     2 RILIVDDNPTNLLLLEALLRSAGYLEVVS-FTDPREALAWCRENPPDLILLDYMMPGMDGLEFIRRLRALPGLEDvpIVM 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1332281222  81 LTVSDSPA-DIEAIvKAGADGYLLKDTEPDELV 112
Cdd:cd17551    81 ITADTDREvRLRAL-EAGATDFLTKPFDPVELL 112
REC_OmpR_CusR-like cd19935
phosphoacceptor receiver (REC) domain of CusR-like OmpR family response regulators; ...
 4-104 8.03e-16

phosphoacceptor receiver (REC) domain of CusR-like OmpR family response regulators; Escherichia coli CusR is part of the CusS/CusR two-component system (TCS) that is involved in response to copper and silver. Other members of this subfamily include Escherichia coli PcoR, Pseudomonas syringae CopR, and Streptomyces coelicolor CutR, which are all transcriptional regulatory proteins and components of TCSs that regulate genes involved in copper resistance and/or metabolism. member of the subfamily is Escherichia coli HprR (hydrogen peroxide response regulator), previously called YdeW, which is part of the HprSR (or YedVW) TCS involved in stress response to hydrogen peroxide, as well as Cupriavidus metallidurans CzcR, which is part of the CzcS/CzcR TCS involved in the control of cobalt, zinc, and cadmium homeostasis. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381162 [Multi-domain]  Cd Length: 100  Bit Score: 69.78  E-value: 8.03e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfEEQFeVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTV 83
Cdd:cd19935     1 ILVVEDEKKLAEYLKKGLT-EEGY-AVDVAYDGEDGLHLALTNEYDLIILDVMLPGLDGLEVLRRLRAAGKQTPVLMLTA 78

                          90       100
                  ....*....|....*....|....
gi 1332281222  84 SDSpadIEAIVK---AGADGYLLK 104
Cdd:cd19935    79 RDS---VEDRVKgldLGADDYLVK 99
REC_DivK-like cd17548
phosphoacceptor receiver (REC) domain of DivK and similar proteins; Caulobacter crescentus ...
 3-117 1.43e-15

phosphoacceptor receiver (REC) domain of DivK and similar proteins; Caulobacter crescentus DivK is an essential response regulator that is involved in the complex phosphorelay pathways controlling both cell division and motility. It localizes cell cycle regulators to specific poles of the cell during division. DivK contains a stand-alone REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381100 [Multi-domain]  Cd Length: 115  Bit Score: 69.49  E-value: 1.43e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEeQFEVVaEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVI-- 80
Cdd:cd17548     1 KILIVEDNPLNMKLARDLLESA-GYEVL-EAADGEEALEIARKEKPDLILMDIQLPGMDGLEATRLLKEDPATRDIPVia 78

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLKDTEPDELVELLEK 117
Cdd:cd17548    79 LTAYAMKGDREKILEAGCDGYISKPIDTREFLETVAK 115
REC_OmpR_EcPhoP-like cd19934
phosphoacceptor receiver (REC) domain of EcPhoP-like OmpR family response regulators; ...
 4-112 2.61e-15

phosphoacceptor receiver (REC) domain of EcPhoP-like OmpR family response regulators; Escherichia coli PhoP (EcPhoP) is part of the PhoQ/PhoP two-component system (TCS) that regulates virulence genes and plays an essential role in the response of the bacteria to the environment of their mammalian hosts, sensing several stimuli such as extracellular magnesium limitation, low pH, the presence of cationic antimicrobial peptides, and osmotic upshift. This subfamily also includes Brucella suis FeuP, part of the FeuPQ TCS that is involved in the regulation of iron uptake, and Microchaete diplosiphon RcaC, which is required for chromatic adaptation. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381161 [Multi-domain]  Cd Length: 117  Bit Score: 68.85  E-value: 2.61e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfeEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTV 83
Cdd:cd19934     1 LLLVEDDALLAAQLKEQLS--DAGYVVDVAEDGEEALFQGEEEPYDLVVLDLGLPGMDGLSVLRRWRSEGRATPVLILTA 78

                          90       100
                  ....*....|....*....|....*....
gi 1332281222  84 SDSPADIEAIVKAGADGYLLKDTEPDELV 112
Cdd:cd19934    79 RDSWQDKVEGLDAGADDYLTKPFHIEELL 107
REC_OmpR_MtPhoP-like cd17615
phosphoacceptor receiver (REC) domain of MtPhoP-like OmpR family response regulators; ...
 3-112 3.64e-15

phosphoacceptor receiver (REC) domain of MtPhoP-like OmpR family response regulators; Mycobacterium tuberculosis PhoP (MtPhoP) is part of the PhoP/PhoR two-component system that is involved in phosphate control by stimulating expression of genes involved in scavenging, transport and mobilization of phosphate, and repressing the utilization of nitrogen sources. Also included in this subfamily is Mycobacterium tuberculosis transcriptional regulatory protein TcrX, part of the two-component regulatory system TcrY/TcrX that may be involved in virulence. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381131 [Multi-domain]  Cd Length: 118  Bit Score: 68.53  E-value: 3.64e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEeQFEVVAeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:cd17615     1 RVLVVDDEPNITELLSMALRYE-GWDVET-AADGAEALAAAREFRPDAVVLDIMLPDMDGLEVLRRLRADGPDVPVLFLT 78

                          90       100       110
                  ....*....|....*....|....*....|
gi 1332281222  83 VSDSPADIEAIVKAGADGYLLKDTEPDELV 112
Cdd:cd17615    79 AKDSVEDRIAGLTAGGDDYVTKPFSLEEVV 108
REC_RegA-like cd17563
phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA; ...
 3-115 3.73e-15

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: 68.24  E-value: 3.73e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQllSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:cd17563     2 SLLLVDDDEVFAERLAR--ALERRGFEVETAHSVEEALALAREEKPDYAVLDLRLGGDSGLDLIPPLRALQPDARIVVLT 79

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1332281222  83 VSDS-PADIEAIvKAGADGYLLKDTEPDELVELL 115
Cdd:cd17563    80 GYASiATAVEAI-KLGADDYLAKPADADEILAAL 112
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
4-192 7.92e-15

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 69.90  E-value: 7.92e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKalRADGCEASIVILTV 83
Cdd:PRK09935    6 VIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYLRTRPVDLIIMDIDLPGTDGFTFLK--RIKQIQSTVKVLFL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  84 SDSPADIEA--IVKAGADGYLLKDTEPDELVELLEKAHLGDKAYSSVVAKYLLQREENTDVFDE--LTERERQILQEVAR 159
Cdd:PRK09935   84 SSKSECFYAgrAIQAGANGFVSKCNDQNDIFHAVQMILSGYTFFPSETLNYIKSNKCSTNSSTDtvLSNREVTILRYLVS 163

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1332281222 160 GFRNKQIADRLFISESTVKVHMKSLLKKLKVPS 192
Cdd:PRK09935  164 GLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHS 196
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
39-203 9.76e-15

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 69.40  E-value: 9.76e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  39 AVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTVSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKA 118
Cdd:COG2771    21 LALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALLALLAALLAR 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222 119 HLGDKAYSSVVAKYLLQREENTDVFDELTERERQILQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAATV 198
Cdd:COG2771   101 LAALLLALALAALLLAALARLLARAPGLTPREREVLRLLAEGLTLKEIARILGISERTVRTHLKRIYRKLGVSSRAELVA 180


                  ....*
gi 1332281222 199 LFLER 203
Cdd:COG2771   181 LALRL 185
REC_PdtaR-like cd19932
phosphoacceptor receiver (REC) domain of PdtaR and similar proteins; This subfamily includes ...
 3-118 5.34e-14

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: 65.51  E-value: 5.34e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCeASIVILT 82
Cdd:cd19932     2 RVLIAEDEALIRMDLREMLE-EAGYEVVGEASDGEEAVELAKKHKPDLVIMDVKMPRLDGIEAAKIITSENI-APIVLLT 79

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1332281222  83 VSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKA 118
Cdd:cd19932    80 AYSQQDLVERAKEAGAMAYLVKPFSESDLIPAIEMA 115
REC_RR468-like cd17552
phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator RR468 and ...
 3-113 5.52e-14

phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator RR468 and similar domains; Thermotoga maritima RR468 (encoded by gene TM0468) is the cognate response regulator (RR) of the class I histidine kinase HK853 (product of gene TM0853). HK853/RR468 comprise a two-component system (TCS) that couples environmental stimuli to adaptive responses. This subfamily also includes Fremyella diplosiphon complementary adaptation response regulator homolog RcaF, a small RR that is involved in four-step phosphorelays of the complementary chromatic adaptation (CCA) system that occurs in many cyanobacteria. Both RR468 and RcaF are stand-alone RRs containing only a REC domain with no output/effector domain. The REC domain itself functions as an effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381104 [Multi-domain]  Cd Length: 121  Bit Score: 65.65  E-value: 5.52e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEEQFEVVaEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASI--VI 80
Cdd:cd17552     3 RILVIDDEEDIREVVQACLEKLAGWEVL-TASSGQEGLEKAATEQPDAILLDVMMPDMDGLATLKKLQANPETQSIpvIL 81

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLKDTEPDELVE 113
Cdd:cd17552    82 LTAKAQPSDRQRFASLGVAGVIAKPFDPLTLAE 114
PRK00742 PRK00742
chemotaxis-specific protein-glutamate methyltransferase CheB;
3-69 5.69e-14

chemotaxis-specific protein-glutamate methyltransferase CheB;


Pssm-ID: 234828 [Multi-domain]  Cd Length: 354  Bit Score: 69.41  E-value: 5.69e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKAL 69
Cdd:PRK00742    5 RVLVVDDSAFMRRLISEILNSDPDIEVVGTAPDGLEAREKIKKLNPDVITLDVEMPVMDGLDALEKI 71
REC_DC-like cd17534
phosphoacceptor receiver (REC) domain of modulated diguanylate cyclase and similar domains; ...
 3-118 8.26e-14

phosphoacceptor receiver (REC) domain of modulated diguanylate cyclase and similar domains; This groups includes a modulated diguanylate cyclase containing a PAS sensor domain from Desulfovibrio desulfuricans G20. Members of this group contain N-terminal REC domains and various output domains including the GGDEF, histidine kinase, and helix-turn-helix (HTH) DNA binding domains. Also included in this family is Mycobacterium tuberculosis PdtaR, a transcriptional antiterminator that contains a REC domain and an ANTAR RNA-binding output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381089 [Multi-domain]  Cd Length: 117  Bit Score: 65.12  E-value: 8.26e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKG-MSGLDTLKALRADgCEASIVIL 81
Cdd:cd17534     2 KILIVEDEAIIALDLKEILE-SLGYEVVGIADSGEEAIELAEENKPDLILMDINLKGdMDGIEAAREIREK-FDIPVIFL 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1332281222  82 TVSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKA 118
Cdd:cd17534    80 TAYSDEETLERAKETNPYGYLVKPFNERELKAAIELA 116
REC_citrate_TCS cd19925
phosphoacceptor receiver (REC) domain of citrate family two-component system response ...
 3-117 1.34e-13

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: 64.57  E-value: 1.34e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHP----LMRRGINQLlsfeEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASI 78
Cdd:cd19925     2 NVLIVEDDPmvaeIHRAYVEQV----PGFTVIGTAGTGEEALKLLKERQPDLILLDIYLPDGNGLDLLRELRAAGHDVDV 77

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1332281222  79 VILTVSDSPADIEAIVKAGADGYLLKDTEPDELVELLEK 117
Cdd:cd19925    78 IVVTAANDVETVREALRLGVVDYLIKPFTFERLRQRLER 116
REC_TrrA-like cd17554
phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator TrrA and ...
 3-111 5.94e-13

phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator TrrA and similar domains; Thermotoga maritima contains a two-component signal transduction system (TCS) composed of the ThkA sensory histidine kinase (HK) and its cognate response regulator (RR) TrrA; the specific function of the system is unknown. TCSs couple environmental stimuli to adaptive responses. TrrA is a stand-alone RR containing only a REC domain with no output/effector domain. The REC domain itself functions as an effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381106 [Multi-domain]  Cd Length: 113  Bit Score: 62.62  E-value: 5.94e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEVVAeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:cd17554     2 KILVVDDEENIRELYKEELE-DEGYEVVT-AGNGEEALEKLESEDPDLVILDIKMPGMDGLETLRKIREKKPDLPVIICT 79

                          90       100       110
                  ....*....|....*....|....*....|
gi 1332281222  83 -VSDSPADIEAIvkaGADGYLLKDTEPDEL 111
Cdd:cd17554    80 aYSEYKSDFSSW---AADAYVVKSSDLTEL 106
REC_OmpR_KdpE-like cd17620
phosphoacceptor receiver (REC) domain of KdpE-like OmpR family response regulators; KdpE is a ...
 4-104 6.62e-13

phosphoacceptor receiver (REC) domain of KdpE-like OmpR family response regulators; KdpE is a component of the KdpD/KdpE two-component system (TCS) and is activated when histidine kinase KdpD senses a drop in external K+ concentration or upshift in ionic osmolarity, resulting in the expression of a heterooligomeric transporter KdpFABC. In addition, the KdpD/KdpE TCS is also an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. KdpE is a member of the OmpR family of DNA-binding response regulators that contain REC and winged helix-turn-helix (wHTH) DNA-binding output effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381135 [Multi-domain]  Cd Length: 99  Bit Score: 62.18  E-value: 6.62e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINqlLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRaDGCEASIVILTV 83
Cdd:cd17620     1 ILVIEDEPQIRRFLR--TALEAHGYRVFEAETGQEGLLEAATRKPDLIILDLGLPDMDGLEVIRRLR-EWSAVPVIVLSA 77

                          90       100
                  ....*....|....*....|.
gi 1332281222  84 SDSPADIEAIVKAGADGYLLK 104
Cdd:cd17620    78 RDEESDKIAALDAGADDYLTK 98
REC_CheC-like cd17593
phosphoacceptor receiver (REC) domain of uncharacterized response regulators containing a CheC ...
 3-117 6.64e-13

phosphoacceptor receiver (REC) domain of uncharacterized response regulators containing a CheC domain; This subfamily is composed of uncharacterized proteins containing an N-terminal REC domain and a C-terminal CheC domain that may function as the output/effector domain of a response regulator. CheC is a CheY-P phosphatase, affecting the level of phosphorylated CheY which controls the sense of flagella rotation and determine swimming behavior of chemotactic bacteria. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381124 [Multi-domain]  Cd Length: 117  Bit Score: 62.55  E-value: 6.64e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEEQFEVVaEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVIlt 82
Cdd:cd17593     2 KVLICDDSSMARKQLARALPADWDVEIT-FAENGEEALEILREGRIDVLFLDLTMPVMDGYEVLEALPVEQLETKVIV-- 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1332281222  83 VSdspADI--EAI--VKA-GADGYLLKDTEPDELVELLEK 117
Cdd:cd17593    79 VS---GDVqpEAKerVLElGALAFLKKPFDPEKLAQLLEE 115
PRK11107 PRK11107
hybrid sensory histidine kinase BarA; Provisional
 3-104 6.69e-13

hybrid sensory histidine kinase BarA; Provisional


Pssm-ID: 236848 [Multi-domain]  Cd Length: 919  Bit Score: 66.80  E-value: 6.69e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLsfEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEAS--IVI 80
Cdd:PRK11107  669 TVMAVDDNPANLKLIGALL--EEQVEHVVLCDSGHQAVEQAKQRPFDLILMDIQMPGMDGIRACELIRQLPHNQNtpIIA 746

                          90       100
                  ....*....|....*....|....
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLK 104
Cdd:PRK11107  747 VTAHAMAGERERLLSAGMDDYLAK 770
PRK15347 PRK15347
two component system sensor kinase;
3-118 7.79e-13

two component system sensor kinase;


Pssm-ID: 237951 [Multi-domain]  Cd Length: 921  Bit Score: 66.59  E-value: 7.79e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfeEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRAD----GCEASI 78
Cdd:PRK15347  692 QILLVDDVETNRDIIGMMLV--ELGQQVTTAASGTEALELGRQHRFDLVLMDIRMPGLDGLETTQLWRDDpnnlDPDCMI 769

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1332281222  79 VILTVSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKA 118
Cdd:PRK15347  770 VALTANAAPEEIHRCKKAGMNHYLTKPVTLAQLARALELA 809
REC_OmpR_DrrD-like cd17625
phosphoacceptor receiver (REC) domain of DrrD-like OmpR family response regulators; DrrD is a ...
 5-115 1.41e-12

phosphoacceptor receiver (REC) domain of DrrD-like OmpR family response regulators; DrrD is a OmpR/PhoB homolog from Thermotoga maritima whose function is not yet known. This subfamily also includes Streptococcus agalactiae transcriptional regulatory protein DltR, part of the DltS/DltR two-component system (TCS), and Pseudomonas aeruginosa transcriptional activator protein PfeR, part of the PfeR/PfeS TCS, which activates expression of the ferric enterobactin receptor. The DltS/DltR TCS regulates the expression of the dlt operon, which comprises four genes (dltA, dltB, dltC, and dltD) that catalyze the incorporation of D-alanine residues into the lipoteichoic acids. Members of this subfamily belong to the OmpR/PhoB family, which comprises of two domains, an N-terminal receiver domain and a C-terminal DNA-binding winged helix-turn-helix effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381140 [Multi-domain]  Cd Length: 115  Bit Score: 61.85  E-value: 1.41e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   5 MLVDDHPLMRRGINQLLSfEEQFEVvAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTVS 84
Cdd:cd17625     1 LVVEDEKDLSEAITKHLK-KEGYTV-DVCFDGEEGLEYALSGIYDLIILDIMLPGMDGLEVLKSLREEGIETPVLLLTAL 78

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1332281222  85 DSPADIEAIVKAGADGYLLKdtePDELVELL 115
Cdd:cd17625    79 DAVEDRVKGLDLGADDYLPK---PFSLAELL 106
PRK11697 PRK11697
two-component system response regulator BtsR;
1-117 1.84e-12

two-component system response regulator BtsR;


Pssm-ID: 236956 [Multi-domain]  Cd Length: 238  Bit Score: 64.10  E-value: 1.84e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   1 MCRVMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEAsIVI 80
Cdd:PRK11697    1 MIKVLIVDDEPLAREELRELLQEEGDIEIVGECSNAIEAIGAIHRLKPDVVFLDIQMPRISGLELVGMLDPEHMPY-IVF 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1332281222  81 LTVSDSPAdIEAIVKAGADgYLLKDTEPDELVELLEK 117
Cdd:PRK11697   80 VTAFDEYA-IKAFEEHAFD-YLLKPIDPARLAKTLAR 114
REC_HupR cd17596
phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR); Members of ...
 3-137 1.95e-12

phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR); Members of this subfamily are 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 belongs to the nitrogen regulatory protein C (NtrC) family of response regulators, which activate transcription by RNA polymerase (RNAP) in response to a change in the environment. HupR is an unusual member of this family as it activates transcription when unphosphorylated, and transcription is inhibited by phosphorylation. Proteins in this subfamily contain an N-terminal REC domain, a central sigma-54 interaction domain that lacks ATPase activity, and a C-terminal DNA-binding domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381127 [Multi-domain]  Cd Length: 133  Bit Score: 62.00  E-value: 1.95e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLsfEEQFEVVAeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:cd17596     2 TILVVDDEVRSLEALRRTL--EEDFDVLT-AASAEEALAILEEEWVQVILCDQRMPGTTGVEFLKEVRERWPEVVRIIIS 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1332281222  83 -VSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKAhlgdkayssvVAKYLLQRE 137
Cdd:cd17596    79 gYTDSEDIIAGINEAGIYQYLTKPWHPDQLLLTVRNA----------ARLFELQRE 124
REC_2_DhkD-like cd17580
second phosphoacceptor receiver (REC) domain of Dictyostelium discoideum hybrid signal ...
 4-115 2.83e-12

second phosphoacceptor receiver (REC) domain of Dictyostelium discoideum hybrid signal transduction histidine kinase D and similar domains; Dictyostelium discoideum hybrid signal transduction histidine kinase D (DhkD) is a large protein that contains two histidine kinase (HK) and two REC domains on the intracellular side of a single pass transmembrane domain, and extracellular PAS and PAC domains that likely are involved in ligand binding. This model represents the second REC domain and similar domains. DhkD activates the cAMP phosphodiesterase RegA to ensure proper prestalk and prespore patterning, tip formation, and the vertical elongation of the mound into a finger, in Dictyostelium discoideum. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381118 [Multi-domain]  Cd Length: 112  Bit Score: 60.93  E-value: 2.83e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfEEQFEVVAeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVI--L 81
Cdd:cd17580     1 ILVVDDNEDAAEMLALLLE-LEGAEVTT-AHSGEEALEAAQRFRPDVILSDIGMPGMDGYELARRLRELPWLANTPAiaL 78

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1332281222  82 TVSDSPADIEAIVKAGADGYLLKDTEPDELVELL 115
Cdd:cd17580    79 TGYGQPEDRERALEAGFDAHLVKPVDPDELIELI 112
REC_DctD-like cd17549
phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and ...
 4-118 3.60e-12

phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and similar proteins; C4-dicarboxylic acid transport protein D (DctD) is part of the two-component regulatory system DctB/DctD, which regulates C4-dicarboxylate transport via regulation of expression of the dctPQM operon and dctA. It is an activator of sigma(54)-RNA polymerase holoenzyme that uses the energy released from ATP hydrolysis to stimulate the isomerization of a closed promoter complex to an open complex capable of initiating transcription. DctD 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. 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: 381101 [Multi-domain]  Cd Length: 130  Bit Score: 60.97  E-value: 3.60e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSFEEqFEVVAeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTV 83
Cdd:cd17549     1 VLLVDDDADVREALQQTLELAG-FRVRA-FADAEEALAALSPDFPGVVISDIRMPGMDGLELLAQIRELDPDLPVILITG 78

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1332281222  84 -SDSPADIEAIvKAGADGYLLKDTEPDELVELLEKA 118
Cdd:cd17549    79 hGDVPMAVEAM-RAGAYDFLEKPFDPERLLDVVRRA 113
REC_OmpR_BsPhoP-like cd19937
phosphoacceptor receiver (REC) domain of BsPhoP-like OmpR family response regulators; Bacillus ...
 5-112 3.61e-12

phosphoacceptor receiver (REC) domain of BsPhoP-like OmpR family response regulators; Bacillus subtilis PhoP (BsPhoP) is part of the PhoPR two-component system that participates in a signal transduction network that controls adaptation of the bacteria to phosphate deficiency by regulating (activating or repressing) genes of the Pho regulon upon phosphorylation by PhoR. When activated, PhoPR directs expression of phosphate scavenging enzymes, lowers synthesis of the phosphate-rich wall teichoic acid (WTA) and initiates synthesis of teichuronic acid, a non-phosphate containing replacement anionic polymer. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381164 [Multi-domain]  Cd Length: 116  Bit Score: 60.75  E-value: 3.61e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   5 MLVDDHPlmrrGINQLLSF---EEQFEVVAeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVIL 81
Cdd:cd19937     1 LVVDDEE----DIVELLKYnleKEGYEVVT-AYDGEEALKRAKDEKPDLIILDLMLPGIDGLEVCRILRSDPKTSSIPII 75

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1332281222  82 TVSDSPADIEAIV--KAGADGYLLKDTEPDELV 112
Cdd:cd19937    76 MLTAKGEEFDKVLglELGADDYITKPFSPRELL 108
REC_HupR-like cd17569
phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR) and similar ...
 3-118 5.92e-12

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: 60.11  E-value: 5.92e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEEqFEVVaEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:cd17569     2 TILLVDDEPNILKALKRLLRREG-YEVL-TATSGEEALEILKQEPVDVVISDQRMPGMDGAELLKRVRERYPDTVRILLT 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1332281222  83 VSdspADIEAIVKAGADG----YLLKDTEPDELVELLEKA 118
Cdd:cd17569    80 GY---ADLDAAIEAINEGeiyrFLTKPWDDEELKETIRQA 116
REC_OmpR_CpxR cd17623
phosphoacceptor receiver (REC) domain of CpxR-like OmpR family response regulators; CpxR is ...
 4-112 1.29e-11

phosphoacceptor receiver (REC) domain of CpxR-like OmpR family response regulators; CpxR is part of the CpxA/CpxR two-component regulatory system that mediates envelope stress responses that is key for virulence and antibiotic resistance in several Gram negative pathogens. CpxR is a transcription factor/response regulator that controls the expression of numerous genes, including those of the classical porins OmpF and OmpC. It belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381138 [Multi-domain]  Cd Length: 115  Bit Score: 59.24  E-value: 1.29e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfEEQFEVVAeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGcEASIVILTV 83
Cdd:cd17623     1 ILLIDDDRELTELLTEYLE-MEGFNVRA-AHDGEQGLAALLEGSPDLVVLDVMLPKMNGLDVLKELRKTS-QVPVLMLTA 77

                          90       100
                  ....*....|....*....|....*....
gi 1332281222  84 SDSPADIEAIVKAGADGYLLKDTEPDELV 112
Cdd:cd17623    78 RGDDIDRILGLELGADDYLPKPFNPRELV 106
REC_OmpR_MtrA-like cd17626
phosphoacceptor receiver (REC) domain of MtrA-like OmpR family response regulators; MtrA is ...
 3-112 2.12e-11

phosphoacceptor receiver (REC) domain of MtrA-like OmpR family response regulators; MtrA is part of MtrA/MtrB (or MtrAB), a highly conserved two-component system (TCS) implicated in the regulation of cell division in the actinobacteria. In unicellular Mycobacterium tuberculosis, MtrAB coordinates DNA replication with cell division and regulates the transcription of resuscitation-promoting factor B. In filamentous Streptomyces venezuelae, it links antibiotic production to sporulation. MtrA belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381141 [Multi-domain]  Cd Length: 115  Bit Score: 58.64  E-value: 2.12e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEVvAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGcEASIVILT 82
Cdd:cd17626     2 RILVVDDDAALAEMIGIVLR-GEGFDP-AFCGDGTQALAAFREVRPDLVLLDLMLPGIDGIEVCRQIRAES-GVPIVMLT 78

                          90       100       110
                  ....*....|....*....|....*....|
gi 1332281222  83 VSDSPADIEAIVKAGADGYLLKDTEPDELV 112
Cdd:cd17626    79 AKSDTVDVVLGLESGADDYVAKPFKPKELV 108
PRK11361 PRK11361
acetoacetate metabolism transcriptional regulator AtoC;
3-118 2.92e-11

acetoacetate metabolism transcriptional regulator AtoC;


Pssm-ID: 183099 [Multi-domain]  Cd Length: 457  Bit Score: 61.79  E-value: 2.92e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEeQFEVVAeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:PRK11361    6 RILIVDDEDNVRRMLSTAFALQ-GFETHC-ANNGRTALHLFADIHPDVVLMDIRMPEMDGIKALKEMRSHETRTPVILMT 83

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1332281222  83 vsdSPADIEAIVKA---GADGYLLKDTEPDELVELLEKA 118
Cdd:PRK11361   84 ---AYAEVETAVEAlrcGAFDYVIKPFDLDELNLIVQRA 119
REC_PA4781-like cd19920
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase PA4781 and similar ...
 4-104 3.33e-11

phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase PA4781 and similar domains; Pseudomonas aeruginosa cyclic di-GMP phosphodiesterase PA4781 contains an N-terminal REC domain and a C-terminal catalytic HD-GYP domain, characteristics of RpfG family response regulators. PA4781 is involved in cyclic di-3',5'-GMP (c-di-GMP) hydrolysis/degradation in a two-step reaction via the linear intermediate pGpG to produce GMP. Its unphosphorylated REC domain prevents accessibility of c-di-GMP to the active site. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381147 [Multi-domain]  Cd Length: 103  Bit Score: 57.52  E-value: 3.33e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfEEQFEVVAeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASI-VI-L 81
Cdd:cd19920     1 ILIVDDVPDNLRLLSELLR-AAGYRVLV-ATDGQQALQRAQAEPPDLILLDVMMPGMDGFEVCRRLKADPATRHIpVIfL 78

                          90       100
                  ....*....|....*....|...
gi 1332281222  82 TVSDSPADIEAIVKAGADGYLLK 104
Cdd:cd19920    79 TALTDTEDKVKGFELGAVDYITK 101
PRK12555 PRK12555
chemotaxis-specific protein-glutamate methyltransferase CheB;
2-84 4.90e-11

chemotaxis-specific protein-glutamate methyltransferase CheB;


Pssm-ID: 237135 [Multi-domain]  Cd Length: 337  Bit Score: 60.66  E-value: 4.90e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   2 CRVMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADgCEASIVIL 81
Cdd:PRK12555    1 MRIGIVNDSPLAVEALRRALARDPDHEVVWVATDGAQAVERCAAQPPDVILMDLEMPRMDGVEATRRIMAE-RPCPILIV 79


                  ...
gi 1332281222  82 TVS 84
Cdd:PRK12555   80 TSL 82
REC_OmpR_ArcA_TorR-like cd17619
phosphoacceptor receiver (REC) domain of ArcA- and TorR-like OmpR family response regulators; ...
 3-112 5.35e-11

phosphoacceptor receiver (REC) domain of ArcA- and TorR-like OmpR family response regulators; This subfamily includes Escherichia coli TorR and ArcA, both OmpR family response regulators that mediate adaptation to changes in various respiratory growth conditions. The TorS-TorR two-component system (TCS) is responsible for the tight regulation of the torCAD operon, which encodes the trimethylamine N-oxide (TMAO) reductase respiratory system in response to anaerobic conditions and the presence of TMAO. The ArcA-ArcB TCS is involved in cell growth during anaerobiosis. ArcA is a global regulator that controls more than 30 operons involved in redox regulation (the Arc modulon). OmpR family DNA-binding response regulators are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381134 [Multi-domain]  Cd Length: 113  Bit Score: 57.40  E-value: 5.35e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRrginQLLS--FEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRAdgcEASIVI 80
Cdd:cd17619     2 HILIVEDEPVTR----ATLKsyFEQEGYDVSEAGDGEEMRQILARQDIDLVLLDINLPGKDGLSLTRELRE---QSEVGI 74

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1332281222  81 LTVSDSPADIEAIV--KAGADGYLLKDTEPDELV 112
Cdd:cd17619    75 ILVTGRDDEVDRIVglEIGADDYVTKPFNPRELL 108
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
147-196 6.05e-11

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 58.95  E-value: 6.05e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1332281222 147 TERERQILQE--VARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAA 196
Cdd:COG2909   122 REEALAALRRrlLAEGLSNKEIAERLFISVNTVKTHLRNIYRKLGVRSRTEA 173
REC_2_GGDEF cd17544
second phosphoacceptor receiver (REC) domain of uncharacterized GGDEF domain proteins; This ...
 2-111 6.73e-11

second phosphoacceptor receiver (REC) domain of uncharacterized GGDEF domain proteins; This family is composed of uncharacterized PleD-like response regulators that contain two N-terminal REC domains and a C-terminal diguanylate cyclase output domain with the characteristic GGDEF motif at the active site. Unlike PleD which contains a REC-like adaptor domain, the second REC domain of these uncharacterized GGDEF domain proteins, described in this model, contains characteristic metal-binding and active site residues. PleD response regulators are global regulators of cell metabolism in some important human pathogens. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381098 [Multi-domain]  Cd Length: 122  Bit Score: 57.53  E-value: 6.73e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   2 CRVMLVDDHPLMRRGINQLLSfEEQFEVVaEASNGTEAVAKAHEN-ELDLILLDLNMKGMSGLDTLKALRA--DGCEASI 78
Cdd:cd17544     1 IKVLVVDDSATSRNHLRALLR-RHNFQVL-EAANGQEALEVLEQHpDIKLVITDYNMPEMDGFELVREIRKkySRDQLAI 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1332281222  79 VILTVSDSPADIEAIVKAGADGYLLKDTEPDEL 111
Cdd:cd17544    79 IGISASGDNALSARFIKAGANDFLTKPFLPEEF 111
PRK10100 PRK10100
transcriptional regulator CsgD;
100-196 8.27e-11

transcriptional regulator CsgD;


Pssm-ID: 182241 [Multi-domain]  Cd Length: 216  Bit Score: 59.11  E-value: 8.27e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222 100 GYLLKDTEPDELVELLEKAHLGDKAYSSVVAKYLLQREENTDvFDE-----LTERERQILQEVARGFRNKQIADRLFISE 174
Cdd:PRK10100  106 GVFYAMEDQERVVNGLQGVLRGECYFTQKLASYLITHSGNYR-YNStesalLTHREKEILNKLRIGASNNEIARSLFISE 184

                          90       100
                  ....*....|....*....|..
gi 1332281222 175 STVKVHMKSLLKKLKVPSRTAA 196
Cdd:PRK10100  185 NTVKTHLYNLFKKIAVKNRTQA 206
REC_OmpR_CtrA cd17616
phosphoacceptor receiver (REC) domain of CtrA-like OmpR family response regulators; CtrA is ...
 4-112 8.57e-11

phosphoacceptor receiver (REC) domain of CtrA-like OmpR family response regulators; CtrA is part of the CckA-ChpT-CtrA phosphorelay that is conserved in alphaproteobacteria and is important in orchestrating the cell cycle, polar development, and flagellar biogenesis. CtrA is the master regulator of flagella synthesis genes and also regulates genes involved in the cell cycle, exopolysaccharide synthesis, and cyclic-di-GMP signaling. CtrA is active as a transcription factor when phosphorylated. It is a member of the OmpR family of DNA-binding response regulators, characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381132 [Multi-domain]  Cd Length: 114  Bit Score: 57.03  E-value: 8.57e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSFEEQfeVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTv 83
Cdd:cd17616     1 VLLIEDDSATAQSIELMLKSEGF--NVYTTDLGEEGLDLGKLYDYDIILLDLNLPDMSGYEVLRTLRLAKVKTPILILS- 77

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1332281222  84 sdSPADIEAIVKA---GADGYLLKDTEPDELV 112
Cdd:cd17616    78 --GLADIEDKVKGlgfGADDYMTKPFHKDELV 107
REC smart00448
cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar ...
 3-57 1.23e-10

cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar motors. This domain contains a phosphoacceptor site that is phosphorylated by histidine kinase homologues.


Pssm-ID: 214668 [Multi-domain]  Cd Length: 55  Bit Score: 54.88  E-value: 1.23e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1332281222    3 RVMLVDDHPLMRRGINQLLsfEEQFEVVAEASNGTEAVAKAHENELDLILLDLNM 57
Cdd:smart00448   2 RILVVDDDPLLRELLKALL--EKEGYEVDEATDGEEALELLKEEKPDLILLDIMM 54
pleD PRK09581
response regulator PleD; Reviewed
 1-104 1.23e-10

response regulator PleD; Reviewed


Pssm-ID: 236577 [Multi-domain]  Cd Length: 457  Bit Score: 59.91  E-value: 1.23e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   1 MCRVMLVDDHPLMRRGINQLLSfEEQFEVVAeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASI-- 78
Cdd:PRK09581    2 TARILVVDDIPANVKLLEAKLL-AEYYTVLT-ASSGAEAIAICEREQPDIILLDVMMPGMDGFEVCRRLKSDPATTHIpv 79

                          90       100
                  ....*....|....*....|....*.
gi 1332281222  79 VILTVSDSPADIEAIVKAGADGYLLK 104
Cdd:PRK09581   80 VMVTALDDPEDRVRGLEAGADDFLTK 105
PRK10365 PRK10365
sigma-54-dependent response regulator transcription factor ZraR;
30-118 1.83e-10

sigma-54-dependent response regulator transcription factor ZraR;


Pssm-ID: 182412 [Multi-domain]  Cd Length: 441  Bit Score: 59.27  E-value: 1.83e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  30 VAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTVSDSPADIEAIVKAGADGYLLKDTEPD 109
Cdd:PRK10365   32 VALANSGRQALEQVREQVFDLVLCDVRMAEMDGIATLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFD 111


                  ....*....
gi 1332281222 110 ELVELLEKA 118
Cdd:PRK10365  112 NLQATLEKA 120
REC_FixJ cd17537
phosphoacceptor receiver (REC) domain of FixJ family response regulators; FixJ family response ...
 4-119 5.87e-10

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: 54.91  E-value: 5.87e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLL-SFeeQFEVVAEASnGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:cd17537     3 VYVVDDDEAVRDSLAFLLrSV--GLAVKTFTS-ASAFLAAAPPDQPGCLVLDVRMPGMSGLELQDELLARGSNIPIIFIT 79

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1332281222  83 V-SDSPADIEAIvKAGADGYLLKDTEPDELVELLEKAH 119
Cdd:cd17537    80 GhGDVPMAVEAM-KAGAVDFLEKPFRDQVLLDAIEQAL 116
REC_NtrX-like cd17550
phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and ...
 4-118 8.45e-10

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: 54.43  E-value: 8.45e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfEEQFEVVAeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTv 83
Cdd:cd17550     1 ILIVDDEEDIRESLSGILE-DEGYEVDT-AADGEEALKLIKERRPDLVLLDIWLPDMDGLELLKEIKEKYPDLPVIMIS- 77

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1332281222  84 sdSPADIEAIVKA---GADGYLLKDTEPDELVELLEKA 118
Cdd:cd17550    78 --GHGTIETAVKAtklGAYDFIEKPLSLDRLLLTIERA 113
PRK10643 PRK10643
two-component system response regulator PmrA;
3-115 8.88e-10

two-component system response regulator PmrA;


Pssm-ID: 182612 [Multi-domain]  Cd Length: 222  Bit Score: 56.20  E-value: 8.88e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFeVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:PRK10643    2 KILIVEDDTLLLQGLILALQ-TEGY-ACDCASTAREAEALLESGHYSLVVLDLGLPDEDGLHLLRRWRQKKYTLPVLILT 79

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1332281222  83 VSDSPADIEAIVKAGADGYLLKdtePDELVELL 115
Cdd:PRK10643   80 ARDTLEDRVAGLDVGADDYLVK---PFALEELH 109
REC_RssB-like cd17555
phosphoacceptor receiver (REC) domain of Pseudomonas aeruginosa RssB and similar domains; ...
 3-118 1.53e-09

phosphoacceptor receiver (REC) domain of Pseudomonas aeruginosa RssB and similar domains; Pseudomonas aeruginosa RssB is an orphan atypical response regulator containing a REC domain and a PP2C-type protein phosphatase output domain. Its function is still unknown. Escherichia RssB, which is not included in this subfamily, is a ClpX adaptor protein which alters ClpX specificity by mediating a specific interaction between ClpX and the substrates such as RpoS, an RNA polymerase sigma factor. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381107 [Multi-domain]  Cd Length: 116  Bit Score: 53.74  E-value: 1.53e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEVVaEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:cd17555     2 TILVIDDDEVVRESIAAYLE-DSGFQVL-QAADGRQGLELFRSEQPDLVLCDLRMPEMDGLEVLKQITKESPDTPVIVVS 79

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1332281222  83 VSDSPADIEAIVKAGADGYLLKdtePDELVELLEKA 118
Cdd:cd17555    80 GAGVMSDAVEALRLGAWDYLTK---PIEDLAVLEHA 112
PRK10955 PRK10955
envelope stress response regulator transcription factor CpxR;
1-194 1.64e-09

envelope stress response regulator transcription factor CpxR;


Pssm-ID: 182864 [Multi-domain]  Cd Length: 232  Bit Score: 55.58  E-value: 1.64e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   1 MCRVMLVDDHPLMRRGINQLLSFEeQFEVVAeASNGTEAVAKAhENELDLILLDLNMKGMSGLDTLKALRADGcEASIVI 80
Cdd:PRK10955    1 MNKILLVDDDRELTSLLKELLEME-GFNVIV-AHDGEQALDLL-DDSIDLLLLDVMMPKKNGIDTLKELRQTH-QTPVIM 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLKDTEPDELV----ELLEKAHLGDKAYSSVVAKYLLQ---------REENTdvFD--- 144
Cdd:PRK10955   77 LTARGSELDRVLGLELGADDYLPKPFNDRELVarirAILRRSHWSEQQQNNDNGSPTLEvdalslnpgRQEAS--FDgqt 154

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222 145 -ELTERERQIL--------QEVARGFRNKQI-ADRLFISESTVKVHMKSLLKKLkvPSRT 194
Cdd:PRK10955  155 lELTGTEFTLLyllaqhlgQVVSREHLSQEVlGKRLTPFDRAIDMHISNLRRKL--PDRK 212
REC_OmpR_PhoB cd17618
phosphoacceptor receiver (REC) domain of PhoB response regulator from the OmpR family; The ...
 3-112 1.96e-09

phosphoacceptor receiver (REC) domain of PhoB response regulator from the OmpR family; The transcription factor PhoB is a component of the PhoR/PhoB two-component system, a key regulatory protein network that facilitates response to inorganic phosphate (Pi) starvation conditions by turning on the phosphate (pho) regulon whose products are involved in phosphorus uptake and metabolism. PhoB is a member of the OmpR family of DNA-binding response regulators that contains REC and winged helix-turn-helix (wHTH) DNA-binding output effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381133 [Multi-domain]  Cd Length: 118  Bit Score: 53.41  E-value: 1.96e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEVVaEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRAD--GCEASIVI 80
Cdd:cd17618     2 TILIVEDEPAIREMIAFNLE-RAGFDVV-EAEDAESAVNLIVEPRPDLILLDWMLPGGSGIQFIRRLKRDemTRDIPIIM 79

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLKDTEPDELV 112
Cdd:cd17618    80 LTARGEEEDKVRGLEAGADDYITKPFSPRELV 111
ompR PRK09468
osmolarity response regulator; Provisional
 1-112 2.60e-09

osmolarity response regulator; Provisional


Pssm-ID: 181883 [Multi-domain]  Cd Length: 239  Bit Score: 54.98  E-value: 2.60e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   1 MCRVMLVDDHPLMRRGINQLLSfEEQFEVVAeASNGtEAVAKAHENEL-DLILLDLNMKGMSGLDTLKALRADGCEASIV 79
Cdd:PRK09468    5 NYKILVVDDDMRLRALLERYLT-EQGFQVRS-AANA-EQMDRLLTRESfHLMVLDLMLPGEDGLSICRRLRSQNNPTPII 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1332281222  80 ILTVSDSpaDIEAIV--KAGADGYLLKDTEPDELV 112
Cdd:PRK09468   82 MLTAKGE--EVDRIVglEIGADDYLPKPFNPRELL 114
REC_Ycf29 cd19927
phosphoacceptor receiver (REC) domain of probable transcriptional regulator Ycf29; Ycf29 is a ...
 4-104 2.76e-09

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: 52.77  E-value: 2.76e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfEEQFEVVAeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALR--ADGCEASIVIL 81
Cdd:cd19927     1 ILLVDDDPGIRLAVKDYLE-DQGFTVIA-ASNGLEALDLLNQYIPDLIISDIIMPGVDGYSLLGKLRknADFDTIPVIFL 78

                          90       100
                  ....*....|....*....|...
gi 1332281222  82 TVSDSPADIEAIVKAGADGYLLK 104
Cdd:cd19927    79 TAKGMTSDRIKGYNAGCDGYLSK 101
REC_NtrC1-like cd17572
phosphoacceptor receiver (REC) domain of nitrogen regulatory protein C 1 (NtrC1) from Aquifex ...
 4-118 3.95e-09

phosphoacceptor receiver (REC) domain of nitrogen regulatory protein C 1 (NtrC1) from Aquifex aeolicus and similar NtrC family response regulators; NtrC family proteins are transcriptional regulators that have REC, AAA+ ATPase/sigma-54 interaction, and DNA-binding output domains. This subfamily of NtrC proteins include Aquifex aeolicus NtrC1 and Vibrio quorum-sensing signal integrator LuxO. The N-terminal REC domain of NtrC proteins regulate the activity of the protein and its phosphorylation controls the AAA+ domain oligomerization, while the central AAA+ domain participates in nucleotide binding, hydrolysis, oligomerization, and sigma54 interaction. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381114 [Multi-domain]  Cd Length: 121  Bit Score: 52.59  E-value: 3.95e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSFEEQFevVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTV 83
Cdd:cd17572     1 VLLVEDSPSLAALYQEYLSDEGYK--VTHVETGKEALAFLSDQPPDVVLLDLKLPDMSGMEILKWIQERSLPTSVIVITA 78

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1332281222  84 SDSpADI--EAIvKAGADGYLLKDTEPDELVELLEKA 118
Cdd:cd17572    79 HGS-VDIavEAM-RLGAYDFLEKPFDADRLRVTVRNA 113
REC_typeB_ARR-like cd17584
phosphoacceptor receiver (REC) domain of type B Arabidopsis response regulators (ARRs) and ...
 4-119 4.69e-09

phosphoacceptor receiver (REC) domain of type B Arabidopsis response regulators (ARRs) and similar domains; Type-B ARRs (Arabidopsis response regulators) are a class of MYB-type transcription factors that act as major players in the transcriptional activation of cytokinin-responsive genes. They directly regulate the expression of type-A ARR genes and other downstream target genes. Cytokinin is a plant hormone implicated in many growth and development processes including shoot organogenesis, leaf senescence, sink/source relationships, vascular development, lateral bud release, and photomorphogenic development. Cytokinin signaling involves a phosphorelay cascade by histidine kinase receptors (AHKs), histidine phosphotransfer proteins (AHPs) and downstream ARRs. ARRs are divided into two groups, type-A and -B, according to their sequence and domain structure. Type-B ARRs contain a receiver (REC) domain and a large C-terminal extension that has characteristics of an effector or output domain, with a Myb-like DNA binding domain referred to as the GARP domain. The GARP domain is a motif specific to plant transcription factors. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381121 [Multi-domain]  Cd Length: 115  Bit Score: 52.25  E-value: 4.69e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLsFEEQFEVVAeASNGTEAVA--KAHENELDLILLDLNMKGMSGLDTLKALRaDGCEASIVIL 81
Cdd:cd17584     1 VLVVDDDPTCLAILKRML-LRCGYQVTT-CTDAEEALSmlRENKDEFDLVITDVHMPDMDGFEFLELIR-LEMDLPVIMM 77

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1332281222  82 TVSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKAH 119
Cdd:cd17584    78 SADGSTSTVMKGLAHGACDYLLKPVSIEDLKNIWQHVV 115
REC_GlnL-like cd17565
phosphoacceptor receiver (REC) domain of transcriptional regulatory protein GlnL and similar ...
 5-104 7.24e-09

phosphoacceptor receiver (REC) domain of transcriptional regulatory protein GlnL and similar proteins; Bacillus subtilis GlnL is part of the GlnK-GlnL (formerly YcbA-YcbB) two-component system that positively regulates the expression of the glsA-glnT (formerly ybgJ-ybgH) operon in response to glutamine. It contains a REC domain and a DNA-binding output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381112 [Multi-domain]  Cd Length: 103  Bit Score: 51.50  E-value: 7.24e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   5 MLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTVS 84
Cdd:cd17565     2 YIVDDDKNIIKILSDIIEDDDLGEVVGEADNGAQAYDEILFLQPDIVLIDLLMPGMDGIQLVRKLKDTGSNGKFIMISQV 81

                          90       100
                  ....*....|....*....|
gi 1332281222  85 DSPADIEAIVKAGADGYLLK 104
Cdd:cd17565    82 SDKEMIGKAYQAGIEFFINK 101
REC_Spo0A cd17561
phosphoacceptor receiver (REC) domain of Spo0A; Spo0A is a response regulator of the ...
 3-104 7.25e-09

phosphoacceptor receiver (REC) domain of Spo0A; Spo0A is a response regulator of the phosphorelay system in the early stage of spore formation. It may be an element of the effector pathway responsible for the activation of sporulation genes in response to nutritional stress and may act in the with sigma factor spo0H to control the expression of some genes that are critical to the sporulation process. Spo0A contains a regulatory N-terminal REC domain and a C-terminal DNA-binding transcription activation domain as its effector/output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381109 [Multi-domain]  Cd Length: 108  Bit Score: 51.46  E-value: 7.25e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEA--SIVI 80
Cdd:cd17561     3 KVLIADDNREFVQLLEEYLNSQPDMEVVGVAHNGQEALELIEEKEPDVLLLDIIMPHLDGIGVLEKLRRMRLEKrpKIIM 82

                          90       100
                  ....*....|....*....|....
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLK 104
Cdd:cd17561    83 LTAFGQEDITQRAVELGASYYILK 106
PRK10693 PRK10693
two-component system response regulator RssB;
31-104 1.27e-08

two-component system response regulator RssB;


Pssm-ID: 182652 [Multi-domain]  Cd Length: 303  Bit Score: 53.46  E-value: 1.27e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1332281222  31 AEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTVSDSPADIEAIVKAGADGYLLK 104
Cdd:PRK10693    1 VLAANGVDALELLGGFTPDLIICDLAMPRMNGIEFVEHLRNRGDQTPVLVISATENMADIAKALRLGVQDVLLK 74
REC_WspR-like cd17575
phosphoacceptor receiver (REC) domain of WspR response regulator and similar proteins; The ...
 3-136 1.46e-08

phosphoacceptor receiver (REC) domain of WspR response regulator and similar proteins; The GGDEF response regulator WspR is part of the Wsp system that is homologous to chemotaxis systems and also includes the membrane-bound receptor protein WspA. In response to growth on surfaces, WspR is phosphorylated by the Wsp signal transduction complex and is activated, functioning as a diguanylate cyclase (DGC) that catalyzes c-di-GMP synthesis. WspR is a hybrid response regulator-diguanylate cyclase, containing an N-terminal REC domain and a C-terminal GGDEF domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381117 [Multi-domain]  Cd Length: 128  Bit Score: 51.25  E-value: 1.46e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEEQFEVvAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGC--EASIVI 80
Cdd:cd17575     2 MVLLVDDQAIIGEAVRRALADEEDIDF-HYCSDPTEAIEVASQIKPTVILQDLVMPGVDGLTLVRFFRANPAtrDIPIIV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLKdtEPDElVELLEKAHLGDKAYSSvvakyLLQR 136
Cdd:cd17575    81 LSTKEEPEVKSEAFALGANDYLVK--LPDK-IELVARIRYHSRSYIN-----LLQR 128
REC_CheV-like cd19924
phosphoacceptor receiver (REC) domain of chemotaxis protein CheV and similar proteins; This ...
 4-104 2.49e-08

phosphoacceptor receiver (REC) domain of chemotaxis protein CheV and similar proteins; This subfamily includes the REC domains of Bacillus subtilis chemotaxis protein CheV, Myxococcus xanthus gliding motility regulatory protein FrzE, and similar proteins. CheV is a hybrid protein with an N-terminal CheW-like domain and a C-terminal CheY-like REC domain. The CheV pathway is one of three systems employed by B. subtilis for sensory adaptation that contribute to chemotaxis. It is involved in the transmission of sensory signals from chemoreceptors to flagellar motors. Together with CheW, it is involved in the coupling of methyl-accepting chemoreceptors to the central two-component histidine kinase CheA. FrzE is a hybrid sensor histidine kinase/response regulator that is part of the Frz pathway that controls cell reversal frequency to support directional motility during swarming and fruiting body formation. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381151 [Multi-domain]  Cd Length: 111  Bit Score: 50.07  E-value: 2.49e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfEEQFEVvAEASNGTEAV---------AKAHENELDLILLDLNMKGMSGLDTLKALRADGC 74
Cdd:cd19924     1 ILVVDDSPTARKQLRDLLK-NLGFEI-AEAVDGEEALnklenlakeGNDLSKELDLIITDIEMPKMDGYELTFELRDDPR 78

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1332281222  75 EASIVILTVS--DSPADIEAIVKAGADGYLLK 104
Cdd:cd19924    79 LANIPVILNSslSGEFSRARGKKVGADAYLAK 110
PRK10336 PRK10336
two-component system response regulator QseB;
3-188 2.94e-08

two-component system response regulator QseB;


Pssm-ID: 182387 [Multi-domain]  Cd Length: 219  Bit Score: 51.82  E-value: 2.94e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEV--VAEASNGTEAVAKAhenELDLILLDLNMKGMSGLDTLKALRADGCEASIVI 80
Cdd:PRK10336    2 RILLIEDDMLIGDGIKTGLS-KMGFSVdwFTQGRQGKEALYSA---PYDAVILDLTLPGMDGRDILREWREKGQREPVLI 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLKdtePDELVE-------LLEKAHlGDKAYSSVVAKYLLQREENTDVFD----ELTER 149
Cdd:PRK10336   78 LTARDALAERVEGLRLGADDYLCK---PFALIEvaarleaLMRRTN-GQASNELRHGNVMLDPGKRIATLAgeplTLKPK 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1332281222 150 ERQILQ----EVARGFRNKQIADRLF-----ISESTVKVHMKSLLKKL 188
Cdd:PRK10336  154 EFALLEllmrNAGRVLPRKLIEEKLYtwdeeVTSNAVEVHVHHLRRKL 201
PRK09959 PRK09959
acid-sensing system histidine kinase EvgS;
4-168 3.13e-08

acid-sensing system histidine kinase EvgS;


Pssm-ID: 182169 [Multi-domain]  Cd Length: 1197  Bit Score: 53.20  E-value: 3.13e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222    4 VMLVDDHP----LMRRGINqLLSFEeqfevVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIV 79
Cdd:PRK09959   961 ILIADDHPtnrlLLKRQLN-LLGYD-----VDEATDGVQALHKVSMQHYDLLITDVNMPNMDGFELTRKLREQNSSLPIW 1034

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   80 ILTVSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKAHlgdkAYSSVVAKYllqREENTDVFDELTERERQILQEVAR 159
Cdd:PRK09959  1035 GLTANAQANEREKGLSCGMNLCLFKPLTLDVLKTHLSQLH----QVAHIAPQY---RHLDIEALKNNTANDLQLMQEILM 1107


                   ....*....
gi 1332281222  160 GFRNKQIAD 168
Cdd:PRK09959  1108 TFQHETHKD 1116
REC_OmpR_RegX3-like cd17621
phosphoacceptor receiver (REC) domain of RegX3-like OmpR family response regulators; RegX3 is ...
 4-104 3.69e-08

phosphoacceptor receiver (REC) domain of RegX3-like OmpR family response regulators; RegX3 is a member of the SenX3-RegX3 two-component system that is involved in phosphate-sensing signal transduction. Phosphorylated RegX3 functions as a transcriptional activator of phoA. It induces transcription in phosphate limiting environment and also controls expression of several critical metabolic enzymes in aerobic condition. RegX3 belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381136 [Multi-domain]  Cd Length: 99  Bit Score: 49.50  E-value: 3.69e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfEEQFEVvAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGcEASIVILTV 83
Cdd:cd17621     1 VLVVEDEESFSDPLAYLLR-KEGFEV-TVATDGPAALAEFDRAGADIVLLDLMLPGLSGTEVCRQLRARS-NVPVIMVTA 77

                          90       100
                  ....*....|....*....|.
gi 1332281222  84 SDSPADIEAIVKAGADGYLLK 104
Cdd:cd17621    78 KDSEIDKVVGLELGADDYVTK 98
REC_OmpR_kpRstA-like cd17622
phosphoacceptor receiver (REC) domain of kpRstA-like OmpR family response regulators; ...
 3-120 4.18e-08

phosphoacceptor receiver (REC) domain of kpRstA-like OmpR family response regulators; Klebsiella pneumoniae RstA (kpRstA) is part of the RstA/RstB two-component regulatory system that may play a regulatory role in virulence. It belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381137 [Multi-domain]  Cd Length: 116  Bit Score: 49.68  E-value: 4.18e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEVVAEaSNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRaDGCEASIVILT 82
Cdd:cd17622     2 RILLVEDDPKLARLIADFLE-SHGFNVVVE-HRGDRALEVIAREKPDAVLLDIMLPGIDGLTLCRDLR-PKYQGPILLLT 78

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1332281222  83 VSDSPADIEAIVKAGADGYLLKDTEPDELVELLeKAHL 120
Cdd:cd17622    79 ALDSDIDHILGLELGADDYVVKPVEPAVLLARL-RALL 115
PRK04841 PRK04841
HTH-type transcriptional regulator MalT;
146-196 4.40e-08

HTH-type transcriptional regulator MalT;


Pssm-ID: 235315 [Multi-domain]  Cd Length: 903  Bit Score: 52.64  E-value: 4.40e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1332281222 146 LTERERQILQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRTAA 196
Cdd:PRK04841  839 LTQREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEA 889
PRK10430 PRK10430
two-component system response regulator DcuR;
1-104 4.72e-08

two-component system response regulator DcuR;


Pssm-ID: 182454 [Multi-domain]  Cd Length: 239  Bit Score: 51.65  E-value: 4.72e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   1 MCRVMLVDDHP----LMRRGINQLlsfeEQFEVVAEASngTEAVAKAH----ENELDLILLDLNMKGMSGLDTLKALRAD 72
Cdd:PRK10430    1 MINVLIVDDDAmvaeLNRRYVAQI----PGFQCCGTAS--TLEQAKEIifnsDTPIDLILLDIYMQQENGLDLLPVLHEA 74

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1332281222  73 GCEASIVILTvsdSPADIEAIVKA---GADGYLLK 104
Cdd:PRK10430   75 GCKSDVIVIS---SAADAATIKDSlhyGVVDYLIK 106
REC_NtrC cd19919
phosphoacceptor receiver (REC) domain of DNA-binding transcriptional regulator NtrC; ...
 3-118 9.43e-08

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: 48.81  E-value: 9.43e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEVVAeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:cd19919     2 TVWIVDDDSSIRWVLERALA-GAGLTVTS-FENAQEALAALASSQPDVLISDIRMPGMDGLALLAQIKQRHPDLPVIIMT 79

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1332281222  83 vsdSPADIEAIVKA---GADGYLLKDTEPDELVELLEKA 118
Cdd:cd19919    80 ---AHSDLDSAVSAyqgGAFEYLPKPFDIDEAVALVERA 115
REC_RocR cd17530
phosphoacceptor receiver (REC) domain of response regulator RocR; The response regulator RocR ...
 3-118 1.11e-07

phosphoacceptor receiver (REC) domain of response regulator RocR; The response regulator RocR from some pathogens contains an N-terminal phosphoreceiver (REC) domain and a C-terminal EAL domain that possesses c-di-GMP specific phosphodiesterase activity. The RocR REC domain is phosphorylated and modulates its EAL domain enzymatic activity, regulating the local level of c-di-GMP. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381086 [Multi-domain]  Cd Length: 123  Bit Score: 48.59  E-value: 1.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEEQFEVvAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:cd17530     2 RVLVLDDDPFQCMMAATILEDLGPGNV-DEADDGREALVILLCNAPDIIICDLKMPDMDGIEFLRHLAESHSNAAVILMS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1332281222  83 VSDSPADIEAIVKAGADG-YLL----KDTEPDELVELLEKA 118
Cdd:cd17530    81 GLDGGILESAETLAGANGlNLLgtlsKPFSPEELTELLTKY 121
PRK14084 PRK14084
DNA-binding response regulator;
3-118 1.14e-07

DNA-binding response regulator;


Pssm-ID: 184495 [Multi-domain]  Cd Length: 246  Bit Score: 50.52  E-value: 1.14e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:PRK14084    2 KALIVDDEPLARNELTYLLNEIGGFEEINEAENVKETLEALLINQYDIIFLDINLMDESGIELAAKIQKMKEPPAIIFAT 81

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1332281222  83 VSDSPAdieaiVKA---GADGYLLKDTEPDELVELLEKA 118
Cdd:PRK14084   82 AHDQFA-----VKAfelNATDYILKPFEQKRIEQAVNKV 115
REC_OmpR_YycF-like cd17614
phosphoacceptor receiver (REC) domain of YrcF-like OmpR family response regulators; YycF ...
 4-120 1.80e-07

phosphoacceptor receiver (REC) domain of YrcF-like OmpR family response regulators; YycF appears to play an important role in cell wall integrity in a wide range of gram-positive bacteria, and may also modulate cell membrane integrity. It functions as part of a phosphotransfer system that ultimately controls the levels of competence within the bacteria. YycF belongs to the OmpR family of response regulators, which are characterized by a REC domain and a winged helix-turn-helix effector domain involved in DNA binding. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381130 [Multi-domain]  Cd Length: 115  Bit Score: 47.80  E-value: 1.80e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHplmrRGINQLLSF---EEQFEVVAeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGcEASIVI 80
Cdd:cd17614     1 ILVVDDE----KPISDILKFnltKEGYEVVT-AYDGREALEKVEEEQPDLILLDLMLPEKDGLEVCREVRKTS-NVPIIM 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLKDTEPDELVELLeKAHL 120
Cdd:cd17614    75 LTAKDSEVDKVLGLELGADDYVTKPFSNRELLARV-KANL 113
PRK11517 PRK11517
DNA-binding response regulator HprR;
3-117 2.51e-07

DNA-binding response regulator HprR;


Pssm-ID: 183172 [Multi-domain]  Cd Length: 223  Bit Score: 49.51  E-value: 2.51e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfeEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRAdGCEASIVILT 82
Cdd:PRK11517    2 KILLIEDNQRTQEWVTQGLS--EAGYVIDAVSDGRDGLYLALKDDYALIILDIMLPGMDGWQILQTLRT-AKQTPVICLT 78

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1332281222  83 VSDSPADIEAIVKAGADGYLLKdtePDELVELLEK 117
Cdd:PRK11517   79 ARDSVDDRVRGLDSGANDYLVK---PFSFSELLAR 110
REC_OmpR_VirG cd17594
phosphoacceptor receiver (REC) domain of VirG-like OmpR family response regulators; VirG is ...
 4-117 2.93e-07

phosphoacceptor receiver (REC) domain of VirG-like OmpR family response regulators; VirG is part of the VirA/VirG two-component system that regulates the expression of virulence (vir) genes. The histidine kinase VirA senses a phenolic wound response signal, undergoes autophosphorylation, and phosphorelays to the VirG response regulator, which induces transcription of the vir regulon. VirG belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381125 [Multi-domain]  Cd Length: 113  Bit Score: 47.44  E-value: 2.93e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfeEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTV 83
Cdd:cd17594     2 VLVVDDDAAMRHLLILYLR--ERGFDVTAAADGAEEARLMLHRRVDLVLLDLRLGQESGLDLLRTIRARSDVPIIIISGD 79

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1332281222  84 SDSPADIEAIVKAGADGYLLKdtePDELVELLEK 117
Cdd:cd17594    80 RRDEIDRVVGLELGADDYLAK---PFGLRELLAR 110
PRK10841 PRK10841
two-component system sensor histidine kinase RcsC;
3-82 3.47e-07

two-component system sensor histidine kinase RcsC;


Pssm-ID: 182772 [Multi-domain]  Cd Length: 924  Bit Score: 49.97  E-value: 3.47e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGI-NQLLSFEEQfevVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVIL 81
Cdd:PRK10841  803 MILVVDDHPINRRLLaDQLGSLGYQ---CKTANDGVDALNVLSKNHIDIVLTDVNMPNMDGYRLTQRLRQLGLTLPVIGV 879


                  .
gi 1332281222  82 T 82
Cdd:PRK10841  880 T 880
PRK10766 PRK10766
two-component system response regulator TorR;
3-115 4.84e-07

two-component system response regulator TorR;


Pssm-ID: 182711 [Multi-domain]  Cd Length: 221  Bit Score: 48.50  E-value: 4.84e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLlsFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRAdgcEASIVILT 82
Cdd:PRK10766    4 HILVVEDEPVTRARLQGY--FEQEGYTVSEAASGAGMREIMQNQHVDLILLDINLPGEDGLMLTRELRS---RSTVGIIL 78

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1332281222  83 VSDSPADIEAIV--KAGADGYLlkdTEPDELVELL 115
Cdd:PRK10766   79 VTGRTDSIDRIVglEMGADDYV---TKPLELRELL 110
PRK11173 PRK11173
two-component response regulator; Provisional
 3-149 5.44e-07

two-component response regulator; Provisional


Pssm-ID: 183013 [Multi-domain]  Cd Length: 237  Bit Score: 48.47  E-value: 5.44e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRrgiNQLLS-FEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGcEASIVIL 81
Cdd:PRK11173    5 HILIVEDELVTR---NTLKSiFEAEGYDVFEATDGAEMHQILSENDINLVIMDINLPGKNGLLLARELREQA-NVALMFL 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1332281222  82 TVSDSPADIEAIVKAGADGYLLKDTEPDELvellekahlgdkaysSVVAKYLLQREENTDVFDELTER 149
Cdd:PRK11173   81 TGRDNEVDKILGLEIGADDYITKPFNPREL---------------TIRARNLLSRTMNLGTVSEERRS 133
PRK10816 PRK10816
two-component system response regulator PhoP;
3-112 8.17e-07

two-component system response regulator PhoP;


Pssm-ID: 182755 [Multi-domain]  Cd Length: 223  Bit Score: 47.81  E-value: 8.17e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINqlLSFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:PRK10816    2 RVLVVEDNALLRHHLK--VQLQDAGHQVDAAEDAKEADYYLNEHLPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLT 79

                          90       100       110
                  ....*....|....*....|....*....|
gi 1332281222  83 VSDSPADIEAIVKAGADGYLLKDTEPDELV 112
Cdd:PRK10816   80 ARESWQDKVEVLSAGADDYVTKPFHIEEVM 109
PRK15479 PRK15479
transcriptional regulator TctD;
3-111 1.15e-06

transcriptional regulator TctD;


Pssm-ID: 185376 [Multi-domain]  Cd Length: 221  Bit Score: 47.41  E-value: 1.15e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFeVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:PRK15479    2 RLLLAEDNRELAHWLEKALV-QNGF-AVDCVFDGLAADHLLQSEMYALAVLDINMPGMDGLEVLQRLRKRGQTLPVLLLT 79

                          90       100
                  ....*....|....*....|....*....
gi 1332281222  83 VSDSPADIEAIVKAGADGYLLKDTEPDEL 111
Cdd:PRK15479   80 ARSAVADRVKGLNVGADDYLPKPFELEEL 108
PRK10710 PRK10710
DNA-binding transcriptional regulator BaeR; Provisional
 34-188 1.93e-06

DNA-binding transcriptional regulator BaeR; Provisional


Pssm-ID: 182665 [Multi-domain]  Cd Length: 240  Bit Score: 46.99  E-value: 1.93e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  34 SNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGcEASIVILTvsdspADIEAI-----VKAGADGYLLKDTEP 108
Cdd:PRK10710   41 SHGDEVLPYVRQTPPDLILLDLMLPGTDGLTLCREIRRFS-DIPIVMVT-----AKIEEIdrllgLEIGADDYICKPYSP 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222 109 DELV----ELLEKAHLGDKAYSSVVAKYLLQREEN-----TDVFDELTERERQIL----QEVARGFRNKQIADRLF---- 171
Cdd:PRK10710  115 REVVarvkTILRRCKPQRELQQQDAESPLIIDESRfqaswRGKMLDLTPAEFRLLktlsHEPGKVFSREQLLNHLYddyr 194

                         170
                  ....*....|....*...
gi 1332281222 172 -ISESTVKVHMKSLLKKL 188
Cdd:PRK10710  195 vVTDRTIDSHIKNLRRKL 212
REC_TrxB cd17595
phosphoacceptor receiver (REC) domain a fused response regulator with a thioredoxin reductase ...
 4-110 2.72e-06

phosphoacceptor receiver (REC) domain a fused response regulator with a thioredoxin reductase output domain; This family is composed of uncharacterized fusion proteins containing a REC domain and a thioredoxin reductase domain. Thioredoxin reductase catalyzes the reduction of thioredoxin and is thus a central component in the thioredoxin system. Fusion proteins containing REC and thioredoxin reductase domains could play an important role in the environmental regulation of the cellular dithiol-disulfide ratio. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381126 [Multi-domain]  Cd Length: 135  Bit Score: 45.02  E-value: 2.72e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLL--SFEEQFEVVAEASnGTEAVA-----KAHENELDLILLDLNMKGMSGLDTLKALRADGCEA 76
Cdd:cd17595     3 ILTVDDDPQVLRAVARDLrrQYGKDYRVLRADS-GAEALDalkelKLRGEAVALFLVDQRMPEMDGVEFLEKAMELFPEA 81

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1332281222  77 SIVILTV-SDSPADIEAIVKAGADGYLLKDTEPDE 110
Cdd:cd17595    82 KRVLLTAyADTDAAIRAINDVQLDYYLLKPWDPPE 116
orf27 CHL00148
Ycf27; Reviewed
 3-111 3.09e-06

Ycf27; Reviewed


Pssm-ID: 214376 [Multi-domain]  Cd Length: 240  Bit Score: 46.25  E-value: 3.09e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSFEeQFEVVaEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGcEASIVILT 82
Cdd:CHL00148    8 KILVVDDEAYIRKILETRLSII-GYEVI-TASDGEEALKLFRKEQPDLVILDVMMPKLDGYGVCQEIRKES-DVPIIMLT 84

                          90       100
                  ....*....|....*....|....*....
gi 1332281222  83 VSDSPADIEAIVKAGADGYLLKDTEPDEL 111
Cdd:CHL00148   85 ALGDVSDRITGLELGADDYVVKPFSPKEL 113
PRK10161 PRK10161
phosphate response regulator transcription factor PhoB;
3-112 3.58e-06

phosphate response regulator transcription factor PhoB;


Pssm-ID: 182277 [Multi-domain]  Cd Length: 229  Bit Score: 46.25  E-value: 3.58e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEVVaEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGC--EASIVI 80
Cdd:PRK10161    4 RILVVEDEAPIREMVCFVLE-QNGFQPV-EAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMtrDIPVVM 81

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLLKDTEPDELV 112
Cdd:PRK10161   82 LTARGEEEDRVRGLETGADDYITKPFSPKELV 113
REC_typeA_ARR cd17581
phosphoacceptor receiver (REC) domain of type A Arabidopsis response regulators (ARRs) and ...
 4-104 3.81e-06

phosphoacceptor receiver (REC) domain of type A Arabidopsis response regulators (ARRs) and similar proteins; Type-A response regulators of Arabidopsis (ARRs) are involved in cytokinin signaling, which involves a phosphorelay cascade by histidine kinase receptors (AHKs), histidine phosphotransfer proteins (AHPs) and downstream ARRs. Cytokinin is a plant hormone implicated in many growth and development processes including shoot organogenesis, leaf senescence, sink/source relationships, vascular development, lateral bud release, and photomorphogenic development. Type-A ARRs function downstream of and are regulated by type-B ARRs, which are a class of MYB-type transcription factors. As primary cytokinin response genes, type-A ARRs act as redundant negative feedback regulators of cytokinin signaling by inactivating the phosphorelay. ARRs are divided into two groups, type-A and -B, according to their sequence and domain structure. Type-A ARRs are similar in domain structure to CheY, in that they lack a typical output domain and only contain a stand-alone receiver (REC) domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381119 [Multi-domain]  Cd Length: 122  Bit Score: 44.28  E-value: 3.81e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfEEQFEVVAEAS----------NGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADG 73
Cdd:cd17581     1 VLAVDDSLVDRKVIERLLR-ISSCRVTAVDSgkraleflglEDEEDSSNFNEPKVNMIITDYCMPGMTGYDLLKKVKESS 79

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1332281222  74 C--EASIVILTVSDSPADIEAIVKAGADGYLLK 104
Cdd:cd17581    80 AlkEIPVVIMSSENIPTRISRCLEEGAEDFLLK 112
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 105-189 5.10e-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: 5.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222 105 DTEPDELVELLEKAHLGDKAYSSVVAKYLLQreentDVFDELTERERQILQEVA-RGFRNKQIADRLFISESTVKVHMKS 183
Cdd:TIGR02937  75 RRELDLLEELLDSDPSPEEELEQEEEREALR-----EALEKLPEREREVLVLRYlEGLSYKEIAEILGISVGTVKRRLKR 149


                  ....*.
gi 1332281222 184 LLKKLK 189
Cdd:TIGR02937 150 ARKKLR 155
PRK11083 PRK11083
DNA-binding response regulator CreB; Provisional
 1-189 6.26e-06

DNA-binding response regulator CreB; Provisional


Pssm-ID: 236838 [Multi-domain]  Cd Length: 228  Bit Score: 45.34  E-value: 6.26e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   1 MCRVMLVDDHPlmrrGINQLLSFEEQFE--VVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASI 78
Cdd:PRK11083    3 QPTILLVEDEQ----AIADTLVYALQSEgfTVEWFERGLPALDKLRQQPPDLVILDVGLPDISGFELCRQLLAFHPALPV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  79 VILTVSDspADIEAIV--KAGADGYLLKDTEPDELVE----LLEKAHLGDKAYSSV-VAKYLLQREENT----DVFDELT 147
Cdd:PRK11083   79 IFLTARS--DEVDRLVglEIGADDYVAKPFSPREVAArvrtILRRVKKFAAPSPVIrIGHFELDEPAARisyfGTPLTLT 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1332281222 148 ERERQILQEV----ARGFRNKQIADRLFIS-----ESTVKVHMKSLLKKLK 189
Cdd:PRK11083  157 RYEFLLLKTLllspGRVFSRQQLMDIVWEDaqdsyDRTVDTHIKTLRAKLR 207
PLN03029 PLN03029
type-a response regulator protein; Provisional
 4-152 9.32e-06

type-a response regulator protein; Provisional


Pssm-ID: 215544 [Multi-domain]  Cd Length: 222  Bit Score: 44.64  E-value: 9.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSFEE-QFEVVAEASNGTEAVAkAHEN------------------ELDLILLDLNMKGMSGLD 64
Cdd:PLN03029   11 VLAVDDSLIDRKLIEKLLKTSSyQVTTVDSGSKALKFLG-LHEDdrsnpdtpsvspnshqevEVNLIITDYCMPGMTGYD 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  65 TLKALRADGCEASI--VILTVSDSPADIEAIVKAGADGYLLKDTEPDELVELleKAHLgdkayssVVAKYLLQREENTDV 142
Cdd:PLN03029   90 LLKKIKESSSLRNIpvVIMSSENVPSRITRCLEEGAEEFFLKPVQLSDLNRL--KPHM-------MKTKSKNQKQENQEK 160

                         170
                  ....*....|
gi 1332281222 143 FDELTERERQ 152
Cdd:PLN03029  161 QEKLEESEIQ 170
REC_hyHK cd17598
phosphoacceptor receiver (REC) domain of uncharacterized hybrid sensor histidine kinase ...
 4-104 1.50e-05

phosphoacceptor receiver (REC) domain of uncharacterized hybrid sensor histidine kinase/response regulators; Typically, two-component regulatory systems (TCSs) consist of a sensor (histidine kinase) that responds to specific input(s) by modifying the output of a cognate response regulator (RR). TCSs allow organisms to sense and respond to changes in environmental conditions. Hybrid sensor histidine kinase/response regulators contain all the elements of a classical TCS in a single polypeptide chain. RRs share the common phosphoacceptor REC domain and different effector/output domains such as DNA, RNA, ligand-binding, protein-binding, or enzymatic domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381128 [Multi-domain]  Cd Length: 118  Bit Score: 42.70  E-value: 1.50e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLsfEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASI--VIL 81
Cdd:cd17598     1 ILIVEDSPTQAEQLKHIL--EEQGYKVQVARNGREALAMLAEHRPTLVISDIVMPEMDGYELCRKIKSDPDLKDIpvILL 78

                          90       100
                  ....*....|....*....|...
gi 1332281222  82 TVSDSPADIEAIVKAGADGYLLK 104
Cdd:cd17598    79 TTLSDPRDVIRGLECGADNFITK 101
pleD PRK09581
response regulator PleD; Reviewed
 3-112 1.68e-05

response regulator PleD; Reviewed


Pssm-ID: 236577 [Multi-domain]  Cd Length: 457  Bit Score: 44.51  E-value: 1.68e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfeEQFEVVAEASNgTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:PRK09581  157 RILLVDDDVSQAERIANILK--EEFRVVVVSDP-SEALFNAAETNYDLVIVSANFENYDPLRLCSQLRSKERTRYVPILL 233

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1332281222  83 VSDsPADIEAIVKA---GADGYLLKDTEPDELV 112
Cdd:PRK09581  234 LVD-EDDDPRLVKAlelGVNDYLMRPIDKNELL 265
REC_LytTR_AgrA-like cd17533
phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AgrA; ...
 3-119 1.82e-05

phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AgrA; Members of the LytTR/AlgR family of response regulators contain a REC domain and a unique LytTR DNA-binding output domain that lacks the helix-turn-helix motif and consists mostly of beta-strands. Transcriptional regulators with the LytTR-type output domains are involved in biosynthesis of extracellular polysaccharides, fimbriation, expression of exoproteins, including toxins, and quorum sensing. Included in this AgrA-like group of LytTR/AlgR family response regulators are Staphylococcus aureus accessory gene regulator protein A (AgrA) and Streptococcus pneumoniae response regulator ComE, which are members of two-component regulatory systems. AgrA is a global regulator that controls the synthesis of virulence factors and other exoproteins. ComE is part of the ComD-ComE system that is part of a quorum-sensing signaling pathway that controls the development of competence, a physiological state required for genetic transformation. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381088 [Multi-domain]  Cd Length: 131  Bit Score: 42.61  E-value: 1.82e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMR----RGINQLLSFEEQFEVVAEASNGTEAVAKAHENE---LDLILLDLNMKGMSGLDTLKALRADGCE 75
Cdd:cd17533     2 NIFILEDDKIQRvrleEIIENILKIENIEYVIELTGKTEELLEKIKERGkngIYFLDIDIKMEEKNGLEVAQKIRKYDPY 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1332281222  76 ASIVILTVSDSPADIEAIVKAGADGYLLKDTEPDE----LVELLEKAH 119
Cdd:cd17533    82 AIIIFVTTHSEFAPLTFEYKVAALDFILKPLKLEEfkkrIEECIKYAQ 129
REC_CpdR_CckA-like cd18160
phosphoacceptor receiver (REC) domain of Brucella abortus CpdR and CckA, and similar domains; ...
 3-70 2.21e-05

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: 42.10  E-value: 2.21e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1332281222   3 RVMLVDDHPLMRRGINQLLsfEEQFEVVAEASNGTEAVAKA-HENELDLILLDLNMKGMSGLDTLKALR 70
Cdd:cd18160     1 TILLADDEPSVRKFIVTTL--KKAGYAVTEAESGAEALEKLqQGKDIDIVVTDIVMPEMDGIELAREAR 67
PRK15115 PRK15115
response regulator GlrR; Provisional
 3-118 2.22e-05

response regulator GlrR; Provisional


Pssm-ID: 185070 [Multi-domain]  Cd Length: 444  Bit Score: 44.44  E-value: 2.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEVVAeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:PRK15115    7 HLLLVDDDPGLLKLLGMRLT-SEGYSVVT-AESGQEALRVLNREKVDLVISDLRMDEMDGMQLFAEIQKVQPGMPVIILT 84

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1332281222  83 VSDSPADIEAIVKAGADGYLLKDTEPDELVELLEKA 118
Cdd:PRK15115   85 AHGSIPDAVAATQQGVFSFLTKPVDRDALYKAIDDA 120
PRK10188 PRK10188
transcriptional regulator SdiA;
146-194 2.64e-05

transcriptional regulator SdiA;


Pssm-ID: 182292 [Multi-domain]  Cd Length: 240  Bit Score: 43.62  E-value: 2.64e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1332281222 146 LTERERQILQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLKVPSRT 194
Cdd:PRK10188  180 FSKREKEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKT 228
REC_OmpR_BfmR-like cd19939
phosphoacceptor receiver (REC) domain of BfmR-like OmpR family response regulators; ...
 3-112 3.17e-05

phosphoacceptor receiver (REC) domain of BfmR-like OmpR family response regulators; Acinetobacter baumannii BfmR is part of the BfmR/S two-component system that functions as the master regulator of biofilm initiation. BfmR confers resistance to complement-mediated bactericidal activity, independent of capsular polysaccharide, and also increases resistance to the clinically important antimicrobials meropenem and colistin, making it a potential antimicrobial target. Its inhibition would have the dual benefit of significantly decreasing in vivo survival and increasing sensitivity to selected antimicrobials. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381166 [Multi-domain]  Cd Length: 116  Bit Score: 41.59  E-value: 3.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEVVAEaSNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRAdgcEASIVILT 82
Cdd:cd19939     1 RILIVEDELELARLTRDYLI-KAGLEVSVF-TDGQRAVRRIIDEQPSLVVLDIMLPGMDGLTVCREVRE---HSHVPILM 75

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1332281222  83 VSDSPADIEAIV--KAGADGYLLKDTEPDELV 112
Cdd:cd19939    76 LTARTEEMDRVLglEMGADDYLCKPFSPRELL 107
REC_PhyR cd17540
phosphoacceptor receiver (REC) domain of response regulator PhyR and similar proteins; PhyR is ...
 3-82 4.97e-05

phosphoacceptor receiver (REC) domain of response regulator PhyR and similar proteins; PhyR is a hybrid stress regulator that contains an N-terminal sigma-like (SL) domain and a C-terminal REC domain. Phosphorylation of the REC domain is known to promote binding of the SL domain to an anti-sigma factor. PhyR thus functions as an anti-anti-sigma factor in its phosphorylated state. It is involved in the general stress response. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381095 [Multi-domain]  Cd Length: 117  Bit Score: 41.08  E-value: 4.97e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLLsfEEQ-FEVVAEASNGTEAVAKAHENELDLILLDLNM-KGMSGLDTLKALRADgCEASIVI 80
Cdd:cd17540     2 RVLIIEDEPLIAMDLEQIV--EDLgHQVVGIARTRDEAVALARRERPDLILADIQLaDGSSGIDAVNEILTT-HDVPVIF 78


                  ..
gi 1332281222  81 LT 82
Cdd:cd17540    79 VT 80
PRK10701 PRK10701
DNA-binding transcriptional regulator RstA; Provisional
 1-120 5.20e-05

DNA-binding transcriptional regulator RstA; Provisional


Pssm-ID: 236738 [Multi-domain]  Cd Length: 240  Bit Score: 42.70  E-value: 5.20e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   1 MCRVMLVDDHPLMRRGINQLLSfEEQFEVVAEaSNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRA--DGceaSI 78
Cdd:PRK10701    1 MNKIVFVEDDAEVGSLIAAYLA-KHDIDVTVE-PRGDRAEATILREQPDLVLLDIMLPGKDGMTICRDLRPkwQG---PI 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1332281222  79 VILTVSDSpaDIEAIV--KAGADGYLLKDTEPDELVELLeKAHL 120
Cdd:PRK10701   76 VLLTSLDS--DMNHILalEMGACDYILKTTPPAVLLARL-RLHL 116
psREC-like_D2_PleD cd17539
REC-like adaptor domain (D2) of response regulator PleD; PleD contains a REC domain (D1) with ...
 4-112 5.24e-05

REC-like adaptor domain (D2) of response regulator PleD; PleD contains a REC domain (D1) with the phosphorylatable aspartate, a pseudo receiver (psREC)-like adaptor domain (D2), and the enzymatic diguanylate cyclase (DGC) domain, also called the GGDEF domain according to a conserved sequence motif, as its output domain. The GGDEF-containing PleD response regulators are global regulators of cell metabolism in some important human pathogens. This model describes the REC-like adaptor domain D2 of PleD, which is an inactive domain.


Pssm-ID: 381094 [Multi-domain]  Cd Length: 124  Bit Score: 41.15  E-value: 5.24e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSFEEQFEVvaeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTV 83
Cdd:cd17539     1 VLLVDDRPSSAERIAAMLSSEHEVVV---EADPDEALFRAAEGPFDLVIVSLALEDFDGLRLCSQLRSLERTRQLPILAV 77

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1332281222  84 SDsPADIEAIVKA---GADGYLLKDTEPDELV 112
Cdd:cd17539    78 AD-PGDRGRLIRAleiGVNDYLVRPIDPNELL 108
REC_OmpR_BaeR-like cd19938
phosphoacceptor receiver (REC) domain of BaeR-like OmpR family response regulators; BaeR is ...
 3-112 5.80e-05

phosphoacceptor receiver (REC) domain of BaeR-like OmpR family response regulators; BaeR is part of the BaeSR two-component system that is involved in regulating genes that confer multidrug and metal resistance. In Salmonella, BaeSR induces AcrD and MdtABC drug efflux systems, increasing multidrug and metal resistance. In Escherichia coli, BaeR stimulates multidrug resistance via mdtABC (multidrug transporter ABC, formerly known as yegMNO) genes, which encode a resistance-nodulation-cell division (RND) drug efflux system. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381165 [Multi-domain]  Cd Length: 114  Bit Score: 40.82  E-value: 5.80e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPlmrrGINQLLSFEEQFEVVAEA--SNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGcEASIVI 80
Cdd:cd19938     1 RILIVEDEP----KLAQLLIDYLRAAGYAPTllAHGDQVLPYVRHTPPDLILLDLMLPGTDGLTLCREIRRFS-DVPIIM 75

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1332281222  81 LTvsdspADIEAI-----VKAGADGYLLKDTEPDELV 112
Cdd:cd19938    76 VT-----ARVEEIdrllgLELGADDYICKPYSPREVV 107
psREC_PRR cd17582
pseudo receiver domain of pseudo-response regulators; In Arabidopsis, five pseudo-response ...
 4-104 9.17e-05

pseudo receiver domain of pseudo-response regulators; In Arabidopsis, five pseudo-response regulators (PRRs), also called APRRs, comprise a core group of clock components that controls the pace of the central oscillator of the circadian clock, an endogenous time-keeping mechanism that enables organisms to adapt to external daily cycles. The coordinated sequential expression of PRR9 (APRR9), PRR7 (APRR7), PRR5 (APRR5), PRR3 (APRR3), and PRR1 (APRR1) results in circadian waves that may be at the basis of the endogenous circadian clock. PRRs contain an N-terminal pseudo receiver (psREC) domain that resembles the receiver domain of a two-component response regulator, but lacks an aspartate residue that accepts a phosphoryl group from the sensor kinase, and a CCT motif at the C-terminus that contains a putative nuclear localization signal. The psREC domain is involved in protein-protein interactions.


Pssm-ID: 381120 [Multi-domain]  Cd Length: 104  Bit Score: 40.08  E-value: 9.17e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfEEQFEVVAeASNGTEA--VAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVIL 81
Cdd:cd17582     1 VLLVENDDSTRQIVTALLR-KCSYEVTA-ASDGLQAwdVLEDEQNEIDLILTEVDLPVSSGFKLLSYIMRHKICKNIPVI 78

                          90       100
                  ....*....|....*....|....*
gi 1332281222  82 TVS--DSPADIEAIVKAGADGYLLK 104
Cdd:cd17582    79 MMSsqDSVGVVFKCLSKGAADYLVK 103
REC_Spo0F-like cd17553
phosphoacceptor receiver (REC) domain of Spo0F and similar domains; Spo0F, a stand-alone ...
 3-117 9.23e-05

phosphoacceptor receiver (REC) domain of Spo0F and similar domains; Spo0F, a stand-alone response regulator containing only a REC domain with no output/effector domain, controls sporulation in Bacillus subtilis through the exchange of a phosphoryl group. Bacillus subtilis forms spores when conditions for growth become unfavorable. The initiation of sporulation is controlled by a phosphorelay (an expanded version of the two-component system) that consists of four main components: a histidine kinase (KinA), a secondary messenger (Spo0F), a phosphotransferase (Spo0B), and a transcription factor (Spo0A). REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381105 [Multi-domain]  Cd Length: 117  Bit Score: 40.62  E-value: 9.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   3 RVMLVDDHPLMRRGINQLlsFEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILT 82
Cdd:cd17553     2 KILIVDDQYGIRILLNEV--FNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMT 79

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1332281222  83 VSDSPADIEAIVKAGADGYLLKDTEPDELVELLEK 117
Cdd:cd17553    80 AYGELDMIQESKELGALTHFAKPFDIDEIRDAVKK 114
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 142-189 1.10e-04

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: 38.56  E-value: 1.10e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1332281222 142 VFDELTERERQILQevARGFRN---KQIADRLFISESTVKVHMKSLLKKLK 189
Cdd:pfam04545   1 ALASLPPRERQVLV--LRYGEGltlEEIGERLGISRERVRQIEKRALRKLR 49
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 144-189 1.13e-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: 1.13e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1332281222 144 DELTERERQILqEVAR--GFRNKQIADRLFISESTVKVHMKSLLKKLK 189
Cdd:TIGR02985 112 EKLPEQCREIF-ILSRfeGLSNKEIAEELGISVKTVEYHITKALKFLR 158
glnG PRK10923
nitrogen regulation protein NR(I); Provisional
 35-118 1.29e-04

nitrogen regulation protein NR(I); Provisional


Pssm-ID: 182842 [Multi-domain]  Cd Length: 469  Bit Score: 42.17  E-value: 1.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  35 NGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTvsdSPADIEAIVKA---GADGYLLKDTEPDEL 111
Cdd:PRK10923   35 NGNEVLEALASKTPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMT---AHSDLDAAVSAyqqGAFDYLPKPFDIDEA 111


                  ....*..
gi 1332281222 112 VELLEKA 118
Cdd:PRK10923  112 VALVERA 118
PRK11091 PRK11091
aerobic respiration control sensor protein ArcB; Provisional
 33-144 1.78e-04

aerobic respiration control sensor protein ArcB; Provisional


Pssm-ID: 236842 [Multi-domain]  Cd Length: 779  Bit Score: 41.85  E-value: 1.78e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  33 ASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEAS---IVILTvSDSPADIEAIVKAGADGYLLKDTEPD 109
Cdd:PRK11091  555 AMTGKEALEMFDPDEYDLVLLDIQLPDMTGLDIARELRERYPREDlppLVALT-ANVLKDKKEYLDAGMDDVLSKPLSVP 633

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1332281222 110 ELVELLEKaHLGDKAYSSVVAKYLLQREENTDVFD 144
Cdd:PRK11091  634 ALTAMIKK-FWDTQDDEESTVTTEESSKANEALLD 667
REC_hyHK_blue-like cd18161
phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinase/response regulators ...
 4-99 2.03e-04

phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinase/response regulators similar to Pseudomonas savastanoi blue-light-activated histidine kinase; Typically, two-component regulatory systems (TCSs) consist of a sensor (histidine kinase) that responds to specific input(s) by modifying the output of a cognate response regulator (RR). TCSs allow organisms to sense and respond to changes in environmental conditions. Hybrid sensor histidine kinase (HK)/response regulators contain all the elements of a classical TCS in a single polypeptide chain. Pseudomonas savastanoi blue-light-activated histidine kinase is a photosensitive HK and RR that is involved in increased bacterial virulence upon exposure to light. RRs share the common phosphoacceptor REC domain and different effector/output domains such as DNA, RNA, ligand-binding, protein-binding, or enzymatic domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381145 [Multi-domain]  Cd Length: 102  Bit Score: 39.25  E-value: 2.03e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLsfEEQFEVVAEASNGTEAVAKAHEN-ELDLILLDLNMKG-MSGLDTLKALRADGCEASIVIL 81
Cdd:cd18161     1 VLVVEDDPDVRRLTAEVL--EDLGYTVLEAASGDEALDLLESGpDIDLLVTDVIMPGgMNGSQLAEEARRRRPDLKVLLT 78

                          90
                  ....*....|....*...
gi 1332281222  82 TVSDSPADIEAIVKAGAD 99
Cdd:cd18161    79 SGYAENAIEGGDLAPGVD 96
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 133-189 2.22e-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: 2.22e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1332281222 133 LLQREENTDV---FDELTERERQILQEVA-RGFRNKQIADRLFISESTVKVHMKSLLKKLK 189
Cdd:COG1595   112 LEAEELLEALlaaLERLPPRQREVLVLRYlEGLSYAEIAEILGISEGTVKSRLSRARKKLR 172
REC_RitR-like cd19922
receiver (REC) domain of orphan response regulator RitR and similar domains; Streptococcus ...
 15-113 2.66e-04

receiver (REC) domain of orphan response regulator RitR and similar domains; Streptococcus pneumoniae RitR (Repressor of iron transport Regulator, formerly RR489) is an orphan two-component signal transduction response regulator that is required for lung pathogenicity. It acts to repress iron uptake via binding the pneumococcal iron uptake (Piu) transporter promoter. Members of this subfamily contain REC and DNA-binding output domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. However, members of this family do not contain the phosphorylatable aspartic acid residue and are phosphorylation-independent.


Pssm-ID: 381149 [Multi-domain]  Cd Length: 110  Bit Score: 39.00  E-value: 2.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  15 RGINQLLSFEEQFE--VVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTVSDSPADIEA 92
Cdd:cd19922     8 RNLAHFLSLELQKEgyRVDLVETGQEALSLALETDYDLILLNVNLSDMSAQDFAEKLSRIKPASVIIVLDHWEDLQEELE 87

                          90       100
                  ....*....|....*....|.
gi 1332281222  93 IVKAGADGYLLKDTEPDELVE 113
Cdd:cd19922    88 EVQRFAVSYVVKPVLISNLVD 108
PRK10529 PRK10529
DNA-binding transcriptional activator KdpE; Provisional
 1-127 4.31e-04

DNA-binding transcriptional activator KdpE; Provisional


Pssm-ID: 182522 [Multi-domain]  Cd Length: 225  Bit Score: 39.79  E-value: 4.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   1 MCRVMLVDDHPLMRRGINQLLsfEEQFEVVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRaDGCEASIVI 80
Cdd:PRK10529    1 MTNVLIVEDEQAIRRFLRTAL--EGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLR-QWSAIPVIV 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1332281222  81 LTVSDSPADIEAIVKAGADGYLlkdTEPDELVELLEKAHLGDKAYSS 127
Cdd:PRK10529   78 LSARSEESDKIAALDAGADDYL---SKPFGIGELQARLRVALRRHSA 121
REC_TPR cd17589
phosphoacceptor receiver (REC) domain of uncharacterized tetratricopeptide repeat (TPR) ...
 4-115 7.24e-04

phosphoacceptor receiver (REC) domain of uncharacterized tetratricopeptide repeat (TPR)-containing response regulators; Response regulators share the common phosphoacceptor REC domain and different output domains. This subfamily contains uncharacterized response regulators with TPR repeats as the effector or output domain, which might contain between 3 to 16 TPR repeats (each about 34 amino acids). TPR-containing proteins occur in all domains of life and the abundance of TPR-containing proteins in a bacterial proteome is not indicative of virulence. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Some members in this subfamily may contain inactive REC domains lacking canonical metal-binding and active site residues.


Pssm-ID: 381123 [Multi-domain]  Cd Length: 115  Bit Score: 38.01  E-value: 7.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfEEQFEVVAEASNGTEAVAKAHENELDLILLDLNM-KGMSG---LDTLKALRADGCEASIV 79
Cdd:cd17589     1 FLIVDDQPTFRSMLKSMLR-SLGVTRIDTASSGEEALRMCENKTYDIVLCDYNLgKGKNGqqlLEELRHKKLISPSTVFI 79

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1332281222  80 ILTVSDSPADIEAIVKAGADGYLLKDTEPDELVELL 115
Cdd:cd17589    80 MVTGESSRAMVLSALELEPDDYLLKPFTVSELRERL 115
HTH_23 pfam13384
Homeodomain-like domain;
146-177 1.35e-03

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 35.71  E-value: 1.35e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1332281222 146 LTERER-QILQEVARGFRNKQIADRLFISESTV 177
Cdd:pfam13384   2 ARERRRaRALLLLAEGLSVKEIAELLGVSRRTV 34
PRK09836 PRK09836
DNA-binding transcriptional activator CusR; Provisional
 29-117 2.35e-03

DNA-binding transcriptional activator CusR; Provisional


Pssm-ID: 182102 [Multi-domain]  Cd Length: 227  Bit Score: 37.60  E-value: 2.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222  29 VVAEASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGCEASIVILTVSDSpadIEAIVKA---GADGYLLKd 105
Cdd:PRK09836   26 VVDLADNGLNGYHLAMTGDYDLIILDIMLPDVNGWDIVRMLRSANKGMPILLLTALGT---IEHRVKGlelGADDYLVK- 101

                          90
                  ....*....|..
gi 1332281222 106 tePDELVELLEK 117
Cdd:PRK09836  102 --PFAFAELLAR 111
PRK09191 PRK09191
two-component response regulator; Provisional
 3-72 3.41e-03

two-component response regulator; Provisional


Pssm-ID: 236402 [Multi-domain]  Cd Length: 261  Bit Score: 37.52  E-value: 3.41e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1332281222   3 RVMLVDDHPLMRRGINQLLSfEEQFEVVAEASNGTEAVAKAHENELDLILLDLNM-KGMSGLDTLKALRAD 72
Cdd:PRK09191  139 RVLIIEDEPIIAMDLEQLVE-SLGHRVTGIARTRAEAVALAKKTRPGLILADIQLaDGSSGIDAVNDILKT 208
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 136-189 4.40e-03

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: 34.39  E-value: 4.40e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1332281222 136 REENTDVFDELTERERQILqeVAR---GFRNKQIADRLFISESTVKVHMKSLLKKLK 189
Cdd:cd06171     1 RERLEEALDKLPEREREVI--LLRfgeGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK15201 PRK15201
fimbriae biosynthesis transcriptional regulator FimW;
150-190 4.77e-03

fimbriae biosynthesis transcriptional regulator FimW;


Pssm-ID: 185123  Cd Length: 198  Bit Score: 36.56  E-value: 4.77e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1332281222 150 ERQILQEVARGFRNKQIADRLFISESTVKVHMKSLLKKLKV 190
Cdd:PRK15201  138 ERHLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLHV 178
REC_PatA-like cd17602
phosphoacceptor receiver (REC) domain of PatA and similar domains; Nostoc sp. (or Anabaena sp.) ...
 4-104 5.60e-03

phosphoacceptor receiver (REC) domain of PatA and similar domains; Nostoc sp. (or Anabaena sp.) PatA is necessary for proper patterning of heterocysts along filaments. PatA contains phosphoacceptor REC domain at its C-terminus and an N-terminal PATAN (PatA N-terminus) domain, which was proposed in a bioinformatics study to mediate protein-protein interactions. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Some members of this group may have an inactive REC domain, lacking canonical metal-binding and active site residues.


Pssm-ID: 381129 [Multi-domain]  Cd Length: 102  Bit Score: 35.04  E-value: 5.60e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfEEQFEVVAeASNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGC--EASIVIL 81
Cdd:cd17602     1 VACVDDRPSIQKMIEYFLE-KQGFRVVV-IDDPLRALTTLLNSKPDLILIDIDMPDLDGYELCSLLRKSSAlkDTPIIML 78

                          90       100
                  ....*....|....*....|...
gi 1332281222  82 TVSDSPADIEAIVKAGADGYLLK 104
Cdd:cd17602    79 TGKDGLVDRIRAKMAGASGYLTK 101
HTH_24 pfam13412
Winged helix-turn-helix DNA-binding;
148-187 7.53e-03

Winged helix-turn-helix DNA-binding;


Pssm-ID: 404317 [Multi-domain]  Cd Length: 45  Bit Score: 33.18  E-value: 7.53e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1332281222 148 ERERQILQEVARGFR--NKQIADRLFISESTVKVHMKSLLKK 187
Cdd:pfam13412   1 ETDRKILNLLQENPRisQRELAERLGLSPSTVNRRLKRLEEE 42
COG4189 COG4189
Predicted transcriptional regulator, ArsR family [Transcription];
136-186 8.82e-03

Predicted transcriptional regulator, ArsR family [Transcription];


Pssm-ID: 443343 [Multi-domain]  Cd Length: 97  Bit Score: 34.55  E-value: 8.82e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1332281222 136 REENTDVFDELTERER-QILQEVARGFRN-KQIADRLFISESTVKVHMKSLLK 186
Cdd:COG4189     6 DEESLEVLKALASETRlRILRLLAEEPLNvNELAEALGLPKSTVSYHIRKLEE 58
REC_OmpR_ChvI-like cd19936
phosphoacceptor receiver (REC) domain of ChvI-like OmpR family response regulators; ...
 4-104 9.00e-03

phosphoacceptor receiver (REC) domain of ChvI-like OmpR family response regulators; Sinorhizobium meliloti ChvI is part of the ExoS/ChvI two-component regulatory system (TCS) that is required for nitrogen-fixing symbiosis and exopolysaccharide synthesis. ExoS/ChvI also play important roles in regulating biofilm formation, motility, nutrient utilization, and the viability of free-living bacteria. ChvI belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381163 [Multi-domain]  Cd Length: 99  Bit Score: 34.34  E-value: 9.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1332281222   4 VMLVDDHPLMRRGINQLLSfEEQFEVVAEAsNGTEAVAKAHENELDLILLDLNMKGMSGLDTLKALRADGcEASIVILTV 83
Cdd:cd19936     1 IALVDDDRNILTSVSMALE-AEGFSVETYT-DGASALDGLNARPPDLAILDIKMPRMDGMELLQRLRQKS-TLPVIFLTS 77

                          90       100
                  ....*....|....*....|.
gi 1332281222  84 SDSPADIEAIVKAGADGYLLK 104
Cdd:cd19936    78 KDDEIDEVFGLRMGADDYITK 98
 
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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