NCBI Conserved Domain Search

Conserved domains on [gi|582378446|gb|EVW73226|]

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DNA-binding response regulator AraC [Staphylococcus aureus S72396]

Protein Classification

response regulator transcription factor( domain architecture ID 11469127)

two-component system response regulator transcription factor that consists of a receiver domain and a helix-turn-helix DNA-binding domain

Graphical summary

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List of domain hits

Name

Accession

Description

Interval

E-value

REC_YesN-like

cd17536

phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response ...

4-121

5.10e-54

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: 170.21 E-value: 5.10e-54

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPWGDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVIILS 81
Cdd:cd17536    1 VLIVDDEPLIREGLKKLIDWEELGFEVVGEAENGEEALELIEEHKPDIVITDIRMPGMDGLELIEKIreLYPDIKIIILS 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 582378446  82 SYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLVRTL 121
Cdd:cd17536   81 GYDDFEYAQKAIRLGVVDYLLKPVDEEELEEALEKAKEEL 120

HTH_ARAC

smart00342

helix_turn_helix, arabinose operon control protein;

166-247

1.15e-18

helix_turn_helix, arabinose operon control protein;

Pssm-ID: 197666 [Multi-domain] Cd Length: 84 Bit Score: 77.98 E-value: 1.15e-18

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   166 KVTVSDLIQHIDVSESYAMRTFKDHVGITIVDYLNRYRILQSLQLL-DRHYKHYEIADKVGFSEYKMFSYHFKKYLQMSP 244
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLrDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ...
gi 582378446   245 SDY 247
Cdd:smart00342  81 SEY 83

Name

Accession

Description

Interval

E-value

REC_YesN-like

cd17536

phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response ...

4-121

5.10e-54

Pssm-ID: 381091 [Multi-domain] Cd Length: 121 Bit Score: 170.21 E-value: 5.10e-54

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPWGDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVIILS 81
Cdd:cd17536    1 VLIVDDEPLIREGLKKLIDWEELGFEVVGEAENGEEALELIEEHKPDIVITDIRMPGMDGLELIEKIreLYPDIKIIILS 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 582378446  82 SYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLVRTL 121
Cdd:cd17536   81 GYDDFEYAQKAIRLGVVDYLLKPVDEEELEEALEKAKEEL 120

YesN

COG4753

Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding ...

3-104

1.37e-37

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: 127.58 E-value: 1.37e-37

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDyHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALL--DCNVIIL 80
Cdd:COG4753    1 KVLIVDDEPLIREGLKRILEWEA-GFEVVGEAENGEEALELLEEHKPDLVITDINMPGMDGLELLEAIRELdpDTKIIIL 79

                         90       100
                 ....*....|....*....|....
gi 582378446  81 SSYDDFEYMKAGIQHHVLDYLLKP 104
Cdd:COG4753   80 SGYSDFEYAQEAIKLGADDYLLKP 103

Response_reg

pfam00072

Response regulator receiver domain; This domain receives the signal from the sensor partner in ...

4-114

1.19e-22

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: 89.13 E-value: 1.19e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446    4 VVICDDERIIREGLKQIIpwGDYHFNtIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLD--CNVIILS 81
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLL--EKEGYV-VAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDptTPVIILT 77

                          90       100       110
                  ....*....|....*....|....*....|...
gi 582378446   82 SYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVIL 114
Cdd:pfam00072  78 AHGDEDDAVEALEAGADDFLSKPFDPDELLAAI 110

HTH_ARAC

smart00342

helix_turn_helix, arabinose operon control protein;

166-247

1.15e-18

helix_turn_helix, arabinose operon control protein;

Pssm-ID: 197666 [Multi-domain] Cd Length: 84 Bit Score: 77.98 E-value: 1.15e-18

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   166 KVTVSDLIQHIDVSESYAMRTFKDHVGITIVDYLNRYRILQSLQLL-DRHYKHYEIADKVGFSEYKMFSYHFKKYLQMSP 244
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLrDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ...
gi 582378446   245 SDY 247
Cdd:smart00342  81 SEY 83

PRK11697

two-component system response regulator BtsR;

1-124

3.09e-17

two-component system response regulator BtsR;

Pssm-ID: 236956 [Multi-domain] Cd Length: 238 Bit Score: 77.96 E-value: 3.09e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   1 MFKVVICDDERIIREGLKQIIPwGDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLndiALLDC----N 76
Cdd:PRK11697   1 MIKVLIVDDEPLAREELRELLQ-EEGDIEIVGECSNAIEAIGAIHRLKPDVVFLDIQMPRISGLELV---GMLDPehmpY 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 582378446  77 VIILSSYDDFEyMKAgIQHHVLDYLLKPVDHAQLEVILGRLVRTLLEQ 124
Cdd:PRK11697  77 IVFVTAFDEYA-IKA-FEEHAFDYLLKPIDPARLAKTLARLRQERSPQ 122

AdaA

COG2169

Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...

152-252

1.16e-14

Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), contains Zn-binding and two AraC-type DNA-binding domains [Replication, recombination and repair];

Pssm-ID: 441772 [Multi-domain] Cd Length: 358 Bit Score: 72.39 E-value: 1.16e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446 152 VNQIVDQIKQSYQTKVTVSDLIQHIDVSESYAMRTFKDHVGITIVDYLNRYRILQSLQLLDRHYKHYEIADKVGFSEYKM 231
Cdd:COG2169   86 VARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQTGLSVTDAAYAAGFGSLSR 165

                         90       100
                 ....*....|....*....|.
gi 582378446 232 FSYHFKKYLQMSPSDYCKQAK 252
Cdd:COG2169  166 FYEAFKKLLGMTPSAYRRGGA 186

HTH_18

pfam12833

Helix-turn-helix domain;

172-247

3.48e-14

Helix-turn-helix domain;

Pssm-ID: 432818 [Multi-domain] Cd Length: 81 Bit Score: 65.69 E-value: 3.48e-14

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 582378446  172 LIQHIDVSESYAMRTFKDHVGITIVDYLNRYRILQSLQLLDRHYKH--YEIADKVGFSEYKMFSYHFKKYLQMSPSDY 247
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDTGLsvAEIALALGFSDASHFSRAFRRLFGLTPSEY 78

REC

smart00448

cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar ...

3-59

5.64e-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: 53.73 E-value: 5.64e-10

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 582378446     3 KVVICDDERIIREGLKQIIpwgDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMP 59
Cdd:smart00448   2 RILVVDDDPLLRELLKALL---EKEGYEVDEATDGEEALELLKEEKPDLILLDIMMP 55

PRK10371

transcriptional regulator MelR;

150-249

4.96e-09

transcriptional regulator MelR;

Pssm-ID: 182416 [Multi-domain] Cd Length: 302 Bit Score: 55.60 E-value: 4.96e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446 150 YYVNQIVDQIKQSYQTKVTVSDLIQHIDVSESYAMRTFKDHVGITIVDYLNRYRILQSLQLL-DRHYKHYEIADKVGFSE 228
Cdd:PRK10371 191 FYVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLsDTDKSILDIALTAGFRS 270

                         90       100
                 ....*....|....*....|.
gi 582378446 229 YKMFSYHFKKYLQMSPSDYCK 249
Cdd:PRK10371 271 SSRFYSTFGKYVGMSPQQYRK 291

Name

Accession

Description

Interval

E-value

REC_YesN-like

cd17536

phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response ...

4-121

5.10e-54

Pssm-ID: 381091 [Multi-domain] Cd Length: 121 Bit Score: 170.21 E-value: 5.10e-54

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPWGDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVIILS 81
Cdd:cd17536    1 VLIVDDEPLIREGLKKLIDWEELGFEVVGEAENGEEALELIEEHKPDIVITDIRMPGMDGLELIEKIreLYPDIKIIILS 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 582378446  82 SYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLVRTL 121
Cdd:cd17536   81 GYDDFEYAQKAIRLGVVDYLLKPVDEEELEEALEKAKEEL 120

YesN

COG4753

Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding ...

3-104

1.37e-37

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: 127.58 E-value: 1.37e-37

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDyHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALL--DCNVIIL 80
Cdd:COG4753    1 KVLIVDDEPLIREGLKRILEWEA-GFEVVGEAENGEEALELLEEHKPDLVITDINMPGMDGLELLEAIRELdpDTKIIIL 79

                         90       100
                 ....*....|....*....|....
gi 582378446  81 SSYDDFEYMKAGIQHHVLDYLLKP 104
Cdd:COG4753   80 SGYSDFEYAQEAIKLGADDYLLKP 103

AtoC

COG2204

DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...

1-174

6.59e-28

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: 110.05 E-value: 6.59e-28

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   1 MFKVVICDDERIIREGLKQIIPWGDYHfntIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLDCN--VI 78
Cdd:COG2204    2 MARILVVDDDPDIRRLLKELLERAGYE---VETAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALDPDlpVI 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  79 ILSSYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLV-RTLLEQQSQNGRSLASCHDAFQpllkveyddyyvnQIVD 157
Cdd:COG2204   79 LLTGYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERALeRRRLRRENAEDSGLIGRSPAMQ-------------EVRR 145

                        170
                 ....*....|....*..
gi 582378446 158 QIKQSYQTKVTVsdLIQ 174
Cdd:COG2204  146 LIEKVAPSDATV--LIT 160

LytT

COG3279

DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction ...

1-131

3.93e-27

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

Pssm-ID: 442510 [Multi-domain] Cd Length: 235 Bit Score: 104.51 E-value: 3.93e-27

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   1 MFKVVICDDERIIREGLKQIIpwGDY-HFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLDCN--V 77
Cdd:COG3279    1 MMKILIVDDEPLARERLERLL--EKYpDLEVVGEASNGEEALELLEEHKPDLVFLDIQMPGLDGFELARQLRELDPPppI 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 582378446  78 IILSSYDdfEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLVRTLLEQQSQNGRS 131
Cdd:COG3279   79 IFTTAYD--EYALEAFEVNAVDYLLKPIDEERLAKALEKAKERLEAKAAAEASP 130

CitB

COG4565

DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ...

1-119

5.41e-25

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

Pssm-ID: 443622 [Multi-domain] Cd Length: 138 Bit Score: 96.19 E-value: 5.41e-25

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   1 MFKVVICDDERIIREGLKQIIpWGDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVI 78
Cdd:COG4565    3 MIRVLIVEDDPMVAELLRRYL-ERLPGFEVVGVASSGEEALALLAEHRPDLILLDIYLPDGDGLELLRELraRGPDVDVI 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 582378446  79 ILSSYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLVR 119
Cdd:COG4565   82 VITAARDPETVREALRAGVVDYLIKPFTFERLREALERYLE 122

RpfG

COG3437

Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ...

3-137

6.33e-25

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: 98.31 E-value: 6.33e-25

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYHfntIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI----ALLDCNVI 78
Cdd:COG3437    8 TVLIVDDDPENLELLRQLLRTLGYD---VVTAESGEEALELLLEAPPDLILLDVRMPGMDGFELLRLLradpSTRDIPVI 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 582378446  79 ILSSYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLVRT-----LLEQQSQNGRSLASCHD 137
Cdd:COG3437   85 FLTALADPEDRERALEAGADDYLTKPFDPEELLARVRNALELrrlqrELDDLVLYLKLAAPLHD 148

REC_NarL-like

cd17535

phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...

4-110

1.17e-23

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: 91.80 E-value: 1.17e-23

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIpWGDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVIILS 81
Cdd:cd17535    1 VLIVDDHPLVREGLRRLL-ESEPDIEVVGEAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLrrRYPDLKVIVLT 79

                         90       100
                 ....*....|....*....|....*....
gi 582378446  82 SYDDFEYMKAGIQHHVLDYLLKPVDHAQL 110
Cdd:cd17535   80 AHDDPEYVLRALKAGAAGYLLKDSSPEEL 108

CheY

COG0784

CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator ...

3-119

2.72e-23

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: 91.45 E-value: 2.72e-23

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQII-PWGdyhfNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLL----NDIALLDCNV 77
Cdd:COG0784    7 RILVVDDNPDNRELLRRLLeRLG----YEVTTAEDGAEALELLRAGPPDLILLDINMPGMDGLELLrrirALPRLPDIPI 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 582378446  78 IILSSYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLVR 119
Cdd:COG0784   83 IALTAYADEEDRERALEAGADDYLTKPVDPEELLEALRRLLA 124

Response_reg

pfam00072

Response regulator receiver domain; This domain receives the signal from the sensor partner in ...

4-114

1.19e-22

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: 89.13 E-value: 1.19e-22

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446    4 VVICDDERIIREGLKQIIpwGDYHFNtIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLD--CNVIILS 81
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLL--EKEGYV-VAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDptTPVIILT 77

                          90       100       110
                  ....*....|....*....|....*....|...
gi 582378446   82 SYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVIL 114
Cdd:pfam00072  78 AHGDEDDAVEALEAGADDFLSKPFDPDELLAAI 110

REC

cd00156

phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...

6-104

3.19e-22

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: 87.67 E-value: 3.19e-22

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   6 ICDDERIIREGLKQIIpwgDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLDCN--VIILSSY 83
Cdd:cd00156    2 IVDDDPAIRELLKSLL---EREGYEVDTAADGEEALELLREERPDLVLLDLMMPGMDGLELLRKLRELPPDipVIVLTAK 78

                         90       100
                 ....*....|....*....|.
gi 582378446  84 DDFEYMKAGIQHHVLDYLLKP 104
Cdd:cd00156   79 ADEEDAVRALELGADDYLVKP 99

PleD

COG3706

Two-component response regulator, PleD family, consists of two REC domains and a diguanylate ...

1-119

4.63e-20

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: 84.19 E-value: 4.63e-20

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   1 MFKVVICDDERIIREGLKQIIPWGDYHfntIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLL----NDIALLDCN 76
Cdd:COG3706    1 PARILVVDDDPTNRKLLRRLLEAAGYE---VVEAADGEEALELLQEHRPDLILLDLEMPDMDGLELCrrlrADPRTADIP 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 582378446  77 VIILSSYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLVR 119
Cdd:COG3706   78 IIFLTALDDEEDRARALEAGADDYLTKPFDPEELLARVDLVAR 120

AmiR

COG3707

Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding ...

3-126

7.16e-19

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: 81.54 E-value: 7.16e-19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYHfnTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI-ALLDCNVIILS 81
Cdd:COG3707    5 RVLVVDDEPLRRADLREGLREAGYE--VVAEAADGEDAVELVRELKPDLVIVDIDMPDRDGLEAARQIsEERPAPVILLT 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 582378446  82 SYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLVRTLLEQQS 126
Cdd:COG3707   83 AYSDPELIERALEAGVSAYLVKPLDPEDLLPALELALARFRELRA 127

OmpR

COG0745

DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...

1-119

7.46e-19

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: 81.54 E-value: 7.46e-19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   1 MFKVVICDDERIIREGLKQIIpwGDYHFNTIyTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLDCN--VI 78
Cdd:COG0745    1 MPRILVVEDDPDIRELLADAL--EREGYEVD-TAADGEEALELLEEERPDLILLDLMLPGMDGLEVCRRLRARPSDipII 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 582378446  79 ILSSYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLVR 119
Cdd:COG0745   78 MLTARDDEEDRVRGLEAGADDYLTKPFDPEELLARIRALLR 118

HTH_ARAC

smart00342

helix_turn_helix, arabinose operon control protein;

166-247

1.15e-18

helix_turn_helix, arabinose operon control protein;

Pssm-ID: 197666 [Multi-domain] Cd Length: 84 Bit Score: 77.98 E-value: 1.15e-18

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   166 KVTVSDLIQHIDVSESYAMRTFKDHVGITIVDYLNRYRILQSLQLL-DRHYKHYEIADKVGFSEYKMFSYHFKKYLQMSP 244
Cdd:smart00342   1 PLTLEDLAEALGVSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLrDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP 80


                   ...
gi 582378446   245 SDY 247
Cdd:smart00342  81 SEY 83

REC_citrate_TCS

cd19925

phosphoacceptor receiver (REC) domain of citrate family two-component system response ...

3-116

1.74e-17

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: 75.74 E-value: 1.74e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYhFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVIIL 80
Cdd:cd19925    2 NVLIVEDDPMVAEIHRAYVEQVPG-FTVIGTAGTGEEALKLLKERQPDLILLDIYLPDGNGLDLLRELraAGHDVDVIVV 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 582378446  81 SSYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGR 116
Cdd:cd19925   81 TAANDVETVREALRLGVVDYLIKPFTFERLRQRLER 116

REC_CheY

cd17542

phosphoacceptor receiver (REC) domain of chemotaxis protein CheY; The chemotaxis response ...

2-113

2.00e-17

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: 75.39 E-value: 2.00e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   2 FKVVICDDERIIREGLKQIIPWGDYHfnTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLDCN--VII 79
Cdd:cd17542    1 KKVLIVDDAAFMRMMLKDILTKAGYE--VVGEAANGEEAVEKYKELKPDLVTMDITMPEMDGIEALKEIKKIDPNakVIM 78

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 582378446  80 LSSYDDFEYMKAGIQHHVLDYLLKPVDHAQ-LEVI 113
Cdd:cd17542   79 CSAMGQEEMVKEAIKAGAKDFIVKPFQPERvLEAV 113

PRK11697

two-component system response regulator BtsR;

1-124

3.09e-17

two-component system response regulator BtsR;

Pssm-ID: 236956 [Multi-domain] Cd Length: 238 Bit Score: 77.96 E-value: 3.09e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   1 MFKVVICDDERIIREGLKQIIPwGDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLndiALLDC----N 76
Cdd:PRK11697   1 MIKVLIVDDEPLAREELRELLQ-EEGDIEIVGECSNAIEAIGAIHRLKPDVVFLDIQMPRISGLELV---GMLDPehmpY 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 582378446  77 VIILSSYDDFEyMKAgIQHHVLDYLLKPVDHAQLEVILGRLVRTLLEQ 124
Cdd:PRK11697  77 IVFVTAFDEYA-IKA-FEEHAFDYLLKPIDPARLAKTLARLRQERSPQ 122

REC_CheB-like

cd17541

phosphoacceptor receiver (REC) domain of chemotaxis response regulator protein-glutamate ...

3-121

4.88e-17

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: 74.74 E-value: 4.88e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPwGDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI-ALLDCNVIILS 81
Cdd:cd17541    2 RVLIVDDSAVMRKLLSRILE-SDPDIEVVGTARDGEEALEKIKELKPDVITLDIEMPVMDGLEALRRImAERPTPVVMVS 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 582378446  82 SYDD------FEYMKAGiqhhVLDYLLKPV--DHAQLEVILGRLVRTL 121
Cdd:cd17541   81 SLTEegaeitLEALELG----AVDFIAKPSggISLDLEEIAEELIEKI 124

REC_HupR-like

cd17569

phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR) and similar ...

2-114

2.49e-16

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: 72.82 E-value: 2.49e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   2 FKVVICDDERIIREGLKQIIPWGDYHfntIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALL--DCNVII 79
Cdd:cd17569    1 PTILLVDDEPNILKALKRLLRREGYE---VLTATSGEEALEILKQEPVDVVISDQRMPGMDGAELLKRVRERypDTVRIL 77

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 582378446  80 LSSYDDFEYMKAGI-QHHVLDYLLKPVDHAQLEVIL 114
Cdd:cd17569   78 LTGYADLDAAIEAInEGEIYRFLTKPWDDEELKETI 113

REC_LytTR_AlgR-like

cd17532

phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR; ...

4-121

2.51e-16

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: 72.57 E-value: 2.51e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPwgdyHFNTIY---TAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLDCN--VI 78
Cdd:cd17532    1 ALIVDDEPLAREELRYLLE----EHPDIEivgEAENGEEALEAIEELKPDVVFLDIQMPGLDGLELAKKLSKLAKPplIV 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 582378446  79 ILSSYDDFEyMKAgIQHHVLDYLLKPVDHAQLEVILGRLVRTL 121
Cdd:cd17532   77 FVTAYDEYA-VEA-FELNAVDYLLKPFSEERLAEALAKLRKRL 117

REC_PdtaR-like

cd19932

phosphoacceptor receiver (REC) domain of PdtaR and similar proteins; This subfamily includes ...

3-110

5.23e-16

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: 71.68 E-value: 5.23e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYhfNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLDCN-VIILS 81
Cdd:cd19932    2 RVLIAEDEALIRMDLREMLEEAGY--EVVGEASDGEEAVELAKKHKPDLVIMDVKMPRLDGIEAAKIITSENIApIVLLT 79

                         90       100
                 ....*....|....*....|....*....
gi 582378446  82 SYDDFEYMKAGIQHHVLDYLLKPVDHAQL 110
Cdd:cd19932   80 AYSQQDLVERAKEAGAMAYLVKPFSESDL 108

AraC

COG2207

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];

69-247

1.02e-15

AraC-type DNA-binding domain and AraC-containing proteins [Transcription];

Pssm-ID: 441809 [Multi-domain] Cd Length: 258 Bit Score: 74.43 E-value: 1.02e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  69 DIALLDCNVIILSSYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLVRTLLEQQSQNGRSLASCHDAFQPLLKVEYD 148
Cdd:COG2207   71 LLLLLLLLGLLLLALLALLLLVGLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLALLRALELLLLLLLLLLLLLLL 150

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446 149 DYYVNQIVDQIKQSYQTKVTVSDLIQHIDVSESYAMRTFKDHVGITIVDYLNRYRILQSLQLL-DRHYKHYEIADKVGFS 227
Cdd:COG2207  151 LLLLLLLLLLLLLLLLLLLTLEELARELGLSPRTLSRLFKEETGTSPKQYLRELRLERAKRLLaETDLSISEIAYELGFS 230

                        170       180
                 ....*....|....*....|
gi 582378446 228 EYKMFSYHFKKYLQMSPSDY 247
Cdd:COG2207  231 SQSHFSRAFKKRFGVTPSEY 250

REC_RpfG-like

cd17551

phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator ...

3-110

1.93e-15

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: 70.16 E-value: 1.93e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYHfnTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLL----NDIALLDCNVI 78
Cdd:cd17551    2 RILIVDDNPTNLLLLEALLRSAGYL--EVVSFTDPREALAWCRENPPDLILLDYMMPGMDGLEFIrrlrALPGLEDVPIV 79

                         90       100       110
                 ....*....|....*....|....*....|..
gi 582378446  79 ILSSYDDFEYMKAGIQHHVLDYLLKPVDHAQL 110
Cdd:cd17551   80 MITADTDREVRLRALEAGATDFLTKPFDPVEL 111

PRK11361

acetoacetate metabolism transcriptional regulator AtoC;

3-132

3.10e-15

acetoacetate metabolism transcriptional regulator AtoC;

Pssm-ID: 183099 [Multi-domain] Cd Length: 457 Bit Score: 74.50 E-value: 3.10e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYhfnTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLD--CNVIIL 80
Cdd:PRK11361   6 RILIVDDEDNVRRMLSTAFALQGF---ETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIKALKEMRSHEtrTPVILM 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 582378446  81 SSYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLVRtlLEQQSQNGRSL 132
Cdd:PRK11361  83 TAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQ--LQSMKKEIRHL 132

CitB

COG2197

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...

1-70

3.45e-15

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: 69.92 E-value: 3.45e-15

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   1 MFKVVICDDERIIREGLKQIIPwGDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI 70
Cdd:COG2197    1 MIRVLIVDDHPLVREGLRALLE-AEPDIEVVGEAADGEEALELLEELRPDVVLLDIRMPGMDGLEALRRL 69

REC_DesR-like

cd19930

phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of ...

4-110

5.12e-15

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: 69.22 E-value: 5.12e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPWGDyHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVIILS 81
Cdd:cd19930    1 VLIAEDQEMVRGALAALLELED-DLEVVAQASNGQEALRLVLKHSPDVAILDIEMPGRTGLEVAAELreELPDTKVLIVT 79

                         90       100
                 ....*....|....*....|....*....
gi 582378446  82 SYDDFEYMKAGIQHHVLDYLLKPVDHAQL 110
Cdd:cd19930   80 TFGRPGYFRRALAAGVDGYVLKDRPIEEL 108

AdaA

COG2169

Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), ...

152-252

1.16e-14

Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), contains Zn-binding and two AraC-type DNA-binding domains [Replication, recombination and repair];

Pssm-ID: 441772 [Multi-domain] Cd Length: 358 Bit Score: 72.39 E-value: 1.16e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446 152 VNQIVDQIKQSYQTKVTVSDLIQHIDVSESYAMRTFKDHVGITIVDYLNRYRILQSLQLLDRHYKHYEIADKVGFSEYKM 231
Cdd:COG2169   86 VARACRLIEAGAEDRPSLEDLAARLGLSPRHLRRLFKAHTGVTPKAYARARRLLRARQLLQTGLSVTDAAYAAGFGSLSR 165

                         90       100
                 ....*....|....*....|.
gi 582378446 232 FSYHFKKYLQMSPSDYCKQAK 252
Cdd:COG2169  166 FYEAFKKLLGMTPSAYRRGGA 186

HTH_18

pfam12833

Helix-turn-helix domain;

172-247

3.48e-14

Helix-turn-helix domain;

Pssm-ID: 432818 [Multi-domain] Cd Length: 81 Bit Score: 65.69 E-value: 3.48e-14

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 582378446  172 LIQHIDVSESYAMRTFKDHVGITIVDYLNRYRILQSLQLLDRHYKH--YEIADKVGFSEYKMFSYHFKKYLQMSPSDY 247
Cdd:pfam12833   1 LAAALGMSPRTLSRLFKRELGLSPKEYLRRLRLERARRLLLEDTGLsvAEIALALGFSDASHFSRAFRRLFGLTPSEY 78

REC_OmpR

cd17574

phosphoacceptor receiver (REC) domain of OmpR family response regulators; OmpR-like proteins ...

6-104

3.85e-14

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: 66.28 E-value: 3.85e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   6 ICDDERIIREGLKqiipwgDY----HFNTIyTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVII 79
Cdd:cd17574    2 VVEDDEEIAELLS------DYlekeGYEVD-TAADGEEALELAREEQPDLIILDVMLPGMDGFEVCRRLreKGSDIPIIM 74

                         90       100
                 ....*....|....*....|....*
gi 582378446  80 LSSYDDFEYMKAGIQHHVLDYLLKP 104
Cdd:cd17574   75 LTAKDEEEDKVLGLELGADDYITKP 99

REC_DctD-like

cd17549

phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and ...

4-126

1.71e-13

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: 65.20 E-value: 1.71e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPWGDYhfnTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLDCN--VIILS 81
Cdd:cd17549    1 VLLVDDDADVREALQQTLELAGF---RVRAFADAEEALAALSPDFPGVVISDIRMPGMDGLELLAQIRELDPDlpVILIT 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 582378446  82 SYDDF----EYMKAGiqhhVLDYLLKPVDHAQLEVILGRLV---RTLLEQQS 126
Cdd:cd17549   78 GHGDVpmavEAMRAG----AYDFLEKPFDPERLLDVVRRALekrRLVLENRR 125

REC_Rcp-like

cd17557

phosphoacceptor receiver (REC) domain of cyanobacterial phytochrome response regulator Rcp and ...

8-123

2.64e-13

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: 64.74 E-value: 2.64e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   8 DDERIIREGLKQI-IPwgdyhfNTIYTAKDGVEALSLIQQH-------QPELVITDIRMPRKNGVDLL----NDIALLDC 75
Cdd:cd17557   10 GDAELIQEAFKEAgVP------NELHVVRDGEEALDFLRGEgeyadapRPDLILLDLNMPRMDGFEVLreikADPDLRRI 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 582378446  76 NVIILSSYDDFEYMKAGIQHHVLDYLLKPVDHAQLEvilgRLVRTLLE 123
Cdd:cd17557   84 PVVVLTTSDAEEDIERAYELGANSYIVKPVDFEEFV----EAIRSLGE 127

REC_DC-like

cd17534

phosphoacceptor receiver (REC) domain of modulated diguanylate cyclase and similar domains; ...

3-114

1.18e-12

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: 62.81 E-value: 1.18e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYhfNTIYTAKDGVEALSLIQQHQPELVITDIRMP-RKNGVDLLNDI-ALLDCNVIIL 80
Cdd:cd17534    2 KILIVEDEAIIALDLKEILESLGY--EVVGIADSGEEAIELAEENKPDLILMDINLKgDMDGIEAAREIrEKFDIPVIFL 79

                         90       100       110
                 ....*....|....*....|....*....|....
gi 582378446  81 SSYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVIL 114
Cdd:cd17534   80 TAYSDEETLERAKETNPYGYLVKPFNERELKAAI 113

REC_TrrA-like

cd17554

phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator TrrA and ...

3-89

1.56e-12

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: 62.24 E-value: 1.56e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYHfntIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLDCN--VIIL 80
Cdd:cd17554    2 KILVVDDEENIRELYKEELEDEGYE---VVTAGNGEEALEKLESEDPDLVILDIKMPGMDGLETLRKIREKKPDlpVIIC 78


                 ....*....
gi 582378446  81 SSYDDFEYM 89
Cdd:cd17554   79 TAYSEYKSD 87

REC_OmpR_PrrA-like

cd17627

phosphoacceptor receiver (REC) domain of PrrA-like OmpR family response regulators; The ...

4-122

2.26e-12

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: 62.02 E-value: 2.26e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPWGDYhfnTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVIILS 81
Cdd:cd17627    1 ILVVDDDRAVRESLRRSLRFEGY---EVETAVDGAEALRVISGNRPDAVVLDVMMPRLDGLEVCRRLraAGNDLPILVLT 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 582378446  82 SYDDFEYMKAGIQHHVLDYLLKPVdhaQLEVILGRlVRTLL 122
Cdd:cd17627   78 ARDSVSDRVAGLDAGADDYLVKPF---ALEELLAR-VRALL 114

REC_CheY_CheY3

cd19923

phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY ...

3-111

3.99e-12

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: 61.59 E-value: 3.99e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDD----ERIIREGLKQIipwgdyHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI----ALLD 74
Cdd:cd19923    2 KVLVVDDfstmRRIIKNLLKEL------GFNNVEEAEDGVDALEKLKAGGFDFVITDWNMPNMDGLELLKTIradgALSH 75

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 582378446  75 CNVIILSSYDDFEYMKAGIQHHVLDYLLKPVDHAQLE 111
Cdd:cd19923   76 LPVLMVTAEAKKENVIAAAQAGVNNYIVKPFTAATLK 112

PRK10651

transcriptional regulator NarL; Provisional

4-191

4.81e-12

transcriptional regulator NarL; Provisional

Pssm-ID: 182619 [Multi-domain] Cd Length: 216 Bit Score: 63.51 E-value: 4.81e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPWGDyHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVIILS 81
Cdd:PRK10651   9 ILLIDDHPMLRTGVKQLISMAP-DITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLreKSLSGRIVVFS 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  82 SYDDFEYMKAGIQHHVLDYLLKPVDHAQL-----EVILGR----------LVRTLLEQQSQNGRSLASchdafqpLLKVE 146
Cdd:PRK10651  88 VSNHEEDVVTALKRGADGYLLKDMEPEDLlkalqQAAAGEmvlsealtpvLAASLRANRATTERDVNQ-------LTPRE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 582378446 147 YDdyyvnqIVDQIKQSYQTKVTVSDLiqhiDVSESyamrTFKDHV 191
Cdd:PRK10651 161 RD------ILKLIAQGLPNKMIARRL----DITES----TVKVHV 191

REC_hyHK_CKI1_RcsC-like

cd17546

phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinases/response regulators ...

4-114

1.72e-11

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: 59.41 E-value: 1.72e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQII-PWGdyhfNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI-----ALLDCNV 77
Cdd:cd17546    1 VLVVDDNPVNRKVLKKLLeKLG----YEVDVAENGQEALELLKEEPFDLVLMDLQMPVMDGLEATRRIrelegGGRRTPI 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 582378446  78 IILSSY----DDFEYMKAGIQhhvlDYLLKPVDHAQLEVIL 114
Cdd:cd17546   77 IALTANaleeDREKCLEAGMD----DYLSKPVKLDQLKEVL 113

REC_NtrC

cd19919

phosphoacceptor receiver (REC) domain of DNA-binding transcriptional regulator NtrC; ...

3-108

2.29e-11

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: 59.21 E-value: 2.29e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYHFNTIytaKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVIIL 80
Cdd:cd19919    2 TVWIVDDDSSIRWVLERALAGAGLTVTSF---ENAQEALAALASSQPDVLISDIRMPGMDGLALLAQIkqRHPDLPVIIM 78

                         90       100       110
                 ....*....|....*....|....*....|
gi 582378446  81 SSYDDFEYMKAGIQHHVLDYLLKP--VDHA 108
Cdd:cd19919   79 TAHSDLDSAVSAYQGGAFEYLPKPfdIDEA 108

GlxA

COG4977

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH ...

152-247

2.51e-11

Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription];

Pssm-ID: 444002 [Multi-domain] Cd Length: 318 Bit Score: 62.48 E-value: 2.51e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446 152 VNQIVDQIKQSYQTKVTVSDLIQHIDVSEsyamRT----FKDHVGITIVDYLNRYRILQSLQLL-------DrhykhyEI 220
Cdd:COG4977  212 LARAQAWMEANLEEPLSVDELARRAGMSP----RTlerrFRAATGTTPARYLQRLRLERARRLLettdlsiE------EI 281

                         90       100
                 ....*....|....*....|....*..
gi 582378446 221 ADKVGFSEYKMFSYHFKKYLQMSPSDY 247
Cdd:COG4977  282 AAACGFGSASHFRRAFRRRFGVSPSAY 308

orf27

CHL00148

Ycf27; Reviewed

3-120

4.51e-11

Ycf27; Reviewed

Pssm-ID: 214376 [Multi-domain] Cd Length: 240 Bit Score: 60.89 E-value: 4.51e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYHfntIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI-ALLDCNVIILS 81
Cdd:CHL00148   8 KILVVDDEAYIRKILETRLSIIGYE---VITASDGEEALKLFRKEQPDLVILDVMMPKLDGYGVCQEIrKESDVPIIMLT 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 582378446  82 SYDDFEYMKAGIQHHVLDYLLKPVDHAQLEV-ILGRLVRT 120
Cdd:CHL00148  85 ALGDVSDRITGLELGADDYVVKPFSPKELEArIRSVLRRT 124

REC_2_DhkD-like

cd17580

second phosphoacceptor receiver (REC) domain of Dictyostelium discoideum hybrid signal ...

4-114

4.78e-11

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: 58.24 E-value: 4.78e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPWgdyHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI----ALLDCNVII 79
Cdd:cd17580    1 ILVVDDNEDAAEMLALLLEL---EGAEVTTAHSGEEALEAAQRFRPDVILSDIGMPGMDGYELARRLrelpWLANTPAIA 77

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 582378446  80 LSSY----DDFEYMKAGIQHHvldyLLKPVDHAQLEVIL 114
Cdd:cd17580   78 LTGYgqpeDRERALEAGFDAH----LVKPVDPDELIELI 112

REC_RssB-like

cd17555

phosphoacceptor receiver (REC) domain of Pseudomonas aeruginosa RssB and similar domains; ...

3-111

6.77e-11

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: 57.98 E-value: 6.77e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYhfnTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALL--DCNVIIL 80
Cdd:cd17555    2 TILVIDDDEVVRESIAAYLEDSGF---QVLQAADGRQGLELFRSEQPDLVLCDLRMPEMDGLEVLKQITKEspDTPVIVV 78

                         90       100       110
                 ....*....|....*....|....*....|..
gi 582378446  81 SSYDDFEYMKAGIQHHVLDYLLKPV-DHAQLE 111
Cdd:cd17555   79 SGAGVMSDAVEALRLGAWDYLTKPIeDLAVLE 110

glnG

PRK10923

nitrogen regulation protein NR(I); Provisional

3-137

7.13e-11

nitrogen regulation protein NR(I); Provisional

Pssm-ID: 182842 [Multi-domain] Cd Length: 469 Bit Score: 61.43 E-value: 7.13e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYHFNTIYTAKDGVEALSliqQHQPELVITDIRMPRKNGVDLLNDIA----LLDcnVI 78
Cdd:PRK10923   5 IVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLEALA---SKTPDVLLSDIRMPGMDGLALLKQIKqrhpMLP--VI 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  79 ILSSYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLVRTLLEQ-QSQNGRSLASCHD 137
Cdd:PRK10923  80 IMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISHYQEQqQPRNIQVNGPTTD 139

COG4567

DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains ...

33-116

9.85e-11

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: 58.77 E-value: 9.85e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  33 TAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALL--DCNVIILSSYDD----FEYMKAGiqhhVLDYLLKPVD 106
Cdd:COG4567   33 TAASVEEALALLEQAPPDYAVLDLRLGDGSGLDLIEALRERdpDARIVVLTGYASiataVEAIKLG----ADDYLAKPAD 108

                         90
                 ....*....|
gi 582378446 107 HAQLEVILGR 116
Cdd:COG4567  109 ADDLLAALER 118

REC_Ycf29

cd19927

phosphoacceptor receiver (REC) domain of probable transcriptional regulator Ycf29; Ycf29 is a ...

4-70

1.32e-10

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: 57.00 E-value: 1.32e-10

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 582378446   4 VVICDDERIIREGLKQIIPWGDYHfntIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI 70
Cdd:cd19927    1 ILLVDDDPGIRLAVKDYLEDQGFT---VIAASNGLEALDLLNQYIPDLIISDIIMPGVDGYSLLGKL 64

REC_NtrX-like

cd17550

phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and ...

4-81

1.61e-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: 56.74 E-value: 1.61e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIpwGDYHFNTIyTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVIILS 81
Cdd:cd17550    1 ILIVDDEEDIRESLSGIL--EDEGYEVD-TAADGEEALKLIKERRPDLVLLDIWLPDMDGLELLKEIkeKYPDLPVIMIS 77

PRK10610

chemotaxis protein CheY;

2-121

3.14e-10

chemotaxis protein CheY;

Pssm-ID: 170568 [Multi-domain] Cd Length: 129 Bit Score: 56.52 E-value: 3.14e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   2 FKVVICDD----ERIIREGLKQIipwgdyHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI----ALL 73
Cdd:PRK10610   6 LKFLVVDDfstmRRIVRNLLKEL------GFNNVEEAEDGVDALNKLQAGGFGFVISDWNMPNMDGLELLKTIradgAMS 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 582378446  74 DCNVIILSSYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLVRTL 121
Cdd:PRK10610  80 ALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEKL 127

REC_typeB_ARR-like

cd17584

phosphoacceptor receiver (REC) domain of type B Arabidopsis response regulators (ARRs) and ...

4-118

4.43e-10

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: 55.71 E-value: 4.43e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPWGDYHfntIYTAKDGVEALSLIQQHQPE--LVITDIRMPRKNGVDLLNDIALL-DCNVIIL 80
Cdd:cd17584    1 VLVVDDDPTCLAILKRMLLRCGYQ---VTTCTDAEEALSMLRENKDEfdLVITDVHMPDMDGFEFLELIRLEmDLPVIMM 77

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 582378446  81 SSYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLV 118
Cdd:cd17584   78 SADGSTSTVMKGLAHGACDYLLKPVSIEDLKNIWQHVV 115

REC_CheC-like

cd17593

phosphoacceptor receiver (REC) domain of uncharacterized response regulators containing a CheC ...

2-117

5.03e-10

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: 55.62 E-value: 5.03e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   2 FKVVICDDERIIREGLKQIIPwGDYHFnTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIAL--LDCNVII 79
Cdd:cd17593    1 MKVLICDDSSMARKQLARALP-ADWDV-EITFAENGEEALEILREGRIDVLFLDLTMPVMDGYEVLEALPVeqLETKVIV 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 582378446  80 LSsyddfeymkAGIQHHV---------LDYLLKPVDHAQLEVILGRL 117
Cdd:cd17593   79 VS---------GDVQPEAkervlelgaLAFLKKPFDPEKLAQLLEEL 116

REC

smart00448

cheY-homologous receiver domain; CheY regulates the clockwise rotation of E. coli flagellar ...

3-59

5.64e-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: 53.73 E-value: 5.64e-10

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 582378446     3 KVVICDDERIIREGLKQIIpwgDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMP 59
Cdd:smart00448   2 RILVVDDDPLLRELLKALL---EKEGYEVDEATDGEEALELLKEEKPDLILLDIMMP 55

REC_2_GGDEF

cd17544

second phosphoacceptor receiver (REC) domain of uncharacterized GGDEF domain proteins; This ...

3-104

1.62e-09

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: 54.45 E-value: 1.62e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPwgDYHFNtIYTAKDGVEALSLIQQHqPE--LVITDIRMPRKNGVDLL---------NDIA 71
Cdd:cd17544    2 KVLVVDDSATSRNHLRALLR--RHNFQ-VLEAANGQEALEVLEQH-PDikLVITDYNMPEMDGFELVreirkkysrDQLA 77

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 582378446  72 lldcnVIILSSYDD----FEYMKAGIQhhvlDYLLKP 104
Cdd:cd17544   78 -----IIGISASGDnalsARFIKAGAN----DFLTKP 105

REC_Spo0A

cd17561

phosphoacceptor receiver (REC) domain of Spo0A; Spo0A is a response regulator of the ...

3-104

3.24e-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: 53.00 E-value: 3.24e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDyHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI----ALLDCNVI 78
Cdd:cd17561    3 KVLIADDNREFVQLLEEYLNSQP-DMEVVGVAHNGQEALELIEEKEPDVLLLDIIMPHLDGIGVLEKLrrmrLEKRPKII 81

                         90       100
                 ....*....|....*....|....*.
gi 582378446  79 ILSSYDDFEYMKAGIQHHVLDYLLKP 104
Cdd:cd17561   82 MLTAFGQEDITQRAVELGASYYILKP 107

REC_Spo0F-like

cd17553

phosphoacceptor receiver (REC) domain of Spo0F and similar domains; Spo0F, a stand-alone ...

3-106

3.50e-09

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: 53.33 E-value: 3.50e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYHfntIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLDCN--VIIL 80
Cdd:cd17553    2 KILIVDDQYGIRILLNEVFNKEGYQ---TFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENirVIIM 78

                         90       100
                 ....*....|....*....|....*.
gi 582378446  81 SSYDDFEYMKAGIQHHVLDYLLKPVD 106
Cdd:cd17553   79 TAYGELDMIQESKELGALTHFAKPFD 104

PRK10371

transcriptional regulator MelR;

150-249

4.96e-09

transcriptional regulator MelR;

Pssm-ID: 182416 [Multi-domain] Cd Length: 302 Bit Score: 55.60 E-value: 4.96e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446 150 YYVNQIVDQIKQSYQTKVTVSDLIQHIDVSESYAMRTFKDHVGITIVDYLNRYRILQSLQLL-DRHYKHYEIADKVGFSE 228
Cdd:PRK10371 191 FYVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLsDTDKSILDIALTAGFRS 270

                         90       100
                 ....*....|....*....|.
gi 582378446 229 YKMFSYHFKKYLQMSPSDYCK 249
Cdd:PRK10371 271 SSRFYSTFGKYVGMSPQQYRK 291

REC_HupR

cd17596

phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR); Members of ...

4-130

6.13e-09

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: 53.14 E-value: 6.13e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIpwgDYHFNtIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLDCNV--IILS 81
Cdd:cd17596    3 ILVVDDEVRSLEALRRTL---EEDFD-VLTAASAEEALAILEEEWVQVILCDQRMPGTTGVEFLKEVRERWPEVvrIIIS 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 582378446  82 SYDDFEYMKAGIQHH-VLDYLLKPVDHAQLEVILGRLVRtLLEQQSQNGR 130
Cdd:cd17596   79 GYTDSEDIIAGINEAgIYQYLTKPWHPDQLLLTVRNAAR-LFELQRENER 127

PRK10693

two-component system response regulator RssB;

32-105

6.46e-09

two-component system response regulator RssB;

Pssm-ID: 182652 [Multi-domain] Cd Length: 303 Bit Score: 55.38 E-value: 6.46e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  32 YTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIAL--LDCNVIILSSYDDF----EYMKAGIQhhvlDYLLKPV 105
Cdd:PRK10693   1 VLAANGVDALELLGGFTPDLIICDLAMPRMNGIEFVEHLRNrgDQTPVLVISATENMadiaKALRLGVQ----DVLLKPV 76

PRK15115

response regulator GlrR; Provisional

30-110

8.58e-09

response regulator GlrR; Provisional

Pssm-ID: 185070 [Multi-domain] Cd Length: 444 Bit Score: 55.23 E-value: 8.58e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  30 TIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLDCN--VIILSSYDDFEYMKAGIQHHVLDYLLKPVDH 107
Cdd:PRK15115  31 SVVTAESGQEALRVLNREKVDLVISDLRMDEMDGMQLFAEIQKVQPGmpVIILTAHGSIPDAVAATQQGVFSFLTKPVDR 110


                 ...
gi 582378446 108 AQL 110
Cdd:PRK15115 111 DAL 113

PRK15347

two component system sensor kinase;

31-173

1.19e-08

two component system sensor kinase;

Pssm-ID: 237951 [Multi-domain] Cd Length: 921 Bit Score: 55.03 E-value: 1.19e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  31 IYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLL----NDIALLD--CNVIILS---SYDDFEYMK-AGIQHhvldY 100
Cdd:PRK15347 717 VTTAASGTEALELGRQHRFDLVLMDIRMPGLDGLETTqlwrDDPNNLDpdCMIVALTanaAPEEIHRCKkAGMNH----Y 792

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446 101 LLKPVDHAQleviLGRLVRTLLEQQSQNGRSLASCHDAFQPLLkvEYDDYYVNQ--------IVDQIKQSYQTKVTVSDL 172
Cdd:PRK15347 793 LTKPVTLAQ----LARALELAAEYQLLRGIELSPQDSSCSPLL--DTDDMALNSklyqslllLLAQIEQAVENQEVLSQL 866


                 .
gi 582378446 173 I 173
Cdd:PRK15347 867 L 867

REC_D1_PleD-like

cd17538

first (D1) phosphoacceptor receiver (REC) domain of response regulator PleD and similar ...

3-105

1.26e-08

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: 51.34 E-value: 1.26e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQII-PWGdYhfnTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVD----LLNDIALLDCNV 77
Cdd:cd17538    1 KILVVDDEPANRELLEALLsAEG-Y---EVLTADSGQEALALAEEELPDLILLDVMMPGMDGFEvcrrLKEDPETRHIPV 76

                         90       100
                 ....*....|....*....|....*...
gi 582378446  78 IILSSYDDFEYMKAGIQHHVLDYLLKPV 105
Cdd:cd17538   77 IMITALDDREDRIRGLEAGADDFLSKPI 104

PRK10403

nitrate/nitrite response regulator protein NarP;

2-113

1.99e-08

nitrate/nitrite response regulator protein NarP;

Pssm-ID: 182431 [Multi-domain] Cd Length: 215 Bit Score: 52.93 E-value: 1.99e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   2 FKVVICDDERIIREGLKQIIPWgDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNdiAL----LDCNV 77
Cdd:PRK10403   7 FQVLIVDDHPLMRRGVRQLLEL-DPGFEVVAEAGDGASAIDLANRLDPDVILLDLNMKGMSGLDTLN--ALrrdgVTAQI 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 582378446  78 IIL----SSYDDFEYMKAGIQhhvlDYLLKPVD-HAQLEVI 113
Cdd:PRK10403  84 IILtvsdASSDVFALIDAGAD----GYLLKDSDpEVLLEAI 120

REC_RocR

cd17530

phosphoacceptor receiver (REC) domain of response regulator RocR; The response regulator RocR ...

3-117

2.54e-08

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: 50.90 E-value: 2.54e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIpwGDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLDCN--VIIL 80
Cdd:cd17530    2 RVLVLDDDPFQCMMAATIL--EDLGPGNVDEADDGREALVILLCNAPDIIICDLKMPDMDGIEFLRHLAESHSNaaVILM 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 582378446  81 SSYDdfeymkAGIQH-----------HVLDYLLKPVDHAQLEVILGRL 117
Cdd:cd17530   80 SGLD------GGILEsaetlaganglNLLGTLSKPFSPEELTELLTKY 121

REC_NarL

cd19931

phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate ...

4-103

2.64e-08

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: 50.81 E-value: 2.64e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPWgDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVIILS 81
Cdd:cd19931    1 VLLIDDHPLLRKGIKQLIEL-DPDFTVVGEASSGEEGIELAERLDPDLILLDLNMKGMSGLDTLKALreEGVSARIVILT 79

                         90       100
                 ....*....|....*....|....*.
gi 582378446  82 SYDD----FEYMKAGIQhhvlDYLLK 103
Cdd:cd19931   80 VSDAeddvVTALRAGAD----GYLLK 101

REC_hyHK

cd17598

phosphoacceptor receiver (REC) domain of uncharacterized hybrid sensor histidine kinase ...

4-122

2.88e-08

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: 50.79 E-value: 2.88e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPWGDYHfntIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI----ALLDCNVII 79
Cdd:cd17598    1 ILIVEDSPTQAEQLKHILEEQGYK---VQVARNGREALAMLAEHRPTLVISDIVMPEMDGYELCRKIksdpDLKDIPVIL 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 582378446  80 LSSYDDFEYMKAGIQHHVLDYLLKPVDHaqlEVILGRLVRTLL 122
Cdd:cd17598   78 LTTLSDPRDVIRGLECGADNFITKPYDE---KYLLSRIKYILV 117

REC_NtrC1-like

cd17572

phosphoacceptor receiver (REC) domain of nitrogen regulatory protein C 1 (NtrC1) from Aquifex ...

31-112

3.62e-08

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: 50.66 E-value: 3.62e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  31 IYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVIILSSYDDF----EYMKAGiqhhVLDYLLKP 104
Cdd:cd17572   25 VTHVETGKEALAFLSDQPPDVVLLDLKLPDMSGMEILKWIqeRSLPTSVIVITAHGSVdiavEAMRLG----AYDFLEKP 100


                 ....*...
gi 582378446 105 VDHAQLEV 112
Cdd:cd17572  101 FDADRLRV 108

PRK10365

sigma-54-dependent response regulator transcription factor ZraR;

23-114

3.85e-08

sigma-54-dependent response regulator transcription factor ZraR;

Pssm-ID: 182412 [Multi-domain] Cd Length: 441 Bit Score: 53.50 E-value: 3.85e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  23 WGdyhFNtIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLD--CNVIILSSYDDFEYMKAGIQHHVLDY 100
Cdd:PRK10365  28 WG---YN-VALANSGRQALEQVREQVFDLVLCDVRMAEMDGIATLKEIKALNpaIPVLIMTAYSSVETAVEALKTGALDY 103

                         90
                 ....*....|....
gi 582378446 101 LLKPVDHAQLEVIL 114
Cdd:PRK10365 104 LIKPLDFDNLQATL 117

REC_OmpR_VirG

cd17594

phosphoacceptor receiver (REC) domain of VirG-like OmpR family response regulators; VirG is ...

3-110

5.13e-08

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: 50.14 E-value: 5.13e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIpwgDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI-ALLDCNVIILS 81
Cdd:cd17594    1 HVLVVDDDAAMRHLLILYL---RERGFDVTAAADGAEEARLMLHRRVDLVLLDLRLGQESGLDLLRTIrARSDVPIIIIS 77

                         90       100       110
                 ....*....|....*....|....*....|
gi 582378446  82 SYDDFEYMK-AGIQHHVLDYLLKPVDHAQL 110
Cdd:cd17594   78 GDRRDEIDRvVGLELGADDYLAKPFGLREL 107

FixJ

COG4566

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...

4-110

5.29e-08

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: 51.64 E-value: 5.29e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIpwGDYHFNTIyTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLDCN--VIILS 81
Cdd:COG4566    2 VYIVDDDEAVRDSLAFLL--ESAGLRVE-TFASAEAFLAALDPDRPGCLLLDVRMPGMSGLELQEELAARGSPlpVIFLT 78

                         90       100       110
                 ....*....|....*....|....*....|...
gi 582378446  82 SYDDF----EYMKAGiqhhVLDYLLKPVDHAQL 110
Cdd:COG4566   79 GHGDVpmavRAMKAG----AVDFLEKPFDDQAL 107

REC_CheY4-like

cd17562

phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY4 and similar CheY ...

3-67

1.01e-07

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: 49.22 E-value: 1.01e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYhfnTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLL 67
Cdd:cd17562    2 KILAVDDSASIRQMVSFTLRGAGY---EVVEAADGRDALSKAQSKKFDLIITDQNMPNMDGIELI 63

REC_OmpR_ChvI-like

cd19936

phosphoacceptor receiver (REC) domain of ChvI-like OmpR family response regulators; ...

4-104

1.28e-07

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: 48.60 E-value: 1.28e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPWGDYHFNTiYTakDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI-ALLDCNVIILSS 82
Cdd:cd19936    1 IALVDDDRNILTSVSMALEAEGFSVET-YT--DGASALDGLNARPPDLAILDIKMPRMDGMELLQRLrQKSTLPVIFLTS 77

                         90       100
                 ....*....|....*....|..
gi 582378446  83 YDDFEYMKAGIQHHVLDYLLKP 104
Cdd:cd19936   78 KDDEIDEVFGLRMGADDYITKP 99

REC_OmpR_YycF-like

cd17614

phosphoacceptor receiver (REC) domain of YrcF-like OmpR family response regulators; YycF ...

4-104

1.84e-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: 48.57 E-value: 1.84e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPWGDYHfntIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLDCNVIILSSY 83
Cdd:cd17614    1 ILVVDDEKPISDILKFNLTKEGYE---VVTAYDGREALEKVEEEQPDLILLDLMLPEKDGLEVCREVRKTSNVPIIMLTA 77

                         90       100
                 ....*....|....*....|..
gi 582378446  84 DDFEYMKA-GIQHHVLDYLLKP 104
Cdd:cd17614   78 KDSEVDKVlGLELGADDYVTKP 99

REC_RegA-like

cd17563

phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA; ...

30-111

2.64e-07

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: 47.82 E-value: 2.64e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  30 TIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI-ALL-DCNVIILSSYDDF----EYMKAGiqhhVLDYLLK 103
Cdd:cd17563   26 EVETAHSVEEALALAREEKPDYAVLDLRLGGDSGLDLIPPLrALQpDARIVVLTGYASIatavEAIKLG----ADDYLAK 101


                 ....*...
gi 582378446 104 PVDHAQLE 111
Cdd:cd17563  102 PADADEIL 109

REC_DivK-like

cd17548

phosphoacceptor receiver (REC) domain of DivK and similar proteins; Caulobacter crescentus ...

30-110

3.68e-07

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: 47.53 E-value: 3.68e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  30 TIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLL----NDIALLDCNVIILSSY----DDFEYMKAGIQhhvlDYL 101
Cdd:cd17548   25 EVLEAADGEEALEIARKEKPDLILMDIQLPGMDGLEATrllkEDPATRDIPVIALTAYamkgDREKILEAGCD----GYI 100


                 ....*....
gi 582378446 102 LKPVDHAQL 110
Cdd:cd17548  101 SKPIDTREF 109

REC_OmpR_kpRstA-like

cd17622

phosphoacceptor receiver (REC) domain of kpRstA-like OmpR family response regulators; ...

36-122

4.11e-07

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: 47.37 E-value: 4.11e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  36 DGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI-ALLDCNVIILSSYDDFEYMKAGIQHHVLDYLLKPVDHAqleVIL 114
Cdd:cd17622   32 RGDRALEVIAREKPDAVLLDIMLPGIDGLTLCRDLrPKYQGPILLLTALDSDIDHILGLELGADDYVVKPVEPA---VLL 108


                 ....*...
gi 582378446 115 GRLvRTLL 122
Cdd:cd17622  109 ARL-RALL 115

PRK10955

envelope stress response regulator transcription factor CpxR;

1-146

4.32e-07

envelope stress response regulator transcription factor CpxR;

Pssm-ID: 182864 [Multi-domain] Cd Length: 232 Bit Score: 49.42 E-value: 4.32e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   1 MFKVVICDDERIIREGLKQIIPWGDYhfnTIYTAKDGVEALSLIQQhQPELVITDIRMPRKNGVDLLNDIALLDCNVIIL 80
Cdd:PRK10955   1 MNKILLVDDDRELTSLLKELLEMEGF---NVIVAHDGEQALDLLDD-SIDLLLLDVMMPKKNGIDTLKELRQTHQTPVIM 76

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 582378446  81 SSYDDFEYMKA-GIQHHVLDYLLKPVDHAQLEV-ILGRLVRTLLEQQSQNGrslaschDAFQPLLKVE 146
Cdd:PRK10955  77 LTARGSELDRVlGLELGADDYLPKPFNDRELVArIRAILRRSHWSEQQQNN-------DNGSPTLEVD 137

REC_RcNtrC-like

cd19928

phosphoacceptor receiver (REC) domain of Rhodobacter capsulatus nitrogen regulatory protein C ...

4-104

4.52e-07

phosphoacceptor receiver (REC) domain of Rhodobacter capsulatus nitrogen regulatory protein C (NtrC) 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 NtrC, also called nitrogen regulator I (NRI), from Rhodobacter capsulatus, Azospirillum brasilense, and Azorhizobium caulinodans. NtrC is part of the NtrB/NtrC two-component system that controls the expression of the nitrogen-regulated (ntr) genes in response to nitrogen limitation. 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: 381155 [Multi-domain] Cd Length: 100 Bit Score: 47.11 E-value: 4.52e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPWGDYHFNTIYTAkdgVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALL--DCNVIILS 81
Cdd:cd19928    1 ILVADDDRAIRTVLTQALGRAGYEVRTTGNA---ATLWRWVEEGEGDLVITDVVMPDENGLDLIPRIKKArpDLPIIVMS 77

                         90       100
                 ....*....|....*....|...
gi 582378446  82 SYDDFEYMKAGIQHHVLDYLLKP 104
Cdd:cd19928   78 AQNTLMTAVKAAERGAFEYLPKP 100

REC_OmpR_PmrA-like

cd17624

phosphoacceptor receiver (REC) domain of PmrA-like OmpR family response regulators; This ...

34-122

4.70e-07

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: 47.09 E-value: 4.70e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  34 AKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVIILSSYDDFEYMKAGIQHHVLDYLLKPVDhaqLE 111
Cdd:cd17624   28 VRTGAEAEAALASGPYDLVILDLGLPDGDGLDLLRRWrrQGQSLPVLILTARDGVDDRVAGLDAGADDYLVKPFA---LE 104

                         90
                 ....*....|.
gi 582378446 112 VILGRLvRTLL 122
Cdd:cd17624  105 ELLARL-RALL 114

REC_FixJ

cd17537

phosphoacceptor receiver (REC) domain of FixJ family response regulators; FixJ family response ...

4-110

5.53e-07

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: 47.20 E-value: 5.53e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPWGDYHFNTIYTAKDGVEALSLIQqhqPELVITDIRMPRKNGVDLLNDIALLDCN--VIILS 81
Cdd:cd17537    3 VYVVDDDEAVRDSLAFLLRSVGLAVKTFTSASAFLAAAPPDQ---PGCLVLDVRMPGMSGLELQDELLARGSNipIIFIT 79

                         90       100       110
                 ....*....|....*....|....*....|...
gi 582378446  82 SYDDF----EYMKAGiqhhVLDYLLKPVDHAQL 110
Cdd:cd17537   80 GHGDVpmavEAMKAG----AVDFLEKPFRDQVL 108

dpiA

PRK10046

two-component response regulator DpiA; Provisional

4-150

5.71e-07

two-component response regulator DpiA; Provisional

Pssm-ID: 182208 [Multi-domain] Cd Length: 225 Bit Score: 48.86 E-value: 5.71e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIpwgdYH---FNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVI 78
Cdd:PRK10046   7 LLIVEDETPLAEMHAEYI----RHipgFSQILLAGNLAQARMMIERFKPGLILLDNYLPDGRGINLLHELvqAHYPGDVV 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 582378446  79 ILSSYDDFEYMKAGIQHHVLDYLLKPVDHAqlevilgRLVRTLLEQQsQNGRSLASCHDAFQPLLKVEYDDY 150
Cdd:PRK10046  83 FTTAASDMETVSEAVRCGVFDYLIKPIAYE-------RLGQTLTRFR-QRKHMLESIDSASQKQIDEMFNAY 146

REC_CpdR_CckA-like

cd18160

phosphoacceptor receiver (REC) domain of Brucella abortus CpdR and CckA, and similar domains; ...

3-80

8.40e-07

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: 46.34 E-value: 8.40e-07

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYHfntIYTAKDGVEALSLIQQHQP-ELVITDIRMPRKNGVDLLNDIALLDCNVIIL 80
Cdd:cd18160    1 TILLADDEPSVRKFIVTTLKKAGYA---VTEAESGAEALEKLQQGKDiDIVVTDIVMPEMDGIELAREARKIDPDVKIL 76

REC_PA4781-like

cd19920

phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase PA4781 and similar ...

30-105

8.86e-07

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: 46.35 E-value: 8.86e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  30 TIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVD----LLNDIALLDCNVIILSSYDDFEYMKAGIQHHVLDYLLKPV 105
Cdd:cd19920   24 RVLVATDGQQALQRAQAEPPDLILLDVMMPGMDGFEvcrrLKADPATRHIPVIFLTALTDTEDKVKGFELGAVDYITKPF 103

PRK10430

two-component system response regulator DcuR;

1-111

1.91e-06

two-component system response regulator DcuR;

Pssm-ID: 182454 [Multi-domain] Cd Length: 239 Bit Score: 47.41 E-value: 1.91e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   1 MFKVVICDDERIIRE----GLKQIipwgdYHFNTIYTAKDGVEALSLIQQHQPE--LVITDIRMPRKNGVDLLNDI--AL 72
Cdd:PRK10430   1 MINVLIVDDDAMVAElnrrYVAQI-----PGFQCCGTASTLEQAKEIIFNSDTPidLILLDIYMQQENGLDLLPVLheAG 75

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 582378446  73 LDCNVIILSSYDDFEYMKAGIQHHVLDYLLKPVDHAQLE 111
Cdd:PRK10430  76 CKSDVIVISSAADAATIKDSLHYGVVDYLIKPFQASRFE 114

REC_PhyR

cd17540

phosphoacceptor receiver (REC) domain of response regulator PhyR and similar proteins; PhyR is ...

3-83

2.16e-06

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: 45.32 E-value: 2.16e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPwgDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMP-RKNGVDLLNDIALL-DCNVIIL 80
Cdd:cd17540    2 RVLIIEDEPLIAMDLEQIVE--DLGHQVVGIARTRDEAVALARRERPDLILADIQLAdGSSGIDAVNEILTThDVPVIFV 79


                 ...
gi 582378446  81 SSY 83
Cdd:cd17540   80 TAY 82

REC_GlnL-like

cd17565

phosphoacceptor receiver (REC) domain of transcriptional regulatory protein GlnL and similar ...

6-105

3.04e-06

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: 44.57 E-value: 3.04e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   6 ICDDERIIREGLKQIIPwgDYHFNTIY-TAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLDCN--VIILSS 82
Cdd:cd17565    3 IVDDDKNIIKILSDIIE--DDDLGEVVgEADNGAQAYDEILFLQPDIVLIDLLMPGMDGIQLVRKLKDTGSNgkFIMISQ 80

                         90       100
                 ....*....|....*....|...
gi 582378446  83 YDDFEYMKAGIQHHVLDYLLKPV 105
Cdd:cd17565   81 VSDKEMIGKAYQAGIEFFINKPI 103

PRK15369

two component system response regulator;

3-103

3.30e-06

two component system response regulator;

Pssm-ID: 185267 [Multi-domain] Cd Length: 211 Bit Score: 46.61 E-value: 3.30e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQII-PWGdyHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLndIALL----DCNV 77
Cdd:PRK15369   5 KILLVDDHELIINGIKNMLaPYP--RYKIVGQVDNGLEVYNACRQLEPDIVILDLGLPGMNGLDVI--PQLHqrwpAMNI 80

                         90       100
                 ....*....|....*....|....*.
gi 582378446  78 IILSSYDDFEYMKAGIQHHVLDYLLK 103
Cdd:PRK15369  81 LVLTARQEEHMASRTLAAGALGYVLK 106

PLN03029

type-a response regulator protein; Provisional

2-127

4.86e-06

type-a response regulator protein; Provisional

Pssm-ID: 215544 [Multi-domain] Cd Length: 222 Bit Score: 46.18 E-value: 4.86e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   2 FKVVICDDERIIREGLKQIIPWGDYHFNTIYTAKDGVEALSLIQ--QHQPE---------------LVITDIRMPRKNGV 64
Cdd:PLN03029   9 FHVLAVDDSLIDRKLIEKLLKTSSYQVTTVDSGSKALKFLGLHEddRSNPDtpsvspnshqevevnLIITDYCMPGMTGY 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 582378446  65 DLLNDI----ALLDCNVIILSSYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLVRTLLEQQSQ 127
Cdd:PLN03029  89 DLLKKIkessSLRNIPVVIMSSENVPSRITRCLEEGAEEFFLKPVQLSDLNRLKPHMMKTKSKNQKQ 155

REC_PilR

cd19926

phosphoacceptor receiver (REC) domain of type 4 fimbriae expression regulatory protein PilR ...

4-104

4.88e-06

phosphoacceptor receiver (REC) domain of type 4 fimbriae expression regulatory protein PilR and similar proteins; Pseudomonas aeruginosa PilR is the response regulator of the PilS/PilR two-component regulatory system (PilSR TCS) that acts in conjunction with sigma-54 to regulate the expression of type 4 pilus (T4P) major subunit PilA. In addition, the PilSR TCS regulates flagellum-dependent swimming motility and pilus-dependent twitching motility. PilR contains an N-terminal REC domain, a central sigma-54 interaction domain, and a C-terminal Fis-type helix-turn-helix DNA-binding domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

Pssm-ID: 381153 [Multi-domain] Cd Length: 100 Bit Score: 44.07 E-value: 4.88e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKqiIPWGDYHFNTiYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIA--LLDCNVIILS 81
Cdd:cd19926    1 VLVVDDEPDIRELLE--ITLGRMGLDV-RSARNVKEARELLASEPYDLCLTDMRLPDGSGLELVQHIQqrLPQTPVAVIT 77

                         90       100
                 ....*....|....*....|...
gi 582378446  82 SYDDFEYMKAGIQHHVLDYLLKP 104
Cdd:cd19926   78 AYGSLDTAIEALKAGAFDFLTKP 100

REC_OmpR_CpxR

cd17623

phosphoacceptor receiver (REC) domain of CpxR-like OmpR family response regulators; CpxR is ...

30-116

6.69e-06

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: 44.22 E-value: 6.69e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  30 TIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI-ALLDCNVIILSSYDDFEYMKAGIQHHVLDYLLKPVDH- 107
Cdd:cd17623   24 NVRAAHDGEQGLAALLEGSPDLVVLDVMLPKMNGLDVLKELrKTSQVPVLMLTARGDDIDRILGLELGADDYLPKPFNPr 103

                         90
                 ....*....|..
gi 582378446 108 ---AQLEVILGR 116
Cdd:cd17623  104 elvARIRAILRR 115

fixJ

PRK09390

response regulator FixJ; Provisional

4-131

1.08e-05

response regulator FixJ; Provisional

Pssm-ID: 181815 [Multi-domain] Cd Length: 202 Bit Score: 44.99 E-value: 1.08e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPWGDYHFNTIYTAKDGVEALSLIQqhqPELVITDIRMPRKNGVDLLNDIALLDCN--VIILS 81
Cdd:PRK09390   6 VHVVDDDEAMRDSLAFLLDSAGFEVRLFESAQAFLDALPGLR---FGCVVTDVRMPGIDGIELLRRLKARGSPlpVIVMT 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 582378446  82 SYDDF----EYMKAGiqhhVLDYLLKPVDHaqlEVILGrLVRTLLEQQSQNGRS 131
Cdd:PRK09390  83 GHGDVplavEAMKLG----AVDFIEKPFED---ERLIG-AIERALAQAPEAAKS 128

REC_OmpR_DrrD-like

cd17625

phosphoacceptor receiver (REC) domain of DrrD-like OmpR family response regulators; DrrD is a ...

6-119

1.12e-05

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: 43.36 E-value: 1.12e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   6 ICDDERIIREGLKQIIPWGDYhfnTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVIILSSY 83
Cdd:cd17625    2 VVEDEKDLSEAITKHLKKEGY---TVDVCFDGEEGLEYALSGIYDLIILDIMLPGMDGLEVLKSLreEGIETPVLLLTAL 78

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 582378446  84 DDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLVR 119
Cdd:cd17625   79 DAVEDRVKGLDLGADDYLPKPFSLAELLARIRALLR 114

PRK11173

two-component response regulator; Provisional

3-132

1.35e-05

two-component response regulator; Provisional

Pssm-ID: 183013 [Multi-domain] Cd Length: 237 Bit Score: 45.01 E-value: 1.35e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYHfntIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLL------NDIALldcn 76
Cdd:PRK11173   5 HILIVEDELVTRNTLKSIFEAEGYD---VFEATDGAEMHQILSENDINLVIMDINLPGKNGLLLArelreqANVAL---- 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 582378446  77 vIILSSYDDfEYMKA-GIQHHVLDYLLKPVDHAQLeVILGR--LVRTLLEQQSQNGRSL 132
Cdd:PRK11173  78 -MFLTGRDN-EVDKIlGLEIGADDYITKPFNPREL-TIRARnlLSRTMNLGTVSEERRS 133

REC_OmpR_ArcA_TorR-like

cd17619

phosphoacceptor receiver (REC) domain of ArcA- and TorR-like OmpR family response regulators; ...

4-112

2.35e-05

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: 42.37 E-value: 2.35e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPWGDYhfnTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI-ALLDCNVIILSS 82
Cdd:cd17619    3 ILIVEDEPVTRATLKSYFEQEGY---DVSEAGDGEEMRQILARQDIDLVLLDINLPGKDGLSLTRELrEQSEVGIILVTG 79

                         90       100       110
                 ....*....|....*....|....*....|
gi 582378446  83 YDDFEYMKAGIQHHVLDYLLKPVDHAQLEV 112
Cdd:cd17619   80 RDDEVDRIVGLEIGADDYVTKPFNPRELLV 109

pleD

PRK09581

response regulator PleD; Reviewed

30-119

3.29e-05

response regulator PleD; Reviewed

Pssm-ID: 236577 [Multi-domain] Cd Length: 457 Bit Score: 44.51 E-value: 3.29e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  30 TIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVD----LLNDIALLDCNVIILSSYDDFEYMKAGIQHHVLDYLLKPV 105
Cdd:PRK09581  28 TVLTASSGAEAIAICEREQPDIILLDVMMPGMDGFEvcrrLKSDPATTHIPVVMVTALDDPEDRVRGLEAGADDFLTKPI 107

                         90
                 ....*....|....
gi 582378446 106 DHAQLEVILGRLVR 119
Cdd:PRK09581 108 NDVALFARVKSLTR 121

REC_OmpR_KdpE-like

cd17620

phosphoacceptor receiver (REC) domain of KdpE-like OmpR family response regulators; KdpE is a ...

4-104

3.47e-05

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: 41.77 E-value: 3.47e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPWGDYhfnTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI-ALLDCNVIILSS 82
Cdd:cd17620    1 ILVIEDEPQIRRFLRTALEAHGY---RVFEAETGQEGLLEAATRKPDLIILDLGLPDMDGLEVIRRLrEWSAVPVIVLSA 77

                         90       100
                 ....*....|....*....|..
gi 582378446  83 YDDFEYMKAGIQHHVLDYLLKP 104
Cdd:cd17620   78 RDEESDKIAALDAGADDYLTKP 99

REC_CheV-like

cd19924

phosphoacceptor receiver (REC) domain of chemotaxis protein CheV and similar proteins; This ...

4-104

3.79e-05

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: 41.98 E-value: 3.79e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIpwGDYHFNtIYTAKDGVEALSLIQQ---------HQPELVITDIRMPRKNGVDLL----NDI 70
Cdd:cd19924    1 ILVVDDSPTARKQLRDLL--KNLGFE-IAEAVDGEEALNKLENlakegndlsKELDLIITDIEMPKMDGYELTfelrDDP 77

                         90       100       110
                 ....*....|....*....|....*....|....
gi 582378446  71 ALLDCNVIILSSYDDFEYMKAGIQHHVLDYLLKP 104
Cdd:cd19924   78 RLANIPVILNSSLSGEFSRARGKKVGADAYLAKF 111

PRK10572

arabinose operon transcriptional regulator AraC;

149-251

4.52e-05

arabinose operon transcriptional regulator AraC;

Pssm-ID: 236717 [Multi-domain] Cd Length: 290 Bit Score: 43.81 E-value: 4.52e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446 149 DYYVNQIVDQIKQSYQTKVTVSDLIQHIDVSESYAMRTFKDHVGITIVDYLNRYRILQSLQLLDR-HYKHYEIADKVGFS 227
Cdd:PRK10572 182 DPRVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRAKLLLQTtRMPIATIGRNVGYD 261

                         90       100
                 ....*....|....*....|....
gi 582378446 228 EYKMFSYHFKKYLQMSPSDYCKQA 251
Cdd:PRK10572 262 DQLYFSRVFKKCTGASPSEFRARC 285

REC_RR468-like

cd17552

phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator RR468 and ...

3-67

5.48e-05

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: 41.77 E-value: 5.48e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 582378446   3 KVVICDDERIIRE----GLKQIIPWgdyhfnTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLL 67
Cdd:cd17552    3 RILVIDDEEDIREvvqaCLEKLAGW------EVLTASSGQEGLEKAATEQPDAILLDVMMPDMDGLATL 65

PRK09685

DNA-binding transcriptional activator FeaR; Provisional

114-251

5.90e-05

DNA-binding transcriptional activator FeaR; Provisional

Pssm-ID: 236612 [Multi-domain] Cd Length: 302 Bit Score: 43.48 E-value: 5.90e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446 114 LGRLVRTLLEQQSQNGrsLASCHD------AFQPLLK---VEYDD---------YYVNQIVDQIKQSYQtkVTVSDLIQH 175
Cdd:PRK09685 148 MVQLSHRLLQQSMNGP--ALSETEsealleALIALLRpalHQRESvqprrerqfQKVVALIDQSIQEEI--LRPEWIAGE 223

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 582378446 176 IDVSESYAMRTFKDHvGITIVDYLNRYRILQSLQLLDRHYKHYEIAD---KVGFSEYKMFSYHFKKYLQMSPSDYCKQA 251
Cdd:PRK09685 224 LGISVRSLYRLFAEQ-GLVVAQYIRNRRLDRCADDLRPAADDEKITSiayKWGFSDSSHFSTAFKQRFGVSPGEYRRKF 301

HTH_AraC

pfam00165

Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the ...

159-200

7.03e-05

Bacterial regulatory helix-turn-helix proteins, AraC family; In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.

Pssm-ID: 425497 [Multi-domain] Cd Length: 42 Bit Score: 39.06 E-value: 7.03e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 582378446  159 IKQSYQTKVTVSDLIQHIDVSESYAMRTFKDHVGITIVDYLN 200
Cdd:pfam00165   1 LRENLSTNLTIADIADELGFSRSYFSRLFKKYTGVTPSQYRH 42

PRK11517

DNA-binding response regulator HprR;

3-126

1.79e-04

DNA-binding response regulator HprR;

Pssm-ID: 183172 [Multi-domain] Cd Length: 223 Bit Score: 41.42 E-value: 1.79e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYhfnTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNdiALLDCN---VII 79
Cdd:PRK11517   2 KILLIEDNQRTQEWVTQGLSEAGY---VIDAVSDGRDGLYLALKDDYALIILDIMLPGMDGWQILQ--TLRTAKqtpVIC 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 582378446  80 LSSYDDFEYMKAGIQHHVLDYLLKPVDHAQLeviLGRlVRTLLEQQS 126
Cdd:PRK11517  77 LTARDSVDDRVRGLDSGANDYLVKPFSFSEL---LAR-VRAQLRQHH 119

PRK13503

HTH-type transcriptional activator RhaS;

185-246

2.09e-04

HTH-type transcriptional activator RhaS;

Pssm-ID: 184094 [Multi-domain] Cd Length: 278 Bit Score: 41.59 E-value: 2.09e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 582378446 185 RTFKDHVGITIVDYLNRYRILQSLQLLdRHYKH--YEIADKVGFSEYKMFSYHFKKYLQMSPSD 246
Cdd:PRK13503 206 RQLKQQTGLTPQRYLNRLRLLKARHLL-RHSDAsvTDIAYRCGFGDSNHFSTLFRREFSWSPRD 268

PRK13501

HTH-type transcriptional activator RhaR;

155-250

2.52e-04

HTH-type transcriptional activator RhaR;

Pssm-ID: 184092 [Multi-domain] Cd Length: 290 Bit Score: 41.43 E-value: 2.52e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446 155 IVDQIKQSYQTKVTVSDLIQHIDVSESYAMRTFKDHVGITIVDYLNRYRILQSLQLLdRHYKHY--EIADKVGFSEYKMF 232
Cdd:PRK13501 181 IMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHAKCLL-RGSEHRisDIAARCGFEDSNYF 259

                         90
                 ....*....|....*...
gi 582378446 233 SYHFKKYLQMSPSDYCKQ 250
Cdd:PRK13501 260 SAVFTREAGMTPRDYRQR 277

REC_OmpR_PhoB

cd17618

phosphoacceptor receiver (REC) domain of PhoB response regulator from the OmpR family; The ...

3-110

2.54e-04

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: 39.54 E-value: 2.54e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYHfntIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLN----DIALLDCNVI 78
Cdd:cd17618    2 TILIVEDEPAIREMIAFNLERAGFD---VVEAEDAESAVNLIVEPRPDLILLDWMLPGGSGIQFIRrlkrDEMTRDIPII 78

                         90       100       110
                 ....*....|....*....|....*....|..
gi 582378446  79 ILSSYDDFEYMKAGIQHHVLDYLLKPVDHAQL 110
Cdd:cd17618   79 MLTARGEEEDKVRGLEAGADDYITKPFSPREL 110

REC_OmpR_EcPhoP-like

cd19934

phosphoacceptor receiver (REC) domain of EcPhoP-like OmpR family response regulators; ...

4-119

2.83e-04

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: 39.57 E-value: 2.83e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIpwGDYHFnTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVIILS 81
Cdd:cd19934    1 LLLVEDDALLAAQLKEQL--SDAGY-VVDVAEDGEEALFQGEEEPYDLVVLDLGLPGMDGLSVLRRWrsEGRATPVLILT 77

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 582378446  82 SYDDFEYMKAGIQHHVLDYLLKPVDHAQLEVILGRLVR 119
Cdd:cd19934   78 ARDSWQDKVEGLDAGADDYLTKPFHIEELLARLRALIR 115

REC_WspR-like

cd17575

phosphoacceptor receiver (REC) domain of WspR response regulator and similar proteins; The ...

2-110

3.63e-04

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: 39.31 E-value: 3.63e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   2 FKVVICDDERIIREGLKQII---PWGDYHFntiytAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI----ALLD 74
Cdd:cd17575    1 IMVLLVDDQAIIGEAVRRALadeEDIDFHY-----CSDPTEAIEVASQIKPTVILQDLVMPGVDGLTLVRFFranpATRD 75

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 582378446  75 CNVIILSSYDDFEYMKAGIQHHVLDYLLKPVDHAQL 110
Cdd:cd17575   76 IPIIVLSTKEEPEVKSEAFALGANDYLVKLPDKIEL 111

PRK13502

HTH-type transcriptional activator RhaR;

104-247

5.33e-04

HTH-type transcriptional activator RhaR;

Pssm-ID: 184093 [Multi-domain] Cd Length: 282 Bit Score: 40.42 E-value: 5.33e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446 104 PVDHAQLEVILGRLVRTLLEQQSQNGRSLASCHDAFqpllkveyddyyVNQIVDQIKQSYQTKVTVSDLIQHIDVSESYA 183
Cdd:PRK13502 142 PLANEMAELLFGQLVMTLKRHRYATDDLPATSRETL------------LDKLITALANSLECPFALDAFCQQEQCSERVL 209

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 582378446 184 MRTFKDHVGITIVDYLNRYRILQSlQLLDRHYKHY--EIADKVGFSEYKMFSYHFKKYLQMSPSDY 247
Cdd:PRK13502 210 RQQFRAQTGMTINQYLRQVRICHA-QYLLQHSPLMisEISMQCGFEDSNYFSVVFTRETGMTPSQW 274

PRK15479

transcriptional regulator TctD;

34-119

5.86e-04

transcriptional regulator TctD;

Pssm-ID: 185376 [Multi-domain] Cd Length: 221 Bit Score: 40.09 E-value: 5.86e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  34 AKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLDCN--VIILSSYDDFEYMKAGIQHHVLDYLLKPVDHAQLE 111
Cdd:PRK15479  30 VFDGLAADHLLQSEMYALAVLDINMPGMDGLEVLQRLRKRGQTlpVLLLTARSAVADRVKGLNVGADDYLPKPFELEELD 109


                 ....*...
gi 582378446 112 VILGRLVR 119
Cdd:PRK15479 110 ARLRALLR 117

PRK10360

transcriptional regulator UhpA;

1-84

5.90e-04

transcriptional regulator UhpA;

Pssm-ID: 182408 [Multi-domain] Cd Length: 196 Bit Score: 39.96 E-value: 5.90e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   1 MFKVVICDDERIIREGLKQIIPWgDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIAlLDCNVIIL 80
Cdd:PRK10360   1 MITVALIDDHLIVRSGFAQLLGL-EPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLP-KGMATIML 78


                 ....
gi 582378446  81 SSYD 84
Cdd:PRK10360  79 SVHD 82

ftrA

PRK09393

transcriptional activator FtrA; Provisional

154-250

6.90e-04

transcriptional activator FtrA; Provisional

Pssm-ID: 181818 [Multi-domain] Cd Length: 322 Bit Score: 40.33 E-value: 6.90e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446 154 QIVDQIKQSYQTKVTVSDLIQHIDVSESYAMRTFKDHVGITIVDYLNRYRILQSLQLLDRHYKHYE-IADKVGFSEYKMF 232
Cdd:PRK09393 222 PLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLLESSALSIDqIAERAGFGSEESL 301

                         90
                 ....*....|....*...
gi 582378446 233 SYHFKKYLQMSPSDYCKQ 250
Cdd:PRK09393 302 RHHFRRRAATSPAAYRKR 319

REC_OmpR_BsPhoP-like

cd19937

phosphoacceptor receiver (REC) domain of BsPhoP-like OmpR family response regulators; Bacillus ...

6-66

7.24e-04

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: 38.41 E-value: 7.24e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 582378446   6 ICDDERIIREGLKqiipwgdyhFN------TIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDL 66
Cdd:cd19937    2 VVDDEEDIVELLK---------YNlekegyEVVTAYDGEEALKRAKDEKPDLIILDLMLPGIDGLEV 59

REC_OmpR_CtrA

cd17616

phosphoacceptor receiver (REC) domain of CtrA-like OmpR family response regulators; CtrA is ...

31-110

7.59e-04

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: 38.16 E-value: 7.59e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  31 IYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVIILSSYDDFEYMKAGIQHHVLDYLLKPVDHA 108
Cdd:cd17616   25 VYTTDLGEEGLDLGKLYDYDIILLDLNLPDMSGYEVLRTLrlAKVKTPILILSGLADIEDKVKGLGFGADDYMTKPFHKD 104


                 ..
gi 582378446 109 QL 110
Cdd:cd17616  105 EL 106

REC_typeA_ARR

cd17581

phosphoacceptor receiver (REC) domain of type A Arabidopsis response regulators (ARRs) and ...

36-105

1.01e-03

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: 38.12 E-value: 1.01e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 582378446  36 DGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI----ALLDCNVIILSSYDDFEY----MKAGIQhhvlDYLLKPV 105
Cdd:cd17581   41 EDEEDSSNFNEPKVNMIITDYCMPGMTGYDLLKKVkessALKEIPVVIMSSENIPTRisrcLEEGAE----DFLLKPV 114

PRK10701

DNA-binding transcriptional regulator RstA; Provisional

37-127

1.35e-03

DNA-binding transcriptional regulator RstA; Provisional

Pssm-ID: 236738 [Multi-domain] Cd Length: 240 Bit Score: 38.85 E-value: 1.35e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  37 GVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI-ALLDCNVIILSSYD-DFeymkagiqHHVL-------DYLLKPVDH 107
Cdd:PRK10701  34 GDRAEATILREQPDLVLLDIMLPGKDGMTICRDLrPKWQGPIVLLTSLDsDM--------NHILalemgacDYILKTTPP 105

                         90       100
                 ....*....|....*....|
gi 582378446 108 AqleVILGRLvRTLLEQQSQ 127
Cdd:PRK10701 106 A---VLLARL-RLHLRQNEQ 121

REC_OmpR_CusR-like

cd19935

phosphoacceptor receiver (REC) domain of CusR-like OmpR family response regulators; ...

34-104

1.55e-03

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: 37.03 E-value: 1.55e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  34 AKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI--ALLDCNVIILSSyddfeymKAGIQHHVL-------DYLLKP 104
Cdd:cd19935   28 AYDGEDGLHLALTNEYDLIILDVMLPGLDGLEVLRRLraAGKQTPVLMLTA-------RDSVEDRVKgldlgadDYLVKP 100

psREC_PRR

cd17582

pseudo receiver domain of pseudo-response regulators; In Arabidopsis, five pseudo-response ...

34-104

1.56e-03

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: 36.99 E-value: 1.56e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446  34 AKDGVEALSLIQQHQPE--LVITDIRMPRKNGVDLLNDI----ALLDCNVIILSSYDD----FEYMKAGiqhhVLDYLLK 103
Cdd:cd17582   28 ASDGLQAWDVLEDEQNEidLILTEVDLPVSSGFKLLSYImrhkICKNIPVIMMSSQDSvgvvFKCLSKG----AADYLVK 103


                 .
gi 582378446 104 P 104
Cdd:cd17582  104 P 104

PRK10529

DNA-binding transcriptional activator KdpE; Provisional

1-123

2.00e-03

DNA-binding transcriptional activator KdpE; Provisional

Pssm-ID: 182522 [Multi-domain] Cd Length: 225 Bit Score: 38.25 E-value: 2.00e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   1 MFKVVICDDERIIREGLKQIIPWGDYHFNTIYTAKDG-VEALSliqqHQPELVITDIRMPRKNGVDLLNDIALLDC-NVI 78
Cdd:PRK10529   1 MTNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGlLEAAT----RKPDLIILDLGLPDGDGIEFIRDLRQWSAiPVI 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 582378446  79 ILSSYDDFEYMKAGIQHHVLDYLLKPVD----HAQLEVILGRLVRTLLE 123
Cdd:PRK10529  77 VLSARSEESDKIAALDAGADDYLSKPFGigelQARLRVALRRHSATPAP 125

REC_LytTR_AgrA-like

cd17533

phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AgrA; ...

2-104

2.42e-03

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: 37.22 E-value: 2.42e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   2 FKVVICDDERIIREGLKQIIP------WGDYHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLD- 74
Cdd:cd17533    1 MNIFILEDDKIQRVRLEEIIEnilkieNIEYVIELTGKTEELLEKIKERGKNGIYFLDIDIKMEEKNGLEVAQKIRKYDp 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 582378446  75 -CNVIILSSYDdfEYMKAGIQHHV--LDYLLKP 104
Cdd:cd17533   81 yAIIIFVTTHS--EFAPLTFEYKVaaLDFILKP 111

PRK09836

DNA-binding transcriptional activator CusR; Provisional

3-124

2.71e-03

DNA-binding transcriptional activator CusR; Provisional

Pssm-ID: 182102 [Multi-domain] Cd Length: 227 Bit Score: 37.98 E-value: 2.71e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDYhfnTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNdiALLDCN----VI 78
Cdd:PRK09836   2 KLLIVEDEKKTGEYLTKGLTEAGF---VVDLADNGLNGYHLAMTGDYDLIILDIMLPDVNGWDIVR--MLRSANkgmpIL 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 582378446  79 ILSSYDDFEYMKAGIQHHVLDYLLKPVDHAQLeviLGRlVRTLLEQ 124
Cdd:PRK09836  77 LLTALGTIEHRVKGLELGADDYLVKPFAFAEL---LAR-VRTLLRR 118

PRK09483

response regulator; Provisional

1-92

2.81e-03

response regulator; Provisional

Pssm-ID: 236538 [Multi-domain] Cd Length: 217 Bit Score: 37.78 E-value: 2.81e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   1 MFKVVICDDERIIREGLKQIIPwgDYH-FNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALL--DCNV 77
Cdd:PRK09483   1 MINVLLVDDHELVRAGIRRILE--DIKgIKVVGEACCGEDAVKWCRTNAVDVVLMDMNMPGIGGLEATRKILRYtpDVKI 78

                         90
                 ....*....|....*....
gi 582378446  78 IILSSYDDFEY----MKAG 92
Cdd:PRK09483  79 IMLTVHTENPLpakvMQAG 97

REC_OmpR_NsrR-like

cd18159

phosphoacceptor receiver (REC) domain of Streptococcus agalactiae NsrR-like OmpR family ...

4-121

3.81e-03

phosphoacceptor receiver (REC) domain of Streptococcus agalactiae NsrR-like OmpR family response regulators; Streptococcus agalactiae NsrR is a lantibiotic resistance-associated response regulator and is part of the nisin resistance operon. It is a member of the NsrRK two-component system (TCS) that is involved in the regulation of lantibiotic resistance genes such as a membrane-associated lipoprotein of LanI, and the nsr gene cluster which encodes for the resistance protein NSR and the ABC transporter NsrFP, both conferring resistance against nisin. This subfamily also includes Staphylococcus epidermidis GraR, part of the GraR/GraS TCS involved in resistance against cationic antimicrobial peptides, and Bacillus subtilis BceR, part of the BceS/BceR TCS involved in the regulation of bacitracin resistance. 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: 381143 [Multi-domain] Cd Length: 113 Bit Score: 36.11 E-value: 3.81e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   4 VVICDDERIIREGLKQIIPwgDYHFNTIYtAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDI-ALLDCNVIILSS 82
Cdd:cd18159    1 ILIVEDDETIASLLKKHLE--KWGYEVVL-IEDFEDVLEEFLQFKPDLVLLDINLPYFDGFYWCREIrQISNVPIIFISS 77

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 582378446  83 YDDFEYMKAGIQHHVLDYLLKPVDhaqLEVILGRLVRTL 121
Cdd:cd18159   78 RDDNMDQVMAINMGGDDYITKPFD---LDVLLAKIKAIL 113

PRK14084

DNA-binding response regulator;

3-154

4.88e-03

DNA-binding response regulator;

Pssm-ID: 184495 [Multi-domain] Cd Length: 246 Bit Score: 37.42 E-value: 4.88e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 582378446   3 KVVICDDERIIREGLKQIIPWGDyHFNTIYTAKDGVEALSLIQQHQPELVITDIRMPRKNGVDLLNDIALLD--CNVIIL 80
Cdd:PRK14084   2 KALIVDDEPLARNELTYLLNEIG-GFEEINEAENVKETLEALLINQYDIIFLDINLMDESGIELAAKIQKMKepPAIIFA 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 582378446  81 SSYDDFEyMKAgIQHHVLDYLLKPVDHAQLEVILGRLVRTLLEQQSQNGRSLASCHDAFQPLLKVEYDD--YYVNQ 154
Cdd:PRK14084  81 TAHDQFA-VKA-FELNATDYILKPFEQKRIEQAVNKVRATKAKDDNNASAIANDMSANFDQSLPIEIDDkiHMLNQ 154

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