NCBI Conserved Domain Search

Conserved domains on [gi|446367907|ref|WP_000445762|]

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sigma-54 dependent transcriptional regulator [Vibrio cholerae]

Protein Classification

sigma-54-dependent transcriptional regulator( domain architecture ID 11454220)

sigma-54 factor interaction domain-containing protein with a domain similar to that found in the response regulator FleR from Pseudomonas aeruginosa

CATH: 3.40.50.2300

Gene Ontology: GO:0006355|GO:0005524|GO:0000160|GO:0000156|GO:0003677

PubMed: 8830233|20226724|12618438|10966457

SCOP: 4003632

Graphical summary

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List of domain hits

Name

Accession

Description

Interval

E-value

AtoC

COG2204

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

2-439

7.40e-173

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: 491.02 E-value: 7.40e-173

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   2 ESQRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILI 81
Cdd:COG2204    1 SMARILVVDDDPDIRRLLKELLERAGYEVETAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALDPDLPVILL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  82 TGHGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQnalssqsrahyLASAKGLEQILIGQCKSIQLLREQIAK 161
Cdd:COG2204   81 TGYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERALERRR-----------LRRENAEDSGLIGRSPAMQEVRRLIEK 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 162 VAAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTGAVKRRIGKLELADKGTL 241
Cdd:COG2204  150 VAPSDATVLITGESGTGKELVARAIHRLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTGAVARRIGKFELADGGTL 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 242 FLDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELRQHAE---FRQDLFYRLNVAQLYLPPLRERGD 318
Cdd:COG2204  230 FLDEIGEMPLALQAKLLRVLQEREFERVGGNKPIPVDVRVIAATNRDLEELVEegrFREDLYYRLNVFPIELPPLRERRE 309

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 319 DILLLFEHFCVQVKPTWR---SLSEADRLALLTYRWPGNVRELRNVALRYAlddsisvgeILASCPGMTEEEasagLPLA 395
Cdd:COG2204  310 DIPLLARHFLARFAAELGkpvKLSPEALEALLAYDWPGNVRELENVIERAV---------ILADGEVITAED----LPEA 376

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....
gi 446367907 396 IQvhNFERKVIAQALHRHQGNISEVMKELDLPRRTLNQKMQKFG 439
Cdd:COG2204  377 LE--EVERELIERALEETGGNVSRAAELLGISRRTLYRKLKKYG 418

Name

Accession

Description

Interval

E-value

AtoC

COG2204

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

2-439

7.40e-173

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: 491.02 E-value: 7.40e-173

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   2 ESQRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILI 81
Cdd:COG2204    1 SMARILVVDDDPDIRRLLKELLERAGYEVETAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALDPDLPVILL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  82 TGHGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQnalssqsrahyLASAKGLEQILIGQCKSIQLLREQIAK 161
Cdd:COG2204   81 TGYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERALERRR-----------LRRENAEDSGLIGRSPAMQEVRRLIEK 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 162 VAAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTGAVKRRIGKLELADKGTL 241
Cdd:COG2204  150 VAPSDATVLITGESGTGKELVARAIHRLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTGAVARRIGKFELADGGTL 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 242 FLDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELRQHAE---FRQDLFYRLNVAQLYLPPLRERGD 318
Cdd:COG2204  230 FLDEIGEMPLALQAKLLRVLQEREFERVGGNKPIPVDVRVIAATNRDLEELVEegrFREDLYYRLNVFPIELPPLRERRE 309

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 319 DILLLFEHFCVQVKPTWR---SLSEADRLALLTYRWPGNVRELRNVALRYAlddsisvgeILASCPGMTEEEasagLPLA 395
Cdd:COG2204  310 DIPLLARHFLARFAAELGkpvKLSPEALEALLAYDWPGNVRELENVIERAV---------ILADGEVITAED----LPEA 376

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....
gi 446367907 396 IQvhNFERKVIAQALHRHQGNISEVMKELDLPRRTLNQKMQKFG 439
Cdd:COG2204  377 LE--EVERELIERALEETGGNVSRAAELLGISRRTLYRKLKKYG 418

ntrC

TIGR01818

nitrogen regulation protein NR(I); This model represents NtrC, a DNA-binding response ...

6-435

1.49e-113

nitrogen regulation protein NR(I); This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc. [Central intermediary metabolism, Nitrogen metabolism, Regulatory functions, DNA interactions, Signal transduction, Two-component systems]

Pssm-ID: 273818 [Multi-domain] Cd Length: 463 Bit Score: 341.72 E-value: 1.49e-113

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907    6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHG 85
Cdd:TIGR01818   1 VWVVDDDRSIRWVLEKALSRAGYEVRTFGNAASVLRALARGQPDLLITDVRMPGEDGLDLLPQIKKRHPQLPVIVMTAHS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   86 DVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQNALSSQSRAHYLASAKGLeqilIGQCKSIQLLREQIAKVAAM 165
Cdd:TIGR01818  81 DLDTAVAAYQRGAFEYLPKPFDLDEAVTLVERALAHAQEQVALPADAGEAEDSAEL----IGEAPAMQEVFRAIGRLSRS 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  166 DTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTGAVKRRIGKLELADKGTLFLDE 245
Cdd:TIGR01818 157 DITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPKDLIESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDE 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  246 IESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELR---QHAEFRQDLFYRLNVAQLYLPPLRERGDDILL 322
Cdd:TIGR01818 237 IGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQNLEalvRQGKFREDLFHRLNVIRIHLPPLRERREDIPR 316

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  323 LFEHFCVQ------VKPtwRSLSEADRLALLTYRWPGNVRELRNVALRYA------------LDDSISVGEILASCPGMT 384
Cdd:TIGR01818 317 LARHFLALaareldVEP--KLLDPEALERLKQLRWPGNVRQLENLCRWLTvmasgdevlvsdLPAELALTGRPASAPDSD 394

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446367907  385 EEE------------ASAGLP---LAIQVHNFERKVIAQALHRHQGNISEVMKELDLPRRTLNQKM 435
Cdd:TIGR01818 395 GQDswdealeawakqALSRGEqglLDRALPEFERPLLEAALQHTRGHKQEAAALLGWGRNTLTRKL 460

PRK11361

acetoacetate metabolism transcriptional regulator AtoC;

4-440

3.15e-113

acetoacetate metabolism transcriptional regulator AtoC;

Pssm-ID: 183099 [Multi-domain] Cd Length: 457 Bit Score: 340.67 E-value: 3.15e-113

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   4 QRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITG 83
Cdd:PRK11361   5 NRILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIKALKEMRSHETRTPVILMTA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  84 HGDVDMAVKALHQGAFDFIEKPFQPERLaNTVAQAVSQYQnALSSQSRAHY--LASAKGLEQILIGQCKSIQLLREqIAK 161
Cdd:PRK11361  85 YAEVETAVEALRCGAFDYVIKPFDLDEL-NLIVQRALQLQ-SMKKEIRHLHqaLSTSWQWGHILTNSPAMMDICKD-TAK 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 162 VAAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTGAVKRRIGKLELADKGTL 241
Cdd:PRK11361 162 IALSQASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGHEKGAFTGAQTLRQGLFERANEGTL 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 242 FLDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELR---QHAEFRQDLFYRLNVAQLYLPPLRERGD 318
Cdd:PRK11361 242 LLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQamvKEGTFREDLFYRLNVIHLILPPLRDRRE 321

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 319 DILLLFEHFCVQVKP-TWRSLSEADRLA---LLTYRWPGNVRELRNVALRYALddsISVGEIL------------ASCPG 382
Cdd:PRK11361 322 DISLLANHFLQKFSSeNQRDIIDIDPMAmslLTAWSWPGNIRELSNVIERAVV---MNSGPIIfsedlppqirqpVCNAG 398

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446367907 383 MTEEEASAGLPLAIQVHNFERKVIAQALHRHQGNISEVMKELDLPRRTLNQKMQKFGL 440
Cdd:PRK11361 399 EVKTAPVGERNLKEEIKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEYGI 456

Sigma54_activat

pfam00158

Sigma-54 interaction domain;

145-309

2.87e-96

Sigma-54 interaction domain;

Pssm-ID: 425491 [Multi-domain] Cd Length: 168 Bit Score: 286.61 E-value: 2.87e-96

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  145 LIGQCKSIQLLREQIAKVAAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTG 224
Cdd:pfam00158   1 IIGESPAMQEVLEQAKRVAPTDAPVLITGESGTGKELFARAIHQLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  225 AVKRRIGKLELADKGTLFLDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELRQ---HAEFRQDLFY 301
Cdd:pfam00158  81 ADSDRKGLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTKPIKVDVRIIAATNRDLEEavaEGRFREDLYY 160


                  ....*...
gi 446367907  302 RLNVAQLY 309
Cdd:pfam00158 161 RLNVIPIE 168

REC_DctD-like

cd17549

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

6-121

9.75e-49

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: 162.66 E-value: 9.75e-49

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHG 85
Cdd:cd17549    1 VLLVDDDADVREALQQTLELAGFRVRAFADAEEALAALSPDFPGVVISDIRMPGMDGLELLAQIRELDPDLPVILITGHG 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 446367907  86 DVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQ 121
Cdd:cd17549   81 DVPMAVEAMRAGAYDFLEKPFDPERLLDVVRRALEK 116

AAA

smart00382

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...

168-285

1.60e-10

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

Pssm-ID: 214640 [Multi-domain] Cd Length: 148 Bit Score: 59.31 E-value: 1.60e-10

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   168 NVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFES---ELFGHEAGAFTGA--VKRRIGKLELADKGTLF 242
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQlllIIVGGKKASGSGElrLRLALALARKLKPDVLI 83

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 446367907   243 LDEIESMPLAMQVKVLRVLQDhvvERVGSNQPITIDLRVIAAA 285
Cdd:smart00382  84 LDEITSLLDAEQEALLLLLEE---LRLLLLLKSEKNLTVILTT 123

Name

Accession

Description

Interval

E-value

AtoC

COG2204

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

2-439

7.40e-173

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: 491.02 E-value: 7.40e-173

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   2 ESQRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILI 81
Cdd:COG2204    1 SMARILVVDDDPDIRRLLKELLERAGYEVETAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALDPDLPVILL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  82 TGHGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQnalssqsrahyLASAKGLEQILIGQCKSIQLLREQIAK 161
Cdd:COG2204   81 TGYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERALERRR-----------LRRENAEDSGLIGRSPAMQEVRRLIEK 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 162 VAAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTGAVKRRIGKLELADKGTL 241
Cdd:COG2204  150 VAPSDATVLITGESGTGKELVARAIHRLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTGAVARRIGKFELADGGTL 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 242 FLDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELRQHAE---FRQDLFYRLNVAQLYLPPLRERGD 318
Cdd:COG2204  230 FLDEIGEMPLALQAKLLRVLQEREFERVGGNKPIPVDVRVIAATNRDLEELVEegrFREDLYYRLNVFPIELPPLRERRE 309

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 319 DILLLFEHFCVQVKPTWR---SLSEADRLALLTYRWPGNVRELRNVALRYAlddsisvgeILASCPGMTEEEasagLPLA 395
Cdd:COG2204  310 DIPLLARHFLARFAAELGkpvKLSPEALEALLAYDWPGNVRELENVIERAV---------ILADGEVITAED----LPEA 376

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....
gi 446367907 396 IQvhNFERKVIAQALHRHQGNISEVMKELDLPRRTLNQKMQKFG 439
Cdd:COG2204  377 LE--EVERELIERALEETGGNVSRAAELLGISRRTLYRKLKKYG 418

RocR

COG3829

RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...

119-440

5.31e-138

RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis domains [Transcription, Signal transduction mechanisms];

Pssm-ID: 443041 [Multi-domain] Cd Length: 448 Bit Score: 403.38 E-value: 5.31e-138

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 119 VSQYQNALSSQSRAHYLASAKGLEQIlIGQCKSIQLLREQIAKVAAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFV 198
Cdd:COG3829  115 LKRLERKLREEELERGLSAKYTFDDI-IGKSPAMKELLELAKRVAKSDSTVLILGESGTGKELFARAIHNASPRRDGPFV 193

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 199 AINCGAIPENLFESELFGHEAGAFTGAVKR-RIGKLELADKGTLFLDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITI 277
Cdd:COG3829  194 AVNCAAIPENLLESELFGYEKGAFTGAKKGgKPGLFELADGGTLFLDEIGEMPLSLQAKLLRVLQEKEVRRVGGTKPIPV 273

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 278 DLRVIAAA----KEELRQHaEFRQDLFYRLNVAQLYLPPLRERGDDILLLFEHF----CVQVKPTWRSLSEADRLALLTY 349
Cdd:COG3829  274 DVRIIAATnrdlEEMVEEG-RFREDLYYRLNVIPIHIPPLRERKEDIPLLAEHFlekfNKKYGKNIKGISPEALELLLAY 352

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 350 RWPGNVRELRNVALRYAL---DDSISVGEILASCPGMTEEEASAG-LPLAIQVHNFERKVIAQALHRHQGNISEVMKELD 425
Cdd:COG3829  353 DWPGNVRELENVIERAVVlseGDVITPEHLPEYLLEEAEAASAAEeGSLKEALEEVEKELIEEALEKTGGNKSKAAKALG 432

                        330
                 ....*....|....*
gi 446367907 426 LPRRTLNQKMQKFGL 440
Cdd:COG3829  433 ISRSTLYRKLKKYGI 447

ntrC

TIGR01818

nitrogen regulation protein NR(I); This model represents NtrC, a DNA-binding response ...

6-435

1.49e-113

Pssm-ID: 273818 [Multi-domain] Cd Length: 463 Bit Score: 341.72 E-value: 1.49e-113

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907    6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHG 85
Cdd:TIGR01818   1 VWVVDDDRSIRWVLEKALSRAGYEVRTFGNAASVLRALARGQPDLLITDVRMPGEDGLDLLPQIKKRHPQLPVIVMTAHS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   86 DVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQNALSSQSRAHYLASAKGLeqilIGQCKSIQLLREQIAKVAAM 165
Cdd:TIGR01818  81 DLDTAVAAYQRGAFEYLPKPFDLDEAVTLVERALAHAQEQVALPADAGEAEDSAEL----IGEAPAMQEVFRAIGRLSRS 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  166 DTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTGAVKRRIGKLELADKGTLFLDE 245
Cdd:TIGR01818 157 DITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPKDLIESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDE 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  246 IESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELR---QHAEFRQDLFYRLNVAQLYLPPLRERGDDILL 322
Cdd:TIGR01818 237 IGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQNLEalvRQGKFREDLFHRLNVIRIHLPPLRERREDIPR 316

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  323 LFEHFCVQ------VKPtwRSLSEADRLALLTYRWPGNVRELRNVALRYA------------LDDSISVGEILASCPGMT 384
Cdd:TIGR01818 317 LARHFLALaareldVEP--KLLDPEALERLKQLRWPGNVRQLENLCRWLTvmasgdevlvsdLPAELALTGRPASAPDSD 394

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446367907  385 EEE------------ASAGLP---LAIQVHNFERKVIAQALHRHQGNISEVMKELDLPRRTLNQKM 435
Cdd:TIGR01818 395 GQDswdealeawakqALSRGEqglLDRALPEFERPLLEAALQHTRGHKQEAAALLGWGRNTLTRKL 460

PRK11361

acetoacetate metabolism transcriptional regulator AtoC;

4-440

3.15e-113

acetoacetate metabolism transcriptional regulator AtoC;

Pssm-ID: 183099 [Multi-domain] Cd Length: 457 Bit Score: 340.67 E-value: 3.15e-113

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   4 QRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITG 83
Cdd:PRK11361   5 NRILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIKALKEMRSHETRTPVILMTA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  84 HGDVDMAVKALHQGAFDFIEKPFQPERLaNTVAQAVSQYQnALSSQSRAHY--LASAKGLEQILIGQCKSIQLLREqIAK 161
Cdd:PRK11361  85 YAEVETAVEALRCGAFDYVIKPFDLDEL-NLIVQRALQLQ-SMKKEIRHLHqaLSTSWQWGHILTNSPAMMDICKD-TAK 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 162 VAAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTGAVKRRIGKLELADKGTL 241
Cdd:PRK11361 162 IALSQASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGHEKGAFTGAQTLRQGLFERANEGTL 241

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 242 FLDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELR---QHAEFRQDLFYRLNVAQLYLPPLRERGD 318
Cdd:PRK11361 242 LLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQamvKEGTFREDLFYRLNVIHLILPPLRDRRE 321

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 319 DILLLFEHFCVQVKP-TWRSLSEADRLA---LLTYRWPGNVRELRNVALRYALddsISVGEIL------------ASCPG 382
Cdd:PRK11361 322 DISLLANHFLQKFSSeNQRDIIDIDPMAmslLTAWSWPGNIRELSNVIERAVV---MNSGPIIfsedlppqirqpVCNAG 398

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446367907 383 MTEEEASAGLPLAIQVHNFERKVIAQALHRHQGNISEVMKELDLPRRTLNQKMQKFGL 440
Cdd:PRK11361 399 EVKTAPVGERNLKEEIKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEYGI 456

PEP_resp_reg

TIGR02915

PEP-CTERM-box response regulator transcription factor; Members of this protein family share ...

8-440

1.09e-111

PEP-CTERM-box response regulator transcription factor; Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC (see SP|Q06065). These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158). [Regulatory functions, DNA interactions]

Pssm-ID: 274348 [Multi-domain] Cd Length: 445 Bit Score: 336.34 E-value: 1.09e-111

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907    8 LIEDDDIVRQATGQWlQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLP-DTDGLSL-LVALKNVQSLMP---VILIT 82
Cdd:TIGR02915   2 LIVEDDLGLQKQLKW-SFADYELAVAADRESAIALVRRHEPAVVTLDLGLPpDADGASEgLAALQQILAIAPdtkVIVIT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   83 GHGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQnaLSSQSRAHYLASAKGLEQILIGQCKSIQLLREQIAKV 162
Cdd:TIGR02915  81 GNDDRENAVKAIGLGAYDFYQKPIDPDVLKLIVDRAFHLYT--LETENRRLQSALGGTALRGLITSSPGMQKICRTIEKI 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  163 AAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTGAVKRRIGKLELADKGTLF 242
Cdd:TIGR02915 159 APSDITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIPENLLESELFGYEKGAFTGAVKQTLGKIEYAHGGTLF 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  243 LDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELRQHAE---FRQDLFYRLNVAQLYLPPLRERGDD 319
Cdd:TIGR02915 239 LDEIGDLPLNLQAKLLRFLQERVIERLGGREEIPVDVRIVCATNQDLKRMIAegtFREDLFYRIAEISITIPPLRSRDGD 318

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  320 ILLL----FEHFCVQVKPTWRSLSEADRLALLTYRWPGNVRELRNVALRYALddsISVGEILAS----CPGMTEEEASAG 391
Cdd:TIGR02915 319 AVLLanafLERFARELKRKTKGFTDDALRALEAHAWPGNVRELENKVKRAVI---MAEGNQITAedlgLDARERAETPLE 395

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*....
gi 446367907  392 LPLAIQVHNFERKVIAQALHRHQGNISEVMKELDLPRRTLNQKMQKFGL 440
Cdd:TIGR02915 396 VNLREVRERAEREAVRKAIARVDGNIARAAELLGITRPTLYDLMKKHGI 444

AcoR

COG3284

Transcriptional regulator DhaR of acetoin/glycerol metabolism [Transcription];

145-439

1.70e-103

Transcriptional regulator DhaR of acetoin/glycerol metabolism [Transcription];

Pssm-ID: 442514 [Multi-domain] Cd Length: 625 Bit Score: 320.69 E-value: 1.70e-103

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 145 LIGQCKSIQLLREQIAKVAAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTG 224
Cdd:COG3284  323 LAGGDPAMRRALRRARRLADRDIPVLILGETGTGKELFARAIHAASPRADGPFVAVNCAAIPEELIESELFGYEPGAFTG 402

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 225 AVKR-RIGKLELADKGTLFLDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELRQHAE---FRQDLF 300
Cdd:COG3284  403 ARRKgRPGKIEQADGGTLFLDEIGDMPLALQARLLRVLQEREVTPLGGTKPIPVDVRLIAATHRDLRELVAagrFREDLY 482

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 301 YRLNVAQLYLPPLRERgDDILLLFEHFCVQVKPTWR--SLSEADRLALLTYRWPGNVRELRNVaLRYAL----DDSISVG 374
Cdd:COG3284  483 YRLNGLTLTLPPLRER-EDLPALIEHLLRELAAGRGplRLSPEALALLAAYPWPGNVRELRNV-LRTALaladGGVITVE 560

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446367907 375 ----EILASCPGMTEEEASAGLPLAIQvhnfERKVIAQALHRHQGNISEVMKELDLPRRTLNQKMQKFG 439
Cdd:COG3284  561 dlpdELRAELAAAAPAAAAPLTSLEEA----ERDAILRALRACGGNVSAAARALGISRSTLYRKLKRYG 625

PRK05022

nitric oxide reductase transcriptional regulator NorR;

123-440

4.11e-99

nitric oxide reductase transcriptional regulator NorR;

Pssm-ID: 235331 [Multi-domain] Cd Length: 509 Bit Score: 305.94 E-value: 4.11e-99

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 123 QNALSSQSRAHYLASAKGLEQILIGQCKSIQLLREQIAKVAAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINC 202
Cdd:PRK05022 167 SQAELPQDVAEFLRQEALKEGEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASPRADKPLVYLNC 246

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 203 GAIPENLFESELFGHEAGAFTGAVKRRIGKLELADKGTLFLDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVI 282
Cdd:PRK05022 247 AALPESLAESELFGHVKGAFTGAISNRSGKFELADGGTLFLDEIGELPLALQAKLLRVLQYGEIQRVGSDRSLRVDVRVI 326

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 283 AAAKEELRQHAE---FRQDLFYRLNVAQLYLPPLRERGDDILLLFEHFCVQVkptwRS--------LSEADRLALLTYRW 351
Cdd:PRK05022 327 AATNRDLREEVRagrFRADLYHRLSVFPLSVPPLRERGDDVLLLAGYFLEQN----RArlglrslrLSPAAQAALLAYDW 402

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 352 PGNVRELRNVALRYAL------DDSISV----------GEILASCPGMTEEEASAGLPLAIQVHNFERKVIAQALHRHQG 415
Cdd:PRK05022 403 PGNVRELEHVISRAALlarargAGRIVTleaqhldlpaEVALPPPEAAAAPAAVVSQNLREATEAFQRQLIRQALAQHQG 482

                        330       340
                 ....*....|....*....|....*
gi 446367907 416 NISEVMKELDLPRRTLNQKMQKFGL 440
Cdd:PRK05022 483 NWAAAARALELDRANLHRLAKRLGL 507

PRK10365

sigma-54-dependent response regulator transcription factor ZraR;

8-437

4.57e-99

sigma-54-dependent response regulator transcription factor ZraR;

Pssm-ID: 182412 [Multi-domain] Cd Length: 441 Bit Score: 303.88 E-value: 4.57e-99

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   8 LIEDDDIVRQATGQWLQLA-GFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHGD 86
Cdd:PRK10365   9 LVVDDDISHCTILQALLRGwGYNVALANSGRQALEQVREQVFDLVLCDVRMAEMDGIATLKEIKALNPAIPVLIMTAYSS 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  87 VDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQyqnalsSQSRAHYLASAKGLEQILIGQCKSIQLLREQIAKVAAMD 166
Cdd:PRK10365  89 VETAVEALKTGALDYLIKPLDFDNLQATLEKALAH------THSIDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSE 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 167 TNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTGAVKRRIGKLELADKGTLFLDEI 246
Cdd:PRK10365 163 ATVLIHGDSGTGKELVARAIHASSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEI 242

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 247 ESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELRQHA---EFRQDLFYRLNVAQLYLPPLRERGDDILLL 323
Cdd:PRK10365 243 GDISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVnagRFRQDLYYRLNVVAIEVPSLRQRREDIPLL 322

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 324 FEHFCvqvkptwRSLSEADRLA-----------LLTYRWPGNVRELRNVALRYAL---DDSISVGEI---LASCPgMTEE 386
Cdd:PRK10365 323 AGHFL-------QRFAERNRKAvkgftpqamdlLIHYDWPGNIRELENAVERAVVlltGEYISERELplaIASTP-IPLG 394

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446367907 387 EASAGLPLAiqvhNFERKVIAQALHRHQGNISEVMKELDLPRRTLNQKMQK 437
Cdd:PRK10365 395 QSQDIQPLV----EVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKLSR 441

PRK15115

response regulator GlrR; Provisional

3-419

2.31e-97

response regulator GlrR; Provisional

Pssm-ID: 185070 [Multi-domain] Cd Length: 444 Bit Score: 299.44 E-value: 2.31e-97

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   3 SQRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILIT 82
Cdd:PRK15115   5 PAHLLLVDDDPGLLKLLGMRLTSEGYSVVTAESGQEALRVLNREKVDLVISDLRMDEMDGMQLFAEIQKVQPGMPVIILT 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  83 GHGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQNALSSQSRAHYLASAKGLEQILigqcksiqllrEQIAKV 162
Cdd:PRK15115  85 AHGSIPDAVAATQQGVFSFLTKPVDRDALYKAIDDALEQSAPATDERWREAIVTRSPLMLRLL-----------EQARMV 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 163 AAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTGAVKRRIGKLELADKGTLF 242
Cdd:PRK15115 154 AQSDVSVLINGQSGTGKEILAQAIHNASPRASKPFIAINCGALPEQLLESELFGHARGAFTGAVSNREGLFQAAEGGTLF 233

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 243 LDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEEL---RQHAEFRQDLFYRLNVAQLYLPPLRERGDD 319
Cdd:PRK15115 234 LDEIGDMPAPLQVKLLRVLQERKVRPLGSNRDIDIDVRIISATHRDLpkaMARGEFREDLYYRLNVVSLKIPALAERTED 313

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 320 ILLLFEHFCVQV----KPTWRSLSEADRLALLTYRWPGNVRELRNVALR-YALDDSISVGEILASCPGMTEEEAsagLPL 394
Cdd:PRK15115 314 IPLLANHLLRQAaerhKPFVRAFSTDAMKRLMTASWPGNVRQLVNVIEQcVALTSSPVISDALVEQALEGENTA---LPT 390

                        410       420
                 ....*....|....*....|....*.
gi 446367907 395 AIQVHN-FERKVIAQALHRHQGNISE 419
Cdd:PRK15115 391 FVEARNqFELNYLRKLLQITKGNVTH 416

Sigma54_activat

pfam00158

Sigma-54 interaction domain;

145-309

2.87e-96

Sigma-54 interaction domain;

Pssm-ID: 425491 [Multi-domain] Cd Length: 168 Bit Score: 286.61 E-value: 2.87e-96

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  145 LIGQCKSIQLLREQIAKVAAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTG 224
Cdd:pfam00158   1 IIGESPAMQEVLEQAKRVAPTDAPVLITGESGTGKELFARAIHQLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  225 AVKRRIGKLELADKGTLFLDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELRQ---HAEFRQDLFY 301
Cdd:pfam00158  81 ADSDRKGLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTKPIKVDVRIIAATNRDLEEavaEGRFREDLYY 160


                  ....*...
gi 446367907  302 RLNVAQLY 309
Cdd:pfam00158 161 RLNVIPIE 168

glnG

PRK10923

nitrogen regulation protein NR(I); Provisional

1-440

3.89e-95

nitrogen regulation protein NR(I); Provisional

Pssm-ID: 182842 [Multi-domain] Cd Length: 469 Bit Score: 294.47 E-value: 3.89e-95

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   1 MESQRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVIL 80
Cdd:PRK10923   1 MQRGIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLEALASKTPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVII 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  81 ITGHGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQNalSSQSRAhylASAKGLEQILIGQCKSIQLLREQIA 160
Cdd:PRK10923  81 MTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISHYQE--QQQPRN---IQVNGPTTDIIGEAPAMQDVFRIIG 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 161 KVAAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTGAVKRRIGKLELADKGT 240
Cdd:PRK10923 156 RLSRSSISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIPKDLIESELFGHEKGAFTGANTIRQGRFEQADGGT 235

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 241 LFLDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELR---QHAEFRQDLFYRLNVAQLYLPPLRERG 317
Cdd:PRK10923 236 LFLDEIGDMPLDVQTRLLRVLADGQFYRVGGYAPVKVDVRIIAATHQNLEqrvQEGKFREDLFHRLNVIRVHLPPLRERR 315

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 318 DDILLLFEHFCVQ------VKPtwRSLSEADRLALLTYRWPGNVRELRNVA--------------------LRYALDDSI 371
Cdd:PRK10923 316 EDIPRLARHFLQVaarelgVEA--KLLHPETEAALTRLAWPGNVRQLENTCrwltvmaagqevliqdlpgeLFESTVPES 393

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446367907 372 SVGEILASCPGMTEEEASAGLP------LAIQVHNFERKVIAQALHRHQGNISEVMKELDLPRRTLNQKMQKFGL 440
Cdd:PRK10923 394 TSQMQPDSWATLLAQWADRALRsghqnlLSEAQPELERTLLTTALRHTQGHKQEAARLLGWGRNTLTRKLKELGM 468

phageshock_pspF

TIGR02974

psp operon transcriptional activator PspF; Members of this protein family are PspF, the ...

145-416

2.35e-85

psp operon transcriptional activator PspF; Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH [Regulatory functions, DNA interactions]

Pssm-ID: 274371 [Multi-domain] Cd Length: 329 Bit Score: 264.54 E-value: 2.35e-85

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  145 LIGQCKSIQLLREQIAKVAAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTG 224
Cdd:TIGR02974   1 LIGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAALSENLLDSELFGHEAGAFTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  225 AVKRRIGKLELADKGTLFLDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELRQHAE---FRQDLFY 301
Cdd:TIGR02974  81 AQKRHQGRFERADGGTLFLDELATASLLVQEKLLRVIEYGEFERVGGSQTLQVDVRLVCATNADLPALAAegrFRADLLD 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  302 RLNVAQLYLPPLRERGDDILLLFEHF----CVQVK-PTWRSLSEADRLALLTYRWPGNVRELRNVALR---------YAL 367
Cdd:TIGR02974 161 RLAFDVITLPPLRERQEDIMLLAEHFairmARELGlPLFPGFTPQAREQLLEYHWPGNVRELKNVVERsvyrhgleeAPI 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446367907  368 DDSI------------------SVGEILASCPGMTEEEASAGLPLAIQVHNFERKVIAQALHRHQGN 416
Cdd:TIGR02974 241 DEIIidpfaspwrpkqaapavdEVNSTPTDLPSPSSIAAAFPLDLKQAQQDYEIELLQQALAEAQFN 307

TyrR

COG3283

Transcriptional regulator TyrR of aromatic amino acids metabolism [Transcription, Amino acid ...

126-364

7.82e-81

Transcriptional regulator TyrR of aromatic amino acids metabolism [Transcription, Amino acid transport and metabolism];

Pssm-ID: 442513 [Multi-domain] Cd Length: 514 Bit Score: 258.97 E-value: 7.82e-81

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 126 LSSQSRAHYLASAKGLEQIlIGQCKSIQLLREQIAKVAAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAI 205
Cdd:COG3283  188 LGEQLQALQVNDDSGFDHI-VASSPKMRQVIRQAKKMAMLDAPLLIQGETGTGKELLARACHLASPRGDKPFLALNCAAL 266

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 206 PENLFESELFGHEAGAFTGAVKRRIGKLELADKGTLFLDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAA 285
Cdd:COG3283  267 PDDVAESELFGYAPGAFGNAREGKKGLFEQANGGTVFLDEIGEMSPQLQAKLLRFLQDGTFRRVGEEQEVKVDVRVICAT 346

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 286 K---EELRQHAEFRQDLFYRLNVAQLYLPPLRERGDDILLLFEHFCVQ-------VKPTwrsLSEADRLALLTYRWPGNV 355
Cdd:COG3283  347 QkdlAELVQEGEFREDLYYRLNVLTLTLPPLRERKSDILPLAEHFVARfsqqlgrPRPR---LSPDLVDFLQSYPWPGNV 423


                 ....*....
gi 446367907 356 RELRNVALR 364
Cdd:COG3283  424 RQLENALYR 432

PRK15424

propionate catabolism operon regulatory protein PrpR; Provisional

112-437

9.93e-81

propionate catabolism operon regulatory protein PrpR; Provisional

Pssm-ID: 237963 [Multi-domain] Cd Length: 538 Bit Score: 259.27 E-value: 9.93e-81

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 112 ANTVAQAVSQYQN--ALSSQSRAHY-----LASAKGLEQILiGQCKSIQLLREQIAKVAAMDTNVIIYGETGCGKELVAQ 184
Cdd:PRK15424 182 AATVRQAFEDALDmtRMTLRHNTHYatrnaLRTRYVLGDLL-GQSPQMEQVRQTILLYARSSAAVLIQGETGTGKELAAQ 260

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 185 CLHQA--------SERQRGQFVAINCGAIPENLFESELFGHEAGAFTGAvKR--RIGKLELADKGTLFLDEIESMPLAMQ 254
Cdd:PRK15424 261 AIHREyfarhdarQGKKSHPFVAVNCGAIAESLLEAELFGYEEGAFTGS-RRggRAGLFEIAHGGTLFLDEIGEMPLPLQ 339

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 255 VKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELRQHAE---FRQDLFYRLNVAQLYLPPLRERGDDILLLFEHFCVQ- 330
Cdd:PRK15424 340 TRLLRVLEEKEVTRVGGHQPVPVDVRVISATHCDLEEDVRqgrFRRDLFYRLSILRLQLPPLRERVADILPLAESFLKQs 419

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 331 -------VKPTWRSLSEADRLALLTYRWPGNVRELRNVALRYAL------DDSISVGEILASCPGMTEEEASAGLPLAiq 397
Cdd:PRK15424 420 laalsapFSAALRQGLQQCETLLLHYDWPGNVRELRNLMERLALflsvepTPDLTPQFLQLLLPELARESAKTPAPRL-- 497

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|
gi 446367907 398 vhnfERKVIAQALHRHQGNISEVMKELDLPRRTLNQKMQK 437
Cdd:PRK15424 498 ----LAATLQQALERFNGDKTAAANYLGISRTTLWRRLKA 533

propionate_PrpR

TIGR02329

propionate catabolism operon regulatory protein PrpR; At least five distinct pathways exists ...

114-437

1.85e-80

propionate catabolism operon regulatory protein PrpR; At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR. [Regulatory functions, DNA interactions]

Pssm-ID: 274079 [Multi-domain] Cd Length: 526 Bit Score: 258.25 E-value: 1.85e-80

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  114 TVAQAVSQYQNALSSQSRAHYLASAkgleqiLIGQCKSIQLLREQIAKVAAMDTNVIIYGETGCGKELVAQCLHQASERQ 193
Cdd:TIGR02329 189 TRLRQAATLRSATRNQLRTRYRLDD------LLGASAPMEQVRALVRLYARSDATVLILGESGTGKELVAQAIHQLSGRR 262

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  194 RGQFVAINCGAIPENLFESELFGHEAGAFTGAVK-RRIGKLELADKGTLFLDEIESMPLAMQVKVLRVLQDHVVERVGSN 272
Cdd:TIGR02329 263 DFPFVAINCGAIAESLLEAELFGYEEGAFTGARRgGRTGLIEAAHRGTLFLDEIGEMPLPLQTRLLRVLEEREVVRVGGT 342

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  273 QPITIDLRVIAA---AKEELRQHAEFRQDLFYRLNVAQLYLPPLRERGDDILLLFEHFCVQ--------VKPTWRSLSEA 341
Cdd:TIGR02329 343 EPVPVDVRVVAAthcALTTAVQQGRFRRDLFYRLSILRIALPPLRERPGDILPLAAEYLVQaaaalrlpDSEAAAQVLAG 422

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  342 DRLALLTYRWPGNVRELRNVALRYALDDS------ISVGEILASCPGMTEEEASAGLPL--AIQVHNFERKVIAQALHRH 413
Cdd:TIGR02329 423 VADPLQRYPWPGNVRELRNLVERLALELSampagaLTPDVLRALAPELAEASGKGKTSAlsLRERSRVEALAVRAALERF 502

                         330       340
                  ....*....|....*....|....
gi 446367907  414 QGNISEVMKELDLPRRTLNQKMQK 437
Cdd:TIGR02329 503 GGDRDAAAKALGISRTTLWRRLKA 526

nifA

TIGR01817

Nif-specific regulatory protein; This model represents NifA, a DNA-binding regulatory protein ...

109-366

1.84e-77

Nif-specific regulatory protein; This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms. [Central intermediary metabolism, Nitrogen fixation, Regulatory functions, DNA interactions]

Pssm-ID: 273817 [Multi-domain] Cd Length: 534 Bit Score: 250.79 E-value: 1.84e-77

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  109 ERLANTVAQAVSQYQNAL---------------SSQSRAHYLASAK-GLEQILIGQCKSIQLLREQIAKVAAMDTNVIIY 172
Cdd:TIGR01817 146 EMVANLIGQTVRLHRLVAqrrerliaeavqlskQLRDKAPEIARRRsGKEDGIIGKSPAMRQVVDQARVVARSNSTVLLR 225

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  173 GETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTGAVKRRIGKLELADKGTLFLDEIESMPLA 252
Cdd:TIGR01817 226 GESGTGKELIAKAIHYLSPRAKRPFVKVNCAALSETLLESELFGHEKGAFTGAIAQRKGRFELADGGTLFLDEIGEISPA 305

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  253 MQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELR---QHAEFRQDLFYRLNVAQLYLPPLRERGDDILLLFEHFCV 329
Cdd:TIGR01817 306 FQAKLLRVLQEGEFERVGGNRTLKVDVRLVAATNRDLEeavAKGEFRADLYYRINVVPIFLPPLRERREDIPLLAEAFLE 385

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 446367907  330 QV-KPTWRSLS---EADRLaLLTYRWPGNVRELRNVALRYA 366
Cdd:TIGR01817 386 KFnRENGRPLTitpSAIRV-LMSCKWPGNVRELENCLERTA 425

pspF

PRK11608

phage shock protein operon transcriptional activator; Provisional

145-416

5.87e-75

phage shock protein operon transcriptional activator; Provisional

Pssm-ID: 236936 [Multi-domain] Cd Length: 326 Bit Score: 237.65 E-value: 5.87e-75

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 145 LIGQCKSIQLLREQIAKVAAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTG 224
Cdd:PRK11608   8 LLGEANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHEAGAFTG 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 225 AVKRRIGKLELADKGTLFLDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELRQHAE---FRQDLFY 301
Cdd:PRK11608  88 AQKRHPGRFERADGGTLFLDELATAPMLVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVAegkFRADLLD 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 302 RLNVAQLYLPPLRERGDDILLLFEHFCVQV-----KPTWRSLSEADRLALLTYRWPGNVRELRNVALR---------YAL 367
Cdd:PRK11608 168 RLAFDVVQLPPLRERQSDIMLMAEHFAIQMcrelgLPLFPGFTERARETLLNYRWPGNIRELKNVVERsvyrhgtseYPL 247

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446367907 368 DDSI-SVGEILASCPGMTEEEASAG--LPLAIQ--VHNFERKVIAQALHRHQGN 416
Cdd:PRK11608 248 DNIIiDPFKRRPAEEAIAVSETTSLptLPLDLRewQHQQEKELLQRSLQQAKFN 301

PRK15429

formate hydrogenlyase transcriptional activator FlhA;

145-440

1.94e-69

formate hydrogenlyase transcriptional activator FlhA;

Pssm-ID: 237965 [Multi-domain] Cd Length: 686 Bit Score: 233.18 E-value: 1.94e-69

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 145 LIGQCKSIQLLREQIAKVAAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTG 224
Cdd:PRK15429 378 IIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPAGLLESDLFGHERGAFTG 457

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 225 AVKRRIGKLELADKGTLFLDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELRQHA---EFRQDLFY 301
Cdd:PRK15429 458 ASAQRIGRFELADKSSLFLDEVGDMPLELQPKLLRVLQEQEFERLGSNKIIQTDVRLIAATNRDLKKMVadrEFRSDLYY 537

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 302 RLNVAQLYLPPLRERGDDILLLFEHFCVQV-KPTWRSLSE--ADRLALLT-YRWPGNVRELRNVALRYALddsISVGEIL 377
Cdd:PRK15429 538 RLNVFPIHLPPLRERPEDIPLLVKAFTFKIaRRMGRNIDSipAETLRTLSnMEWPGNVRELENVIERAVL---LTRGNVL 614

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446367907 378 A-SCPGMT--EEEASAGLPLAIQVHNFERKVIAQALHRHQGNIS---EVMKELDLPRRTLNQKMQKFGL 440
Cdd:PRK15429 615 QlSLPDITlpEPETPPAATVVAQEGEDEYQLIVRVLKETNGVVAgpkGAAQRLGLKRTTLLSRMKRLGI 683

FhlA

COG3604

FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...

157-440

3.18e-62

FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis domains [Transcription, Signal transduction mechanisms];

Pssm-ID: 442823 [Multi-domain] Cd Length: 338 Bit Score: 205.08 E-value: 3.18e-62

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 157 EQIAKVAAmdtnVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESelfgheagaftgavkrrigklela 236
Cdd:COG3604  110 ETLASLAA----VAILGETGTGKELVANAIHELSPRADKPFVKVNCAALPESLLES------------------------ 161

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 237 dkgtlfldeiesmplamqvkvlrvLQDHVVERVGSNQPITIDLRVIAAAK---EELRQHAEFRQDLFYRLNVAQLYLPPL 313
Cdd:COG3604  162 ------------------------LQEGEFERVGGDETIKVDVRIIAATNrdlEEEVAEGRFREDLYYRLNVFPIRLPPL 217

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 314 RERGDDILLLFEHF----CVQVKPTWRSLSEADRLALLTYRWPGNVRELRNVALRYAlddsisvgeILASCPGMTEEEAS 389
Cdd:COG3604  218 RERREDIPLLAEHFlekfSRRLGKPILRLSPEALEALMAYPWPGNVRELENVIERAV---------ILAEGGVLDADDLA 288

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446367907 390 AGLPLAIQvhNFERKVIAQALHRHQGNISEVMKELDLPRRTLNQKMQKFGL 440
Cdd:COG3604  289 PGSREALE--EVEREHILEALERTGGNIAGAARLLGLTPSTLRSRMKKLGI 337

PRK10820

transcriptional regulator TyrR;

142-367

3.23e-59

transcriptional regulator TyrR;

Pssm-ID: 236769 [Multi-domain] Cd Length: 520 Bit Score: 202.22 E-value: 3.23e-59

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 142 EQILIGQCKSIQLLrEQIAKVAAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGA 221
Cdd:PRK10820 204 SQIVAVSPKMRQVV-EQARKLAMLDAPLLITGDTGTGKDLLAYACHLRSPRGKKPFLALNCASIPDDVVESELFGHAPGA 282

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 222 FTGAVKRRIGKLELADKGTLFLDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKE---ELRQHAEFRQD 298
Cdd:PRK10820 283 YPNALEGKKGFFEQANGGSVLLDEIGEMSPRMQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQKnlvELVQKGEFRED 362

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446367907 299 LFYRLNVAQLYLPPLRERGDDILLLFEHFCVQ-------VKPtwrSLSeADRLALLT-YRWPGNVRELRNvALRYAL 367
Cdd:PRK10820 363 LYYRLNVLTLNLPPLRDRPQDIMPLTELFVARfadeqgvPRP---KLA-ADLNTVLTrYGWPGNVRQLKN-AIYRAL 434

REC_DctD-like

cd17549

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

6-121

9.75e-49

Pssm-ID: 381101 [Multi-domain] Cd Length: 130 Bit Score: 162.66 E-value: 9.75e-49

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHG 85
Cdd:cd17549    1 VLLVDDDADVREALQQTLELAGFRVRAFADAEEALAALSPDFPGVVISDIRMPGMDGLELLAQIRELDPDLPVILITGHG 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 446367907  86 DVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQ 121
Cdd:cd17549   81 DVPMAVEAMRAGAYDFLEKPFDPERLLDVVRRALEK 116

PRK11388

DNA-binding transcriptional regulator DhaR; Provisional

141-445

2.68e-48

DNA-binding transcriptional regulator DhaR; Provisional

Pssm-ID: 183114 [Multi-domain] Cd Length: 638 Bit Score: 174.87 E-value: 2.68e-48

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 141 LEQILIGQCKSIQLLReqIAKVAAMDTN-VIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGhea 219
Cdd:PRK11388 324 FDHMPQDSPQMRRLIH--FGRQAAKSSFpVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPDEALAEEFLG--- 398

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 220 GAFTGAVKRRIGKLELADKGTLFLDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELRQHAE---FR 296
Cdd:PRK11388 399 SDRTDSENGRLSKFELAHGGTLFLEKVEYLSPELQSALLQVLKTGVITRLDSRRLIPVDVRVIATTTADLAMLVEqnrFS 478

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 297 QDLFYRLNVAQLYLPPLRERGDDILLLFEH--------FCVQVKPTWRSLSeadrlALLTYRWPGNVRELRNVALRYALD 368
Cdd:PRK11388 479 RQLYYALHAFEITIPPLRMRREDIPALVNNklrslekrFSTRLKIDDDALA-----RLVSYRWPGNDFELRSVIENLALS 553

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 369 DS---ISVGEILASCPGMTEEEASAG--LPLAIQVHNFERKVIAQALHRHQGNISEVMKELDLPRRTLNQKMQKFGLLRG 443
Cdd:PRK11388 554 SDngrIRLSDLPEHLFTEQATDDVSAtrLSTSLSLAELEKEAIINAAQVCGGRIQEMAALLGIGRTTLWRKMKQHGIDAG 633


                 ..
gi 446367907 444 DF 445
Cdd:PRK11388 634 QF 635

FixJ

COG4566

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

6-133

4.33e-37

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: 134.46 E-value: 4.33e-37

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHG 85
Cdd:COG4566    2 VYIVDDDEAVRDSLAFLLESAGLRVETFASAEAFLAALDPDRPGCLLLDVRMPGMSGLELQEELAARGSPLPVIFLTGHG 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 446367907  86 DVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQNALSSQSRAH 133
Cdd:COG4566   82 DVPMAVRAMKAGAVDFLEKPFDDQALLDAVRRALARDRARRAERARRA 129

fixJ

PRK09390

response regulator FixJ; Provisional

1-130

5.23e-33

response regulator FixJ; Provisional

Pssm-ID: 181815 [Multi-domain] Cd Length: 202 Bit Score: 123.57 E-value: 5.23e-33

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   1 MESQRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVIL 80
Cdd:PRK09390   1 SDKGVVHVVDDDEAMRDSLAFLLDSAGFEVRLFESAQAFLDALPGLRFGCVVTDVRMPGIDGIELLRRLKARGSPLPVIV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 446367907  81 ITGHGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQNALSSQS 130
Cdd:PRK09390  81 MTGHGDVPLAVEAMKLGAVDFIEKPFEDERLIGAIERALAQAPEAAKSEA 130

REC_NtrX-like

cd17550

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

8-119

8.81e-31

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: 114.52 E-value: 8.81e-31

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   8 LIEDDDI-VRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHGD 86
Cdd:cd17550    2 LIVDDEEdIRESLSGILEDEGYEVDTAADGEEALKLIKERRPDLVLLDIWLPDMDGLELLKEIKEKYPDLPVIMISGHGT 81

                         90       100       110
                 ....*....|....*....|....*....|...
gi 446367907  87 VDMAVKALHQGAFDFIEKPFQPERLANTVAQAV 119
Cdd:cd17550   82 IETAVKATKLGAYDFIEKPLSLDRLLLTIERAL 114

REC_FixJ

cd17537

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

6-118

9.21e-31

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: 114.61 E-value: 9.21e-31

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHG 85
Cdd:cd17537    3 VYVVDDDEAVRDSLAFLLRSVGLAVKTFTSASAFLAAAPPDQPGCLVLDVRMPGMSGLELQDELLARGSNIPIIFITGHG 82

                         90       100       110
                 ....*....|....*....|....*....|...
gi 446367907  86 DVDMAVKALHQGAFDFIEKPFQPERLANTVAQA 118
Cdd:cd17537   83 DVPMAVEAMKAGAVDFLEKPFRDQVLLDAIEQA 115

Response_reg

pfam00072

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

6-111

8.74e-30

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

Pssm-ID: 395025 [Multi-domain] Cd Length: 111 Bit Score: 111.86 E-value: 8.74e-30

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907    6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHG 85
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEKEGYVVAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTAHG 80

                          90       100
                  ....*....|....*....|....*.
gi 446367907   86 DVDMAVKALHQGAFDFIEKPFQPERL 111
Cdd:pfam00072  81 DEDDAVEALEAGADDFLSKPFDPDEL 106

CheY

COG0784

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

1-124

4.14e-29

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: 110.71 E-value: 4.14e-29

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   1 MESQRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSL--MPV 78
Cdd:COG0784    3 LGGKRILVVDDNPDNRELLRRLLERLGYEVTTAEDGAEALELLRAGPPDLILLDINMPGMDGLELLRRIRALPRLpdIPI 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 446367907  79 ILITGHGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQN 124
Cdd:COG0784   83 IALTAYADEEDRERALEAGADDYLTKPVDPEELLEALRRLLARASA 128

RpfG

COG3437

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

5-144

1.03e-27

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: 109.87 E-value: 1.03e-27

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSL--MPVILIT 82
Cdd:COG3437    8 TVLIVDDDPENLELLRQLLRTLGYDVVTAESGEEALELLLEAPPDLILLDVRMPGMDGFELLRLLRADPSTrdIPVIFLT 87

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446367907  83 GHGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQNALSSQSRAHYLASAKGLEQI 144
Cdd:COG3437   88 ALADPEDRERALEAGADDYLTKPFDPEELLARVRNALELRRLQRELDDLVLYLKLAAPLHDI 149

REC_NtrC

cd19919

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

4-106

1.24e-27

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: 106.20 E-value: 1.24e-27

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   4 QRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITG 83
Cdd:cd19919    1 KTVWIVDDDSSIRWVLERALAGAGLTVTSFENAQEALAALASSQPDVLISDIRMPGMDGLALLAQIKQRHPDLPVIIMTA 80

                         90       100
                 ....*....|....*....|...
gi 446367907  84 HGDVDMAVKALHQGAFDFIEKPF 106
Cdd:cd19919   81 HSDLDSAVSAYQGGAFEYLPKPF 103

REC

cd00156

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

8-105

3.19e-27

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: 104.62 E-value: 3.19e-27

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   8 LIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHGDV 87
Cdd:cd00156    2 IVDDDPAIRELLKSLLEREGYEVDTAADGEEALELLREERPDLVLLDLMMPGMDGLELLRKLRELPPDIPVIVLTAKADE 81

                         90
                 ....*....|....*...
gi 446367907  88 DMAVKALHQGAFDFIEKP 105
Cdd:cd00156   82 EDAVRALELGADDYLVKP 99

OmpR

COG0745

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

3-115

4.83e-27

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: 107.35 E-value: 4.83e-27

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   3 SQRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILIT 82
Cdd:COG0745    1 MPRILVVEDDPDIRELLADALEREGYEVDTAADGEEALELLEEERPDLILLDLMLPGMDGLEVCRRLRARPSDIPIIMLT 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 446367907  83 GHGDVDMAVKALHQGAFDFIEKPFQPERLANTV 115
Cdd:COG0745   81 ARDDEEDRVRGLEAGADDYLTKPFDPEELLARI 113

RtcR

COG4650

Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a ...

157-358

2.27e-26

Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription, Signal transduction mechanisms];

Pssm-ID: 443688 [Multi-domain] Cd Length: 534 Bit Score: 111.46 E-value: 2.27e-26

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 157 EQIAKVAAMDTNVI-IYGETGCGKELVAQ---CLHQASERQRGQFVAINC------GAIpenlfeSELFGHEAGAFTGAV 226
Cdd:COG4650  198 EQIERVAIRSRAPIlLTGPTGAGKSQLARriyELKKARHQVSGRFVEVNCatlrgdGAM------SALFGHVKGAFTGAV 271

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 227 KRRIGKLELADKGTLFLDEIESMPLAMQVKVLRVLQDHVVERVGSNQPITIDLRVIAAAKEELRQ---HAEFRQDLFYRL 303
Cdd:COG4650  272 SDRAGLLRSADGGVLFLDEIGELGLDEQAMLLRAIEEKRFLPVGSDKEVSSDFQLIAGTNRDLRQevaEGRFREDLLARI 351

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446367907 304 NVAQLYLPPLRERGDDIL--LLFE--HFCVQVKPTWRSLSEAdRLALLTY------RWPGNVREL 358
Cdd:COG4650  352 NLWTFRLPGLAERREDIEpnLDYElaRFAREQGRRVRFNKEA-RARYLAFatspeaLWSGNFRDL 415

CitB

COG4565

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

1-130

2.37e-26

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

Pssm-ID: 443622 [Multi-domain] Cd Length: 138 Bit Score: 103.51 E-value: 2.37e-26

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   1 MESQRIALIEDDDIVRQATGQWL-QLAGFD-VAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPV 78
Cdd:COG4565    1 MKMIRVLIVEDDPMVAELLRRYLeRLPGFEvVGVASSGEEALALLAEHRPDLILLDIYLPDGDGLELLRELRARGPDVDV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446367907  79 ILITGHGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQNALSSQS 130
Cdd:COG4565   81 IVITAARDPETVREALRAGVVDYLIKPFTFERLREALERYLEYRRLLREDQE 132

REC_NtrC1-like

cd17572

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

6-123

6.51e-26

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: 101.51 E-value: 6.51e-26

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHG 85
Cdd:cd17572    1 VLLVEDSPSLAALYQEYLSDEGYKVTHVETGKEALAFLSDQPPDVVLLDLKLPDMSGMEILKWIQERSLPTSVIVITAHG 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 446367907  86 DVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQ 123
Cdd:cd17572   81 SVDIAVEAMRLGAYDFLEKPFDADRLRVTVRNALKHRK 118

PleD

COG3706

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

5-115

9.59e-26

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: 103.06 E-value: 9.59e-26

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSL--MPVILIT 82
Cdd:COG3706    3 RILVVDDDPTNRKLLRRLLEAAGYEVVEAADGEEALELLQEHRPDLILLDLEMPDMDGLELCRRLRADPRTadIPIIFLT 82

                         90       100       110
                 ....*....|....*....|....*....|...
gi 446367907  83 GHGDVDMAVKALHQGAFDFIEKPFQPERLANTV 115
Cdd:COG3706   83 ALDDEEDRARALEAGADDYLTKPFDPEELLARV 115

COG4567

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

2-121

2.13e-22

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: 93.83 E-value: 2.13e-22

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   2 ESQRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILI 81
Cdd:COG4567    3 EDRSLLLVDDDEAFARVLARALERRGFEVTTAASVEEALALLEQAPPDYAVLDLRLGDGSGLDLIEALRERDPDARIVVL 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446367907  82 TGHGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQ 121
Cdd:COG4567   83 TGYASIATAVEAIKLGADDYLAKPADADDLLAALERAEGD 122

YesN

COG4753

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

5-105

3.23e-22

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: 90.99 E-value: 3.23e-22

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQ-LAGFDVAMFA-DGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILIT 82
Cdd:COG4753    1 KVLIVDDEPLIREGLKRILEwEAGFEVVGEAeNGEEALELLEEHKPDLVITDINMPGMDGLELLEAIRELDPDTKIIILS 80

                         90       100
                 ....*....|....*....|...
gi 446367907  83 GHGDVDMAVKALHQGAFDFIEKP 105
Cdd:COG4753   81 GYSDFEYAQEAIKLGADDYLLKP 103

REC_RssB-like

cd17555

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

5-107

4.64e-22

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: 90.72 E-value: 4.64e-22

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGH 84
Cdd:cd17555    2 TILVIDDDEVVRESIAAYLEDSGFQVLQAADGRQGLELFRSEQPDLVLCDLRMPEMDGLEVLKQITKESPDTPVIVVSGA 81

                         90       100
                 ....*....|....*....|...
gi 446367907  85 GDVDMAVKALHQGAFDFIEKPFQ 107
Cdd:cd17555   82 GVMSDAVEALRLGAWDYLTKPIE 104

PspF

COG1221

Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain ...

145-361

7.91e-22

Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription, Signal transduction mechanisms];

Pssm-ID: 440834 [Multi-domain] Cd Length: 835 Bit Score: 98.64 E-value: 7.91e-22

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 145 LIGQCKSiqlLREQI--AKVAAM----DTNVIIYGETGCGKELVAQCLHQ-ASERQR----GQFVAINCGAIPEN--LFE 211
Cdd:COG1221  106 LIGANGS---LKNAIeqAKAAILyppkGLHTLILGPTGVGKSFFAELMYEyAIEIGVlpedAPFVVFNCADYANNpqLLM 182

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 212 SELFGHEAGAFTGAVKRRIGKLELADKGTLFLDEIESMPLAMQVKvLRVLQDH-VVERVG-SNQPITIDLRVIAAAKEEL 289
Cdd:COG1221  183 SQLFGYVKGAFTGADKDKEGLIEKADGGILFLDEVHRLPPEGQEM-LFTFMDKgIYRRLGeTEKTRKANVRIIFATTEDP 261

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 290 RQH--AEFRQdlfyRLNVaQLYLPPLRERG-----DDILLLFEHfcvqvkptwrslsEADRL------------ALLTYR 350
Cdd:COG1221  262 ESSllKTFLR----RIPM-VIKLPSLEERSleerlELIKHFFKE-------------EAKRLnkpikvskevlkALLLYD 323

                        250
                 ....*....|.
gi 446367907 351 WPGNVRELRNV 361
Cdd:COG1221  324 CPGNIGQLKSD 334

AAA

cd00009

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...

168-304

2.98e-21

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

Pssm-ID: 99707 [Multi-domain] Cd Length: 151 Bit Score: 89.90 E-value: 2.98e-21

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 168 NVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEagaftgAVKRRIGKLELADKGTLFLDEIE 247
Cdd:cd00009   21 NLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHF------LVRLLFELAEKAKPGVLFIDEID 94

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446367907 248 SMPLAMQVKVLRVLQDHVVERVGSNqpitiDLRVIAAAKEELRQhaEFRQDLFYRLN 304
Cdd:cd00009   95 SLSRGAQNALLRVLETLNDLRIDRE-----NVRVIGATNRPLLG--DLDRALYDRLD 144

REC_YesN-like

cd17536

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

8-123

1.34e-19

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: 83.93 E-value: 1.34e-19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   8 LIEDDDIVRQA---TGQWLQLaGFD-VAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITG 83
Cdd:cd17536    3 IVDDEPLIREGlkkLIDWEEL-GFEvVGEAENGEEALELIEEHKPDIVITDIRMPGMDGLELIEKIRELYPDIKIIILSG 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446367907  84 HGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQ 123
Cdd:cd17536   82 YDDFEYAQKAIRLGVVDYLLKPVDEEELEEALEKAKEELD 121

LytT

COG3279

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

5-172

7.98e-19

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

Pssm-ID: 442510 [Multi-domain] Cd Length: 235 Bit Score: 85.25 E-value: 7.98e-19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWL-QLAGFD-VAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILIT 82
Cdd:COG3279    3 KILIVDDEPLARERLERLLeKYPDLEvVGEASNGEEALELLEEHKPDLVFLDIQMPGLDGFELARQLRELDPPPPIIFTT 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  83 GHGdvDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQNALSSQSRAHYlasakgLEQILIGQCKSIQLLR-EQIAK 161
Cdd:COG3279   83 AYD--EYALEAFEVNAVDYLLKPIDEERLAKALEKAKERLEAKAAAEASPEE------KDRIFVKSGGKLVKIPlDDILY 154

                        170
                 ....*....|.
gi 446367907 162 VAAMDTNVIIY 172
Cdd:COG3279  155 IEAEGNYVKIH 165

REC_OmpR

cd17574

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

8-105

1.02e-18

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: 80.91 E-value: 1.02e-18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   8 LIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHGDV 87
Cdd:cd17574    2 VVEDDEEIAELLSDYLEKEGYEVDTAADGEEALELAREEQPDLIILDVMLPGMDGFEVCRRLREKGSDIPIIMLTAKDEE 81

                         90
                 ....*....|....*...
gi 446367907  88 DMAVKALHQGAFDFIEKP 105
Cdd:cd17574   82 EDKVLGLELGADDYITKP 99

REC_OmpR_PmrA-like

cd17624

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

6-112

2.28e-18

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: 80.61 E-value: 2.28e-18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHG 85
Cdd:cd17624    1 ILLVEDDALLGDGLKTGLRKAGYAVDWVRTGAEAEAALASGPYDLVILDLGLPDGDGLDLLRRWRRQGQSLPVLILTARD 80

                         90       100
                 ....*....|....*....|....*..
gi 446367907  86 DVDMAVKALHQGAFDFIEKPFQPERLA 112
Cdd:cd17624   81 GVDDRVAGLDAGADDYLVKPFALEELL 107

AmiR

COG3707

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

1-123

4.88e-18

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

Pssm-ID: 442921 [Multi-domain] Cd Length: 194 Bit Score: 81.93 E-value: 4.88e-18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   1 MESQRIALIEDDDIVRQATGQWLQLAGFDV-AMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALkNVQSLMPVI 79
Cdd:COG3707    1 MRGLRVLVVDDEPLRRADLREGLREAGYEVvAEAADGEDAVELVRELKPDLVIVDIDMPDRDGLEAARQI-SEERPAPVI 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 446367907  80 LITGHGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQ 123
Cdd:COG3707   80 LLTAYSDPELIERALEAGVSAYLVKPLDPEDLLPALELALARFR 123

REC_RegA-like

cd17563

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

4-105

1.16e-17

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: 78.25 E-value: 1.16e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   4 QRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITG 83
Cdd:cd17563    1 KSLLLVDDDEVFAERLARALERRGFEVETAHSVEEALALAREEKPDYAVLDLRLGGDSGLDLIPPLRALQPDARIVVLTG 80

                         90       100
                 ....*....|....*....|..
gi 446367907  84 HGDVDMAVKALHQGAFDFIEKP 105
Cdd:cd17563   81 YASIATAVEAIKLGADDYLAKP 102

REC_OmpR_CpxR

cd17623

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

6-112

7.27e-17

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: 76.19 E-value: 7.27e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVqSLMPVILITGHG 85
Cdd:cd17623    1 ILLIDDDRELTELLTEYLEMEGFNVRAAHDGEQGLAALLEGSPDLVVLDVMLPKMNGLDVLKELRKT-SQVPVLMLTARG 79

                         90       100
                 ....*....|....*....|....*..
gi 446367907  86 DVDMAVKALHQGAFDFIEKPFQPERLA 112
Cdd:cd17623   80 DDIDRILGLELGADDYLPKPFNPRELV 106

REC_typeB_ARR-like

cd17584

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

8-113

2.39e-16

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: 74.59 E-value: 2.39e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   8 LIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQ--SFAAVVSDVRLPDTDGLSLLVALKNVQSLmPVILITGHG 85
Cdd:cd17584    3 VVDDDPTCLAILKRMLLRCGYQVTTCTDAEEALSMLRENkdEFDLVITDVHMPDMDGFEFLELIRLEMDL-PVIMMSADG 81

                         90       100
                 ....*....|....*....|....*...
gi 446367907  86 DVDMAVKALHQGAFDFIEKPFQPERLAN 113
Cdd:cd17584   82 STSTVMKGLAHGACDYLLKPVSIEDLKN 109

REC_CheY4-like

cd17562

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

5-116

3.08e-16

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: 74.64 E-value: 3.08e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDI-VRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLM--PVILI 81
Cdd:cd17562    1 KKILAVDDSAsIRQMVSFTLRGAGYEVVEAADGRDALSKAQSKKFDLIITDQNMPNMDGIELIKELRKLPAYKftPILML 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 446367907  82 TGHGDVDMAVKALHQGAFDFIEKPFQPERLANTVA 116
Cdd:cd17562   81 TTESSDEKKQEGKAAGATGWLVKPFDPEQLLEVVK 115

REC_OmpR_PrrA-like

cd17627

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

6-111

4.50e-16

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: 73.96 E-value: 4.50e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHG 85
Cdd:cd17627    1 ILVVDDDRAVRESLRRSLRFEGYEVETAVDGAEALRVISGNRPDAVVLDVMMPRLDGLEVCRRLRAAGNDLPILVLTARD 80

                         90       100
                 ....*....|....*....|....*.
gi 446367907  86 DVDMAVKALHQGAFDFIEKPFQPERL 111
Cdd:cd17627   81 SVSDRVAGLDAGADDYLVKPFALEEL 106

REC_HupR-like

cd17569

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

5-119

5.07e-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: 73.98 E-value: 5.07e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLlvaLKNVQSLMPV---ILI 81
Cdd:cd17569    2 TILLVDDEPNILKALKRLLRREGYEVLTATSGEEALEILKQEPVDVVISDQRMPGMDGAEL---LKRVRERYPDtvrILL 78

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 446367907  82 TGHGDVDMAVKALHQGA-FDFIEKPFQPERLANTVAQAV 119
Cdd:cd17569   79 TGYADLDAAIEAINEGEiYRFLTKPWDDEELKETIRQAL 117

REC_CpdR_CckA-like

cd18160

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

5-106

8.95e-16

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: 72.92 E-value: 8.95e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQS-FAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITG 83
Cdd:cd18160    1 TILLADDEPSVRKFIVTTLKKAGYAVTEAESGAEALEKLQQGKdIDIVVTDIVMPEMDGIELAREARKIDPDVKILFISG 80

                         90       100
                 ....*....|....*....|...
gi 446367907  84 HGDVDMAVKALHQGAFDFIEKPF 106
Cdd:cd18160   81 GAAAAPELLSDAVGDNATLKKPF 103

REC_NarL-like

cd17535

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

6-118

1.91e-15

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: 72.16 E-value: 1.91e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLA-GFDVAM-FADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITG 83
Cdd:cd17535    1 VLIVDDHPLVREGLRRLLESEpDIEVVGeAADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRRYPDLKVIVLTA 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 446367907  84 HGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQA 118
Cdd:cd17535   81 HDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAV 115

REC_OmpR_DrrD-like

cd17625

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

8-112

1.94e-15

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: 72.25 E-value: 1.94e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   8 LIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHGDV 87
Cdd:cd17625    2 VVEDEKDLSEAITKHLKKEGYTVDVCFDGEEGLEYALSGIYDLIILDIMLPGMDGLEVLKSLREEGIETPVLLLTALDAV 81

                         90       100
                 ....*....|....*....|....*.
gi 446367907  88 DMAVKALHQGAFDFIEKPFQ-PERLA 112
Cdd:cd17625   82 EDRVKGLDLGADDYLPKPFSlAELLA 107

REC_OmpR_ArcA_TorR-like

cd17619

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

5-111

3.13e-15

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: 71.65 E-value: 3.13e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKnVQSLMPVILITGH 84
Cdd:cd17619    2 HILIVEDEPVTRATLKSYFEQEGYDVSEAGDGEEMRQILARQDIDLVLLDINLPGKDGLSLTRELR-EQSEVGIILVTGR 80

                         90       100
                 ....*....|....*....|....*...
gi 446367907  85 G-DVDMAVkALHQGAFDFIEKPFQPERL 111
Cdd:cd17619   81 DdEVDRIV-GLEIGADDYVTKPFNPREL 107

REC_hyHK_CKI1_RcsC-like

cd17546

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

6-115

3.83e-15

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: 71.35 E-value: 3.83e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSL---LVALKNVQSLMPVILIT 82
Cdd:cd17546    1 VLVVDDNPVNRKVLKKLLEKLGYEVDVAENGQEALELLKEEPFDLVLMDLQMPVMDGLEAtrrIRELEGGGRRTPIIALT 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 446367907  83 GHGDVDMAVKALHQGAFDFIEKPFQPERLANTV 115
Cdd:cd17546   81 ANALEEDREKCLEAGMDDYLSKPVKLDQLKEVL 113

REC_OmpR_MtPhoP-like

cd17615

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

5-111

1.55e-14

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

Pssm-ID: 381131 [Multi-domain] Cd Length: 118 Bit Score: 69.69 E-value: 1.55e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGH 84
Cdd:cd17615    1 RVLVVDDEPNITELLSMALRYEGWDVETAADGAEALAAAREFRPDAVVLDIMLPDMDGLEVLRRLRADGPDVPVLFLTAK 80

                         90       100
                 ....*....|....*....|....*..
gi 446367907  85 GDVDMAVKALHQGAFDFIEKPFQPERL 111
Cdd:cd17615   81 DSVEDRIAGLTAGGDDYVTKPFSLEEV 107

REC_citrate_TCS

cd19925

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

5-117

1.68e-14

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: 69.58 E-value: 1.68e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWL-QLAGFDVAMFAD-GASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILIT 82
Cdd:cd19925    2 NVLIVEDDPMVAEIHRAYVeQVPGFTVIGTAGtGEEALKLLKERQPDLILLDIYLPDGNGLDLLRELRAAGHDVDVIVVT 81

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 446367907  83 GHGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQ 117
Cdd:cd19925   82 AANDVETVREALRLGVVDYLIKPFTFERLRQRLER 116

Sigma54_activ_2

pfam14532

Sigma-54 interaction domain;

146-313

3.60e-14

Sigma-54 interaction domain;

Pssm-ID: 434021 [Multi-domain] Cd Length: 138 Bit Score: 69.29 E-value: 3.60e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  146 IGQCKSIQLLREQIAKVAAMDTNVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESelfgheagaftga 225
Cdd:pfam14532   1 LGASAAIQEIKRRLEQAAQSTLPVFLTGEPGSGKEFCARYLHNPSTPWVQPFDIEYLAHAPLELLEQ------------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  226 vkrrigklelADKGTLFLDEIESMPlamqvkvlRVLQDHVVERVGSNQPitIDLRVIAAAKEELRQHAE---FRQDLFYR 302
Cdd:pfam14532  68 ----------AKGGTLYLKDIADLS--------KALQKGLLLLLAKAEG--YRVRLVCTSSKDLPQLAAaglFDEQLYFE 127

                         170
                  ....*....|.
gi 446367907  303 LNVAQLYLPPL 313
Cdd:pfam14532 128 LSALRLHVPPL 138

PRK15479

transcriptional regulator TctD;

5-111

6.73e-14

transcriptional regulator TctD;

Pssm-ID: 185376 [Multi-domain] Cd Length: 221 Bit Score: 70.52 E-value: 6.73e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDivrqATGQWLQLA----GFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVIL 80
Cdd:PRK15479   2 RLLLAEDNR----ELAHWLEKAlvqnGFAVDCVFDGLAADHLLQSEMYALAVLDINMPGMDGLEVLQRLRKRGQTLPVLL 77

                         90       100       110
                 ....*....|....*....|....*....|.
gi 446367907  81 ITGHGDVDMAVKALHQGAFDFIEKPFQPERL 111
Cdd:PRK15479  78 LTARSAVADRVKGLNVGADDYLPKPFELEEL 108

REC_OmpR_CusR-like

cd19935

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

6-105

1.36e-13

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: 66.31 E-value: 1.36e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHG 85
Cdd:cd19935    1 ILVVEDEKKLAEYLKKGLTEEGYAVDVAYDGEDGLHLALTNEYDLIILDVMLPGLDGLEVLRRLRAAGKQTPVLMLTARD 80

                         90       100
                 ....*....|....*....|
gi 446367907  86 DVDMAVKALHQGAFDFIEKP 105
Cdd:cd19935   81 SVEDRVKGLDLGADDYLVKP 100

REC_OmpR_ChvI-like

cd19936

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

6-105

1.40e-13

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: 66.31 E-value: 1.40e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNvQSLMPVILITGHG 85
Cdd:cd19936    1 IALVDDDRNILTSVSMALEAEGFSVETYTDGASALDGLNARPPDLAILDIKMPRMDGMELLQRLRQ-KSTLPVIFLTSKD 79

                         90       100
                 ....*....|....*....|
gi 446367907  86 DVDMAVKALHQGAFDFIEKP 105
Cdd:cd19936   80 DEIDEVFGLRMGADDYITKP 99

REC_2_DhkD-like

cd17580

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

6-115

4.82e-13

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: 65.17 E-value: 4.82e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSL--MPVILITG 83
Cdd:cd17580    1 ILVVDDNEDAAEMLALLLELEGAEVTTAHSGEEALEAAQRFRPDVILSDIGMPGMDGYELARRLRELPWLanTPAIALTG 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 446367907  84 HGDVDMAVKALHQGaFDF-IEKPFQPERLANTV 115
Cdd:cd17580   81 YGQPEDRERALEAG-FDAhLVKPVDPDELIELI 112

REC_OmpR_MtrA-like

cd17626

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

4-111

1.14e-12

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

Pssm-ID: 381141 [Multi-domain] Cd Length: 115 Bit Score: 64.41 E-value: 1.14e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   4 QRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVqSLMPVILITG 83
Cdd:cd17626    1 ARILVVDDDAALAEMIGIVLRGEGFDPAFCGDGTQALAAFREVRPDLVLLDLMLPGIDGIEVCRQIRAE-SGVPIVMLTA 79

                         90       100
                 ....*....|....*....|....*...
gi 446367907  84 HGDVDMAVKALHQGAFDFIEKPFQPERL 111
Cdd:cd17626   80 KSDTVDVVLGLESGADDYVAKPFKPKEL 107

REC_OmpR_VirG

cd17594

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

6-106

1.15e-12

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: 64.39 E-value: 1.15e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKnVQSLMPVILITGHG 85
Cdd:cd17594    2 VLVVDDDAAMRHLLILYLRERGFDVTAAADGAEEARLMLHRRVDLVLLDLRLGQESGLDLLRTIR-ARSDVPIIIISGDR 80

                         90       100
                 ....*....|....*....|..
gi 446367907  86 DVDMA-VKALHQGAFDFIEKPF 106
Cdd:cd17594   81 RDEIDrVVGLELGADDYLAKPF 102

REC_OmpR_EcPhoP-like

cd19934

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

6-112

1.20e-12

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: 64.23 E-value: 1.20e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHG 85
Cdd:cd19934    1 LLLVEDDALLAAQLKEQLSDAGYVVDVAEDGEEALFQGEEEPYDLVVLDLGLPGMDGLSVLRRWRSEGRATPVLILTARD 80

                         90       100
                 ....*....|....*....|....*..
gi 446367907  86 DVDMAVKALHQGAFDFIEKPFQPERLA 112
Cdd:cd19934   81 SWQDKVEGLDAGADDYLTKPFHIEELL 107

REC_CheY

cd17542

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

8-119

1.29e-12

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: 64.22 E-value: 1.29e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   8 LIEDDDI-VRQATGQWLQLAGFDVAMFA-DGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHG 85
Cdd:cd17542    4 LIVDDAAfMRMMLKDILTKAGYEVVGEAaNGEEAVEKYKELKPDLVTMDITMPEMDGIEALKEIKKIDPNAKVIMCSAMG 83

                         90       100       110
                 ....*....|....*....|....*....|....
gi 446367907  86 DVDMAVKALHQGAFDFIEKPFQPERLANTVAQAV 119
Cdd:cd17542   84 QEEMVKEAIKAGAKDFIVKPFQPERVLEAVEKVL 117

REC_OmpR_BfmR-like

cd19939

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

5-111

1.41e-12

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

Pssm-ID: 381166 [Multi-domain] Cd Length: 116 Bit Score: 63.93 E-value: 1.41e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNvQSLMPVILITGH 84
Cdd:cd19939    1 RILIVEDELELARLTRDYLIKAGLEVSVFTDGQRAVRRIIDEQPSLVVLDIMLPGMDGLTVCREVRE-HSHVPILMLTAR 79

                         90       100
                 ....*....|....*....|....*..
gi 446367907  85 GDVDMAVKALHQGAFDFIEKPFQPERL 111
Cdd:cd19939   80 TEEMDRVLGLEMGADDYLCKPFSPREL 106

PRK11517

DNA-binding response regulator HprR;

5-117

2.03e-12

DNA-binding response regulator HprR;

Pssm-ID: 183172 [Multi-domain] Cd Length: 223 Bit Score: 66.46 E-value: 2.03e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSlMPVILITGH 84
Cdd:PRK11517   2 KILLIEDNQRTQEWVTQGLSEAGYVIDAVSDGRDGLYLALKDDYALIILDIMLPGMDGWQILQTLRTAKQ-TPVICLTAR 80

                         90       100       110
                 ....*....|....*....|....*....|....
gi 446367907  85 GDVDMAVKALHQGAFDFIEKPFQ-PERLANTVAQ 117
Cdd:PRK11517  81 DSVDDRVRGLDSGANDYLVKPFSfSELLARVRAQ 114

REC_OmpR_PhoB

cd17618

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

5-111

5.53e-12

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: 62.27 E-value: 5.53e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSL--MPVILIT 82
Cdd:cd17618    2 TILIVEDEPAIREMIAFNLERAGFDVVEAEDAESAVNLIVEPRPDLILLDWMLPGGSGIQFIRRLKRDEMTrdIPIIMLT 81

                         90       100
                 ....*....|....*....|....*....
gi 446367907  83 GHGDVDMAVKALHQGAFDFIEKPFQPERL 111
Cdd:cd17618   82 ARGEEEDKVRGLEAGADDYITKPFSPREL 110

REC_Ycf29

cd19927

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

6-105

8.46e-12

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: 61.62 E-value: 8.46e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSL--MPVILITG 83
Cdd:cd19927    1 ILLVDDDPGIRLAVKDYLEDQGFTVIAASNGLEALDLLNQYIPDLIISDIIMPGVDGYSLLGKLRKNADFdtIPVIFLTA 80

                         90       100
                 ....*....|....*....|..
gi 446367907  84 HGDVDMAVKALHQGAFDFIEKP 105
Cdd:cd19927   81 KGMTSDRIKGYNAGCDGYLSKP 102

REC_OmpR_BsPhoP-like

cd19937

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

9-111

8.83e-12

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

Pssm-ID: 381164 [Multi-domain] Cd Length: 116 Bit Score: 61.91 E-value: 8.83e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   9 IEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALK--NVQSLMPVILITGHGD 86
Cdd:cd19937    3 VDDEEDIVELLKYNLEKEGYEVVTAYDGEEALKRAKDEKPDLIILDLMLPGIDGLEVCRILRsdPKTSSIPIIMLTAKGE 82

                         90       100
                 ....*....|....*....|....*
gi 446367907  87 VDMAVKALHQGAFDFIEKPFQPERL 111
Cdd:cd19937   83 EFDKVLGLELGADDYITKPFSPREL 107

PRK11083

DNA-binding response regulator CreB; Provisional

1-115

1.47e-11

DNA-binding response regulator CreB; Provisional

Pssm-ID: 236838 [Multi-domain] Cd Length: 228 Bit Score: 63.83 E-value: 1.47e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   1 MESQRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVIL 80
Cdd:PRK11083   1 MQQPTILLVEDEQAIADTLVYALQSEGFTVEWFERGLPALDKLRQQPPDLVILDVGLPDISGFELCRQLLAFHPALPVIF 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 446367907  81 ITG-HGDVDMAVkALHQGAFDFIEKPFQPERLANTV 115
Cdd:PRK11083  81 LTArSDEVDRLV-GLEIGADDYVAKPFSPREVAARV 115

orf27

CHL00148

Ycf27; Reviewed

4-111

1.56e-11

Ycf27; Reviewed

Pssm-ID: 214376 [Multi-domain] Cd Length: 240 Bit Score: 63.97 E-value: 1.56e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   4 QRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNvQSLMPVILITG 83
Cdd:CHL00148   7 EKILVVDDEAYIRKILETRLSIIGYEVITASDGEEALKLFRKEQPDLVILDVMMPKLDGYGVCQEIRK-ESDVPIIMLTA 85

                         90       100
                 ....*....|....*....|....*...
gi 446367907  84 HGDVDMAVKALHQGAFDFIEKPFQPERL 111
Cdd:CHL00148  86 LGDVSDRITGLELGADDYVVKPFSPKEL 113

REC_OmpR_BaeR-like

cd19938

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

5-108

1.57e-11

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

Pssm-ID: 381165 [Multi-domain] Cd Length: 114 Bit Score: 60.85 E-value: 1.57e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLmPVILITGH 84
Cdd:cd19938    1 RILIVEDEPKLAQLLIDYLRAAGYAPTLLAHGDQVLPYVRHTPPDLILLDLMLPGTDGLTLCREIRRFSDV-PIIMVTAR 79

                         90       100
                 ....*....|....*....|....
gi 446367907  85 GDVDMAVKALHQGAFDFIEKPFQP 108
Cdd:cd19938   80 VEEIDRLLGLELGADDYICKPYSP 103

REC_RR468-like

cd17552

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

3-118

1.89e-11

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: 61.03 E-value: 1.89e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   3 SQRIALIEDDDIVRQATGQWLQ-LAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALK---NVQSLmPV 78
Cdd:cd17552    1 SKRILVIDDEEDIREVVQACLEkLAGWEVLTASSGQEGLEKAATEQPDAILLDVMMPDMDGLATLKKLQanpETQSI-PV 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446367907  79 ILITGHGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQA 118
Cdd:cd17552   80 ILLTAKAQPSDRQRFASLGVAGVIAKPFDPLTLAEQIAKL 119

ompR

PRK09468

osmolarity response regulator; Provisional

2-111

2.79e-11

osmolarity response regulator; Provisional

Pssm-ID: 181883 [Multi-domain] Cd Length: 239 Bit Score: 63.45 E-value: 2.79e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   2 ESQRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILI 81
Cdd:PRK09468   4 ENYKILVVDDDMRLRALLERYLTEQGFQVRSAANAEQMDRLLTRESFHLMVLDLMLPGEDGLSICRRLRSQNNPTPIIML 83

                         90       100       110
                 ....*....|....*....|....*....|.
gi 446367907  82 TGHGD-VDMAVkALHQGAFDFIEKPFQPERL 111
Cdd:PRK09468  84 TAKGEeVDRIV-GLEIGADDYLPKPFNPREL 113

REC_OmpR_kpRstA-like

cd17622

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

5-111

2.82e-11

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: 60.47 E-value: 2.82e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLmPVILITGH 84
Cdd:cd17622    2 RILLVEDDPKLARLIADFLESHGFNVVVEHRGDRALEVIAREKPDAVLLDIMLPGIDGLTLCRDLRPKYQG-PILLLTAL 80

                         90       100
                 ....*....|....*....|....*..
gi 446367907  85 GDVDMAVKALHQGAFDFIEKPFQPERL 111
Cdd:cd17622   81 DSDIDHILGLELGADDYVVKPVEPAVL 107

REC_LytTR_AlgR-like

cd17532

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

30-118

3.71e-11

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: 60.24 E-value: 3.71e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  30 VAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHGDvdMAVKALHQGAFDFIEKPFQPE 109
Cdd:cd17532   27 VGEAENGEEALEAIEELKPDVVFLDIQMPGLDGLELAKKLSKLAKPPLIVFVTAYDE--YAVEAFELNAVDYLLKPFSEE 104


                 ....*....
gi 446367907 110 RLANTVAQA 118
Cdd:cd17532  105 RLAEALAKL 113

REC_RcNtrC-like

cd19928

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

8-105

4.13e-11

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: 59.44 E-value: 4.13e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   8 LIEDDD-IVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHGD 86
Cdd:cd19928    2 LVADDDrAIRTVLTQALGRAGYEVRTTGNAATLWRWVEEGEGDLVITDVVMPDENGLDLIPRIKKARPDLPIIVMSAQNT 81

                         90
                 ....*....|....*....
gi 446367907  87 VDMAVKALHQGAFDFIEKP 105
Cdd:cd19928   82 LMTAVKAAERGAFEYLPKP 100

PRK10643

two-component system response regulator PmrA;

5-124

5.66e-11

two-component system response regulator PmrA;

Pssm-ID: 182612 [Multi-domain] Cd Length: 222 Bit Score: 61.98 E-value: 5.66e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGH 84
Cdd:PRK10643   2 KILIVEDDTLLLQGLILALQTEGYACDCASTAREAEALLESGHYSLVVLDLGLPDEDGLHLLRRWRQKKYTLPVLILTAR 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446367907  85 GDVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQN 124
Cdd:PRK10643  82 DTLEDRVAGLDVGADDYLVKPFALEELHARIRALIRRHQG 121

REC_PA4781-like

cd19920

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

8-106

8.46e-11

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

Pssm-ID: 381147 [Multi-domain] Cd Length: 103 Bit Score: 58.68 E-value: 8.46e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   8 LIEDD--DIVRqATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSL--MPVILITG 83
Cdd:cd19920    2 LIVDDvpDNLR-LLSELLRAAGYRVLVATDGQQALQRAQAEPPDLILLDVMMPGMDGFEVCRRLKADPATrhIPVIFLTA 80

                         90       100
                 ....*....|....*....|...
gi 446367907  84 HGDVDMAVKALHQGAFDFIEKPF 106
Cdd:cd19920   81 LTDTEDKVKGFELGAVDYITKPF 103

REC_CheY_CheY3

cd19923

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

7-111

9.81e-11

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: 58.89 E-value: 9.81e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   7 ALIEDD-----DIVRQATGQwlqlAGF-DVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSL--MPV 78
Cdd:cd19923    3 VLVVDDfstmrRIIKNLLKE----LGFnNVEEAEDGVDALEKLKAGGFDFVITDWNMPNMDGLELLKTIRADGALshLPV 78

                         90       100       110
                 ....*....|....*....|....*....|...
gi 446367907  79 ILITGHGDVDMAVKALHQGAFDFIEKPFQPERL 111
Cdd:cd19923   79 LMVTAEAKKENVIAAAQAGVNNYIVKPFTAATL 111

REC_RpfG-like

cd17551

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

5-108

1.18e-10

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: 58.61 E-value: 1.18e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGF-DVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSL--MPVILI 81
Cdd:cd17551    2 RILIVDDNPTNLLLLEALLRSAGYlEVVSFTDPREALAWCRENPPDLILLDYMMPGMDGLEFIRRLRALPGLedVPIVMI 81

                         90       100
                 ....*....|....*....|....*..
gi 446367907  82 TGHGDVDMAVKALHQGAFDFIEKPFQP 108
Cdd:cd17551   82 TADTDREVRLRALEAGATDFLTKPFDP 108

AAA

smart00382

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...

168-285

1.60e-10

Pssm-ID: 214640 [Multi-domain] Cd Length: 148 Bit Score: 59.31 E-value: 1.60e-10

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   168 NVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFES---ELFGHEAGAFTGA--VKRRIGKLELADKGTLF 242
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQlllIIVGGKKASGSGElrLRLALALARKLKPDVLI 83

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 446367907   243 LDEIESMPLAMQVKVLRVLQDhvvERVGSNQPITIDLRVIAAA 285
Cdd:smart00382  84 LDEITSLLDAEQEALLLLLEE---LRLLLLLKSEKNLTVILTT 123

PRK10336

two-component system response regulator QseB;

5-126

1.64e-10

two-component system response regulator QseB;

Pssm-ID: 182387 [Multi-domain] Cd Length: 219 Bit Score: 60.68 E-value: 1.64e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGH 84
Cdd:PRK10336   2 RILLIEDDMLIGDGIKTGLSKMGFSVDWFTQGRQGKEALYSAPYDAVILDLTLPGMDGRDILREWREKGQREPVLILTAR 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 446367907  85 GDVDMAVKALHQGAFDFIEKPFQ----PERLANTVAQAVSQYQNAL 126
Cdd:PRK10336  82 DALAERVEGLRLGADDYLCKPFAlievAARLEALMRRTNGQASNEL 127

REC_2_GGDEF

cd17544

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

7-111

1.75e-10

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: 58.30 E-value: 1.75e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   7 ALIEDDD-IVRQATGQWLQLAGFDVAMFADGASALAAIEQQS-FAAVVSDVRLPDTDGLSLLVALKNVQSL--MPVILIT 82
Cdd:cd17544    3 VLVVDDSaTSRNHLRALLRRHNFQVLEAANGQEALEVLEQHPdIKLVITDYNMPEMDGFELVREIRKKYSRdqLAIIGIS 82

                         90       100
                 ....*....|....*....|....*....
gi 446367907  83 GHGDVDMAVKALHQGAFDFIEKPFQPERL 111
Cdd:cd17544   83 ASGDNALSARFIKAGANDFLTKPFLPEEF 111

REC_D1_PleD-like

cd17538

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

8-106

2.21e-10

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: 57.51 E-value: 2.21e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   8 LIEDDDIV-RQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLM--PVILITGH 84
Cdd:cd17538    3 LVVDDEPAnRELLEALLSAEGYEVLTADSGQEALALAEEELPDLILLDVMMPGMDGFEVCRRLKEDPETRhiPVIMITAL 82

                         90       100
                 ....*....|....*....|..
gi 446367907  85 GDVDMAVKALHQGAFDFIEKPF 106
Cdd:cd17538   83 DDREDRIRGLEAGADDFLSKPI 104

REC_TrrA-like

cd17554

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

5-99

4.11e-10

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: 56.85 E-value: 4.11e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGH 84
Cdd:cd17554    2 KILVVDDEENIRELYKEELEDEGYEVVTAGNGEEALEKLESEDPDLVILDIKMPGMDGLETLRKIREKKPDLPVIICTAY 81

                         90
                 ....*....|....*
gi 446367907  85 GDVDMAVKALHQGAF 99
Cdd:cd17554   82 SEYKSDFSSWAADAY 96

REC_hyHK

cd17598

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

6-112

4.27e-10

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: 56.95 E-value: 4.27e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSL--MPVILITG 83
Cdd:cd17598    1 ILIVEDSPTQAEQLKHILEEQGYKVQVARNGREALAMLAEHRPTLVISDIVMPEMDGYELCRKIKSDPDLkdIPVILLTT 80

                         90       100
                 ....*....|....*....|....*....
gi 446367907  84 HGDVDMAVKALHQGAFDFIEKPFQPERLA 112
Cdd:cd17598   81 LSDPRDVIRGLECGADNFITKPYDEKYLL 109

REC_PilR

cd19926

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

7-105

6.29e-10

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: 56.01 E-value: 6.29e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   7 ALIEDDDI-VRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHG 85
Cdd:cd19926    1 VLVVDDEPdIRELLEITLGRMGLDVRSARNVKEARELLASEPYDLCLTDMRLPDGSGLELVQHIQQRLPQTPVAVITAYG 80

                         90       100
                 ....*....|....*....|
gi 446367907  86 DVDMAVKALHQGAFDFIEKP 105
Cdd:cd19926   81 SLDTAIEALKAGAFDFLTKP 100

PRK10766

two-component system response regulator TorR;

3-111

2.25e-09

two-component system response regulator TorR;

Pssm-ID: 182711 [Multi-domain] Cd Length: 221 Bit Score: 57.36 E-value: 2.25e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   3 SQRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNvQSLMPVILIT 82
Cdd:PRK10766   2 SYHILVVEDEPVTRARLQGYFEQEGYTVSEAASGAGMREIMQNQHVDLILLDINLPGEDGLMLTRELRS-RSTVGIILVT 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 446367907  83 GHGD-VDMAVkALHQGAFDFIEKPFQPERL 111
Cdd:PRK10766  81 GRTDsIDRIV-GLEMGADDYVTKPLELREL 109

REC_HupR

cd17596

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

8-123

2.77e-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: 55.07 E-value: 2.77e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   8 LIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLlvaLKNVQSLMP---VILITGH 84
Cdd:cd17596    4 LVVDDEVRSLEALRRTLEEDFDVLTAASAEEALAILEEEWVQVILCDQRMPGTTGVEF---LKEVRERWPevvRIIISGY 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446367907  85 GDVDMAVKALHQ-GAFDFIEKPFQPERLANTVAQAVSQYQ 123
Cdd:cd17596   81 TDSEDIIAGINEaGIYQYLTKPWHPDQLLLTVRNAARLFE 120

REC_OmpR_CtrA

cd17616

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

6-111

2.90e-09

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: 54.72 E-value: 2.90e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHG 85
Cdd:cd17616    1 VLLIEDDSATAQSIELMLKSEGFNVYTTDLGEEGLDLGKLYDYDIILLDLNLPDMSGYEVLRTLRLAKVKTPILILSGLA 80

                         90       100
                 ....*....|....*....|....*.
gi 446367907  86 DVDMAVKALHQGAFDFIEKPFQPERL 111
Cdd:cd17616   81 DIEDKVKGLGFGADDYMTKPFHKDEL 106

PRK10360

transcriptional regulator UhpA;

6-115

3.33e-09

transcriptional regulator UhpA;

Pssm-ID: 182408 [Multi-domain] Cd Length: 196 Bit Score: 56.52 E-value: 3.33e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQL-AGFD-VAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLlvaLKNVQSLMPVILITG 83
Cdd:PRK10360   4 VALIDDHLIVRSGFAQLLGLePDLQvVAEFGSGREALAGLPGRGVQVCICDISMPDISGLEL---LSQLPKGMATIMLSV 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 446367907  84 HGDVDMAVKALHQGAFDFIEKPFQPERLANTV 115
Cdd:PRK10360  81 HDSPALVEQALNAGARGFLSKRCSPDELIAAV 112

REC_DesR-like

cd19930

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

6-115

4.11e-09

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: 54.20 E-value: 4.11e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAG--FDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITG 83
Cdd:cd19930    1 VLIAEDQEMVRGALAALLELEDdlEVVAQASNGQEALRLVLKHSPDVAILDIEMPGRTGLEVAAELREELPDTKVLIVTT 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 446367907  84 HGDVDMAVKALHQGAFDFIEKPFQPERLANTV 115
Cdd:cd19930   81 FGRPGYFRRALAAGVDGYVLKDRPIEELADAI 112

REC_OmpR_NsrR-like

cd18159

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

6-106

9.26e-09

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: 53.05 E-value: 9.26e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVqSLMPVILITGH- 84
Cdd:cd18159    1 ILIVEDDETIASLLKKHLEKWGYEVVLIEDFEDVLEEFLQFKPDLVLLDINLPYFDGFYWCREIRQI-SNVPIIFISSRd 79

                         90       100
                 ....*....|....*....|..
gi 446367907  85 GDVDMaVKALHQGAFDFIEKPF 106
Cdd:cd18159   80 DNMDQ-VMAINMGGDDYITKPF 100

PRK10610

chemotaxis protein CheY;

5-106

1.01e-08

chemotaxis protein CheY;

Pssm-ID: 170568 [Multi-domain] Cd Length: 129 Bit Score: 53.44 E-value: 1.01e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGF-DVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSL--MPVILI 81
Cdd:PRK10610   7 KFLVVDDFSTMRRIVRNLLKELGFnNVEEAEDGVDALNKLQAGGFGFVISDWNMPNMDGLELLKTIRADGAMsaLPVLMV 86

                         90       100
                 ....*....|....*....|....*
gi 446367907  82 TGHGDVDMAVKALHQGAFDFIEKPF 106
Cdd:PRK10610  87 TAEAKKENIIAAAQAGASGYVVKPF 111

REC_OmpR_KdpE-like

cd17620

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

6-105

1.57e-08

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: 52.17 E-value: 1.57e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNvQSLMPVILITGHG 85
Cdd:cd17620    1 ILVIEDEPQIRRFLRTALEAHGYRVFEAETGQEGLLEAATRKPDLIILDLGLPDMDGLEVIRRLRE-WSAVPVIVLSARD 79

                         90       100
                 ....*....|....*....|
gi 446367907  86 DVDMAVKALHQGAFDFIEKP 105
Cdd:cd17620   80 EESDKIAALDAGADDYLTKP 99

REC_DivK-like

cd17548

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

5-117

1.58e-08

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: 52.54 E-value: 1.58e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSL--MPVILIT 82
Cdd:cd17548    1 KILIVEDNPLNMKLARDLLESAGYEVLEAADGEEALEIARKEKPDLILMDIQLPGMDGLEATRLLKEDPATrdIPVIALT 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 446367907  83 GH---GDVDmavKALHQGAFDFIEKPFQPERLANTVAQ 117
Cdd:cd17548   81 AYamkGDRE---KILEAGCDGYISKPIDTREFLETVAK 115

PRK09836

DNA-binding transcriptional activator CusR; Provisional

5-106

2.34e-08

DNA-binding transcriptional activator CusR; Provisional

Pssm-ID: 182102 [Multi-domain] Cd Length: 227 Bit Score: 54.55 E-value: 2.34e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGH 84
Cdd:PRK09836   2 KLLIVEDEKKTGEYLTKGLTEAGFVVDLADNGLNGYHLAMTGDYDLIILDIMLPDVNGWDIVRMLRSANKGMPILLLTAL 81

                         90       100
                 ....*....|....*....|..
gi 446367907  85 GDVDMAVKALHQGAFDFIEKPF 106
Cdd:PRK09836  82 GTIEHRVKGLELGADDYLVKPF 103

REC_PdtaR-like

cd19932

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

5-121

2.50e-08

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: 52.03 E-value: 2.50e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFA-DGASALAAIEQQSFAAVVSDVRLPDTDGLSllvALKNV--QSLMPVILI 81
Cdd:cd19932    2 RVLIAEDEALIRMDLREMLEEAGYEVVGEAsDGEEAVELAKKHKPDLVIMDVKMPRLDGIE---AAKIItsENIAPIVLL 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446367907  82 TGHGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQ 121
Cdd:cd19932   79 TAYSQQDLVERAKEAGAMAYLVKPFSESDLIPAIEMAIAR 118

REC_Spo0F-like

cd17553

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

4-115

2.97e-08

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: 51.79 E-value: 2.97e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   4 QRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITG 83
Cdd:cd17553    1 EKILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTA 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 446367907  84 HGDVDMAVKALHQGAFDFIEKPFQPERLANTV 115
Cdd:cd17553   81 YGELDMIQESKELGALTHFAKPFDIDEIRDAV 112

CitB

COG2197

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

5-69

4.42e-08

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: 51.82 E-value: 4.42e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446367907   5 RIALIEDDDIVRQATGQWLQLA-GFDV-AMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVAL 69
Cdd:COG2197    3 RVLIVDDHPLVREGLRALLEAEpDIEVvGEAADGEEALELLEELRPDVVLLDIRMPGMDGLEALRRL 69

dpiA

PRK10046

two-component response regulator DpiA; Provisional

8-143

4.87e-08

two-component response regulator DpiA; Provisional

Pssm-ID: 182208 [Multi-domain] Cd Length: 225 Bit Score: 53.48 E-value: 4.87e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   8 LIEDDDIVRQATGQWLQ-LAGFDVAMFADG-ASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALknVQSLMP--VILITG 83
Cdd:PRK10046   9 IVEDETPLAEMHAEYIRhIPGFSQILLAGNlAQARMMIERFKPGLILLDNYLPDGRGINLLHEL--VQAHYPgdVVFTTA 86

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  84 HGDVDMAVKALHQGAFDFIEKPFQPERLantvAQAVSQYQNalssqsRAHYLASAKGLEQ 143
Cdd:PRK10046  87 ASDMETVSEAVRCGVFDYLIKPIAYERL----GQTLTRFRQ------RKHMLESIDSASQ 136

REC_CheB-like

cd17541

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

5-105

5.94e-08

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: 51.24 E-value: 5.94e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWL-QLAGFDVAMFA-DGASALAAIEQQSFAAVVSDVRLPDTDGLSllvALKNVQSL--MPVIL 80
Cdd:cd17541    2 RVLIVDDSAVMRKLLSRILeSDPDIEVVGTArDGEEALEKIKELKPDVITLDIEMPVMDGLE---ALRRIMAErpTPVVM 78

                         90       100
                 ....*....|....*....|....*..
gi 446367907  81 ITGH--GDVDMAVKALHQGAFDFIEKP 105
Cdd:cd17541   79 VSSLteEGAEITLEALELGAVDFIAKP 105

PRK10161

phosphate response regulator transcription factor PhoB;

3-111

9.98e-08

phosphate response regulator transcription factor PhoB;

Pssm-ID: 182277 [Multi-domain] Cd Length: 229 Bit Score: 52.80 E-value: 9.98e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   3 SQRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKN--VQSLMPVIL 80
Cdd:PRK10161   2 ARRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKResMTRDIPVVM 81

                         90       100       110
                 ....*....|....*....|....*....|.
gi 446367907  81 ITGHGDVDMAVKALHQGAFDFIEKPFQPERL 111
Cdd:PRK10161  82 LTARGEEEDRVRGLETGADDYITKPFSPKEL 112

REC_OmpR_RegX3-like

cd17621

phosphoacceptor receiver (REC) domain of RegX3-like OmpR family response regulators; RegX3 is ...

6-105

2.20e-07

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

Pssm-ID: 381136 [Multi-domain] Cd Length: 99 Bit Score: 48.73 E-value: 2.20e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNvQSLMPVILITGHG 85
Cdd:cd17621    1 VLVVEDEESFSDPLAYLLRKEGFEVTVATDGPAALAEFDRAGADIVLLDLMLPGLSGTEVCRQLRA-RSNVPVIMVTAKD 79

                         90       100
                 ....*....|....*....|
gi 446367907  86 DVDMAVKALHQGAFDFIEKP 105
Cdd:cd17621   80 SEIDKVVGLELGADDYVTKP 99

HTH_8

pfam02954

Bacterial regulatory protein, Fis family;

401-437

2.38e-07

Bacterial regulatory protein, Fis family;

Pssm-ID: 427077 [Multi-domain] Cd Length: 40 Bit Score: 47.00 E-value: 2.38e-07

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 446367907  401 FERKVIAQALHRHQGNISEVMKELDLPRRTLNQKMQK 437
Cdd:pfam02954   4 VEKELIEAALERTGGNKSKAARLLGISRRTLYRKLKK 40

REC_CheV-like

cd19924

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

6-105

2.73e-07

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: 48.91 E-value: 2.73e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQ---------QSFAAVVSDVRLPDTDGLSLLVALKN---VQ 73
Cdd:cd19924    1 ILVVDDSPTARKQLRDLLKNLGFEIAEAVDGEEALNKLENlakegndlsKELDLIITDIEMPKMDGYELTFELRDdprLA 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 446367907  74 SLmPVILITGHGDVDMAVKALHQGAFDFIEKP 105
Cdd:cd19924   81 NI-PVILNSSLSGEFSRARGKKVGADAYLAKF 111

PRK11173

two-component response regulator; Provisional

1-111

4.39e-07

two-component response regulator; Provisional

Pssm-ID: 183013 [Multi-domain] Cd Length: 237 Bit Score: 50.78 E-value: 4.39e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   1 MESQRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNvQSLMPVIL 80
Cdd:PRK11173   1 MQTPHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSENDINLVIMDINLPGKNGLLLARELRE-QANVALMF 79

                         90       100       110
                 ....*....|....*....|....*....|..
gi 446367907  81 ITGH-GDVDmAVKALHQGAFDFIEKPFQPERL 111
Cdd:PRK11173  80 LTGRdNEVD-KILGLEIGADDYITKPFNPREL 110

PRK10816

two-component system response regulator PhoP;

5-129

4.42e-07

two-component system response regulator PhoP;

Pssm-ID: 182755 [Multi-domain] Cd Length: 223 Bit Score: 50.51 E-value: 4.42e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGH 84
Cdd:PRK10816   2 RVLVVEDNALLRHHLKVQLQDAGHQVDAAEDAKEADYYLNEHLPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTAR 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 446367907  85 GDVDMAVKALHQGAFDFIEKPFQPERLANTVaQAVSQYQNALSSQ 129
Cdd:PRK10816  82 ESWQDKVEVLSAGADDYVTKPFHIEEVMARM-QALMRRNSGLASQ 125

REC_DC-like

cd17534

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

5-119

9.95e-07

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: 47.40 E-value: 9.95e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDV-AMFADGASALAAIEQQSFAAVVSDVRLP-DTDGLSLLVALKNVQSLmPVILIT 82
Cdd:cd17534    2 KILIVEDEAIIALDLKEILESLGYEVvGIADSGEEAIELAEENKPDLILMDINLKgDMDGIEAAREIREKFDI-PVIFLT 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 446367907  83 GHGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQAV 119
Cdd:cd17534   81 AYSDEETLERAKETNPYGYLVKPFNERELKAAIELAL 117

psREC_PRR

cd17582

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

6-105

1.04e-06

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: 47.01 E-value: 1.04e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAA--VVSDVRLPDTDGLSLLV------ALKNVqslmP 77
Cdd:cd17582    1 VLLVENDDSTRQIVTALLRKCSYEVTAASDGLQAWDVLEDEQNEIdlILTEVDLPVSSGFKLLSyimrhkICKNI----P 76

                         90       100
                 ....*....|....*....|....*...
gi 446367907  78 VILITGHGDVDMAVKALHQGAFDFIEKP 105
Cdd:cd17582   77 VIMMSSQDSVGVVFKCLSKGAADYLVKP 104

PRK09959

acid-sensing system histidine kinase EvgS;

2-124

1.15e-06

acid-sensing system histidine kinase EvgS;

Pssm-ID: 182169 [Multi-domain] Cd Length: 1197 Bit Score: 51.27 E-value: 1.15e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907    2 ESQRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILI 81
Cdd:PRK09959  957 EKLSILIADDHPTNRLLLKRQLNLLGYDVDEATDGVQALHKVSMQHYDLLITDVNMPNMDGFELTRKLREQNSSLPIWGL 1036

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 446367907   82 TGHGDVDMAVKALHQGAFDFIEKPFQPERLA------NTVAQAVSQYQN 124
Cdd:PRK09959 1037 TANAQANEREKGLSCGMNLCLFKPLTLDVLKthlsqlHQVAHIAPQYRH 1085

REC_HP-RR-like

cd17573

phosphoacceptor receiver (REC) domain of orphan response regulator HP-RR and similar proteins; ...

6-106

1.42e-06

phosphoacceptor receiver (REC) domain of orphan response regulator HP-RR and similar proteins; Helicobacter pylori response regulator hp1043 (HP-RR) is an orphan response regulator which is phosphorylation-independent and is essential for growth. HP-RR functions as a cell growth-associated regulator in the absence of post-translational modification. Members of this subfamily contain REC and DNA-binding output domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

Pssm-ID: 381115 [Multi-domain] Cd Length: 110 Bit Score: 46.65 E-value: 1.42e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGF--DVAMFADGASALAAIeqQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITG 83
Cdd:cd17573    1 ILLIEDDSTLGKEISKGLNEKGYqaDVAESLKDGEYYIDI--RNYDLVLVSDKLPDGNGLSIVSRIKEKHPSIVVIVLSD 78

                         90       100
                 ....*....|....*....|...
gi 446367907  84 HGDVDMAVKALHQGAFDFIEKPF 106
Cdd:cd17573   79 NPKTEQEIEAFKEGADDYIAKPF 101

PRK13558

bacterio-opsin activator; Provisional

3-133

1.46e-06

bacterio-opsin activator; Provisional

Pssm-ID: 237426 [Multi-domain] Cd Length: 665 Bit Score: 50.61 E-value: 1.46e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   3 SQRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILIT 82
Cdd:PRK13558   7 TRGVLFVGDDPEAGPVDCDLDEDGRLDVTQIRDFVAARDRVEAGEIDCVVADHEPDGFDGLALLEAVRQTTAVPPVVVVP 86

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446367907  83 GHGDVDMAVKALHQGAFDFIekpfqPERLANTVAQAVSQYQNALSSQSRAH 133
Cdd:PRK13558  87 TAGDEAVARRAVDADAAAYV-----PAVSDDATAAIAERIESAVPEHSRDT 132

PRK10955

envelope stress response regulator transcription factor CpxR;

5-111

1.66e-06

envelope stress response regulator transcription factor CpxR;

Pssm-ID: 182864 [Multi-domain] Cd Length: 232 Bit Score: 49.03 E-value: 1.66e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQqSFAAVVSDVRLPDTDGLSLLVALKNVQSLmPVILITGH 84
Cdd:PRK10955   3 KILLVDDDRELTSLLKELLEMEGFNVIVAHDGEQALDLLDD-SIDLLLLDVMMPKKNGIDTLKELRQTHQT-PVIMLTAR 80

                         90       100
                 ....*....|....*....|....*..
gi 446367907  85 GDVDMAVKALHQGAFDFIEKPFQPERL 111
Cdd:PRK10955  81 GSELDRVLGLELGADDYLPKPFNDREL 107

REC_CheC-like

cd17593

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

27-117

2.22e-06

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: 46.38 E-value: 2.22e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  27 GFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGhgDV-DMA---VKALhqGAFDFI 102
Cdd:cd17593   25 DVEITFAENGEEALEILREGRIDVLFLDLTMPVMDGYEVLEALPVEQLETKVIVVSG--DVqPEAkerVLEL--GALAFL 100

                         90
                 ....*....|....*
gi 446367907 103 EKPFQPERLANTVAQ 117
Cdd:cd17593  101 KKPFDPEKLAQLLEE 115

PRK10701

DNA-binding transcriptional regulator RstA; Provisional

4-104

2.91e-06

DNA-binding transcriptional regulator RstA; Provisional

Pssm-ID: 236738 [Multi-domain] Cd Length: 240 Bit Score: 48.48 E-value: 2.91e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   4 QRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNvQSLMPVILITG 83
Cdd:PRK10701   2 NKIVFVEDDAEVGSLIAAYLAKHDIDVTVEPRGDRAEATILREQPDLVLLDIMLPGKDGMTICRDLRP-KWQGPIVLLTS 80

                         90       100
                 ....*....|....*....|..
gi 446367907  84 HgDVDM-AVKALHQGAFDFIEK 104
Cdd:PRK10701  81 L-DSDMnHILALEMGACDYILK 101

PRK10710

DNA-binding transcriptional regulator BaeR; Provisional

2-108

3.05e-06

DNA-binding transcriptional regulator BaeR; Provisional

Pssm-ID: 182665 [Multi-domain] Cd Length: 240 Bit Score: 48.14 E-value: 3.05e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   2 ESQRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVqSLMPVILI 81
Cdd:PRK10710   9 NTPRILIVEDEPKLGQLLIDYLQAASYATTLLSHGDEVLPYVRQTPPDLILLDLMLPGTDGLTLCREIRRF-SDIPIVMV 87

                         90       100
                 ....*....|....*....|....*..
gi 446367907  82 TGHGDVDMAVKALHQGAFDFIEKPFQP 108
Cdd:PRK10710  88 TAKIEEIDRLLGLEIGADDYICKPYSP 114

PRK10430

two-component system response regulator DcuR;

8-123

5.40e-06

two-component system response regulator DcuR;

Pssm-ID: 182454 [Multi-domain] Cd Length: 239 Bit Score: 47.41 E-value: 5.40e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   8 LIEDDD-IVRQATGQWL-QLAGFD---VAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILIT 82
Cdd:PRK10430   5 LIVDDDaMVAELNRRYVaQIPGFQccgTASTLEQAKEIIFNSDTPIDLILLDIYMQQENGLDLLPVLHEAGCKSDVIVIS 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 446367907  83 GHGDVDMAVKALHQGAFDFIEKPFQPERLantvAQAVSQYQ 123
Cdd:PRK10430  85 SAADAATIKDSLHYGVVDYLIKPFQASRF----EEALTGWR 121

AAA_5

pfam07728

AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...

168-294

8.11e-06

AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.

Pssm-ID: 400191 [Multi-domain] Cd Length: 135 Bit Score: 45.36 E-value: 8.11e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  168 NVIIYGETGCGKELVAQCLHQASERQRGQFVAINCGAIPENLFESELFGHEAGAFTGAVKRRIGKlelaDKGTLFLDEIE 247
Cdd:pfam07728   1 GVLLVGPPGTGKTELAERLAAALSNRPVFYVQLTRDTTEEDLFGRRNIDPGGASWVDGPLVRAAR----EGEIAVLDEIN 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 446367907  248 SMPLAMQVKVLRVLQD---HVVERVGSNQPITIDLRVIAAAKEELRQHAE 294
Cdd:pfam07728  77 RANPDVLNSLLSLLDErrlLLPDGGELVKAAPDGFRLIATMNPLDRGLNE 126

PRK14084

DNA-binding response regulator;

7-139

1.36e-05

DNA-binding response regulator;

Pssm-ID: 184495 [Multi-domain] Cd Length: 246 Bit Score: 46.28 E-value: 1.36e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   7 ALIEDDDIVRQATGQWL--QLAGFDVAMFADGAS-ALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITG 83
Cdd:PRK14084   3 ALIVDDEPLARNELTYLlnEIGGFEEINEAENVKeTLEALLINQYDIIFLDINLMDESGIELAAKIQKMKEPPAIIFATA 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446367907  84 HGDvdMAVKALHQGAFDFIEKPFQPERLANTV--AQAVSQYQNALSSQSRAHYLASAK 139
Cdd:PRK14084  83 HDQ--FAVKAFELNATDYILKPFEQKRIEQAVnkVRATKAKDDNNASAIANDMSANFD 138

PRK15347

two component system sensor kinase;

5-123

1.74e-05

two component system sensor kinase;

Pssm-ID: 237951 [Multi-domain] Cd Length: 921 Bit Score: 47.33 E-value: 1.74e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLL----VALKNVQSLMPVIL 80
Cdd:PRK15347 692 QILLVDDVETNRDIIGMMLVELGQQVTTAASGTEALELGRQHRFDLVLMDIRMPGLDGLETTqlwrDDPNNLDPDCMIVA 771

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 446367907  81 ITGH---GDVDMAVKAlhqGAFDFIEKPFQPERLANTVAQAVsQYQ 123
Cdd:PRK15347 772 LTANaapEEIHRCKKA---GMNHYLTKPVTLAQLARALELAA-EYQ 813

REC_PatA-like

cd17602

phosphoacceptor receiver (REC) domain of PatA and similar domains; Nostoc sp. (or Anabaena sp.) ...

6-105

2.49e-05

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

Pssm-ID: 381129 [Multi-domain] Cd Length: 102 Bit Score: 43.13 E-value: 2.49e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSL--MPVILITG 83
Cdd:cd17602    1 VACVDDRPSIQKMIEYFLEKQGFRVVVIDDPLRALTTLLNSKPDLILIDIDMPDLDGYELCSLLRKSSALkdTPIIMLTG 80

                         90       100
                 ....*....|....*....|..
gi 446367907  84 HGDVDMAVKALHQGAFDFIEKP 105
Cdd:cd17602   81 KDGLVDRIRAKMAGASGYLTKP 102

PRK11466

hybrid sensory histidine kinase TorS; Provisional

5-125

3.21e-05

hybrid sensory histidine kinase TorS; Provisional

Pssm-ID: 236914 [Multi-domain] Cd Length: 914 Bit Score: 46.44 E-value: 3.21e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAI-EQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITG 83
Cdd:PRK11466 683 RLLLIEDNPLTQRITAEMLNTSGAQVVAVGNAAQALETLqNSEPFAAALVDFDLPDYDGITLARQLAQQYPSLVLIGFSA 762

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 446367907  84 HgDVDMAVKALHQGAF-DFIEKPFQPERLANTVAQAVS-QYQNA 125
Cdd:PRK11466 763 H-VIDETLRQRTSSLFrGIIPKPVPREVLGQLLAHYLQlQVNND 805

pleD

PRK09581

response regulator PleD; Reviewed

2-126

6.60e-05

response regulator PleD; Reviewed

Pssm-ID: 236577 [Multi-domain] Cd Length: 457 Bit Score: 45.28 E-value: 6.60e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   2 ESQRIALIEDDDIVRQATGQWLQlAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQ--SLMPVI 79
Cdd:PRK09581 154 EDGRILLVDDDVSQAERIANILK-EEFRVVVVSDPSEALFNAAETNYDLVIVSANFENYDPLRLCSQLRSKErtRYVPIL 232

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446367907  80 LITGHGDVDMAVKALHQGAFDFIEKPFQPERLantVAQAVSQ-----YQNAL 126
Cdd:PRK09581 233 LLVDEDDDPRLVKALELGVNDYLMRPIDKNEL---LARVRTQirrkrYQDAL 281

PRK13856

two-component response regulator VirG; Provisional

4-134

1.20e-04

two-component response regulator VirG; Provisional

Pssm-ID: 172377 [Multi-domain] Cd Length: 241 Bit Score: 43.26 E-value: 1.20e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   4 QRIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNvQSLMPVILITG 83
Cdd:PRK13856   2 KHVLVIDDDVAMRHLIVEYLTIHAFKVTAVADSQQFNRVLASETVDVVVVDLNLGREDGLEIVRSLAT-KSDVPIIIISG 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446367907  84 HG-DVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQNALSSQSRAHY 134
Cdd:PRK13856  81 DRlEEADKVVALELGATDFIAKPFGTREFLARIRVALRVRPNVVRTKDRRSF 132

REC_OmpR_YycF-like

cd17614

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

6-106

1.66e-04

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: 40.87 E-value: 1.66e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSlMPVILITGHG 85
Cdd:cd17614    1 ILVVDDEKPISDILKFNLTKEGYEVVTAYDGREALEKVEEEQPDLILLDLMLPEKDGLEVCREVRKTSN-VPIIMLTAKD 79

                         90       100
                 ....*....|....*....|.
gi 446367907  86 DVDMAVKALHQGAFDFIEKPF 106
Cdd:cd17614   80 SEVDKVLGLELGADDYVTKPF 100

pleD

PRK09581

response regulator PleD; Reviewed

28-105

2.15e-04

response regulator PleD; Reviewed

Pssm-ID: 236577 [Multi-domain] Cd Length: 457 Bit Score: 43.35 E-value: 2.15e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  28 FDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLM--PVILITGHGDVDMAVKALHQGAFDFIEKP 105
Cdd:PRK09581  27 YTVLTASSGAEAIAICEREQPDIILLDVMMPGMDGFEVCRRLKSDPATThiPVVMVTALDDPEDRVRGLEAGADDFLTKP 106

REC_hyHK_blue-like

cd18161

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

6-106

2.66e-04

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

Pssm-ID: 381145 [Multi-domain] Cd Length: 102 Bit Score: 40.02 E-value: 2.66e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAIEQQS-FAAVVSDVRLPD-TDGLSLLVALKNVQSLMPVILITG 83
Cdd:cd18161    1 VLVVEDDPDVRRLTAEVLEDLGYTVLEAASGDEALDLLESGPdIDLLVTDVIMPGgMNGSQLAEEARRRRPDLKVLLTSG 80

                         90       100
                 ....*....|....*....|...
gi 446367907  84 HGDVDMAVKALHQGaFDFIEKPF 106
Cdd:cd18161   81 YAENAIEGGDLAPG-VDVLSKPF 102

REC_RocR

cd17530

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

5-118

2.73e-04

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: 40.50 E-value: 2.73e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFD-VAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITG 83
Cdd:cd17530    2 RVLVLDDDPFQCMMAATILEDLGPGnVDEADDGREALVILLCNAPDIIICDLKMPDMDGIEFLRHLAESHSNAAVILMSG 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446367907  84 HG-----DVDMAVKALHQGAFDFIEKPFQPERLANTVAQA 118
Cdd:cd17530   82 LDggileSAETLAGANGLNLLGTLSKPFSPEELTELLTKY 121

REC_PhyR

cd17540

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

4-118

3.01e-04

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: 40.31 E-value: 3.01e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   4 QRIALIEDDDIVRQATGQWLQLAGFDV---AMFADGASALAAIEQQsfAAVVSDVRLpdTDGLSLLVALKNVQSLM--PV 78
Cdd:cd17540    1 TRVLIIEDEPLIAMDLEQIVEDLGHQVvgiARTRDEAVALARRERP--DLILADIQL--ADGSSGIDAVNEILTTHdvPV 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 446367907  79 ILITGHGDvdmavkALHQG-----AFdFIEKPFQPERLANTVAQA 118
Cdd:cd17540   77 IFVTAYPE------RLLTGerpepTF-LITKPFDPEMVKAAISQA 114

REC_1_GGDEF

cd19921

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

5-104

3.90e-04

first 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 contains characteristic metal-binding and active site residues. PleD response regulators are global regulators of cell metabolism in some important human pathogens. This model describes the first REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

Pssm-ID: 381148 [Multi-domain] Cd Length: 115 Bit Score: 39.86 E-value: 3.90e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWL-QLAGFDVAMFADGASALAAIE--QQSFAAVVsDVRLPDT-DGLSLLVALKNVqslMPVIL 80
Cdd:cd19921    1 KVLIVEDSKTFSKVLKHLIaQELGLEVDVAETLAEAKALLEegDDYFAALV-DLNLPDApNGEAVDLVLEKG---IPVIV 76

                         90       100
                 ....*....|....*....|....
gi 446367907  81 ITGHGDVDMAVKALHQGAFDFIEK 104
Cdd:cd19921   77 LTGSFDEDKRETLLSKGVVDYVLK 100

PRK00742

chemotaxis-specific protein-glutamate methyltransferase CheB;

34-111

3.94e-04

chemotaxis-specific protein-glutamate methyltransferase CheB;

Pssm-ID: 234828 [Multi-domain] Cd Length: 354 Bit Score: 42.44 E-value: 3.94e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  34 ADGASALAAIEQQSFAAVVSDVRLPDTDGLSllvALKNVQSL--MPVILI---TGHGdVDMAVKALHQGAFDFIEKPFQP 108
Cdd:PRK00742  36 PDGLEAREKIKKLNPDVITLDVEMPVMDGLD---ALEKIMRLrpTPVVMVsslTERG-AEITLRALELGAVDFVTKPFLG 111


                 ...
gi 446367907 109 ERL 111
Cdd:PRK00742 112 ISL 114

PRK11697

two-component system response regulator BtsR;

39-144

4.77e-04

two-component system response regulator BtsR;

Pssm-ID: 236956 [Multi-domain] Cd Length: 238 Bit Score: 41.76 E-value: 4.77e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  39 ALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKnvQSLMP-VILITGHGDvdMAVKALHQGAFDFIEKPFQPERLANTVAq 117
Cdd:PRK11697  39 AIGAIHRLKPDVVFLDIQMPRISGLELVGMLD--PEHMPyIVFVTAFDE--YAIKAFEEHAFDYLLKPIDPARLAKTLA- 113

                         90       100
                 ....*....|....*....|....*..
gi 446367907 118 avsQYQNALSSQSRAHyLASAKGLEQI 144
Cdd:PRK11697 114 ---RLRQERSPQDVLL-PEAQPPLKHI 136

REC_Spo0A

cd17561

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

35-106

6.01e-04

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: 39.13 E-value: 6.01e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446367907  35 DGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVAL--KNVQSLMPVILITGHGDVDMAVKALHQGAFDFIEKPF 106
Cdd:cd17561   35 NGQEALELIEEKEPDVLLLDIIMPHLDGIGVLEKLrrMRLEKRPKIIMLTAFGQEDITQRAVELGASYYILKPF 108

COG4567

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

371-437

6.45e-04

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: 40.67 E-value: 6.45e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446367907 371 ISVGEILASCPGmTEEEASAGLPLAIQVHNFERKVIAQALHRHQGNISEVMKELDLPRRTLNQKMQK 437
Cdd:COG4567  107 ADADDLLAALER-AEGDAPAPPENPMSLDRLEWEHIQRVLAECDGNISATARALGMHRRTLQRKLAK 172

PRK10529

DNA-binding transcriptional activator KdpE; Provisional

51-134

1.80e-03

DNA-binding transcriptional activator KdpE; Provisional

Pssm-ID: 182522 [Multi-domain] Cd Length: 225 Bit Score: 39.79 E-value: 1.80e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907  51 VVSDVRLPDTDGLSLLVALKNvQSLMPVILITGHGDVDMAVKALHQGAFDFIEKPFQPERLANTVAQAVSQYQNALSSQS 130
Cdd:PRK10529  49 IILDLGLPDGDGIEFIRDLRQ-WSAIPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRHSATPAPDP 127


                 ....
gi 446367907 131 RAHY 134
Cdd:PRK10529 128 LVKF 131

REC_TrxB

cd17595

phosphoacceptor receiver (REC) domain a fused response regulator with a thioredoxin reductase ...

6-111

2.82e-03

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

Pssm-ID: 381126 [Multi-domain] Cd Length: 135 Bit Score: 38.09 E-value: 2.82e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDDDIVRQATGQWLQL---AGFDVAMFADGASALAAIEQ-----QSFAAVVSDVRLPDTDGLSLlvaLKNVQSLMP 77
Cdd:cd17595    3 ILTVDDDPQVLRAVARDLRRqygKDYRVLRADSGAEALDALKElklrgEAVALFLVDQRMPEMDGVEF---LEKAMELFP 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446367907  78 ---VILITGHGDVDMAVKALHQGAFDF-IEKPFQP--ERL 111
Cdd:cd17595   80 eakRVLLTAYADTDAAIRAINDVQLDYyLLKPWDPpeEKL 119

REC_ETR-like

cd19933

phosphoacceptor receiver (REC) domain of plant ethylene receptors ETR1, ETR2, and EIN4, and ...

5-105

3.03e-03

phosphoacceptor receiver (REC) domain of plant ethylene receptors ETR1, ETR2, and EIN4, and similar proteins; Plant ethylene receptors contain N-terminal transmembrane domains that contain an ethylene binding site and also serve in localization of the receptor to the endoplasmic reticulum or the Golgi apparatus and a C-terminal histidine kinase (HK)-like domain. There are five ethylene receptors (ETR1, ERS1, ETR2, ERS2, and EIN4) in Arabidopsis thaliana. ETR1, ETR2, and EIN4 also contain REC domains C-terminal to the HK domain. ETR1 and ERS1 belong to subfamily 1, and have functional HK domains while ETR2, ERS2, and EIN4 belong to subfamily 2, and lack the necessary residues for HK activity and may function as serine/threonine kinases. The plant hormone ethylene plays an important role in plant growth and development. It regulates seed germination, seedling growth, leaf and petal abscission, fruit ripening, organ senescence, and pathogen responses. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

Pssm-ID: 381160 [Multi-domain] Cd Length: 117 Bit Score: 37.38 E-value: 3.03e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   5 RIALIEDDDIVRQATGQWLQLAGFDVAMFADGASALAAI--EQQSFAAVVSDVRLPDTDGLSllVALKnVQSLMP----- 77
Cdd:cd19933    2 KVLLVDDNAVNRMVTKGLLEKLGCEVTTVSSGEECLNLLasAEHSFQLVLLDLCMPEMDGFE--VALR-IRKLFGrrerp 78

                         90       100
                 ....*....|....*....|....*....
gi 446367907  78 -VILITGHGDVDMAVKALHQGAFDFIEKP 105
Cdd:cd19933   79 lIVALTANTDDSTREKCLSLGMNGVITKP 107

psREC-like_D2_PleD

cd17539

REC-like adaptor domain (D2) of response regulator PleD; PleD contains a REC domain (D1) with ...

6-124

3.47e-03

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

Pssm-ID: 381094 [Multi-domain] Cd Length: 124 Bit Score: 37.29 E-value: 3.47e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   6 IALIEDddivRQATGQWLQ--LAGF-DVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQS--LMPVIL 80
Cdd:cd17539    1 VLLVDD----RPSSAERIAamLSSEhEVVVEADPDEALFRAAEGPFDLVIVSLALEDFDGLRLCSQLRSLERtrQLPILA 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 446367907  81 ITGHGDVDMAVKALHQGAFDFIEKPFQPERLantVAQAVSQYQN 124
Cdd:cd17539   77 VADPGDRGRLIRALEIGVNDYLVRPIDPNEL---LARVRTQIRR 117

PRK10841

two-component system sensor histidine kinase RcsC;

27-82

4.36e-03

two-component system sensor histidine kinase RcsC;

Pssm-ID: 182772 [Multi-domain] Cd Length: 924 Bit Score: 39.57 E-value: 4.36e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446367907  27 GFDVAMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILIT 82
Cdd:PRK10841 825 GYQCKTANDGVDALNVLSKNHIDIVLTDVNMPNMDGYRLTQRLRQLGLTLPVIGVT 880

RecA-like_CDC48_r2-like

cd19511

second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...

169-249

4.67e-03

second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase domains; This subfamily includes the second of two ATPase domains of the molecular chaperone CDC48 in yeast and p97 or VCP in metazoans, Peroxisomal biogenesis factor 1 (PEX1) and -6 (PEX6), Valosin-containing protein-like ATPase (VAT), and nuclear VCP-like protein (NVL). This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

Pssm-ID: 410919 [Multi-domain] Cd Length: 159 Bit Score: 37.65 E-value: 4.67e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907 169 VIIYGETGCGKELVAQCLhqASERQRgQFVAINCgaipenlfeSELFGHEAGAFTGAVKRRIGKLELADKGTLFLDEIES 248
Cdd:cd19511   30 VLLYGPPGCGKTLLAKAL--ASEAGL-NFISVKG---------PELFSKYVGESERAVREIFQKARQAAPCIIFFDEIDS 97


                 .
gi 446367907 249 M 249
Cdd:cd19511   98 L 98

PRK09958

acid-sensing system DNA-binding response regulator EvgA;

8-127

5.05e-03

acid-sensing system DNA-binding response regulator EvgA;

Pssm-ID: 182168 [Multi-domain] Cd Length: 204 Bit Score: 38.34 E-value: 5.05e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446367907   8 LIEDDDIVRQATGQWLQLAGFDV-AMFADGASALAAIEQQSFAAVVSDVRLPDTDGLSLLVALKNVQSLMPVILITGHGD 86
Cdd:PRK09958   5 IIDDHPLAIAAIRNLLIKNDIEIlAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSAKND 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 446367907  87 VDMAVKALHQGAFDFIEKpfqPERLANTVAqAVSQYQNALS 127
Cdd:PRK09958  85 HFYGKHCADAGANGFVSK---KEGMNNIIA-AIEAAKNGYC 121

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