NCBI Conserved Domain Search

Conserved domains on [gi|489048862|ref|WP_002959078|]

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MULTISPECIES: sigma-54 dependent transcriptional regulator [Pseudoalteromonas]

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, ...

8-446

6.15e-176

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: 499.10 E-value: 6.15e-176

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTG 87
Cdd:COG2204    3 ARILVVDDDPDIRRLLKELLERAGYEVETAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALDPDLPVILLTG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  88 YADVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARACDKRSLVIQNRAlklavqktsapGVRILGDTPKMQDMMHLLNTVI 166
Cdd:COG2204   83 YGDVETAVEAIKAGAFDYLTKPFDlEELLAAVERALERRRLRRENAE-----------DSGLIGRSPAMQEVRRLIEKVA 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 167 DTPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTGATHTRKGKFEFAQGGTVFL 246
Cdd:COG2204  152 PSDATVLITGESGTGKELVARAIHRLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTGAVARRIGKFELADGGTLFL 231

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 247 DEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYYRLSLVKVDIPPLRARKADI 326
Cdd:COG2204  232 DEIGEMPLALQAKLLRVLQEREFERVGGNKPIPVDVRVIAATNRDLEELVEEGRFREDLYYRLNVFPIELPPLRERREDI 311

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 327 VLLFKHFSSIAATRYHKPPaPLNSEIQQRLLAYDWPGNVRELRNQAERAVLLgvelafsvsktqAKGELSPDLSLSEKVA 406
Cdd:COG2204  312 PLLARHFLARFAAELGKPV-KLSPEALEALLAYDWPGNVRELENVIERAVIL------------ADGEVITAEDLPEALE 378

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|
gi 489048862 407 FYEQSLIEEALERNHGSIKNTMDTLQIARKTLYDKMSKYN 446
Cdd:COG2204  379 EVERELIERALEETGGNVSRAAELLGISRRTLYRKLKKYG 418

Name

Accession

Description

Interval

E-value

AtoC

COG2204

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

8-446

6.15e-176

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: 499.10 E-value: 6.15e-176

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTG 87
Cdd:COG2204    3 ARILVVDDDPDIRRLLKELLERAGYEVETAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALDPDLPVILLTG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  88 YADVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARACDKRSLVIQNRAlklavqktsapGVRILGDTPKMQDMMHLLNTVI 166
Cdd:COG2204   83 YGDVETAVEAIKAGAFDYLTKPFDlEELLAAVERALERRRLRRENAE-----------DSGLIGRSPAMQEVRRLIEKVA 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 167 DTPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTGATHTRKGKFEFAQGGTVFL 246
Cdd:COG2204  152 PSDATVLITGESGTGKELVARAIHRLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTGAVARRIGKFELADGGTLFL 231

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 247 DEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYYRLSLVKVDIPPLRARKADI 326
Cdd:COG2204  232 DEIGEMPLALQAKLLRVLQEREFERVGGNKPIPVDVRVIAATNRDLEELVEEGRFREDLYYRLNVFPIELPPLRERREDI 311

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 327 VLLFKHFSSIAATRYHKPPaPLNSEIQQRLLAYDWPGNVRELRNQAERAVLLgvelafsvsktqAKGELSPDLSLSEKVA 406
Cdd:COG2204  312 PLLARHFLARFAAELGKPV-KLSPEALEALLAYDWPGNVRELENVIERAVIL------------ADGEVITAEDLPEALE 378

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|
gi 489048862 407 FYEQSLIEEALERNHGSIKNTMDTLQIARKTLYDKMSKYN 446
Cdd:COG2204  379 EVERELIERALEETGGNVSRAAELLGISRRTLYRKLKKYG 418

ntrC

TIGR01818

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

10-442

4.66e-120

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: 358.28 E-value: 4.66e-120

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:TIGR01818   1 VWVVDDDRSIRWVLEKALSRAGYEVRTFGNAASVLRALARGQPDLLITDVRMPGEDGLDLLPQIKKRHPQLPVIVMTAHS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   90 DVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARACDKRslviQNRALKLAVQKTSAPGVRILGDTPKMQDMMHLLNTVIDT 168
Cdd:TIGR01818  81 DLDTAVAAYQRGAFEYLPKPFDlDEAVTLVERALAHA----QEQVALPADAGEAEDSAELIGEAPAMQEVFRAIGRLSRS 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  169 PADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTGATHTRKGKFEFAQGGTVFLDE 248
Cdd:TIGR01818 157 DITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPKDLIESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDE 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  249 IESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYYRLSLVKVDIPPLRARKADIVL 328
Cdd:TIGR01818 237 IGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQNLEALVRQGKFREDLFHRLNVIRIHLPPLRERREDIPR 316

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  329 LFKHFSSIAATRYHKPPAPLNSEIQQRLLAYDWPGNVRELRNQAER-AVL----------LGVELAFSVSKTQAKGELSP 397
Cdd:TIGR01818 317 LARHFLALAARELDVEPKLLDPEALERLKQLRWPGNVRQLENLCRWlTVMasgdevlvsdLPAELALTGRPASAPDSDGQ 396

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489048862  398 D-------------LS------LSEKVAFYEQSLIEEALERNHGSIKNTMDTLQIARKTLYDKM 442
Cdd:TIGR01818 397 DswdealeawakqaLSrgeqglLDRALPEFERPLLEAALQHTRGHKQEAAALLGWGRNTLTRKL 460

PRK11361

acetoacetate metabolism transcriptional regulator AtoC;

5-448

1.07e-117

acetoacetate metabolism transcriptional regulator AtoC;

Pssm-ID: 183099 [Multi-domain] Cd Length: 457 Bit Score: 352.23 E-value: 1.07e-117

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   5 SPCKHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIF 84
Cdd:PRK11361   2 TAINRILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIKALKEMRSHETRTPVIL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  85 LTGYADVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARACDKRSLVIQNRALKLAVQKTSAPGvRILGDTPKMQDMMHLLN 163
Cdd:PRK11361  82 MTAYAEVETAVEALRCGAFDYVIKPFDlDELNLIVQRALQLQSMKKEIRHLHQALSTSWQWG-HILTNSPAMMDICKDTA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 164 TVIDTPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTGATHTRKGKFEFAQGGT 243
Cdd:PRK11361 161 KIALSQASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGHEKGAFTGAQTLRQGLFERANEGT 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 244 VFLDEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYYRLSLVKVDIPPLRARK 323
Cdd:PRK11361 241 LLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFREDLFYRLNVIHLILPPLRDRR 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 324 ADIVLLFKHFSSIAATRYHKPPAPLNSEIQQRLLAYDWPGNVRELRNQAERAVLLGV----------------ELAFSVS 387
Cdd:PRK11361 321 EDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWPGNIRELSNVIERAVVMNSgpiifsedlppqirqpVCNAGEV 400

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489048862 388 KTQAKGElspdLSLSEKVAFYEQSLIEEALERNHGSIKNTMDTLQIARKTLYDKMSKYNLN 448
Cdd:PRK11361 401 KTAPVGE----RNLKEEIKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEYGID 457

Sigma54_activat

pfam00158

Sigma-54 interaction domain;

148-312

3.82e-93

Sigma-54 interaction domain;

Pssm-ID: 425491 [Multi-domain] Cd Length: 168 Bit Score: 278.52 E-value: 3.82e-93

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  148 ILGDTPKMQDMMHLLNTVIDTPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTG 227
Cdd:pfam00158   1 IIGESPAMQEVLEQAKRVAPTDAPVLITGESGTGKELFARAIHQLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  228 ATHTRKGKFEFAQGGTVFLDEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYY 307
Cdd:pfam00158  81 ADSDRKGLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTKPIKVDVRIIAATNRDLEEAVAEGRFREDLYY 160


                  ....*
gi 489048862  308 RLSLV 312
Cdd:pfam00158 161 RLNVI 165

REC_DctD-like

cd17549

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

10-135

7.39e-58

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: 186.54 E-value: 7.39e-58

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:cd17549    1 VLLVDDDADVREALQQTLELAGFRVRAFADAEEALAALSPDFPGVVISDIRMPGMDGLELLAQIRELDPDLPVILITGHG 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 489048862  90 DVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARACDKRSLVIQNRALK 135
Cdd:cd17549   81 DVPMAVEAMRAGAYDFLEKPFDpERLLDVVRRALEKRRLVLENRRLR 127

REC

smart00448

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

8-62

1.66e-10

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

Pssm-ID: 214668 [Multi-domain] Cd Length: 55 Bit Score: 56.42 E-value: 1.66e-10

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 489048862     8 KHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMP 62
Cdd:smart00448   1 MRILVVDDDPLLRELLKALLEKEGYEVDEATDGEEALELLKEEKPDLILLDIMMP 55

Name

Accession

Description

Interval

E-value

AtoC

COG2204

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

8-446

6.15e-176

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: 499.10 E-value: 6.15e-176

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTG 87
Cdd:COG2204    3 ARILVVDDDPDIRRLLKELLERAGYEVETAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALDPDLPVILLTG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  88 YADVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARACDKRSLVIQNRAlklavqktsapGVRILGDTPKMQDMMHLLNTVI 166
Cdd:COG2204   83 YGDVETAVEAIKAGAFDYLTKPFDlEELLAAVERALERRRLRRENAE-----------DSGLIGRSPAMQEVRRLIEKVA 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 167 DTPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTGATHTRKGKFEFAQGGTVFL 246
Cdd:COG2204  152 PSDATVLITGESGTGKELVARAIHRLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTGAVARRIGKFELADGGTLFL 231

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 247 DEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYYRLSLVKVDIPPLRARKADI 326
Cdd:COG2204  232 DEIGEMPLALQAKLLRVLQEREFERVGGNKPIPVDVRVIAATNRDLEELVEEGRFREDLYYRLNVFPIELPPLRERREDI 311

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 327 VLLFKHFSSIAATRYHKPPaPLNSEIQQRLLAYDWPGNVRELRNQAERAVLLgvelafsvsktqAKGELSPDLSLSEKVA 406
Cdd:COG2204  312 PLLARHFLARFAAELGKPV-KLSPEALEALLAYDWPGNVRELENVIERAVIL------------ADGEVITAEDLPEALE 378

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|
gi 489048862 407 FYEQSLIEEALERNHGSIKNTMDTLQIARKTLYDKMSKYN 446
Cdd:COG2204  379 EVERELIERALEETGGNVSRAAELLGISRRTLYRKLKKYG 418

RocR

COG3829

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

148-448

5.06e-134

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: 393.37 E-value: 5.06e-134

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 148 ILGDTPKMQDMMHLLNTVIDTPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTG 227
Cdd:COG3829  140 IIGKSPAMKELLELAKRVAKSDSTVLILGESGTGKELFARAIHNASPRRDGPFVAVNCAAIPENLLESELFGYEKGAFTG 219

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 228 ATHT-RKGKFEFAQGGTVFLDEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLY 306
Cdd:COG3829  220 AKKGgKPGLFELADGGTLFLDEIGEMPLSLQAKLLRVLQEKEVRRVGGTKPIPVDVRIIAATNRDLEEMVEEGRFREDLY 299

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 307 YRLSLVKVDIPPLRARKADIVLLFKHFSSIAATRYHKPPAPLNSEIQQRLLAYDWPGNVRELRNQAERAVLLGVE----- 381
Cdd:COG3829  300 YRLNVIPIHIPPLRERKEDIPLLAEHFLEKFNKKYGKNIKGISPEALELLLAYDWPGNVRELENVIERAVVLSEGdvitp 379

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489048862 382 --LAFSVSKTQAKGELSPDLSLSEKVAFYEQSLIEEALERNHGSIKNTMDTLQIARKTLYDKMSKYNLN 448
Cdd:COG3829  380 ehLPEYLLEEAEAASAAEEGSLKEALEEVEKELIEEALEKTGGNKSKAAKALGISRSTLYRKLKKYGIK 448

ntrC

TIGR01818

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

10-442

4.66e-120

Pssm-ID: 273818 [Multi-domain] Cd Length: 463 Bit Score: 358.28 E-value: 4.66e-120

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:TIGR01818   1 VWVVDDDRSIRWVLEKALSRAGYEVRTFGNAASVLRALARGQPDLLITDVRMPGEDGLDLLPQIKKRHPQLPVIVMTAHS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   90 DVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARACDKRslviQNRALKLAVQKTSAPGVRILGDTPKMQDMMHLLNTVIDT 168
Cdd:TIGR01818  81 DLDTAVAAYQRGAFEYLPKPFDlDEAVTLVERALAHA----QEQVALPADAGEAEDSAELIGEAPAMQEVFRAIGRLSRS 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  169 PADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTGATHTRKGKFEFAQGGTVFLDE 248
Cdd:TIGR01818 157 DITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPKDLIESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDE 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  249 IESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYYRLSLVKVDIPPLRARKADIVL 328
Cdd:TIGR01818 237 IGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQNLEALVRQGKFREDLFHRLNVIRIHLPPLRERREDIPR 316

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  329 LFKHFSSIAATRYHKPPAPLNSEIQQRLLAYDWPGNVRELRNQAER-AVL----------LGVELAFSVSKTQAKGELSP 397
Cdd:TIGR01818 317 LARHFLALAARELDVEPKLLDPEALERLKQLRWPGNVRQLENLCRWlTVMasgdevlvsdLPAELALTGRPASAPDSDGQ 396

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489048862  398 D-------------LS------LSEKVAFYEQSLIEEALERNHGSIKNTMDTLQIARKTLYDKM 442
Cdd:TIGR01818 397 DswdealeawakqaLSrgeqglLDRALPEFERPLLEAALQHTRGHKQEAAALLGWGRNTLTRKL 460

PRK11361

acetoacetate metabolism transcriptional regulator AtoC;

5-448

1.07e-117

acetoacetate metabolism transcriptional regulator AtoC;

Pssm-ID: 183099 [Multi-domain] Cd Length: 457 Bit Score: 352.23 E-value: 1.07e-117

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   5 SPCKHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIF 84
Cdd:PRK11361   2 TAINRILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIKALKEMRSHETRTPVIL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  85 LTGYADVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARACDKRSLVIQNRALKLAVQKTSAPGvRILGDTPKMQDMMHLLN 163
Cdd:PRK11361  82 MTAYAEVETAVEALRCGAFDYVIKPFDlDELNLIVQRALQLQSMKKEIRHLHQALSTSWQWG-HILTNSPAMMDICKDTA 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 164 TVIDTPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTGATHTRKGKFEFAQGGT 243
Cdd:PRK11361 161 KIALSQASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGHEKGAFTGAQTLRQGLFERANEGT 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 244 VFLDEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYYRLSLVKVDIPPLRARK 323
Cdd:PRK11361 241 LLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFREDLFYRLNVIHLILPPLRDRR 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 324 ADIVLLFKHFSSIAATRYHKPPAPLNSEIQQRLLAYDWPGNVRELRNQAERAVLLGV----------------ELAFSVS 387
Cdd:PRK11361 321 EDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWPGNIRELSNVIERAVVMNSgpiifsedlppqirqpVCNAGEV 400

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489048862 388 KTQAKGElspdLSLSEKVAFYEQSLIEEALERNHGSIKNTMDTLQIARKTLYDKMSKYNLN 448
Cdd:PRK11361 401 KTAPVGE----RNLKEEIKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEYGID 457

PEP_resp_reg

TIGR02915

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

10-447

4.69e-109

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: 329.40 E-value: 4.69e-109

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   10 IIVVDDEAMIRDSLKqlLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMP-----AMDGLTLLEQVTAFDSELPVIF 84
Cdd:TIGR02915   1 LLIVEDDLGLQKQLK--WSFADYELAVAADRESAIALVRRHEPAVVTLDLGLPpdadgASEGLAALQQILAIAPDTKVIV 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   85 LTGYADVTIAVKAMQLGAYDLFEKPVNETLLDC-IARACDKRSLVIQNRALKLAVQKTSAPGvrILGDTPKMQDMMHLLN 163
Cdd:TIGR02915  79 ITGNDDRENAVKAIGLGAYDFYQKPIDPDVLKLiVDRAFHLYTLETENRRLQSALGGTALRG--LITSSPGMQKICRTIE 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  164 TVIDTPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTGATHTRKGKFEFAQGGT 243
Cdd:TIGR02915 157 KIAPSDITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIPENLLESELFGYEKGAFTGAVKQTLGKIEYAHGGT 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  244 VFLDEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYYRLSLVKVDIPPLRARK 323
Cdd:TIGR02915 237 LFLDEIGDLPLNLQAKLLRFLQERVIERLGGREEIPVDVRIVCATNQDLKRMIAEGTFREDLFYRIAEISITIPPLRSRD 316

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  324 ADIVLLFKHFSSIAATRYHKPPAPLNSEIQQRLLAYDWPGNVRELRNQAERAVLLG-------VELAFSVSktqAKGELS 396
Cdd:TIGR02915 317 GDAVLLANAFLERFARELKRKTKGFTDDALRALEAHAWPGNVRELENKVKRAVIMAegnqitaEDLGLDAR---ERAETP 393

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|.
gi 489048862  397 PDLSLSEKVAFYEQSLIEEALERNHGSIKNTMDTLQIARKTLYDKMSKYNL 447
Cdd:TIGR02915 394 LEVNLREVRERAEREAVRKAIARVDGNIARAAELLGITRPTLYDLMKKHGI 444

AcoR

COG3284

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

137-446

2.32e-102

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

Pssm-ID: 442514 [Multi-domain] Cd Length: 625 Bit Score: 318.00 E-value: 2.32e-102

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 137 AVQKTSAPGVRILGDTPKMQDMMHLLNTVIDTPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESE 216
Cdd:COG3284  312 AGAPAPAALAALAGGDPAMRRALRRARRLADRDIPVLILGETGTGKELFARAIHAASPRADGPFVAVNCAAIPEELIESE 391

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 217 LFGAASGAYTGA-THTRKGKFEFAQGGTVFLDEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLL 295
Cdd:COG3284  392 LFGYEPGAFTGArRKGRPGKIEQADGGTLFLDEIGDMPLALQARLLRVLQEREVTPLGGTKPIPVDVRLIAATHRDLREL 471

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 296 VEKGEFRADLYYRLSLVKVDIPPLRARkADIVLLFKHFssIAATRYHKPPAPLNSEIQQRLLAYDWPGNVRELRNQAERA 375
Cdd:COG3284  472 VAAGRFREDLYYRLNGLTLTLPPLRER-EDLPALIEHL--LRELAAGRGPLRLSPEALALLAAYPWPGNVRELRNVLRTA 548

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 376 VLLG----VELA------FSVSKTQAKGELSPDLSLSEKvafyEQSLIEEALERNHGSIKNTMDTLQIARKTLYDKMSKY 445
Cdd:COG3284  549 LALAdggvITVEdlpdelRAELAAAAPAAAAPLTSLEEA----ERDAILRALRACGGNVSAAARALGISRSTLYRKLKRY 624


                 .
gi 489048862 446 N 446
Cdd:COG3284  625 G 625

PRK10365

sigma-54-dependent response regulator transcription factor ZraR;

10-444

3.28e-102

sigma-54-dependent response regulator transcription factor ZraR;

Pssm-ID: 182412 [Multi-domain] Cd Length: 441 Bit Score: 311.96 E-value: 3.28e-102

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:PRK10365   8 ILVVDDDISHCTILQALLRGWGYNVALANSGRQALEQVREQVFDLVLCDVRMAEMDGIATLKEIKALNPAIPVLIMTAYS 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  90 DVTIAVKAMQLGAYDLFEKPVN-----ETLLDCIARAcdkrslviQNRALKLAVQKTSAPGvrILGDTPKMQDMMHLLNT 164
Cdd:PRK10365  88 SVETAVEALKTGALDYLIKPLDfdnlqATLEKALAHT--------HSIDAETPAVTASQFG--MVGKSPAMQHLLSEIAL 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 165 VIDTPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTGATHTRKGKFEFAQGGTV 244
Cdd:PRK10365 158 VAPSEATVLIHGDSGTGKELVARAIHASSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTL 237

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 245 FLDEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYYRLSLVKVDIPPLRARKA 324
Cdd:PRK10365 238 FLDEIGDISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNVVAIEVPSLRQRRE 317

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 325 DIVLLFKHFSSIAATRYHKPPAPLNSEIQQRLLAYDWPGNVRELRNQAERAVLLGV-------ELAFSVSKTQAKGELSP 397
Cdd:PRK10365 318 DIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAVERAVVLLTgeyiserELPLAIASTPIPLGQSQ 397

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....*..
gi 489048862 398 DLSLSEKVafyEQSLIEEALERNHGSIKNTMDTLQIARKTLYDKMSK 444
Cdd:PRK10365 398 DIQPLVEV---EKEVILAALEKTGGNKTEAARQLGITRKTLLAKLSR 441

glnG

PRK10923

nitrogen regulation protein NR(I); Provisional

10-442

2.66e-98

nitrogen regulation protein NR(I); Provisional

Pssm-ID: 182842 [Multi-domain] Cd Length: 469 Bit Score: 302.95 E-value: 2.66e-98

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:PRK10923   6 VWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLEALASKTPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHS 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  90 DVTIAVKAMQLGAYDLFEKP--VNETLLdCIARACDKRSLVIQNRAlklavQKTSAPGVRILGDTPKMQDMMHLLNTVID 167
Cdd:PRK10923  86 DLDAAVSAYQQGAFDYLPKPfdIDEAVA-LVERAISHYQEQQQPRN-----IQVNGPTTDIIGEAPAMQDVFRIIGRLSR 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 168 TPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTGATHTRKGKFEFAQGGTVFLD 247
Cdd:PRK10923 160 SSISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIPKDLIESELFGHEKGAFTGANTIRQGRFEQADGGTLFLD 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 248 EIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYYRLSLVKVDIPPLRARKADIV 327
Cdd:PRK10923 240 EIGDMPLDVQTRLLRVLADGQFYRVGGYAPVKVDVRIIAATHQNLEQRVQEGKFREDLFHRLNVIRVHLPPLRERREDIP 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 328 LLFKHFSSIAATRYHKPPAPLNSEIQQRLLAYDWPGNVRELRN--------QAERAVL---LGVELaFSVSKTQAKGELS 396
Cdd:PRK10923 320 RLARHFLQVAARELGVEAKLLHPETEAALTRLAWPGNVRQLENtcrwltvmAAGQEVLiqdLPGEL-FESTVPESTSQMQ 398

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489048862 397 PD-----LS--------------LSEKVAFYEQSLIEEALERNHGSIKNTMDTLQIARKTLYDKM 442
Cdd:PRK10923 399 PDswatlLAqwadralrsghqnlLSEAQPELERTLLTTALRHTQGHKQEAARLLGWGRNTLTRKL 463

PRK15115

response regulator GlrR; Provisional

9-378

2.85e-98

response regulator GlrR; Provisional

Pssm-ID: 185070 [Multi-domain] Cd Length: 444 Bit Score: 301.76 E-value: 2.85e-98

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGY 88
Cdd:PRK15115   7 HLLLVDDDPGLLKLLGMRLTSEGYSVVTAESGQEALRVLNREKVDLVISDLRMDEMDGMQLFAEIQKVQPGMPVIILTAH 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  89 ADVTIAVKAMQLGAYDLFEKPVNEtllDCIARACDKrslviqnrALKLavqktSAPGV------RILGDTPKMQDMMHLL 162
Cdd:PRK15115  87 GSIPDAVAATQQGVFSFLTKPVDR---DALYKAIDD--------ALEQ-----SAPATderwreAIVTRSPLMLRLLEQA 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 163 NTVIDTPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTGATHTRKGKFEFAQGG 242
Cdd:PRK15115 151 RMVAQSDVSVLINGQSGTGKEILAQAIHNASPRASKPFIAINCGALPEQLLESELFGHARGAFTGAVSNREGLFQAAEGG 230

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 243 TVFLDEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYYRLSLVKVDIPPLRAR 322
Cdd:PRK15115 231 TLFLDEIGDMPAPLQVKLLRVLQERKVRPLGSNRDIDIDVRIISATHRDLPKAMARGEFREDLYYRLNVVSLKIPALAER 310

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 489048862 323 KADIVLLFKHFSSIAATRyHKPPA-PLNSEIQQRLLAYDWPGNVRELRNQAERAVLL 378
Cdd:PRK15115 311 TEDIPLLANHLLRQAAER-HKPFVrAFSTDAMKRLMTASWPGNVRQLVNVIEQCVAL 366

Sigma54_activat

pfam00158

Sigma-54 interaction domain;

148-312

3.82e-93

Sigma-54 interaction domain;

Pssm-ID: 425491 [Multi-domain] Cd Length: 168 Bit Score: 278.52 E-value: 3.82e-93

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  148 ILGDTPKMQDMMHLLNTVIDTPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTG 227
Cdd:pfam00158   1 IIGESPAMQEVLEQAKRVAPTDAPVLITGESGTGKELFARAIHQLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  228 ATHTRKGKFEFAQGGTVFLDEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYY 307
Cdd:pfam00158  81 ADSDRKGLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTKPIKVDVRIIAATNRDLEEAVAEGRFREDLYY 160


                  ....*
gi 489048862  308 RLSLV 312
Cdd:pfam00158 161 RLNVI 165

PRK05022

nitric oxide reductase transcriptional regulator NorR;

97-444

1.80e-91

nitric oxide reductase transcriptional regulator NorR;

Pssm-ID: 235331 [Multi-domain] Cd Length: 509 Bit Score: 286.30 E-value: 1.80e-91

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  97 AMQLGAYDLFEkpvNETL--LDCIARACDKRSLVIqnRALKLAVQKTSAP----------GVRILGDTPKMQDMMHLLNT 164
Cdd:PRK05022 131 ALDPGQFDAFS---DEELraLAALAAATLRNALLI--EQLESQAELPQDVaeflrqealkEGEMIGQSPAMQQLKKEIEV 205

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 165 VIDTPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTGATHTRKGKFEFAQGGTV 244
Cdd:PRK05022 206 VAASDLNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAALPESLAESELFGHVKGAFTGAISNRSGKFELADGGTL 285

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 245 FLDEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYYRLSLVKVDIPPLRARKA 324
Cdd:PRK05022 286 FLDEIGELPLALQAKLLRVLQYGEIQRVGSDRSLRVDVRVIAATNRDLREEVRAGRFRADLYHRLSVFPLSVPPLRERGD 365

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 325 DIVLLFKHFSSIAATRYHKPPAPLNSEIQQRLLAYDWPGNVRELRNQAERAVL-------------------LGVELAFS 385
Cdd:PRK05022 366 DVLLLAGYFLEQNRARLGLRSLRLSPAAQAALLAYDWPGNVRELEHVISRAALlarargagrivtleaqhldLPAEVALP 445

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489048862 386 VSKTQAKGELSPDLSLSEKVAFYEQSLIEEALERNHGSIKNTMDTLQIARKTLYdKMSK 444
Cdd:PRK05022 446 PPEAAAAPAAVVSQNLREATEAFQRQLIRQALAQHQGNWAAAARALELDRANLH-RLAK 503

PRK15424

propionate catabolism operon regulatory protein PrpR; Provisional

148-449

7.18e-88

propionate catabolism operon regulatory protein PrpR; Provisional

Pssm-ID: 237963 [Multi-domain] Cd Length: 538 Bit Score: 278.14 E-value: 7.18e-88

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 148 ILGDTPKMQDMMHLLNTVIDTPADVMIEGETGTGKELVARYLH--------DQSIRSASNFVAINCGAVPEQLIESELFG 219
Cdd:PRK15424 221 LLGQSPQMEQVRQTILLYARSSAAVLIQGETGTGKELAAQAIHreyfarhdARQGKKSHPFVAVNCGAIAESLLEAELFG 300

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 220 AASGAYTGATHT-RKGKFEFAQGGTVFLDEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEK 298
Cdd:PRK15424 301 YEEGAFTGSRRGgRAGLFEIAHGGTLFLDEIGEMPLPLQTRLLRVLEEKEVTRVGGHQPVPVDVRVISATHCDLEEDVRQ 380

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 299 GEFRADLYYRLSLVKVDIPPLRARKADIVLLFKHF--SSIAATryhkpPAPLNSEIQQRL-------LAYDWPGNVRELR 369
Cdd:PRK15424 381 GRFRRDLFYRLSILRLQLPPLRERVADILPLAESFlkQSLAAL-----SAPFSAALRQGLqqcetllLHYDWPGNVRELR 455

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 370 NQAER-AVLLGVELAFSVSKTQAKgELSPDLSLSEKV---AFYEQSLIEEALERNHGSIKNTMDTLQIARKTLYDKMSKY 445
Cdd:PRK15424 456 NLMERlALFLSVEPTPDLTPQFLQ-LLLPELARESAKtpaPRLLAATLQQALERFNGDKTAAANYLGISRTTLWRRLKAE 534


                 ....
gi 489048862 446 NLNR 449
Cdd:PRK15424 535 AKAQ 538

propionate_PrpR

TIGR02329

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

148-444

1.04e-81

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: 261.72 E-value: 1.04e-81

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  148 ILGDTPKMQDMMHLLNTVIDTPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTG 227
Cdd:TIGR02329 214 LLGASAPMEQVRALVRLYARSDATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIAESLLEAELFGYEEGAFTG 293

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  228 ATHT-RKGKFEFAQGGTVFLDEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLY 306
Cdd:TIGR02329 294 ARRGgRTGLIEAAHRGTLFLDEIGEMPLPLQTRLLRVLEEREVVRVGGTEPVPVDVRVVAATHCALTTAVQQGRFRRDLF 373

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  307 YRLSLVKVDIPPLRARKADIVLLFKHFSSIAATRYHKPPAPLNSE----IQQRLLAYDWPGNVRELRNQAER-AVLLGVE 381
Cdd:TIGR02329 374 YRLSILRIALPPLRERPGDILPLAAEYLVQAAAALRLPDSEAAAQvlagVADPLQRYPWPGNVRELRNLVERlALELSAM 453

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489048862  382 ------------LAFSVSKTQAKGELSPDlSLSEKvAFYEQSLIEEALERNHGSIKNTMDTLQIARKTLYDKMSK 444
Cdd:TIGR02329 454 pagaltpdvlraLAPELAEASGKGKTSAL-SLRER-SRVEALAVRAALERFGGDRDAAAKALGISRTTLWRRLKA 526

TyrR

COG3283

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

147-418

1.92e-80

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

Pssm-ID: 442513 [Multi-domain] Cd Length: 514 Bit Score: 257.81 E-value: 1.92e-80

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 147 RILGDTPKMQdmmHLLNT-----VIDTPadVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAA 221
Cdd:COG3283  205 HIVASSPKMR---QVIRQakkmaMLDAP--LLIQGETGTGKELLARACHLASPRGDKPFLALNCAALPDDVAESELFGYA 279

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 222 SGAYTGATHTRKGKFEFAQGGTVFLDEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEF 301
Cdd:COG3283  280 PGAFGNAREGKKGLFEQANGGTVFLDEIGEMSPQLQAKLLRFLQDGTFRRVGEEQEVKVDVRVICATQKDLAELVQEGEF 359

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 302 RADLYYRLSLVKVDIPPLRARKADIVLLFKHFSSIAATRYHKPPAPLNSEIQQRLLAYDWPGNVRELRNQAERAVllgve 381
Cdd:COG3283  360 REDLYYRLNVLTLTLPPLRERKSDILPLAEHFVARFSQQLGRPRPRLSPDLVDFLQSYPWPGNVRQLENALYRAV----- 434

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 489048862 382 lafsvskTQAKG-ELSP-DLSLSEKVAfyEQSLIEEALE 418
Cdd:COG3283  435 -------SLLEGdELTPeDLQLPEYAA--SAGLLDDLLE 464

phageshock_pspF

TIGR02974

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

166-431

2.78e-78

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: 246.44 E-value: 2.78e-78

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  166 IDTPadVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTGATHTRKGKFEFAQGGTVF 245
Cdd:TIGR02974  21 LDRP--VLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAALSENLLDSELFGHEAGAFTGAQKRHQGRFERADGGTLF 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  246 LDEIESTPMSLQVKLLRVLE----ERkvtpVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYYRLSLVKVDIPPLRA 321
Cdd:TIGR02974  99 LDELATASLLVQEKLLRVIEygefER----VGGSQTLQVDVRLVCATNADLPALAAEGRFRADLLDRLAFDVITLPPLRE 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  322 RKADIVLLFKHFSSIAATRYHKPPAP-LNSEIQQRLLAYDWPGNVRELRNQAERAVL----------------------- 377
Cdd:TIGR02974 175 RQEDIMLLAEHFAIRMARELGLPLFPgFTPQAREQLLEYHWPGNVRELKNVVERSVYrhgleeapideiiidpfaspwrp 254

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489048862  378 -LGVELAFSVSKTQAKGEL------SPDLSLSEKVAFYEQSLIEEALERNHGSIKNTMDTL 431
Cdd:TIGR02974 255 kQAAPAVDEVNSTPTDLPSpssiaaAFPLDLKQAQQDYEIELLQQALAEAQFNQRKAAELL 315

nifA

TIGR01817

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

148-378

4.29e-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: 249.63 E-value: 4.29e-77

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  148 ILGDTPKMQDMMHLLNTVIDTPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTG 227
Cdd:TIGR01817 198 IIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYLSPRAKRPFVKVNCAALSETLLESELFGHEKGAFTG 277

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  228 ATHTRKGKFEFAQGGTVFLDEI-ESTPMsLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLY 306
Cdd:TIGR01817 278 AIAQRKGRFELADGGTLFLDEIgEISPA-FQAKLLRVLQEGEFERVGGNRTLKVDVRLVAATNRDLEEAVAKGEFRADLY 356

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489048862  307 YRLSLVKVDIPPLRARKADIVLLFKHFSSIAATRYHKPPAPLNSEIqQRLLAYDWPGNVRELRNQAERAVLL 378
Cdd:TIGR01817 357 YRINVVPIFLPPLRERREDIPLLAEAFLEKFNRENGRPLTITPSAI-RVLMSCKWPGNVRELENCLERTATL 427

PRK15429

formate hydrogenlyase transcriptional activator FlhA;

124-450

5.29e-69

formate hydrogenlyase transcriptional activator FlhA;

Pssm-ID: 237965 [Multi-domain] Cd Length: 686 Bit Score: 232.03 E-value: 5.29e-69

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 124 KRSLVIQNRALKLAVQKTSAPGVRILGDTPKMQDMMHLLNTVIDTPADVMIEGETGTGKELVARYLHDQSIRSASNFVAI 203
Cdd:PRK15429 354 KERLVDENLALTEQLNNVDSEFGEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLSGRNNRRMVKM 433

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 204 NCGAVPEQLIESELFGAASGAYTGATHTRKGKFEFAQGGTVFLDEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIR 283
Cdd:PRK15429 434 NCAAMPAGLLESDLFGHERGAFTGASAQRIGRFELADKSSLFLDEVGDMPLELQPKLLRVLQEQEFERLGSNKIIQTDVR 513

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 284 IVAATKVDLLLLVEKGEFRADLYYRLSLVKVDIPPLRARKADIVLLFKHFSSIAATRYHKPPAPLNSEIQQRLLAYDWPG 363
Cdd:PRK15429 514 LIAATNRDLKKMVADREFRSDLYYRLNVFPIHLPPLRERPEDIPLLVKAFTFKIARRMGRNIDSIPAETLRTLSNMEWPG 593

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 364 NVRELRNQAERAVLL--GVELAFSVSK-TQAKGELSPDLSLSEKVAFYEQSLIEEALERNHGSI---KNTMDTLQIARKT 437
Cdd:PRK15429 594 NVRELENVIERAVLLtrGNVLQLSLPDiTLPEPETPPAATVVAQEGEDEYQLIVRVLKETNGVVagpKGAAQRLGLKRTT 673

                        330
                 ....*....|...
gi 489048862 438 LYDKMSKYNLNRD 450
Cdd:PRK15429 674 LLSRMKRLGIDKS 686

FhlA

COG3604

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

156-448

4.05e-66

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: 215.48 E-value: 4.05e-66

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 156 QDMMHLLNTVIDtPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESelfgaasgaytgathtrkgk 235
Cdd:COG3604  103 EEDLRLLETLAS-LAAVAILGETGTGKELVANAIHELSPRADKPFVKVNCAALPESLLES-------------------- 161

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 236 fefaqggtvfldeiestpmslqvkllrvLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYYRLSLVKVD 315
Cdd:COG3604  162 ----------------------------LQEGEFERVGGDETIKVDVRIIAATNRDLEEEVAEGRFREDLYYRLNVFPIR 213

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 316 IPPLRARKADIVLLFKHFSSIAATRYHKPPAPLNSEIQQRLLAYDWPGNVRELRNQAERAVLLgvelafsvskTQAKGEL 395
Cdd:COG3604  214 LPPLRERREDIPLLAEHFLEKFSRRLGKPILRLSPEALEALMAYPWPGNVRELENVIERAVIL----------AEGGVLD 283

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489048862 396 SPDLSLSEKVAF--YEQSLIEEALERNHGSIKNTMDTLQIARKTLYDKMSKYNLN 448
Cdd:COG3604  284 ADDLAPGSREALeeVEREHILEALERTGGNIAGAARLLGLTPSTLRSRMKKLGIK 338

pspF

PRK11608

phage shock protein operon transcriptional activator; Provisional

172-376

7.14e-66

phage shock protein operon transcriptional activator; Provisional

Pssm-ID: 236936 [Multi-domain] Cd Length: 326 Bit Score: 214.15 E-value: 7.14e-66

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 172 VMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTGATHTRKGKFEFAQGGTVFLDEIES 251
Cdd:PRK11608  32 VLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELAT 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 252 TPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYYRLSLVKVDIPPLRARKADIVLLFK 331
Cdd:PRK11608 112 APMLVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVAEGKFRADLLDRLAFDVVQLPPLRERQSDIMLMAE 191

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 489048862 332 HFSSIAATRYHKPPAP-LNSEIQQRLLAYDWPGNVRELRNQAERAV 376
Cdd:PRK11608 192 HFAIQMCRELGLPLFPgFTERARETLLNYRWPGNIRELKNVVERSV 237

PRK10820

transcriptional regulator TyrR;

125-418

2.74e-64

transcriptional regulator TyrR;

Pssm-ID: 236769 [Multi-domain] Cd Length: 520 Bit Score: 215.71 E-value: 2.74e-64

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 125 RSLVIQNRAL-KLAVQKTSAPGvRILGDTPKMQdmmHLLN-----TVIDTPadVMIEGETGTGKELVARYLHDQSIRSAS 198
Cdd:PRK10820 183 RSTARMGRQLqNLAVNDDSAFS-QIVAVSPKMR---QVVEqarklAMLDAP--LLITGDTGTGKDLLAYACHLRSPRGKK 256

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 199 NFVAINCGAVPEQLIESELFGAASGAYTGATHTRKGKFEFAQGGTVFLDEI-ESTPmSLQVKLLRVLEERKVTPVGDNKA 277
Cdd:PRK10820 257 PFLALNCASIPDDVVESELFGHAPGAYPNALEGKKGFFEQANGGSVLLDEIgEMSP-RMQAKLLRFLNDGTFRRVGEDHE 335

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 278 IELDIRIVAATKVDLLLLVEKGEFRADLYYRLSLVKVDIPPLRARKADIVLLFKHFSSIAATRYHKPPAPLNSEIQQRLL 357
Cdd:PRK10820 336 VHVDVRVICATQKNLVELVQKGEFREDLYYRLNVLTLNLPPLRDRPQDIMPLTELFVARFADEQGVPRPKLAADLNTVLT 415

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489048862 358 AYDWPGNVRELRNQAERAVllgvelafsvskTQAKG-ELSP-DLSLSEKVAfyEQSLIEEALE 418
Cdd:PRK10820 416 RYGWPGNVRQLKNAIYRAL------------TQLEGyELRPqDILLPDYDA--AVAVGEDAME 464

REC_DctD-like

cd17549

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

10-135

7.39e-58

Pssm-ID: 381101 [Multi-domain] Cd Length: 130 Bit Score: 186.54 E-value: 7.39e-58

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:cd17549    1 VLLVDDDADVREALQQTLELAGFRVRAFADAEEALAALSPDFPGVVISDIRMPGMDGLELLAQIRELDPDLPVILITGHG 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 489048862  90 DVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARACDKRSLVIQNRALK 135
Cdd:cd17549   81 DVPMAVEAMRAGAYDFLEKPFDpERLLDVVRRALEKRRLVLENRRLR 127

PRK11388

DNA-binding transcriptional regulator DhaR; Provisional

150-452

2.16e-53

DNA-binding transcriptional regulator DhaR; Provisional

Pssm-ID: 183114 [Multi-domain] Cd Length: 638 Bit Score: 189.12 E-value: 2.16e-53

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 150 GDTPKMQDMMHLLNTVIDTPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASgayTGAT 229
Cdd:PRK11388 329 QDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPDEALAEEFLGSDR---TDSE 405

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 230 HTRKGKFEFAQGGTVFLDEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYYRL 309
Cdd:PRK11388 406 NGRLSKFELAHGGTLFLEKVEYLSPELQSALLQVLKTGVITRLDSRRLIPVDVRVIATTTADLAMLVEQNRFSRQLYYAL 485

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 310 SLVKVDIPPLRARKADIVLLFKHFSSiAATRYHKPPAPLNSEIQQRLLAYDWPGNVRELRNQAERAVL------LGVE-L 382
Cdd:PRK11388 486 HAFEITIPPLRMRREDIPALVNNKLR-SLEKRFSTRLKIDDDALARLVSYRWPGNDFELRSVIENLALssdngrIRLSdL 564

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489048862 383 AFSVSKTQAKGE-----LSPDLSLSEkvafYEQSLIEEALERNHGSIKNTMDTLQIARKTLYDKMSKYNLNRDMF 452
Cdd:PRK11388 565 PEHLFTEQATDDvsatrLSTSLSLAE----LEKEAIINAAQVCGGRIQEMAALLGIGRTTLWRKMKQHGIDAGQF 635

FixJ

COG4566

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

9-124

1.21e-36

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: 133.30 E-value: 1.21e-36

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGY 88
Cdd:COG4566    1 TVYIVDDDEAVRDSLAFLLESAGLRVETFASAEAFLAALDPDRPGCLLLDVRMPGMSGLELQEELAARGSPLPVIFLTGH 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 489048862  89 ADVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARACDK 124
Cdd:COG4566   81 GDVPMAVRAMKAGAVDFLEKPFDdQALLDAVRRALAR 117

REC_FixJ

cd17537

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

9-121

6.56e-32

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: 117.69 E-value: 6.56e-32

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGY 88
Cdd:cd17537    2 TVYVVDDDEAVRDSLAFLLRSVGLAVKTFTSASAFLAAAPPDQPGCLVLDVRMPGMSGLELQDELLARGSNIPIIFITGH 81

                         90       100       110
                 ....*....|....*....|....*....|....
gi 489048862  89 ADVTIAVKAMQLGAYDLFEKPVNET-LLDCIARA 121
Cdd:cd17537   82 GDVPMAVEAMKAGAVDFLEKPFRDQvLLDAIEQA 115

REC_NtrX-like

cd17550

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

10-123

2.37e-29

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: 110.66 E-value: 2.37e-29

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:cd17550    1 ILIVDDEEDIRESLSGILEDEGYEVDTAADGEEALKLIKERRPDLVLLDIWLPDMDGLELLKEIKEKYPDLPVIMISGHG 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 489048862  90 DVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARACD 123
Cdd:cd17550   81 TIETAVKATKLGAYDFIEKPLSlDRLLLTIERALE 115

CheY

COG0784

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

8-126

1.96e-28

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: 108.78 E-value: 1.96e-28

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFD--SELPVIFL 85
Cdd:COG0784    6 KRILVVDDNPDNRELLRRLLERLGYEVTTAEDGAEALELLRAGPPDLILLDINMPGMDGLELLRRIRALPrlPDIPIIAL 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 489048862  86 TGYADVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARACDKRS 126
Cdd:COG0784   86 TAYADEEDRERALEAGADDYLTKPVDpEELLEALRRLLARAS 127

Response_reg

pfam00072

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

10-115

1.48e-27

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: 105.70 E-value: 1.48e-27

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEKEGYVVAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTAHG 80

                          90       100
                  ....*....|....*....|....*.
gi 489048862   90 DVTIAVKAMQLGAYDLFEKPVNETLL 115
Cdd:pfam00072  81 DEDDAVEALEAGADDFLSKPFDPDEL 106

REC

cd00156

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

12-109

3.16e-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: 3.16e-27

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  12 VVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYADV 91
Cdd:cd00156    2 IVDDDPAIRELLKSLLEREGYEVDTAADGEEALELLREERPDLVLLDLMMPGMDGLELLRKLRELPPDIPVIVLTAKADE 81

                         90
                 ....*....|....*...
gi 489048862  92 TIAVKAMQLGAYDLFEKP 109
Cdd:cd00156   82 EDAVRALELGADDYLVKP 99

RpfG

COG3437

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

10-142

4.76e-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: 107.94 E-value: 4.76e-27

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDS--ELPVIFLTG 87
Cdd:COG3437    9 VLIVDDDPENLELLRQLLRTLGYDVVTAESGEEALELLLEAPPDLILLDVRMPGMDGFELLRLLRADPStrDIPVIFLTA 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 489048862  88 YADVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARACDKRSLVIQNRALKLAVQKTS 142
Cdd:COG3437   89 LADPEDRERALEAGADDYLTKPFDpEELLARVRNALELRRLQRELDDLVLYLKLAA 144

fixJ

PRK09390

response regulator FixJ; Provisional

12-121

3.01e-26

response regulator FixJ; Provisional

Pssm-ID: 181815 [Multi-domain] Cd Length: 202 Bit Score: 105.08 E-value: 3.01e-26

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  12 VVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYADV 91
Cdd:PRK09390   8 VVDDDEAMRDSLAFLLDSAGFEVRLFESAQAFLDALPGLRFGCVVTDVRMPGIDGIELLRRLKARGSPLPVIVMTGHGDV 87

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489048862  92 TIAVKAMQLGAYDLFEKPVNET-LLDCIARA 121
Cdd:PRK09390  88 PLAVEAMKLGAVDFIEKPFEDErLIGAIERA 118

RtcR

COG4650

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

168-368

4.48e-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: 110.69 E-value: 4.48e-26

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 168 TPADVMIEGETGTGKELVAR--YLHDQSIRSAS-NFVAINC------GAVpeqlieSELFGAASGAYTGATHTRKGKFEF 238
Cdd:COG4650  207 SRAPILLTGPTGAGKSQLARriYELKKARHQVSgRFVEVNCatlrgdGAM------SALFGHVKGAFTGAVSDRAGLLRS 280

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 239 AQGGTVFLDEIESTPMSLQVKLLRVLEERKVTPVGDNKAIELDIRIVAATKVDLLLLVEKGEFRADLYYRLSLVKVDIPP 318
Cdd:COG4650  281 ADGGVLFLDEIGELGLDEQAMLLRAIEEKRFLPVGSDKEVSSDFQLIAGTNRDLRQEVAEGRFREDLLARINLWTFRLPG 360

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 319 LRARKADIV--LLF--KHFSSIAATRyhkppAPLNSEIQQRLLAYD------WPGNVREL 368
Cdd:COG4650  361 LAERREDIEpnLDYelARFAREQGRR-----VRFNKEARARYLAFAtspealWSGNFRDL 415

YesN

COG4753

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

10-109

4.14e-25

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: 98.69 E-value: 4.14e-25

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLT-LEGY-TVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTG 87
Cdd:COG4753    2 VLIVDDEPLIREGLKRILEwEAGFeVVGEAENGEEALELLEEHKPDLVITDINMPGMDGLELLEAIRELDPDTKIIILSG 81

                         90       100
                 ....*....|....*....|..
gi 489048862  88 YADVTIAVKAMQLGAYDLFEKP 109
Cdd:COG4753   82 YSDFEYAQEAIKLGADDYLLKP 103

PleD

COG3706

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

9-120

5.26e-25

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

Pssm-ID: 442920 [Multi-domain] Cd Length: 179 Bit Score: 101.14 E-value: 5.26e-25

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQV--TAFDSELPVIFLT 86
Cdd:COG3706    3 RILVVDDDPTNRKLLRRLLEAAGYEVVEAADGEEALELLQEHRPDLILLDLEMPDMDGLELCRRLraDPRTADIPIIFLT 82

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 489048862  87 GYADVTIAVKAMQLGAYDLFEKPVNETLL----DCIAR 120
Cdd:COG3706   83 ALDDEEDRARALEAGADDYLTKPFDPEELlarvDLVAR 120

OmpR

COG0745

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

8-162

5.28e-25

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: 101.96 E-value: 5.28e-25

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTG 87
Cdd:COG0745    2 PRILVVEDDPDIRELLADALEREGYEVDTAADGEEALELLEEERPDLILLDLMLPGMDGLEVCRRLRARPSDIPIIMLTA 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489048862  88 YADVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARACDKRSL-VIQNRALKLAVQKTSAPGVRILGDTPKMQDMMHLL 162
Cdd:COG0745   82 RDDEEDRVRGLEAGADDYLTKPFDpEELLARIRALLRRRAAeVLRVGDLLDLAAREVTRDGEPVELTPKEFRLLELL 158

REC_YesN-like

cd17536

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

10-124

8.45e-25

phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response regulators; This family is composed of uncharacterized response regulators that contain a REC domain and a AraC family helix-turn-helix (HTH) DNA-binding output domain, including Bacillus subtilis uncharacterized transcriptional regulatory protein YesN and Staphylococcus aureus uncharacterized response regulatory protein SAR0214. YesN is a member of the two-component regulatory system YesM/YesN and SAR0214 is a member of the probable two-component regulatory system SAR0215/SAR0214. Also included in this family is the AlgR-like group of LytTR/AlgR family response, which includes Pseudomonas aeruginosa positive alginate biosynthesis regulatory protein AlgR and Bacillus subtilis sensory transduction protein LytT, among others. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

Pssm-ID: 381091 [Multi-domain] Cd Length: 121 Bit Score: 98.56 E-value: 8.45e-25

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGY---TVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLT 86
Cdd:cd17536    1 VLIVDDEPLIREGLKKLIDWEELgfeVVGEAENGEEALELIEEHKPDIVITDIRMPGMDGLELIEKIRELYPDIKIIILS 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 489048862  87 GYADVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARACDK 124
Cdd:cd17536   81 GYDDFEYAQKAIRLGVVDYLLKPVDeEELEEALEKAKEE 119

REC_NtrC

cd19919

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

8-122

2.04e-24

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: 97.34 E-value: 2.04e-24

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTG 87
Cdd:cd19919    1 KTVWIVDDDSSIRWVLERALAGAGLTVTSFENAQEALAALASSQPDVLISDIRMPGMDGLALLAQIKQRHPDLPVIIMTA 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 489048862  88 YADVTIAVKAMQLGAYDLFEKP--VNETlLDCIARAC 122
Cdd:cd19919   81 HSDLDSAVSAYQGGAFEYLPKPfdIDEA-VALVERAI 116

CitB

COG4565

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

9-136

3.87e-22

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

Pssm-ID: 443622 [Multi-domain] Cd Length: 138 Bit Score: 91.95 E-value: 3.87e-22

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLL-TLEGYT-VECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLT 86
Cdd:COG4565    5 RVLIVEDDPMVAELLRRYLeRLPGFEvVGVASSGEEALALLAEHRPDLILLDIYLPDGDGLELLRELRARGPDVDVIVIT 84

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 489048862  87 GYADVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARACDKRSLVIQNRALKL 136
Cdd:COG4565   85 AARDPETVREALRAGVVDYLIKPFTfERLREALERYLEYRRLLREDQEEDL 135

REC_OmpR

cd17574

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

12-109

3.68e-21

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: 87.85 E-value: 3.68e-21

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  12 VVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYADV 91
Cdd:cd17574    2 VVEDDEEIAELLSDYLEKEGYEVDTAADGEEALELAREEQPDLIILDVMLPGMDGFEVCRRLREKGSDIPIIMLTAKDEE 81

                         90
                 ....*....|....*...
gi 489048862  92 TIAVKAMQLGAYDLFEKP 109
Cdd:cd17574   82 EDKVLGLELGADDYITKP 99

Spo0F

COG5803

Stage 0 sporulation initiation response regulator Spo0F [Cell cycle control, cell division, ...

8-111

7.86e-21

Stage 0 sporulation initiation response regulator Spo0F [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];

Pssm-ID: 444505 [Multi-domain] Cd Length: 119 Bit Score: 87.54 E-value: 7.86e-21

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTG 87
Cdd:COG5803    3 KKILIVDDQAGIRMLLKEVLKKEGYEVFQAANGKEALEKVKELKPDLVLLDMKMPGMDGIEILKEIKEIDPDIPVIMMTA 82

                         90       100
                 ....*....|....*....|....
gi 489048862  88 YADVTIAVKAMQLGAYDLFEKPVN 111
Cdd:COG5803   83 YGELDMVEEAKELGAKGYFTKPFD 106

REC_HupR-like

cd17569

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

8-123

3.06e-20

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: 85.92 E-value: 3.06e-20

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTG 87
Cdd:cd17569    1 PTILLVDDEPNILKALKRLLRREGYEVLTATSGEEALEILKQEPVDVVISDQRMPGMDGAELLKRVRERYPDTVRILLTG 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 489048862  88 YADVTIAVKAMQLGA-YDLFEKP-VNETLLDCIARACD 123
Cdd:cd17569   81 YADLDAAIEAINEGEiYRFLTKPwDDEELKETIRQALE 118

REC_typeB_ARR-like

cd17584

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

10-112

5.37e-20

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: 84.99 E-value: 5.37e-20

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKL--NRRFMGVVLSDINMPAMDGLTLLEQVTAfDSELPVIFLTG 87
Cdd:cd17584    1 VLVVDDDPTCLAILKRMLLRCGYQVTTCTDAEEALSMLreNKDEFDLVITDVHMPDMDGFEFLELIRL-EMDLPVIMMSA 79

                         90       100
                 ....*....|....*....|....*
gi 489048862  88 YADVTIAVKAMQLGAYDLFEKPVNE 112
Cdd:cd17584   80 DGSTSTVMKGLAHGACDYLLKPVSI 104

LytT

COG3279

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

9-149

2.53e-19

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

Pssm-ID: 442510 [Multi-domain] Cd Length: 235 Bit Score: 86.79 E-value: 2.53e-19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLLT-LEGYT-VECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLT 86
Cdd:COG3279    3 KILIVDDEPLARERLERLLEkYPDLEvVGEASNGEEALELLEEHKPDLVFLDIQMPGLDGFELARQLRELDPPPPIIFTT 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489048862  87 GYADVtiAVKAMQLGAYDLFEKPVNETLLdciARACDKrslVIQNRALKLAVQKTSAPGVRIL 149
Cdd:COG3279   83 AYDEY--ALEAFEVNAVDYLLKPIDEERL---AKALEK---AKERLEAKAAAEASPEEKDRIF 137

COG4567

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

4-121

3.35e-19

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: 84.58 E-value: 3.35e-19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   4 NSPCKHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVI 83
Cdd:COG4567    1 SAEDRSLLLVDDDEAFARVLARALERRGFEVTTAASVEEALALLEQAPPDYAVLDLRLGDGSGLDLIEALRERDPDARIV 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 489048862  84 FLTGYADVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARA 121
Cdd:COG4567   81 VLTGYASIATAVEAIKLGADDYLAKPADaDDLLAALERA 119

Sigma54_activ_2

pfam14532

Sigma-54 interaction domain;

149-319

3.72e-19

Sigma-54 interaction domain;

Pssm-ID: 434021 [Multi-domain] Cd Length: 138 Bit Score: 83.55 E-value: 3.72e-19

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  149 LGDTPKMQDMMHLLNTVIDTPADVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLieselfgaasgaytga 228
Cdd:pfam14532   1 LGASAAIQEIKRRLEQAAQSTLPVFLTGEPGSGKEFCARYLHNPSTPWVQPFDIEYLAHAPLEL---------------- 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  229 thtrkgkFEFAQGGTVFLDEIESTPMSLQVKLLRVLEerkvtpvgdnKAIELDIRIVAATKVDLLLLVEKGEFRADLYYR 308
Cdd:pfam14532  65 -------LEQAKGGTLYLKDIADLSKALQKGLLLLLA----------KAEGYRVRLVCTSSKDLPQLAAAGLFDEQLYFE 127

                         170
                  ....*....|.
gi 489048862  309 LSLVKVDIPPL 319
Cdd:pfam14532 128 LSALRLHVPPL 138

AAA

cd00009

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

153-318

2.80e-18

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: 81.42 E-value: 2.80e-18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 153 PKMQDMMHLLNTVIDTPAD--VMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGaasgayTGATH 230
Cdd:cd00009    1 VGQEEAIEALREALELPPPknLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFG------HFLVR 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 231 TRKGKFEFAQGGTVFLDEIESTPMSLQVKLLRVLEERKVTPVgdnkaIELDIRIVAATKVDLLllvekGEFRADLYYRLS 310
Cdd:cd00009   75 LLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRI-----DRENVRVIGATNRPLL-----GDLDRALYDRLD 144


                 ....*...
gi 489048862 311 LvKVDIPP 318
Cdd:cd00009  145 I-RIVIPL 151

REC_RssB-like

cd17555

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

10-110

9.24e-18

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: 78.78 E-value: 9.24e-18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:cd17555    3 ILVIDDDEVVRESIAAYLEDSGFQVLQAADGRQGLELFRSEQPDLVLCDLRMPEMDGLEVLKQITKESPDTPVIVVSGAG 82

                         90       100
                 ....*....|....*....|.
gi 489048862  90 DVTIAVKAMQLGAYDLFEKPV 110
Cdd:cd17555   83 VMSDAVEALRLGAWDYLTKPI 103

REC_OmpR_ChvI-like

cd19936

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

10-109

1.57e-17

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: 77.49 E-value: 1.57e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAfDSELPVIFLTGYA 89
Cdd:cd19936    1 IALVDDDRNILTSVSMALEAEGFSVETYTDGASALDGLNARPPDLAILDIKMPRMDGMELLQRLRQ-KSTLPVIFLTSKD 79

                         90       100
                 ....*....|....*....|
gi 489048862  90 DVTIAVKAMQLGAYDLFEKP 109
Cdd:cd19936   80 DEIDEVFGLRMGADDYITKP 99

REC_TrrA-like

cd17554

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

8-90

1.77e-17

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: 78.03 E-value: 1.77e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTG 87
Cdd:cd17554    1 KKILVVDDEENIRELYKEELEDEGYEVVTAGNGEEALEKLESEDPDLVILDIKMPGMDGLETLRKIREKKPDLPVIICTA 80


                 ...
gi 489048862  88 YAD 90
Cdd:cd17554   81 YSE 83

PspF

COG1221

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

172-370

2.35e-17

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: 84.77 E-value: 2.35e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 172 VMIEGETGTGKELVARYLH-----DQSIRSASNFVAINCG--AVPEQLIESELFGAASGAYTGATHTRKGKFEFAQGGTV 244
Cdd:COG1221  133 TLILGPTGVGKSFFAELMYeyaieIGVLPEDAPFVVFNCAdyANNPQLLMSQLFGYVKGAFTGADKDKEGLIEKADGGIL 212

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862 245 FLDEIESTPMSLQVKLLRVLEERKVTPVGD-NKAIELDIRIVAAT--KVDLLLLvekGEF-RadlyyRLSLVkVDIPPLR 320
Cdd:COG1221  213 FLDEVHRLPPEGQEMLFTFMDKGIYRRLGEtEKTRKANVRIIFATteDPESSLL---KTFlR-----RIPMV-IKLPSLE 283

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 489048862 321 AR----KADIVllfKHFSSIAATRYHKpPAPLNSEIQQRLLAYDWPGNVRELRN 370
Cdd:COG1221  284 ERsleeRLELI---KHFFKEEAKRLNK-PIKVSKEVLKALLLYDCPGNIGQLKS 333

REC_RegA-like

cd17563

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

8-111

3.48e-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: 77.10 E-value: 3.48e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLN-RRFMGVVLsDINMPAMDGLTLLEQVTAFDSELPVIFLT 86
Cdd:cd17563    1 KSLLLVDDDEVFAERLARALERRGFEVETAHSVEEALALAReEKPDYAVL-DLRLGGDSGLDLIPPLRALQPDARIVVLT 79

                         90       100
                 ....*....|....*....|....*
gi 489048862  87 GYADVTIAVKAMQLGAYDLFEKPVN 111
Cdd:cd17563   80 GYASIATAVEAIKLGADDYLAKPAD 104

REC_OmpR_PrrA-like

cd17627

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

10-109

7.84e-17

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: 76.27 E-value: 7.84e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:cd17627    1 ILVVDDDRAVRESLRRSLRFEGYEVETAVDGAEALRVISGNRPDAVVLDVMMPRLDGLEVCRRLRAAGNDLPILVLTARD 80

                         90       100
                 ....*....|....*....|
gi 489048862  90 DVTIAVKAMQLGAYDLFEKP 109
Cdd:cd17627   81 SVSDRVAGLDAGADDYLVKP 100

REC_RpfG-like

cd17551

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

9-121

8.43e-17

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: 75.94 E-value: 8.43e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLLTLEGYT-VECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAF--DSELPVIFL 85
Cdd:cd17551    2 RILIVDDNPTNLLLLEALLRSAGYLeVVSFTDPREALAWCRENPPDLILLDYMMPGMDGLEFIRRLRALpgLEDVPIVMI 81

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489048862  86 TGYADVTIAVKAMQLGAYDLFEKPVNETllDCIARA 121
Cdd:cd17551   82 TADTDREVRLRALEAGATDFLTKPFDPV--ELLARV 115

REC_NtrC1-like

cd17572

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

10-111

8.44e-17

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: 76.08 E-value: 8.44e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:cd17572    1 VLLVEDSPSLAALYQEYLSDEGYKVTHVETGKEALAFLSDQPPDVVLLDLKLPDMSGMEILKWIQERSLPTSVIVITAHG 80

                         90       100
                 ....*....|....*....|..
gi 489048862  90 DVTIAVKAMQLGAYDLFEKPVN 111
Cdd:cd17572   81 SVDIAVEAMRLGAYDFLEKPFD 102

REC_OmpR_ArcA_TorR-like

cd17619

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

9-111

9.31e-17

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: 75.89 E-value: 9.31e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAfDSELPVIFLTGY 88
Cdd:cd17619    2 HILIVEDEPVTRATLKSYFEQEGYDVSEAGDGEEMRQILARQDIDLVLLDINLPGKDGLSLTRELRE-QSEVGIILVTGR 80

                         90       100
                 ....*....|....*....|...
gi 489048862  89 ADVTIAVKAMQLGAYDLFEKPVN 111
Cdd:cd17619   81 DDEVDRIVGLEIGADDYVTKPFN 103

REC_2_DhkD-like

cd17580

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

10-118

3.79e-16

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: 74.03 E-value: 3.79e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQV--TAFDSELPVIFLTG 87
Cdd:cd17580    1 ILVVDDNEDAAEMLALLLELEGAEVTTAHSGEEALEAAQRFRPDVILSDIGMPGMDGYELARRLreLPWLANTPAIALTG 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 489048862  88 YADVTIAVKAMQLGaYDL-FEKPVN-ETLLDCI 118
Cdd:cd17580   81 YGQPEDRERALEAG-FDAhLVKPVDpDELIELI 112

REC_D1_PleD-like

cd17538

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

9-110

8.25e-16

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: 72.92 E-value: 8.25e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDS--ELPVIFLT 86
Cdd:cd17538    1 KILVVDDEPANRELLEALLSAEGYEVLTADSGQEALALAEEELPDLILLDVMMPGMDGFEVCRRLKEDPEtrHIPVIMIT 80

                         90       100
                 ....*....|....*....|....
gi 489048862  87 GYADVTIAVKAMQLGAYDLFEKPV 110
Cdd:cd17538   81 ALDDREDRIRGLEAGADDFLSKPI 104

PRK11083

DNA-binding response regulator CreB; Provisional

9-109

1.15e-15

DNA-binding response regulator CreB; Provisional

Pssm-ID: 236838 [Multi-domain] Cd Length: 228 Bit Score: 75.77 E-value: 1.15e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGY 88
Cdd:PRK11083   5 TILLVEDEQAIADTLVYALQSEGFTVEWFERGLPALDKLRQQPPDLVILDVGLPDISGFELCRQLLAFHPALPVIFLTAR 84

                         90       100
                 ....*....|....*....|.
gi 489048862  89 ADVTIAVKAMQLGAYDLFEKP 109
Cdd:PRK11083  85 SDEVDRLVGLEIGADDYVAKP 105

REC_OmpR_PmrA-like

cd17624

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

10-109

1.52e-15

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: 72.52 E-value: 1.52e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKL-NRRFMGVVLsDINMPAMDGLTLLEQVTAFDSELPVIFLTGY 88
Cdd:cd17624    1 ILLVEDDALLGDGLKTGLRKAGYAVDWVRTGAEAEAALaSGPYDLVIL-DLGLPDGDGLDLLRRWRRQGQSLPVLILTAR 79

                         90       100
                 ....*....|....*....|.
gi 489048862  89 ADVTIAVKAMQLGAYDLFEKP 109
Cdd:cd17624   80 DGVDDRVAGLDAGADDYLVKP 100

REC_OmpR_CusR-like

cd19935

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

10-109

2.05e-15

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: 71.70 E-value: 2.05e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:cd19935    1 ILVVEDEKKLAEYLKKGLTEEGYAVDVAYDGEDGLHLALTNEYDLIILDVMLPGLDGLEVLRRLRAAGKQTPVLMLTARD 80

                         90       100
                 ....*....|....*....|
gi 489048862  90 DVTIAVKAMQLGAYDLFEKP 109
Cdd:cd19935   81 SVEDRVKGLDLGADDYLVKP 100

REC_NarL-like

cd17535

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

10-102

2.19e-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: 2.19e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLL-TLEGYTV--ECfNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLT 86
Cdd:cd17535    1 VLIVDDHPLVREGLRRLLeSEPDIEVvgEA-ADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRRYPDLKVIVLT 79

                         90
                 ....*....|....*.
gi 489048862  87 GYADVTIAVKAMQLGA 102
Cdd:cd17535   80 AHDDPEYVLRALKAGA 95

REC_CheY4-like

cd17562

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

8-122

2.22e-15

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: 71.95 E-value: 2.22e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTL---LEQVTAFDSeLPVIF 84
Cdd:cd17562    1 KKILAVDDSASIRQMVSFTLRGAGYEVVEAADGRDALSKAQSKKFDLIITDQNMPNMDGIELikeLRKLPAYKF-TPILM 79

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 489048862  85 LTGYADVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARAC 122
Cdd:cd17562   80 LTTESSDEKKQEGKAAGATGWLVKPFDpEQLLEVVKKVL 118

REC_hyHK_CKI1_RcsC-like

cd17546

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

10-115

3.10e-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: 3.10e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSE---LPVIFLT 86
Cdd:cd17546    1 VLVVDDNPVNRKVLKKLLEKLGYEVDVAENGQEALELLKEEPFDLVLMDLQMPVMDGLEATRRIRELEGGgrrTPIIALT 80

                         90       100
                 ....*....|....*....|....*....
gi 489048862  87 GYADVTIAVKAMQLGAYDLFEKPVNETLL 115
Cdd:cd17546   81 ANALEEDREKCLEAGMDDYLSKPVKLDQL 109

REC_CheY_CheY3

cd19923

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

10-115

3.87e-15

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: 71.60 E-value: 3.87e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYT-VECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFD--SELPVIFLT 86
Cdd:cd19923    3 VLVVDDFSTMRRIIKNLLKELGFNnVEEAEDGVDALEKLKAGGFDFVITDWNMPNMDGLELLKTIRADGalSHLPVLMVT 82

                         90       100
                 ....*....|....*....|....*....
gi 489048862  87 GYADVTIAVKAMQLGAYDLFEKPVNETLL 115
Cdd:cd19923   83 AEAKKENVIAAAQAGVNNYIVKPFTAATL 111

REC_Ycf29

cd19927

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

10-109

6.35e-15

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: 70.48 E-value: 6.35e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQV---TAFDSeLPVIFLT 86
Cdd:cd19927    1 ILLVDDDPGIRLAVKDYLEDQGFTVIAASNGLEALDLLNQYIPDLIISDIIMPGVDGYSLLGKLrknADFDT-IPVIFLT 79

                         90       100
                 ....*....|....*....|...
gi 489048862  87 GYADVTIAVKAMQLGAYDLFEKP 109
Cdd:cd19927   80 AKGMTSDRIKGYNAGCDGYLSKP 102

REC_PA4781-like

cd19920

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

10-110

9.72e-15

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: 69.85 E-value: 9.72e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDS--ELPVIFLTG 87
Cdd:cd19920    1 ILIVDDVPDNLRLLSELLRAAGYRVLVATDGQQALQRAQAEPPDLILLDVMMPGMDGFEVCRRLKADPAtrHIPVIFLTA 80

                         90       100
                 ....*....|....*....|...
gi 489048862  88 YADVTIAVKAMQLGAYDLFEKPV 110
Cdd:cd19920   81 LTDTEDKVKGFELGAVDYITKPF 103

REC_OmpR_CpxR

cd17623

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

10-134

1.16e-14

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: 70.03 E-value: 1.16e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAfDSELPVIFLTGYA 89
Cdd:cd17623    1 ILLIDDDRELTELLTEYLEMEGFNVRAAHDGEQGLAALLEGSPDLVVLDVMLPKMNGLDVLKELRK-TSQVPVLMLTARG 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 489048862  90 DVTIAVKAMQLGAYDLFEKPvnetlldciaraCDKRSLVIQNRAL 134
Cdd:cd17623   80 DDIDRILGLELGADDYLPKP------------FNPRELVARIRAI 112

orf27

CHL00148

Ycf27; Reviewed

2-109

4.85e-14

Ycf27; Reviewed

Pssm-ID: 214376 [Multi-domain] Cd Length: 240 Bit Score: 71.67 E-value: 4.85e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   2 IENSPCKHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAfDSELP 81
Cdd:CHL00148   1 TMENSKEKILVVDDEAYIRKILETRLSIIGYEVITASDGEEALKLFRKEQPDLVILDVMMPKLDGYGVCQEIRK-ESDVP 79

                         90       100
                 ....*....|....*....|....*...
gi 489048862  82 VIFLTGYADVTIAVKAMQLGAYDLFEKP 109
Cdd:CHL00148  80 IIMLTALGDVSDRITGLELGADDYVVKP 107

AmiR

COG3707

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

10-135

7.50e-14

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: 69.99 E-value: 7.50e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTV-ECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAfDSELPVIFLTGY 88
Cdd:COG3707    6 VLVVDDEPLRRADLREGLREAGYEVvAEAADGEDAVELVRELKPDLVIVDIDMPDRDGLEAARQISE-ERPAPVILLTAY 84

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489048862  89 ADVTIAVKAMQLGAYDLFEKPVNE-----TLLDCIARACDKRSLVIQNRALK 135
Cdd:COG3707   85 SDPELIERALEAGVSAYLVKPLDPedllpALELALARFRELRALRRELAKLR 136

REC_OmpR_DrrD-like

cd17625

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

12-109

7.84e-14

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: 67.63 E-value: 7.84e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  12 VVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYADV 91
Cdd:cd17625    2 VVEDEKDLSEAITKHLKKEGYTVDVCFDGEEGLEYALSGIYDLIILDIMLPGMDGLEVLKSLREEGIETPVLLLTALDAV 81

                         90
                 ....*....|....*...
gi 489048862  92 TIAVKAMQLGAYDLFEKP 109
Cdd:cd17625   82 EDRVKGLDLGADDYLPKP 99

REC_OmpR_MtPhoP-like

cd17615

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

10-120

1.23e-13

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: 66.99 E-value: 1.23e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:cd17615    2 VLVVDDEPNITELLSMALRYEGWDVETAADGAEALAAAREFRPDAVVLDIMLPDMDGLEVLRRLRADGPDVPVLFLTAKD 81

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489048862  90 DVTIAVKAMQLGAYDLFEKPVneTLLDCIAR 120
Cdd:cd17615   82 SVEDRIAGLTAGGDDYVTKPF--SLEEVVAR 110

REC_CpdR_CckA-like

cd18160

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

10-109

5.06e-13

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: 64.83 E-value: 5.06e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNR-RFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGY 88
Cdd:cd18160    2 ILLADDEPSVRKFIVTTLKKAGYAVTEAESGAEALEKLQQgKDIDIVVTDIVMPEMDGIELAREARKIDPDVKILFISGG 81

                         90       100
                 ....*....|....*....|.
gi 489048862  89 ADVTIAVKAMQLGAYDLFEKP 109
Cdd:cd18160   82 AAAAPELLSDAVGDNATLKKP 102

REC_hyHK

cd17598

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

10-115

6.07e-13

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: 65.04 E-value: 6.07e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDS--ELPVIFLTG 87
Cdd:cd17598    1 ILIVEDSPTQAEQLKHILEEQGYKVQVARNGREALAMLAEHRPTLVISDIVMPEMDGYELCRKIKSDPDlkDIPVILLTT 80

                         90       100
                 ....*....|....*....|....*...
gi 489048862  88 YADVTIAVKAMQLGAYDLFEKPVNETLL 115
Cdd:cd17598   81 LSDPRDVIRGLECGADNFITKPYDEKYL 108

REC_CheY

cd17542

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

10-121

7.65e-13

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: 64.99 E-value: 7.65e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTV--ECfNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTG 87
Cdd:cd17542    3 VLIVDDAAFMRMMLKDILTKAGYEVvgEA-ANGEEAVEKYKELKPDLVTMDITMPEMDGIEALKEIKKIDPNAKVIMCSA 81

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 489048862  88 YADVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARA 121
Cdd:cd17542   82 MGQEEMVKEAIKAGAKDFIVKPFQpERVLEAVEKV 116

REC_LytTR_AlgR-like

cd17532

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

10-124

8.39e-13

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: 64.87 E-value: 8.39e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGY--TVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTG 87
Cdd:cd17532    1 ALIVDDEPLAREELRYLLEEHPDieIVGEAENGEEALEAIEELKPDVVFLDIQMPGLDGLELAKKLSKLAKPPLIVFVTA 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 489048862  88 YADvtIAVKAMQLGAYDLFEKPVNEtllDCIARACDK 124
Cdd:cd17532   81 YDE--YAVEAFELNAVDYLLKPFSE---ERLAEALAK 112

REC_PdtaR-like

cd19932

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

8-120

1.01e-12

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: 64.74 E-value: 1.01e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTLEGYTV--ECfNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAfDSELPVIFL 85
Cdd:cd19932    1 VRVLIAEDEALIRMDLREMLEEAGYEVvgEA-SDGEEAVELAKKHKPDLVIMDVKMPRLDGIEAAKIITS-ENIAPIVLL 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 489048862  86 TGYADVTIAVKAMQLGAYDLFEKPVNE-----TLLDCIAR 120
Cdd:cd19932   79 TAYSQQDLVERAKEAGAMAYLVKPFSEsdlipAIEMAIAR 118

REC_Spo0F-like

cd17553

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

8-109

3.05e-12

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: 63.34 E-value: 3.05e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTG 87
Cdd:cd17553    1 EKILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTA 80

                         90       100
                 ....*....|....*....|..
gi 489048862  88 YADVTIAVKAMQLGAYDLFEKP 109
Cdd:cd17553   81 YGELDMIQESKELGALTHFAKP 102

REC_CheB-like

cd17541

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

10-116

4.34e-12

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: 62.79 E-value: 4.34e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGY-----TVEcfnDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAfDSELPVIF 84
Cdd:cd17541    3 VLIVDDSAVMRKLLSRILESDPDievvgTAR---DGEEALEKIKELKPDVITLDIEMPVMDGLEALRRIMA-ERPTPVVM 78

                         90       100       110
                 ....*....|....*....|....*....|....
gi 489048862  85 LTGY--ADVTIAVKAMQLGAYDLFEKPVNETLLD 116
Cdd:cd17541   79 VSSLteEGAEITLEALELGAVDFIAKPSGGISLD 112

REC_OmpR_YycF-like

cd17614

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

10-109

6.99e-12

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: 62.06 E-value: 6.99e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAfDSELPVIFLTGYA 89
Cdd:cd17614    1 ILVVDDEKPISDILKFNLTKEGYEVVTAYDGREALEKVEEEQPDLILLDLMLPEKDGLEVCREVRK-TSNVPIIMLTAKD 79

                         90       100
                 ....*....|....*....|
gi 489048862  90 DVTIAVKAMQLGAYDLFEKP 109
Cdd:cd17614   80 SEVDKVLGLELGADDYVTKP 99

REC_DC-like

cd17534

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

8-112

1.29e-11

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: 61.27 E-value: 1.29e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTLEGYTV-ECFNDASTALTKLNRRFMGVVLSDINMP-AMDGLTLLEQV-TAFDseLPVIF 84
Cdd:cd17534    1 KKILIVEDEAIIALDLKEILESLGYEVvGIADSGEEAIELAEENKPDLILMDINLKgDMDGIEAAREIrEKFD--IPVIF 78

                         90       100
                 ....*....|....*....|....*...
gi 489048862  85 LTGYADVTIAVKAMQLGAYDLFEKPVNE 112
Cdd:cd17534   79 LTAYSDEETLERAKETNPYGYLVKPFNE 106

REC_OmpR_BsPhoP-like

cd19937

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

12-109

2.68e-11

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

Pssm-ID: 381164 [Multi-domain] Cd Length: 116 Bit Score: 60.36 E-value: 2.68e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  12 VVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQV--TAFDSELPVIFLTGYA 89
Cdd:cd19937    2 VVDDEEDIVELLKYNLEKEGYEVVTAYDGEEALKRAKDEKPDLIILDLMLPGIDGLEVCRILrsDPKTSSIPIIMLTAKG 81

                         90       100
                 ....*....|....*....|
gi 489048862  90 DVTIAVKAMQLGAYDLFEKP 109
Cdd:cd19937   82 EEFDKVLGLELGADDYITKP 101

PRK15479

transcriptional regulator TctD;

10-136

3.03e-11

transcriptional regulator TctD;

Pssm-ID: 185376 [Multi-domain] Cd Length: 221 Bit Score: 62.82 E-value: 3.03e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:PRK15479   3 LLLAEDNRELAHWLEKALVQNGFAVDCVFDGLAADHLLQSEMYALAVLDINMPGMDGLEVLQRLRKRGQTLPVLLLTARS 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 489048862  90 DVTIAVKAMQLGAYDLFEKPVNETLLDCIARACDKRSLVIQNRALKL 136
Cdd:PRK15479  83 AVADRVKGLNVGADDYLPKPFELEELDARLRALLRRSAGQVQEVQQL 129

REC_RcNtrC-like

cd19928

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

10-109

6.47e-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: 59.05 E-value: 6.47e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:cd19928    1 ILVADDDRAIRTVLTQALGRAGYEVRTTGNAATLWRWVEEGEGDLVITDVVMPDENGLDLIPRIKKARPDLPIIVMSAQN 80

                         90       100
                 ....*....|....*....|
gi 489048862  90 DVTIAVKAMQLGAYDLFEKP 109
Cdd:cd19928   81 TLMTAVKAAERGAFEYLPKP 100

REC_OmpR_BfmR-like

cd19939

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

9-120

9.73e-11

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: 58.92 E-value: 9.73e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFdSELPVIFLTGY 88
Cdd:cd19939    1 RILIVEDELELARLTRDYLIKAGLEVSVFTDGQRAVRRIIDEQPSLVVLDIMLPGMDGLTVCREVREH-SHVPILMLTAR 79

                         90       100       110
                 ....*....|....*....|....*....|..
gi 489048862  89 ADVTIAVKAMQLGAYDLFEKPVNETLLdcIAR 120
Cdd:cd19939   80 TEEMDRVLGLEMGADDYLCKPFSPREL--LAR 109

REC_2_GGDEF

cd17544

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

9-109

1.14e-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: 58.68 E-value: 1.14e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNR-RFMGVVLSDINMPAMDGLTLLEQV-TAFDSE-LPVIFL 85
Cdd:cd17544    2 KVLVVDDSATSRNHLRALLRRHNFQVLEAANGQEALEVLEQhPDIKLVITDYNMPEMDGFELVREIrKKYSRDqLAIIGI 81

                         90       100
                 ....*....|....*....|....
gi 489048862  86 TGYADVTIAVKAMQLGAYDLFEKP 109
Cdd:cd17544   82 SASGDNALSARFIKAGANDFLTKP 105

PRK10610

chemotaxis protein CheY;

11-116

1.41e-10

chemotaxis protein CheY;

Pssm-ID: 170568 [Multi-domain] Cd Length: 129 Bit Score: 58.83 E-value: 1.41e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  11 IVVDDEAMIRDSLKQLLTLEGY-TVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFD--SELPVIFLTG 87
Cdd:PRK10610   9 LVVDDFSTMRRIVRNLLKELGFnNVEEAEDGVDALNKLQAGGFGFVISDWNMPNMDGLELLKTIRADGamSALPVLMVTA 88

                         90       100
                 ....*....|....*....|....*....
gi 489048862  88 YADVTIAVKAMQLGAYDLFEKPVNETLLD 116
Cdd:PRK10610  89 EAKKENIIAAAQAGASGYVVKPFTAATLE 117

REC_HupR

cd17596

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

10-136

1.53e-10

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: 58.92 E-value: 1.53e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTlEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:cd17596    3 ILVVDDEVRSLEALRRTLE-EDFDVLTAASAEEALAILEEEWVQVILCDQRMPGTTGVEFLKEVRERWPEVVRIIISGYT 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 489048862  90 DVTIAVKAM-QLGAYDLFEKPVN-ETLLDCIARACDKRSLVIQNRALKL 136
Cdd:cd17596   82 DSEDIIAGInEAGIYQYLTKPWHpDQLLLTVRNAARLFELQRENERLSL 130

REC

smart00448

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

8-62

1.66e-10

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

Pssm-ID: 214668 [Multi-domain] Cd Length: 55 Bit Score: 56.42 E-value: 1.66e-10

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 489048862     8 KHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMP 62
Cdd:smart00448   1 MRILVVDDDPLLRELLKALLEKEGYEVDEATDGEEALELLKEEKPDLILLDIMMP 55

REC_hyHK_blue-like

cd18161

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

10-110

1.95e-10

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: 57.74 E-value: 1.95e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRF-MGVVLSDINMPA-MDGLTLLEQVTAFDSELPVIFLTG 87
Cdd:cd18161    1 VLVVEDDPDVRRLTAEVLEDLGYTVLEAASGDEALDLLESGPdIDLLVTDVIMPGgMNGSQLAEEARRRRPDLKVLLTSG 80

                         90       100
                 ....*....|....*....|...
gi 489048862  88 YADVTIaVKAMQLGAYDLFEKPV 110
Cdd:cd18161   81 YAENAI-EGGDLAPGVDVLSKPF 102

REC_OmpR_PhoB

cd17618

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

8-109

2.64e-10

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: 57.64 E-value: 2.64e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQV--TAFDSELPVIFL 85
Cdd:cd17618    1 RTILIVEDEPAIREMIAFNLERAGFDVVEAEDAESAVNLIVEPRPDLILLDWMLPGGSGIQFIRRLkrDEMTRDIPIIML 80

                         90       100
                 ....*....|....*....|....
gi 489048862  86 TGYADVTIAVKAMQLGAYDLFEKP 109
Cdd:cd17618   81 TARGEEEDKVRGLEAGADDYITKP 104

PRK10766

two-component system response regulator TorR;

8-110

2.95e-10

two-component system response regulator TorR;

Pssm-ID: 182711 [Multi-domain] Cd Length: 221 Bit Score: 60.05 E-value: 2.95e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAfDSELPVIFLTG 87
Cdd:PRK10766   3 YHILVVEDEPVTRARLQGYFEQEGYTVSEAASGAGMREIMQNQHVDLILLDINLPGEDGLMLTRELRS-RSTVGIILVTG 81

                         90       100
                 ....*....|....*....|...
gi 489048862  88 YADVTIAVKAMQLGAYDLFEKPV 110
Cdd:PRK10766  82 RTDSIDRIVGLEMGADDYVTKPL 104

REC_OmpR_BaeR-like

cd19938

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

9-109

3.08e-10

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: 57.39 E-value: 3.08e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFdSELPVIFLTGY 88
Cdd:cd19938    1 RILIVEDEPKLAQLLIDYLRAAGYAPTLLAHGDQVLPYVRHTPPDLILLDLMLPGTDGLTLCREIRRF-SDVPIIMVTAR 79

                         90       100
                 ....*....|....*....|.
gi 489048862  89 ADVTIAVKAMQLGAYDLFEKP 109
Cdd:cd19938   80 VEEIDRLLGLELGADDYICKP 100

PRK10955

envelope stress response regulator transcription factor CpxR;

10-126

4.32e-10

envelope stress response regulator transcription factor CpxR;

Pssm-ID: 182864 [Multi-domain] Cd Length: 232 Bit Score: 59.82 E-value: 4.32e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRfMGVVLSDINMPAMDGLTLLEQVTAfDSELPVIFLTGYA 89
Cdd:PRK10955   4 ILLVDDDRELTSLLKELLEMEGFNVIVAHDGEQALDLLDDS-IDLLLLDVMMPKKNGIDTLKELRQ-THQTPVIMLTARG 81

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 489048862  90 DVTIAVKAMQLGAYDLFEKPVNETLLDCIARACDKRS 126
Cdd:PRK10955  82 SELDRVLGLELGADDYLPKPFNDRELVARIRAILRRS 118

REC_RR468-like

cd17552

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

8-121

5.42e-10

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: 56.79 E-value: 5.42e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKqlLTLE---GYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAfDSE---LP 81
Cdd:cd17552    2 KRILVIDDEEDIREVVQ--ACLEklaGWEVLTASSGQEGLEKAATEQPDAILLDVMMPDMDGLATLKKLQA-NPEtqsIP 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 489048862  82 VIFLTGYADVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARA 121
Cdd:cd17552   79 VILLTAKAQPSDRQRFASLGVAGVIAKPFDpLTLAEQIAKL 119

REC_OmpR_KdpE-like

cd17620

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

10-109

6.29e-10

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: 56.02 E-value: 6.29e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVEcfnDASTALTKLN----RRFmGVVLSDINMPAMDGLTLLEQVTAFdSELPVIFL 85
Cdd:cd17620    1 ILVIEDEPQIRRFLRTALEAHGYRVF---EAETGQEGLLeaatRKP-DLIILDLGLPDMDGLEVIRRLREW-SAVPVIVL 75

                         90       100
                 ....*....|....*....|....
gi 489048862  86 TGYADVTIAVKAMQLGAYDLFEKP 109
Cdd:cd17620   76 SARDEESDKIAALDAGADDYLTKP 99

ompR

PRK09468

osmolarity response regulator; Provisional

9-111

7.09e-10

osmolarity response regulator; Provisional

Pssm-ID: 181883 [Multi-domain] Cd Length: 239 Bit Score: 59.22 E-value: 7.09e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLLTLEGYTVECFNDAStALTKLNRR--FMGVVLsDINMPAMDGLTLLEQVTAFDSELPVIFLT 86
Cdd:PRK09468   7 KILVVDDDMRLRALLERYLTEQGFQVRSAANAE-QMDRLLTResFHLMVL-DLMLPGEDGLSICRRLRSQNNPTPIIMLT 84

                         90       100
                 ....*....|....*....|....*
gi 489048862  87 GYADVTIAVKAMQLGAYDLFEKPVN 111
Cdd:PRK09468  85 AKGEEVDRIVGLEIGADDYLPKPFN 109

REC_CheC-like

cd17593

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

8-111

7.72e-10

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

Pssm-ID: 381124 [Multi-domain] Cd Length: 117 Bit Score: 56.39 E-value: 7.72e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTlEGYTVECFN--DASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFL 85
Cdd:cd17593    1 MKVLICDDSSMARKQLARALP-ADWDVEITFaeNGEEALEILREGRIDVLFLDLTMPVMDGYEVLEALPVEQLETKVIVV 79

                         90       100
                 ....*....|....*....|....*...
gi 489048862  86 TGyaDVTIAVK--AMQLGAYDLFEKPVN 111
Cdd:cd17593   80 SG--DVQPEAKerVLELGALAFLKKPFD 105

REC_OmpR_VirG

cd17594

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

9-110

9.21e-10

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: 55.92 E-value: 9.21e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAfDSELPVIFLTGY 88
Cdd:cd17594    1 HVLVVDDDAAMRHLLILYLRERGFDVTAAADGAEEARLMLHRRVDLVLLDLRLGQESGLDLLRTIRA-RSDVPIIIISGD 79

                         90       100
                 ....*....|....*....|...
gi 489048862  89 ADVTIA-VKAMQLGAYDLFEKPV 110
Cdd:cd17594   80 RRDEIDrVVGLELGADDYLAKPF 102

REC_DivK-like

cd17548

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

10-120

9.73e-10

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: 56.01 E-value: 9.73e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFD--SELPVIFLTG 87
Cdd:cd17548    2 ILIVEDNPLNMKLARDLLESAGYEVLEAADGEEALEIARKEKPDLILMDIQLPGMDGLEATRLLKEDPatRDIPVIALTA 81

                         90       100       110
                 ....*....|....*....|....*....|....
gi 489048862  88 YADVTIAVKAMQLGAYDLFEKPVN-ETLLDCIAR 120
Cdd:cd17548   82 YAMKGDREKILEAGCDGYISKPIDtREFLETVAK 115

REC_OmpR_RegX3-like

cd17621

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

10-109

9.77e-10

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: 55.67 E-value: 9.77e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAfDSELPVIFLTGYA 89
Cdd:cd17621    1 VLVVEDEESFSDPLAYLLRKEGFEVTVATDGPAALAEFDRAGADIVLLDLMLPGLSGTEVCRQLRA-RSNVPVIMVTAKD 79

                         90       100
                 ....*....|....*....|
gi 489048862  90 DVTIAVKAMQLGAYDLFEKP 109
Cdd:cd17621   80 SEIDKVVGLELGADDYVTKP 99

PRK10643

two-component system response regulator PmrA;

10-109

1.22e-09

two-component system response regulator PmrA;

Pssm-ID: 182612 [Multi-domain] Cd Length: 222 Bit Score: 58.12 E-value: 1.22e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:PRK10643   3 ILIVEDDTLLLQGLILALQTEGYACDCASTAREAEALLESGHYSLVVLDLGLPDEDGLHLLRRWRQKKYTLPVLILTARD 82

                         90       100
                 ....*....|....*....|
gi 489048862  90 DVTIAVKAMQLGAYDLFEKP 109
Cdd:PRK10643  83 TLEDRVAGLDVGADDYLVKP 102

REC_OmpR_EcPhoP-like

cd19934

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

10-109

1.50e-09

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: 55.37 E-value: 1.50e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:cd19934    1 LLLVEDDALLAAQLKEQLSDAGYVVDVAEDGEEALFQGEEEPYDLVVLDLGLPGMDGLSVLRRWRSEGRATPVLILTARD 80

                         90       100
                 ....*....|....*....|
gi 489048862  90 DVTIAVKAMQLGAYDLFEKP 109
Cdd:cd19934   81 SWQDKVEGLDAGADDYLTKP 100

PRK11173

two-component response regulator; Provisional

9-120

1.51e-09

two-component response regulator; Provisional

Pssm-ID: 183013 [Multi-domain] Cd Length: 237 Bit Score: 58.10 E-value: 1.51e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAfDSELPVIFLTGY 88
Cdd:PRK11173   5 HILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSENDINLVIMDINLPGKNGLLLARELRE-QANVALMFLTGR 83

                         90       100       110
                 ....*....|....*....|....*....|..
gi 489048862  89 ADVTIAVKAMQLGAYDLFEKPVNETLLDCIAR 120
Cdd:PRK11173  84 DNEVDKILGLEIGADDYITKPFNPRELTIRAR 115

REC_PilR

cd19926

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

10-109

1.70e-09

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: 54.85 E-value: 1.70e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:cd19926    1 VLVVDDEPDIRELLEITLGRMGLDVRSARNVKEARELLASEPYDLCLTDMRLPDGSGLELVQHIQQRLPQTPVAVITAYG 80

                         90       100
                 ....*....|....*....|
gi 489048862  90 DVTIAVKAMQLGAYDLFEKP 109
Cdd:cd19926   81 SLDTAIEALKAGAFDFLTKP 100

REC_OmpR_NsrR-like

cd18159

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

10-109

1.71e-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: 55.37 E-value: 1.71e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFdSELPVIFLTGYA 89
Cdd:cd18159    1 ILIVEDDETIASLLKKHLEKWGYEVVLIEDFEDVLEEFLQFKPDLVLLDINLPYFDGFYWCREIRQI-SNVPIIFISSRD 79

                         90       100
                 ....*....|....*....|
gi 489048862  90 DVTIAVKAMQLGAYDLFEKP 109
Cdd:cd18159   80 DNMDQVMAINMGGDDYITKP 99

REC_PatA-like

cd17602

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

10-109

1.80e-09

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: 54.68 E-value: 1.80e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTL---LEQVTAFdSELPVIFLT 86
Cdd:cd17602    1 VACVDDRPSIQKMIEYFLEKQGFRVVVIDDPLRALTTLLNSKPDLILIDIDMPDLDGYELcslLRKSSAL-KDTPIIMLT 79

                         90       100
                 ....*....|....*....|...
gi 489048862  87 GYADVTIAVKAMQLGAYDLFEKP 109
Cdd:cd17602   80 GKDGLVDRIRAKMAGASGYLTKP 102

CitB

COG2197

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

9-73

3.55e-09

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: 54.90 E-value: 3.55e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489048862   9 HIIVVDDEAMIRDSLKQLLTLE-GYTV-ECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQV 73
Cdd:COG2197    3 RVLIVDDHPLVREGLRALLEAEpDIEVvGEAADGEEALELLEELRPDVVLLDIRMPGMDGLEALRRL 69

REC_OmpR_MtrA-like

cd17626

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

10-120

5.61e-09

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: 53.63 E-value: 5.61e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAfDSELPVIFLTGYA 89
Cdd:cd17626    3 ILVVDDDAALAEMIGIVLRGEGFDPAFCGDGTQALAAFREVRPDLVLLDLMLPGIDGIEVCRQIRA-ESGVPIVMLTAKS 81

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489048862  90 DVTIAVKAMQLGAYDLFEKPVNETLLdcIAR 120
Cdd:cd17626   82 DTVDVVLGLESGADDYVAKPFKPKEL--VAR 110

PRK10693

two-component system response regulator RssB;

39-118

1.75e-08

two-component system response regulator RssB;

Pssm-ID: 182652 [Multi-domain] Cd Length: 303 Bit Score: 55.77 E-value: 1.75e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  39 DASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYADVTIAVKAMQLGAYDLFEKPVN------E 112
Cdd:PRK10693   5 NGVDALELLGGFTPDLIICDLAMPRMNGIEFVEHLRNRGDQTPVLVISATENMADIAKALRLGVQDVLLKPVKdlnrlrE 84


                 ....*.
gi 489048862 113 TLLDCI 118
Cdd:PRK10693  85 MVFACL 90

REC_CheV-like

cd19924

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

10-109

3.88e-08

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

Pssm-ID: 381151 [Multi-domain] Cd Length: 111 Bit Score: 51.23 E-value: 3.88e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKL-NRRFMG--------VVLSDINMPAMDGLTLLEQVTAfD--- 77
Cdd:cd19924    1 ILVVDDSPTARKQLRDLLKNLGFEIAEAVDGEEALNKLeNLAKEGndlskeldLIITDIEMPKMDGYELTFELRD-Dprl 79

                         90       100       110
                 ....*....|....*....|....*....|..
gi 489048862  78 SELPVIFLTGYADVTIAVKAMQLGAYDLFEKP 109
Cdd:cd19924   80 ANIPVILNSSLSGEFSRARGKKVGADAYLAKF 111

PRK10336

two-component system response regulator QseB;

10-120

4.47e-08

two-component system response regulator QseB;

Pssm-ID: 182387 [Multi-domain] Cd Length: 219 Bit Score: 53.36 E-value: 4.47e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:PRK10336   3 ILLIEDDMLIGDGIKTGLSKMGFSVDWFTQGRQGKEALYSAPYDAVILDLTLPGMDGRDILREWREKGQREPVLILTARD 82

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489048862  90 DVTIAVKAMQLGAYDLFEKPVneTLLDCIAR 120
Cdd:PRK10336  83 ALAERVEGLRLGADDYLCKPF--ALIEVAAR 111

PRK10841

two-component system sensor histidine kinase RcsC;

9-89

7.95e-08

two-component system sensor histidine kinase RcsC;

Pssm-ID: 182772 [Multi-domain] Cd Length: 924 Bit Score: 54.98 E-value: 7.95e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSL-KQLLTLeGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTG 87
Cdd:PRK10841 803 MILVVDDHPINRRLLaDQLGSL-GYQCKTANDGVDALNVLSKNHIDIVLTDVNMPNMDGYRLTQRLRQLGLTLPVIGVTA 881


                 ..
gi 489048862  88 YA 89
Cdd:PRK10841 882 NA 883

pleD

PRK09581

response regulator PleD; Reviewed

10-128

1.43e-07

response regulator PleD; Reviewed

Pssm-ID: 236577 [Multi-domain] Cd Length: 457 Bit Score: 53.37 E-value: 1.43e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDD-EAMIRdSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQV-----TAFdseLPVI 83
Cdd:PRK09581   5 ILVVDDiPANVK-LLEAKLLAEYYTVLTASSGAEAIAICEREQPDIILLDVMMPGMDGFEVCRRLksdpaTTH---IPVV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 489048862  84 FLTGYADVTIAVKAMQLGAYDLFEKPVNETLLdcIARAcdkRSLV 128
Cdd:PRK09581  81 MVTALDDPEDRVRGLEAGADDFLTKPINDVAL--FARV---KSLT 120

PRK09959

acid-sensing system histidine kinase EvgS;

10-115

1.65e-07

acid-sensing system histidine kinase EvgS;

Pssm-ID: 182169 [Multi-domain] Cd Length: 1197 Bit Score: 53.97 E-value: 1.65e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:PRK09959  961 ILIADDHPTNRLLLKRQLNLLGYDVDEATDGVQALHKVSMQHYDLLITDVNMPNMDGFELTRKLREQNSSLPIWGLTANA 1040

                          90       100
                  ....*....|....*....|....*.
gi 489048862   90 DVTIAVKAMQLGAYDLFEKPVNETLL 115
Cdd:PRK09959 1041 QANEREKGLSCGMNLCLFKPLTLDVL 1066

PRK00742

chemotaxis-specific protein-glutamate methyltransferase CheB;

10-116

1.89e-07

chemotaxis-specific protein-glutamate methyltransferase CheB;

Pssm-ID: 234828 [Multi-domain] Cd Length: 354 Bit Score: 52.84 E-value: 1.89e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLE-GYTVECF-NDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAfDSELPVIF--- 84
Cdd:PRK00742   6 VLVVDDSAFMRRLISEILNSDpDIEVVGTaPDGLEAREKIKKLNPDVITLDVEMPVMDGLDALEKIMR-LRPTPVVMvss 84

                         90       100       110
                 ....*....|....*....|....*....|....
gi 489048862  85 LT--GyADVTIavKAMQLGAYDLFEKPVNETLLD 116
Cdd:PRK00742  85 LTerG-AEITL--RALELGAVDFVTKPFLGISLG 115

REC_OmpR_CtrA

cd17616

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

10-120

2.73e-07

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: 48.94 E-value: 2.73e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:cd17616    1 VLLIEDDSATAQSIELMLKSEGFNVYTTDLGEEGLDLGKLYDYDIILLDLNLPDMSGYEVLRTLRLAKVKTPILILSGLA 80

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489048862  90 DVTIAVKAMQLGAYDLFEKPVNETLLdcIAR 120
Cdd:cd17616   81 DIEDKVKGLGFGADDYMTKPFHKDEL--VAR 109

AAA

smart00382

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

172-288

2.80e-07

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: 49.68 E-value: 2.80e-07

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   172 VMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTGATHTRKGK--FEFAQG---GTVFL 246
Cdd:smart00382   5 ILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRlaLALARKlkpDVLIL 84

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 489048862   247 DEIESTPMSLQVKLLRVLEErkvTPVGDNKAIELDIRIVAAT 288
Cdd:smart00382  85 DEITSLLDAEQEALLLLLEE---LRLLLLLKSEKNLTVILTT 123

REC_DesR-like

cd19930

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

10-120

3.23e-07

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: 48.81 E-value: 3.23e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEG--YTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTG 87
Cdd:cd19930    1 VLIAEDQEMVRGALAALLELEDdlEVVAQASNGQEALRLVLKHSPDVAILDIEMPGRTGLEVAAELREELPDTKVLIVTT 80

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 489048862  88 YADVTIAVKAMQ--LGAYDLFEKPVnETLLDCIAR 120
Cdd:cd19930   81 FGRPGYFRRALAagVDGYVLKDRPI-EELADAIRT 114

PRK10161

phosphate response regulator transcription factor PhoB;

8-125

7.47e-07

phosphate response regulator transcription factor PhoB;

Pssm-ID: 182277 [Multi-domain] Cd Length: 229 Bit Score: 50.10 E-value: 7.47e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVT--AFDSELPVIFL 85
Cdd:PRK10161   3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKreSMTRDIPVVML 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 489048862  86 TGYADVTIAVKAMQLGAYDLFEKPVNETLLDCIARACDKR 125
Cdd:PRK10161  83 TARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR 122

REC_citrate_TCS

cd19925

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

9-110

1.08e-06

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: 47.24 E-value: 1.08e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLLT-LEGYTV--ECFNDAStALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFL 85
Cdd:cd19925    2 NVLIVEDDPMVAEIHRAYVEqVPGFTVigTAGTGEE-ALKLLKERQPDLILLDIYLPDGNGLDLLRELRAAGHDVDVIVV 80

                         90       100
                 ....*....|....*....|....*
gi 489048862  86 TGYADVTIAVKAMQLGAYDLFEKPV 110
Cdd:cd19925   81 TAANDVETVREALRLGVVDYLIKPF 105

PRK13856

two-component response regulator VirG; Provisional

8-109

1.34e-06

two-component response regulator VirG; Provisional

Pssm-ID: 172377 [Multi-domain] Cd Length: 241 Bit Score: 49.43 E-value: 1.34e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   8 KHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAfDSELPVIFLTG 87
Cdd:PRK13856   2 KHVLVIDDDVAMRHLIVEYLTIHAFKVTAVADSQQFNRVLASETVDVVVVDLNLGREDGLEIVRSLAT-KSDVPIIIISG 80

                         90       100
                 ....*....|....*....|...
gi 489048862  88 -YADVTIAVKAMQLGAYDLFEKP 109
Cdd:PRK13856  81 dRLEEADKVVALELGATDFIAKP 103

PRK10360

transcriptional regulator UhpA;

10-108

1.97e-06

transcriptional regulator UhpA;

Pssm-ID: 182408 [Multi-domain] Cd Length: 196 Bit Score: 48.43 E-value: 1.97e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEG--YTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTafdSELPVIFLTG 87
Cdd:PRK10360   4 VALIDDHLIVRSGFAQLLGLEPdlQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLP---KGMATIMLSV 80

                         90       100
                 ....*....|....*....|.
gi 489048862  88 YADVTIAVKAMQLGAYDLFEK 108
Cdd:PRK10360  81 HDSPALVEQALNAGARGFLSK 101

REC_OmpR_kpRstA-like

cd17622

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

10-120

2.73e-06

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: 46.22 E-value: 2.73e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFdSELPVIFLTGYA 89
Cdd:cd17622    3 ILLVEDDPKLARLIADFLESHGFNVVVEHRGDRALEVIAREKPDAVLLDIMLPGIDGLTLCRDLRPK-YQGPILLLTALD 81

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489048862  90 DVTIAVKAMQLGAYDLFEKPVNETLLdcIAR 120
Cdd:cd17622   82 SDIDHILGLELGADDYVVKPVEPAVL--LAR 110

REC_ETR-like

cd19933

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

10-110

3.54e-06

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: 45.85 E-value: 3.54e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMG--VVLSDINMPAMDGLTLLEQVTAF--DSELPVIF- 84
Cdd:cd19933    3 VLLVDDNAVNRMVTKGLLEKLGCEVTTVSSGEECLNLLASAEHSfqLVLLDLCMPEMDGFEVALRIRKLfgRRERPLIVa 82

                         90       100
                 ....*....|....*....|....*.
gi 489048862  85 LTGYADVTIAVKAMQLGAYDLFEKPV 110
Cdd:cd19933   83 LTANTDDSTREKCLSLGMNGVITKPV 108

PRK15347

two component system sensor kinase;

9-139

4.55e-06

two component system sensor kinase;

Pssm-ID: 237951 [Multi-domain] Cd Length: 921 Bit Score: 49.26 E-value: 4.55e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQ----VTAFDSELPVIF 84
Cdd:PRK15347 692 QILLVDDVETNRDIIGMMLVELGQQVTTAASGTEALELGRQHRFDLVLMDIRMPGLDGLETTQLwrddPNNLDPDCMIVA 771

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489048862  85 LTGYADVTIAVKAMQLGAYDLFEKPVnetlldciaracdkrSLVIQNRALKLAVQ 139
Cdd:PRK15347 772 LTANAAPEEIHRCKKAGMNHYLTKPV---------------TLAQLARALELAAE 811

PRK12555

chemotaxis-specific protein-glutamate methyltransferase CheB;

10-110

6.82e-06

chemotaxis-specific protein-glutamate methyltransferase CheB;

Pssm-ID: 237135 [Multi-domain] Cd Length: 337 Bit Score: 47.95 E-value: 6.82e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLE-GYTVE-CFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAfDSELPVIFLTG 87
Cdd:PRK12555   3 IGIVNDSPLAVEALRRALARDpDHEVVwVATDGAQAVERCAAQPPDVILMDLEMPRMDGVEATRRIMA-ERPCPILIVTS 81

                         90       100
                 ....*....|....*....|....*
gi 489048862  88 Y--ADVTIAVKAMQLGAYDLFEKPV 110
Cdd:PRK12555  82 LteRNASRVFEAMGAGALDAVDTPT 106

AAA_5

pfam07728

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

171-288

1.87e-05

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: 44.21 E-value: 1.87e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  171 DVMIEGETGTGKELVARYLHDQSIRSASNFVAINCGAVPEQLIESELFGAASGAYTGATHTRKGKfefaQGGTVFLDEIE 250
Cdd:pfam07728   1 GVLLVGPPGTGKTELAERLAAALSNRPVFYVQLTRDTTEEDLFGRRNIDPGGASWVDGPLVRAAR----EGEIAVLDEIN 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 489048862  251 STPMSLQVKLLRVLEERKVTP---VGDNKAIELDIRIVAAT 288
Cdd:pfam07728  77 RANPDVLNSLLSLLDERRLLLpdgGELVKAAPDGFRLIATM 117

PRK09935

fimbriae biosynthesis transcriptional regulator FimZ;

10-102

1.92e-05

fimbriae biosynthesis transcriptional regulator FimZ;

Pssm-ID: 182154 [Multi-domain] Cd Length: 210 Bit Score: 45.64 E-value: 1.92e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLL--TLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTG 87
Cdd:PRK09935   6 VIIMDTHPIIRMSIEVLLqkNSELQIVLKTDDYRITIDYLRTRPVDLIIMDIDLPGTDGFTFLKRIKQIQSTVKVLFLSS 85

                         90
                 ....*....|....*
gi 489048862  88 YADVTIAVKAMQLGA 102
Cdd:PRK09935  86 KSECFYAGRAIQAGA 100

PRK11517

DNA-binding response regulator HprR;

10-109

2.25e-05

DNA-binding response regulator HprR;

Pssm-ID: 183172 [Multi-domain] Cd Length: 223 Bit Score: 45.66 E-value: 2.25e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQV-TAfdSELPVIFLTGY 88
Cdd:PRK11517   3 ILLIEDNQRTQEWVTQGLSEAGYVIDAVSDGRDGLYLALKDDYALIILDIMLPGMDGWQILQTLrTA--KQTPVICLTAR 80

                         90       100
                 ....*....|....*....|.
gi 489048862  89 ADVTIAVKAMQLGAYDLFEKP 109
Cdd:PRK11517  81 DSVDDRVRGLDSGANDYLVKP 101

PRK09483

response regulator; Provisional

10-102

2.37e-05

response regulator; Provisional

Pssm-ID: 236538 [Multi-domain] Cd Length: 217 Bit Score: 45.48 E-value: 2.37e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLT-LEGYTV--ECfNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLT 86
Cdd:PRK09483   4 VLLVDDHELVRAGIRRILEdIKGIKVvgEA-CCGEDAVKWCRTNAVDVVLMDMNMPGIGGLEATRKILRYTPDVKIIMLT 82

                         90
                 ....*....|....*.
gi 489048862  87 GYADVTIAVKAMQLGA 102
Cdd:PRK09483  83 VHTENPLPAKVMQAGA 98

REC_TrxB

cd17595

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

10-98

3.49e-05

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: 43.48 E-value: 3.49e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDE-----AMIRDSLKQLLtlEGYTV---ECFNDASTALTKLNRR--FMGVVLSDINMPAMDGLTLLEQVTAFDSE 79
Cdd:cd17595    3 ILTVDDDpqvlrAVARDLRRQYG--KDYRVlraDSGAEALDALKELKLRgeAVALFLVDQRMPEMDGVEFLEKAMELFPE 80

                         90
                 ....*....|....*....
gi 489048862  80 LPVIFLTGYADVTIAVKAM 98
Cdd:cd17595   81 AKRVLLTAYADTDAAIRAI 99

psREC_PRR

cd17582

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

10-109

6.11e-05

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

Pssm-ID: 381120 [Multi-domain] Cd Length: 104 Bit Score: 42.00 E-value: 6.11e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLN--RRFMGVVLSDINMPAMDGLTLLEQVTAFDS--ELPVIFL 85
Cdd:cd17582    1 VLLVENDDSTRQIVTALLRKCSYEVTAASDGLQAWDVLEdeQNEIDLILTEVDLPVSSGFKLLSYIMRHKIckNIPVIMM 80

                         90       100
                 ....*....|....*....|....
gi 489048862  86 TGYADVTIAVKAMQLGAYDLFEKP 109
Cdd:cd17582   81 SSQDSVGVVFKCLSKGAADYLVKP 104

REC_NarL

cd19931

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

10-122

6.21e-05

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

Pssm-ID: 381158 [Multi-domain] Cd Length: 117 Bit Score: 42.33 E-value: 6.21e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGyTVECFNDAST---ALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLT 86
Cdd:cd19931    1 VLLIDDHPLLRKGIKQLIELDP-DFTVVGEASSgeeGIELAERLDPDLILLDLNMKGMSGLDTLKALREEGVSARIVILT 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 489048862  87 GYADVTIAVKAMQLGAYDLFEKPVN-ETLLDCIARAC 122
Cdd:cd19931   80 VSDAEDDVVTALRAGADGYLLKDMEpEDLLEALKQAA 116

PRK10816

two-component system response regulator PhoP;

10-109

6.37e-05

two-component system response regulator PhoP;

Pssm-ID: 182755 [Multi-domain] Cd Length: 223 Bit Score: 43.96 E-value: 6.37e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:PRK10816   3 VLVVEDNALLRHHLKVQLQDAGHQVDAAEDAKEADYYLNEHLPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTARE 82

                         90       100
                 ....*....|....*....|
gi 489048862  90 DVTIAVKAMQLGAYDLFEKP 109
Cdd:PRK10816  83 SWQDKVEVLSAGADDYVTKP 102

REC_RocR

cd17530

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

10-118

9.00e-05

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: 42.04 E-value: 9.00e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLL-TLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGY 88
Cdd:cd17530    3 VLVLDDDPFQCMMAATILeDLGPGNVDEADDGREALVILLCNAPDIIICDLKMPDMDGIEFLRHLAESHSNAAVILMSGL 82

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 489048862  89 ADVTIAVKAMQLGAYDL-----FEKPVNETLLDCI 118
Cdd:cd17530   83 DGGILESAETLAGANGLnllgtLSKPFSPEELTEL 117

PRK13557

histidine kinase; Provisional

7-115

9.09e-05

histidine kinase; Provisional

Pssm-ID: 237425 [Multi-domain] Cd Length: 540 Bit Score: 44.66 E-value: 9.09e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   7 CKHIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKL--NRRFmGVVLSDINMP-AMDGLTLLEQVTAFDSELPVI 83
Cdd:PRK13557 415 TETILIVDDRPDVAELARMILEDFGYRTLVASNGREALEILdsHPEV-DLLFTDLIMPgGMNGVMLAREARRRQPKIKVL 493

                         90       100       110
                 ....*....|....*....|....*....|..
gi 489048862  84 FLTGYADVTIAVKAMQLGAYDLFEKPVNETLL 115
Cdd:PRK13557 494 LTTGYAEASIERTDAGGSEFDILNKPYRRAEL 525

PLN03029

type-a response regulator protein; Provisional

9-110

9.97e-05

type-a response regulator protein; Provisional

Pssm-ID: 215544 [Multi-domain] Cd Length: 222 Bit Score: 43.48 E-value: 9.97e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   9 HIIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKL------------------NRRFMGV--VLSDINMPAMDGLT 68
Cdd:PLN03029  10 HVLAVDDSLIDRKLIEKLLKTSSYQVTTVDSGSKALKFLglheddrsnpdtpsvspnSHQEVEVnlIITDYCMPGMTGYD 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 489048862  69 LLEQVTAFDS--ELPVIFLTGYADVTIAVKAMQLGAYDLFEKPV 110
Cdd:PLN03029  90 LLKKIKESSSlrNIPVVIMSSENVPSRITRCLEEGAEEFFLKPV 133

REC_Spo0A

cd17561

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

54-109

1.05e-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: 41.44 E-value: 1.05e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489048862  54 VVLSDINMPAMDGLTLLE--QVTAFDSELPVIFLTGYADVTIAVKAMQLGAYDLFEKP 109
Cdd:cd17561   50 VLLLDIIMPHLDGIGVLEklRRMRLEKRPKIIMLTAFGQEDITQRAVELGASYYILKP 107

PRK14084

DNA-binding response regulator;

10-109

1.18e-04

DNA-binding response regulator;

Pssm-ID: 184495 [Multi-domain] Cd Length: 246 Bit Score: 43.59 E-value: 1.18e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGyTVECFNDA---STALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLT 86
Cdd:PRK14084   3 ALIVDDEPLARNELTYLLNEIG-GFEEINEAenvKETLEALLINQYDIIFLDINLMDESGIELAAKIQKMKEPPAIIFAT 81

                         90       100
                 ....*....|....*....|...
gi 489048862  87 gyADVTIAVKAMQLGAYDLFEKP 109
Cdd:PRK14084  82 --AHDQFAVKAFELNATDYILKP 102

PRK10430

two-component system response regulator DcuR;

10-109

1.34e-04

two-component system response regulator DcuR;

Pssm-ID: 182454 [Multi-domain] Cd Length: 239 Bit Score: 43.17 E-value: 1.34e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLT-LEGYTveCFNDAST-----ALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVI 83
Cdd:PRK10430   4 VLIVDDDAMVAELNRRYVAqIPGFQ--CCGTASTleqakEIIFNSDTPIDLILLDIYMQQENGLDLLPVLHEAGCKSDVI 81

                         90       100
                 ....*....|....*....|....*.
gi 489048862  84 FLTGYADVTIAVKAMQLGAYDLFEKP 109
Cdd:PRK10430  82 VISSAADAATIKDSLHYGVVDYLIKP 107

REC_WspR-like

cd17575

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

10-108

1.72e-04

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

Pssm-ID: 381117 [Multi-domain] Cd Length: 128 Bit Score: 41.24 E-value: 1.72e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECF-NDASTALTKLNRRFMGVVLSDINMPAMDGLTLLE--QVTAFDSELPVIFLT 86
Cdd:cd17575    3 VLLVDDQAIIGEAVRRALADEEDIDFHYcSDPTEAIEVASQIKPTVILQDLVMPGVDGLTLVRffRANPATRDIPIIVLS 82

                         90       100
                 ....*....|....*....|..
gi 489048862  87 GYADVTIAVKAMQLGAYDLFEK 108
Cdd:cd17575   83 TKEEPEVKSEAFALGANDYLVK 104

HTH_8

pfam02954

Bacterial regulatory protein, Fis family;

409-444

1.87e-04

Bacterial regulatory protein, Fis family;

Pssm-ID: 427077 [Multi-domain] Cd Length: 40 Bit Score: 38.53 E-value: 1.87e-04

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 489048862  409 EQSLIEEALERNHGSIKNTMDTLQIARKTLYDKMSK 444
Cdd:pfam02954   5 EKELIEAALERTGGNKSKAARLLGISRRTLYRKLKK 40

PRK10651

transcriptional regulator NarL; Provisional

1-97

2.26e-04

transcriptional regulator NarL; Provisional

Pssm-ID: 182619 [Multi-domain] Cd Length: 216 Bit Score: 42.32 E-value: 2.26e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862   1 MIENSPCKhIIVVDDEAMIRDSLKQLLTLEGyTVECFNDAST---ALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFD 77
Cdd:PRK10651   1 MSNQEPAT-ILLIDDHPMLRTGVKQLISMAP-DITVVGEASNgeqGIELAESLDPDLILLDLNMPGMNGLETLDKLREKS 78

                         90       100
                 ....*....|....*....|...
gi 489048862  78 SELPVIFLT---GYADVTIAVKA 97
Cdd:PRK10651  79 LSGRIVVFSvsnHEEDVVTALKR 101

PRK10529

DNA-binding transcriptional activator KdpE; Provisional

10-109

3.10e-04

DNA-binding transcriptional activator KdpE; Provisional

Pssm-ID: 182522 [Multi-domain] Cd Length: 225 Bit Score: 42.10 E-value: 3.10e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFdSELPVIFLTGYA 89
Cdd:PRK10529   4 VLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQW-SAIPVIVLSARS 82

                         90       100
                 ....*....|....*....|
gi 489048862  90 DVTIAVKAMQLGAYDLFEKP 109
Cdd:PRK10529  83 EESDKIAALDAGADDYLSKP 102

REC_Rcp-like

cd17557

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

54-111

3.12e-04

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

Pssm-ID: 381108 [Multi-domain] Cd Length: 129 Bit Score: 40.48 E-value: 3.12e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489048862  54 VVLSDINMPAMDGLTLLEQVTAfDSEL---PVIFLTG-YADVTIaVKAMQLGAYDLFEKPVN 111
Cdd:cd17557   55 LILLDLNMPRMDGFEVLREIKA-DPDLrriPVVVLTTsDAEEDI-ERAYELGANSYIVKPVD 114

PRK15369

two component system response regulator;

10-128

5.97e-04

two component system response regulator;

Pssm-ID: 185267 [Multi-domain] Cd Length: 211 Bit Score: 41.22 E-value: 5.97e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLT-LEGYTVECFNDASTALTKLNRRFM-GVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTG 87
Cdd:PRK15369   6 ILLVDDHELIINGIKNMLApYPRYKIVGQVDNGLEVYNACRQLEpDIVILDLGLPGMNGLDVIPQLHQRWPAMNILVLTA 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 489048862  88 YADVTIAVKAMQLGA--YDLFEKPvNETLLDCIARACDKRSLV 128
Cdd:PRK15369  86 RQEEHMASRTLAAGAlgYVLKKSP-QQILLAAIQTVAVGKRYI 127

PRK09836

DNA-binding transcriptional activator CusR; Provisional

10-149

6.57e-04

DNA-binding transcriptional activator CusR; Provisional

Pssm-ID: 182102 [Multi-domain] Cd Length: 227 Bit Score: 41.06 E-value: 6.57e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTGYA 89
Cdd:PRK09836   3 LLIVEDEKKTGEYLTKGLTEAGFVVDLADNGLNGYHLAMTGDYDLIILDIMLPDVNGWDIVRMLRSANKGMPILLLTALG 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489048862  90 DVTIAVKAMQLGAYDLFEKPVN--------ETLLDCIARACDKRSLVIQNRALKLAVQKTSAPGVRIL 149
Cdd:PRK09836  83 TIEHRVKGLELGADDYLVKPFAfaellarvRTLLRRGAAVIIESQFQVADLMVDLVSRKVTRSGTRIT 150

PRK13435

response regulator; Provisional

10-125

1.66e-03

response regulator; Provisional

Pssm-ID: 184052 [Multi-domain] Cd Length: 145 Bit Score: 38.88 E-value: 1.66e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGY-TVECFNDASTALTKLNRRFMGVVLSDINMpaMDGLTLLE--QVTAFDSELPVIFLT 86
Cdd:PRK13435   8 VLIVEDEALIALELEKLVEEAGHeVVGIAMSSEQAIALGRRRQPDVALVDVHL--ADGPTGVEvaRRLSADGGVEVVFMT 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 489048862  87 GYADVtiaVKAMQLGAYDLFEKPVNET-LLDCIARACDKR 125
Cdd:PRK13435  86 GNPER---VPHDFAGALGVIAKPYSPRgVARALSYLSARR 122

REC_GlnL-like

cd17565

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

10-110

2.12e-03

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

Pssm-ID: 381112 [Multi-domain] Cd Length: 103 Bit Score: 37.64 E-value: 2.12e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLE--GYTVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLLEQVTAFDSELPVIFLTG 87
Cdd:cd17565    1 FYIVDDDKNIIKILSDIIEDDdlGEVVGEADNGAQAYDEILFLQPDIVLIDLLMPGMDGIQLVRKLKDTGSNGKFIMISQ 80

                         90       100
                 ....*....|....*....|...
gi 489048862  88 YADVTIAVKAMQLGAYDLFEKPV 110
Cdd:cd17565   81 VSDKEMIGKAYQAGIEFFINKPI 103

PRK10403

nitrate/nitrite response regulator protein NarP;

1-70

5.79e-03

nitrate/nitrite response regulator protein NarP;

Pssm-ID: 182431 [Multi-domain] Cd Length: 215 Bit Score: 38.29 E-value: 5.79e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489048862   1 MIENSPCkHIIVVDDEAMIRDSLKQLLTLEGY--TVECFNDASTALTKLNRRFMGVVLSDINMPAMDGLTLL 70
Cdd:PRK10403   1 MPEATPF-QVLIVDDHPLMRRGVRQLLELDPGfeVVAEAGDGASAIDLANRLDPDVILLDLNMKGMSGLDTL 71

REC_PhyR

cd17540

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

10-90

8.11e-03

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: 36.07 E-value: 8.11e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489048862  10 IIVVDDEAMIRDSLKQLLTLEGYTVecfndASTALTK------LNRRFMGVVLSDINMPamDGLTLLEQVTAF--DSELP 81
Cdd:cd17540    3 VLIIEDEPLIAMDLEQIVEDLGHQV-----VGIARTRdeavalARRERPDLILADIQLA--DGSSGIDAVNEIltTHDVP 75


                 ....*....
gi 489048862  82 VIFLTGYAD 90
Cdd:cd17540   76 VIFVTAYPE 84

CDC6

COG1474

Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];

147-205

8.13e-03

Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];

Pssm-ID: 441083 [Multi-domain] Cd Length: 389 Bit Score: 38.29 E-value: 8.13e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489048862 147 RILGDTPKMQDMMHLLNTVID--TPADVMIEGETGTGKELVARYLHDQSIRSASN------FVAINC 205
Cdd:COG1474   27 RLPHREEEIEELASALRPALRgeRPSNVLIYGPTGTGKTAVAKYVLEELEEEAEErgvdvrVVYVNC 93

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