NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1544283978|gb|RUD77397|]
View 

sigma-54-dependent Fis family transcriptional regulator [Pseudomonas aeruginosa]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 5-423 2.69e-180

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: 508.73  E-value: 2.69e-180
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAY 84
Cdd:COG2204    19 KELLERAGYEVETAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALDPDLPVILLTGYGDVETAVEAIKAGAF 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  85 DFMEKPFSPERLVEVARRALEQRGLAREVSALRRqlagrqdlaqrIIGRSPAIQALRELIANVGDTSANVLILGETGTGK 164
Cdd:COG2204    99 DYLTKPFDLEELLAAVERALERRRLRRENAEDSG-----------LIGRSPAMQEVRRLIEKVAPSDATVLITGESGTGK 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 165 ELVARCLHDYSRRHQHAFVALNCGGLPENLFDSEIFGHEAHAFTGANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLR 244
Cdd:COG2204   168 ELVARAIHRLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTGAVARRIGKFELADGGTLFLDEIGEMPLALQAKLLR 247

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 245 VLQEHTLERLGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEHFLQQSSLRFD 324
Cdd:COG2204   248 VLQEREFERVGGNKPIPVDVRVIAATNRDLEELVEEGRFREDLYYRLNVFPIELPPLRERREDIPLLARHFLARFAAELG 327

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 325 RPAPeLDRATVASLMAHDWPGNVRELRNVAERFALGLPvfnkgGQAVQTGGprFAEAVEAFEKALLGDALARHHGNLTQA 404
Cdd:COG2204   328 KPVK-LSPEALEALLAYDWPGNVRELENVIERAVILAD-----GEVITAED--LPEALEEVERELIERALEETGGNVSRA 399

                         410
                  ....*....|....*....
gi 1544283978 405 SQDLGMAKTTLFDKVKKYG 423
Cdd:COG2204   400 AELLGISRRTLYRKLKKYG 418
 
Name Accession Description Interval E-value
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 5-423 2.69e-180

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: 508.73  E-value: 2.69e-180
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAY 84
Cdd:COG2204    19 KELLERAGYEVETAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALDPDLPVILLTGYGDVETAVEAIKAGAF 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  85 DFMEKPFSPERLVEVARRALEQRGLAREVSALRRqlagrqdlaqrIIGRSPAIQALRELIANVGDTSANVLILGETGTGK 164
Cdd:COG2204    99 DYLTKPFDLEELLAAVERALERRRLRRENAEDSG-----------LIGRSPAMQEVRRLIEKVAPSDATVLITGESGTGK 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 165 ELVARCLHDYSRRHQHAFVALNCGGLPENLFDSEIFGHEAHAFTGANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLR 244
Cdd:COG2204   168 ELVARAIHRLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTGAVARRIGKFELADGGTLFLDEIGEMPLALQAKLLR 247

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 245 VLQEHTLERLGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEHFLQQSSLRFD 324
Cdd:COG2204   248 VLQEREFERVGGNKPIPVDVRVIAATNRDLEELVEEGRFREDLYYRLNVFPIELPPLRERREDIPLLARHFLARFAAELG 327

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 325 RPAPeLDRATVASLMAHDWPGNVRELRNVAERFALGLPvfnkgGQAVQTGGprFAEAVEAFEKALLGDALARHHGNLTQA 404
Cdd:COG2204   328 KPVK-LSPEALEALLAYDWPGNVRELENVIERAVILAD-----GEVITAED--LPEALEEVERELIERALEETGGNVSRA 399

                         410
                  ....*....|....*....
gi 1544283978 405 SQDLGMAKTTLFDKVKKYG 423
Cdd:COG2204   400 AELLGISRRTLYRKLKKYG 418
ntrC TIGR01818
nitrogen regulation protein NR(I); This model represents NtrC, a DNA-binding response ...
 5-420 2.73e-126

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: 373.30  E-value: 2.73e-126
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAY 84
Cdd:TIGR01818  15 EKALSRAGYEVRTFGNAASVLRALARGQPDLLITDVRMPGEDGLDLLPQIKKRHPQLPVIVMTAHSDLDTAVAAYQRGAF 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  85 DFMEKPFSPERLVEVARRALEQRGLAREVSALrrqlAGRQDLAQRIIGRSPAIQALRELIANVGDTSANVLILGETGTGK 164
Cdd:TIGR01818  95 EYLPKPFDLDEAVTLVERALAHAQEQVALPAD----AGEAEDSAELIGEAPAMQEVFRAIGRLSRSDITVLINGESGTGK 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 165 ELVARCLHDYSRRHQHAFVALNCGGLPENLFDSEIFGHEAHAFTGANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLR 244
Cdd:TIGR01818 171 ELVARALHRHSPRANGPFIALNMAAIPKDLIESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDEIGDMPLDAQTRLLR 250

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 245 VLQEHTLERLGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEHFLQQSSLRFD 324
Cdd:TIGR01818 251 VLADGEFYRVGGRTPIKVDVRIVAATHQNLEALVRQGKFREDLFHRLNVIRIHLPPLRERREDIPRLARHFLALAARELD 330

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 325 RPAPELDRATVASLMAHDWPGNVRELRNVAER------------------FALGLPVFNKGGQAVQTG------------ 374
Cdd:TIGR01818 331 VEPKLLDPEALERLKQLRWPGNVRQLENLCRWltvmasgdevlvsdlpaeLALTGRPASAPDSDGQDSwdealeawakqa 410

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1544283978 375 ---GPR--FAEAVEAFEKALLGDALARHHGNLTQASQDLGMAKTTLFDKVK 420
Cdd:TIGR01818 411 lsrGEQglLDRALPEFERPLLEAALQHTRGHKQEAAALLGWGRNTLTRKLK 461
PRK11361 PRK11361
acetoacetate metabolism transcriptional regulator AtoC;
7-424 1.68e-125

acetoacetate metabolism transcriptional regulator AtoC;


Pssm-ID: 183099 [Multi-domain]  Cd Length: 457  Bit Score: 371.10  E-value: 1.68e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   7 ALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDF 86
Cdd:PRK11361   23 AFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIKALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDY 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  87 MEKPFSPERLVEVARRALEQRGLAREVSALRRQLAGRQDlAQRIIGRSPAIQALRELIANVGDTSANVLILGETGTGKEL 166
Cdd:PRK11361  103 VIKPFDLDELNLIVQRALQLQSMKKEIRHLHQALSTSWQ-WGHILTNSPAMMDICKDTAKIALSQASVLISGESGTGKEL 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 167 VARCLHDYSRRHQHAFVALNCGGLPENLFDSEIFGHEAHAFTGANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLRVL 246
Cdd:PRK11361  182 IARAIHYNSRRAKGPFIKVNCAALPESLLESELFGHEKGAFTGAQTLRQGLFERANEGTLLLDEIGEMPLVLQAKLLRIL 261

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 247 QEHTLERLGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEHFLQQSSLRFDRP 326
Cdd:PRK11361  262 QEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFREDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRD 341

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 327 APELDRATVASLMAHDWPGNVRELRNVAER----------FALGLP------VFNKGG-QAVQTGGPRFAEAVEAFEKAL 389
Cdd:PRK11361  342 IIDIDPMAMSLLTAWSWPGNIRELSNVIERavvmnsgpiiFSEDLPpqirqpVCNAGEvKTAPVGERNLKEEIKRVEKRI 421

                         410       420       430
                  ....*....|....*....|....*....|....*
gi 1544283978 390 LGDALARHHGNLTQASQDLGMAKTTLFDKVKKYGL 424
Cdd:PRK11361  422 IMEVLEQQEGNRTRTALMLGISRRALMYKLQEYGI 456
Sigma54_activat pfam00158
Sigma-54 interaction domain;
130-297 6.17e-99

Sigma-54 interaction domain;


Pssm-ID: 425491 [Multi-domain]  Cd Length: 168  Bit Score: 292.38  E-value: 6.17e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 130 IIGRSPAIQALRELIANVGDTSANVLILGETGTGKELVARCLHDYSRRHQHAFVALNCGGLPENLFDSEIFGHEAHAFTG 209
Cdd:pfam00158   1 IIGESPAMQEVLEQAKRVAPTDAPVLITGESGTGKELFARAIHQLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 210 ANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLRVLQEHTLERLGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLYY 289
Cdd:pfam00158  81 ADSDRKGLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTKPIKVDVRIIAATNRDLEEAVAEGRFREDLYY 160


                  ....*...
gi 1544283978 290 RLNVVSLE 297
Cdd:pfam00158 161 RLNVIPIE 168
REC_DctD-like cd17549
phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and ...
 4-120 8.05e-62

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: 196.17  E-value: 8.05e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   4 CQQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGA 83
Cdd:cd17549    14 LQQTLELAGFRVRAFADAEEALAALSPDFPGVVISDIRMPGMDGLELLAQIRELDPDLPVILITGHGDVPMAVEAMRAGA 93

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1544283978  84 YDFMEKPFSPERLVEVARRALEQRGLAREVSALRRQL 120
Cdd:cd17549    94 YDFLEKPFDPERLLDVVRRALEKRRLVLENRRLRQQL 130
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 153-270 5.56e-10

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 57.38  E-value: 5.56e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  153 NVLILGETGTGKELVARCLHDYSRRHQHAFVALNCGGLPENLFDS---EIFGHEAHAFTGANKRRIG--KIEHANGGTLF 227
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQlllIIVGGKKASGSGELRLRLAlaLARKLKPDVLI 83

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1544283978  228 LDEIESMPVNLQIKLLRVLQEhtlERLGSNQSIPVDCRVIAAT 270
Cdd:smart00382  84 LDEITSLLDAEQEALLLLLEE---LRLLLLLKSEKNLTVILTT 123
 
Name Accession Description Interval E-value
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 5-423 2.69e-180

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: 508.73  E-value: 2.69e-180
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAY 84
Cdd:COG2204    19 KELLERAGYEVETAASGEEALALLREEPPDLVLLDLRMPGMDGLELLRELRALDPDLPVILLTGYGDVETAVEAIKAGAF 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  85 DFMEKPFSPERLVEVARRALEQRGLAREVSALRRqlagrqdlaqrIIGRSPAIQALRELIANVGDTSANVLILGETGTGK 164
Cdd:COG2204    99 DYLTKPFDLEELLAAVERALERRRLRRENAEDSG-----------LIGRSPAMQEVRRLIEKVAPSDATVLITGESGTGK 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 165 ELVARCLHDYSRRHQHAFVALNCGGLPENLFDSEIFGHEAHAFTGANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLR 244
Cdd:COG2204   168 ELVARAIHRLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTGAVARRIGKFELADGGTLFLDEIGEMPLALQAKLLR 247

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 245 VLQEHTLERLGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEHFLQQSSLRFD 324
Cdd:COG2204   248 VLQEREFERVGGNKPIPVDVRVIAATNRDLEELVEEGRFREDLYYRLNVFPIELPPLRERREDIPLLARHFLARFAAELG 327

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 325 RPAPeLDRATVASLMAHDWPGNVRELRNVAERFALGLPvfnkgGQAVQTGGprFAEAVEAFEKALLGDALARHHGNLTQA 404
Cdd:COG2204   328 KPVK-LSPEALEALLAYDWPGNVRELENVIERAVILAD-----GEVITAED--LPEALEEVERELIERALEETGGNVSRA 399

                         410
                  ....*....|....*....
gi 1544283978 405 SQDLGMAKTTLFDKVKKYG 423
Cdd:COG2204   400 AELLGISRRTLYRKLKKYG 418
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 97-425 2.78e-149

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: 431.12  E-value: 2.78e-149
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  97 VEVARRALEQRGLAREVS-ALRRQLAGRQDLAQRIIGRSPAIQALRELIANVGDTSANVLILGETGTGKELVARCLHDYS 175
Cdd:COG3829   106 VETFRDITELKRLERKLReEELERGLSAKYTFDDIIGKSPAMKELLELAKRVAKSDSTVLILGESGTGKELFARAIHNAS 185

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 176 RRHQHAFVALNCGGLPENLFDSEIFGHEAHAFTGANKR-RIGKIEHANGGTLFLDEIESMPVNLQIKLLRVLQEHTLERL 254
Cdd:COG3829   186 PRRDGPFVAVNCAAIPENLLESELFGYEKGAFTGAKKGgKPGLFELADGGTLFLDEIGEMPLSLQAKLLRVLQEKEVRRV 265

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 255 GSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEHFLQQSSLRFDRPAPELDRAT 334
Cdd:COG3829   266 GGTKPIPVDVRIIAATNRDLEEMVEEGRFREDLYYRLNVIPIHIPPLRERKEDIPLLAEHFLEKFNKKYGKNIKGISPEA 345

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 335 VASLMAHDWPGNVRELRNVAERFA------------LGLPVFNKGGQAVQTGGPRFAEAVEAFEKALLGDALARHHGNLT 402
Cdd:COG3829   346 LELLLAYDWPGNVRELENVIERAVvlsegdvitpehLPEYLLEEAEAASAAEEGSLKEALEEVEKELIEEALEKTGGNKS 425

                         330       340
                  ....*....|....*....|...
gi 1544283978 403 QASQDLGMAKTTLFDKVKKYGLQ 425
Cdd:COG3829   426 KAAKALGISRSTLYRKLKKYGIK 448
ntrC TIGR01818
nitrogen regulation protein NR(I); This model represents NtrC, a DNA-binding response ...
 5-420 2.73e-126

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: 373.30  E-value: 2.73e-126
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAY 84
Cdd:TIGR01818  15 EKALSRAGYEVRTFGNAASVLRALARGQPDLLITDVRMPGEDGLDLLPQIKKRHPQLPVIVMTAHSDLDTAVAAYQRGAF 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  85 DFMEKPFSPERLVEVARRALEQRGLAREVSALrrqlAGRQDLAQRIIGRSPAIQALRELIANVGDTSANVLILGETGTGK 164
Cdd:TIGR01818  95 EYLPKPFDLDEAVTLVERALAHAQEQVALPAD----AGEAEDSAELIGEAPAMQEVFRAIGRLSRSDITVLINGESGTGK 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 165 ELVARCLHDYSRRHQHAFVALNCGGLPENLFDSEIFGHEAHAFTGANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLR 244
Cdd:TIGR01818 171 ELVARALHRHSPRANGPFIALNMAAIPKDLIESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDEIGDMPLDAQTRLLR 250

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 245 VLQEHTLERLGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEHFLQQSSLRFD 324
Cdd:TIGR01818 251 VLADGEFYRVGGRTPIKVDVRIVAATHQNLEALVRQGKFREDLFHRLNVIRIHLPPLRERREDIPRLARHFLALAARELD 330

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 325 RPAPELDRATVASLMAHDWPGNVRELRNVAER------------------FALGLPVFNKGGQAVQTG------------ 374
Cdd:TIGR01818 331 VEPKLLDPEALERLKQLRWPGNVRQLENLCRWltvmasgdevlvsdlpaeLALTGRPASAPDSDGQDSwdealeawakqa 410

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1544283978 375 ---GPR--FAEAVEAFEKALLGDALARHHGNLTQASQDLGMAKTTLFDKVK 420
Cdd:TIGR01818 411 lsrGEQglLDRALPEFERPLLEAALQHTRGHKQEAAALLGWGRNTLTRKLK 461
PRK11361 PRK11361
acetoacetate metabolism transcriptional regulator AtoC;
7-424 1.68e-125

acetoacetate metabolism transcriptional regulator AtoC;


Pssm-ID: 183099 [Multi-domain]  Cd Length: 457  Bit Score: 371.10  E-value: 1.68e-125
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   7 ALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDF 86
Cdd:PRK11361   23 AFALQGFETHCANNGRTALHLFADIHPDVVLMDIRMPEMDGIKALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDY 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  87 MEKPFSPERLVEVARRALEQRGLAREVSALRRQLAGRQDlAQRIIGRSPAIQALRELIANVGDTSANVLILGETGTGKEL 166
Cdd:PRK11361  103 VIKPFDLDELNLIVQRALQLQSMKKEIRHLHQALSTSWQ-WGHILTNSPAMMDICKDTAKIALSQASVLISGESGTGKEL 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 167 VARCLHDYSRRHQHAFVALNCGGLPENLFDSEIFGHEAHAFTGANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLRVL 246
Cdd:PRK11361  182 IARAIHYNSRRAKGPFIKVNCAALPESLLESELFGHEKGAFTGAQTLRQGLFERANEGTLLLDEIGEMPLVLQAKLLRIL 261

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 247 QEHTLERLGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEHFLQQSSLRFDRP 326
Cdd:PRK11361  262 QEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFREDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRD 341

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 327 APELDRATVASLMAHDWPGNVRELRNVAER----------FALGLP------VFNKGG-QAVQTGGPRFAEAVEAFEKAL 389
Cdd:PRK11361  342 IIDIDPMAMSLLTAWSWPGNIRELSNVIERavvmnsgpiiFSEDLPpqirqpVCNAGEvKTAPVGERNLKEEIKRVEKRI 421

                         410       420       430
                  ....*....|....*....|....*....|....*
gi 1544283978 390 LGDALARHHGNLTQASQDLGMAKTTLFDKVKKYGL 424
Cdd:PRK11361  422 IMEVLEQQEGNRTRTALMLGISRRALMYKLQEYGI 456
PEP_resp_reg TIGR02915
PEP-CTERM-box response regulator transcription factor; Members of this protein family share ...
 2-424 5.69e-117

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: 348.66  E-value: 5.69e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   2 LGCQQALE--LEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLP-----GIDGLTLLERLKSLDPSLPVVLITGHGDISM 74
Cdd:TIGR02915   8 LGLQKQLKwsFADYELAVAADRESAIALVRRHEPAVVTLDLGLPpdadgASEGLAALQQILAIAPDTKVIVITGNDDREN 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  75 AVQAMHAGAYDFMEKPFSPERLVEVARRALEQRGLAREVSALRRQLAGRQDlaQRIIGRSPAIQALRELIANVGDTSANV 154
Cdd:TIGR02915  88 AVKAIGLGAYDFYQKPIDPDVLKLIVDRAFHLYTLETENRRLQSALGGTAL--RGLITSSPGMQKICRTIEKIAPSDITV 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 155 LILGETGTGKELVARCLHDYSRRHQHAFVALNCGGLPENLFDSEIFGHEAHAFTGANKRRIGKIEHANGGTLFLDEIESM 234
Cdd:TIGR02915 166 LLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIPENLLESELFGYEKGAFTGAVKQTLGKIEYAHGGTLFLDEIGDL 245

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 235 PVNLQIKLLRVLQEHTLERLGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEH 314
Cdd:TIGR02915 246 PLNLQAKLLRFLQERVIERLGGREEIPVDVRIVCATNQDLKRMIAEGTFREDLFYRIAEISITIPPLRSRDGDAVLLANA 325

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 315 FLQQSSLRFDRPAPELDRATVASLMAHDWPGNVRELRNVAER------------FALGLPvfnKGGQAVQTGGPRFAEAV 382
Cdd:TIGR02915 326 FLERFARELKRKTKGFTDDALRALEAHAWPGNVRELENKVKRavimaegnqitaEDLGLD---ARERAETPLEVNLREVR 402

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|..
gi 1544283978 383 EAFEKALLGDALARHHGNLTQASQDLGMAKTTLFDKVKKYGL 424
Cdd:TIGR02915 403 ERAEREAVRKAIARVDGNIARAAELLGITRPTLYDLMKKHGI 444
PRK10365 PRK10365
sigma-54-dependent response regulator transcription factor ZraR;
20-421 2.05e-108

sigma-54-dependent response regulator transcription factor ZraR;


Pssm-ID: 182412 [Multi-domain]  Cd Length: 441  Bit Score: 326.99  E-value: 2.05e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  20 SAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLVEV 99
Cdd:PRK10365   37 SGRQALEQVREQVFDLVLCDVRMAEMDGIATLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQAT 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 100 ARRALEQrglAREVSAlrrQLAGRQDLAQRIIGRSPAIQALRELIANVGDTSANVLILGETGTGKELVARCLHDYSRRHQ 179
Cdd:PRK10365  117 LEKALAH---THSIDA---ETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHASSARSE 190

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 180 HAFVALNCGGLPENLFDSEIFGHEAHAFTGANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLRVLQEHTLERLGSNQS 259
Cdd:PRK10365  191 KPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPMMQVRLLRAIQEREVQRVGSNQT 270

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 260 IPVDCRVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEHFLQQSSLRFDRPAPELDRATVASLM 339
Cdd:PRK10365  271 ISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNVVAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLI 350

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 340 AHDWPGNVRELRNVAERFAL----------GLPVfNKGGQAVQTGGPRFAEAVEAFEKALLGDALARHHGNLTQASQDLG 409
Cdd:PRK10365  351 HYDWPGNIRELENAVERAVVlltgeyiserELPL-AIASTPIPLGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLG 429

                         410
                  ....*....|..
gi 1544283978 410 MAKTTLFDKVKK 421
Cdd:PRK10365  430 ITRKTLLAKLSR 441
AcoR COG3284
Transcriptional regulator DhaR of acetoin/glycerol metabolism [Transcription];
129-423 3.26e-103

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


Pssm-ID: 442514 [Multi-domain]  Cd Length: 625  Bit Score: 319.15  E-value: 3.26e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 129 RIIGRSPAIQALRELIANVGDTSANVLILGETGTGKELVARCLHDYSRRHQHAFVALNCGGLPENLFDSEIFGHEAHAFT 208
Cdd:COG3284   322 ALAGGDPAMRRALRRARRLADRDIPVLILGETGTGKELFARAIHAASPRADGPFVAVNCAAIPEELIESELFGYEPGAFT 401

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 209 GANKR-RIGKIEHANGGTLFLDEIESMPVNLQIKLLRVLQEHTLERLGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDL 287
Cdd:COG3284   402 GARRKgRPGKIEQADGGTLFLDEIGDMPLALQARLLRVLQEREVTPLGGTKPIPVDVRLIAATHRDLRELVAAGRFREDL 481

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 288 YYRLNVVSLELPALRDrREDILLLFEHFLQQssLRFDRPAPELDRATVASLMAHDWPGNVRELRNVAERfALGL------ 361
Cdd:COG3284   482 YYRLNGLTLTLPPLRE-REDLPALIEHLLRE--LAAGRGPLRLSPEALALLAAYPWPGNVRELRNVLRT-ALALadggvi 557

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1544283978 362 ------PVFNKGGQAVQTGGPRFAEAVEAFEKALLGDALARHHGNLTQASQDLGMAKTTLFDKVKKYG 423
Cdd:COG3284   558 tvedlpDELRAELAAAAPAAAAPLTSLEEAERDAILRALRACGGNVSAAARALGISRSTLYRKLKRYG 625
PRK15115 PRK15115
response regulator GlrR; Provisional
 19-424 5.05e-101

response regulator GlrR; Provisional


Pssm-ID: 185070 [Multi-domain]  Cd Length: 444  Bit Score: 307.92  E-value: 5.05e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  19 GSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLVE 98
Cdd:PRK15115   36 ESGQEALRVLNREKVDLVISDLRMDEMDGMQLFAEIQKVQPGMPVIILTAHGSIPDAVAATQQGVFSFLTKPVDRDALYK 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  99 VARRALEQRGLArevsalrrqlaGRQDLAQRIIGRSPAIQALRELIANVGDTSANVLILGETGTGKELVARCLHDYSRRH 178
Cdd:PRK15115  116 AIDDALEQSAPA-----------TDERWREAIVTRSPLMLRLLEQARMVAQSDVSVLINGQSGTGKEILAQAIHNASPRA 184

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 179 QHAFVALNCGGLPENLFDSEIFGHEAHAFTGANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLRVLQEHTLERLGSNQ 258
Cdd:PRK15115  185 SKPFIAINCGALPEQLLESELFGHARGAFTGAVSNREGLFQAAEGGTLFLDEIGDMPAPLQVKLLRVLQERKVRPLGSNR 264

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 259 SIPVDCRVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEHFLQQSSLRFDRPAPELDRATVASL 338
Cdd:PRK15115  265 DIDIDVRIISATHRDLPKAMARGEFREDLYYRLNVVSLKIPALAERTEDIPLLANHLLRQAAERHKPFVRAFSTDAMKRL 344

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 339 MAHDWPGNVRELRNVAER-FAL-GLPVFNKG--GQAVQ---TGGPRFAEAVEAFEKALLGDALARHHGNLTQASQDLGMA 411
Cdd:PRK15115  345 MTASWPGNVRQLVNVIEQcVALtSSPVISDAlvEQALEgenTALPTFVEARNQFELNYLRKLLQITKGNVTHAARMAGRN 424

                         410
                  ....*....|...
gi 1544283978 412 KTTLFDKVKKYGL 424
Cdd:PRK15115  425 RTEFYKLLSRHEL 437
glnG PRK10923
nitrogen regulation protein NR(I); Provisional
 5-425 1.92e-100

nitrogen regulation protein NR(I); Provisional


Pssm-ID: 182842 [Multi-domain]  Cd Length: 469  Bit Score: 307.18  E-value: 1.92e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAY 84
Cdd:PRK10923   20 ERALAGAGLTCTTFENGNEVLEALASKTPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAF 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  85 DFMEKPFSPERLVEVARRALEQrglAREVSALRRQLAgrQDLAQRIIGRSPAIQALRELIANVGDTSANVLILGETGTGK 164
Cdd:PRK10923  100 DYLPKPFDIDEAVALVERAISH---YQEQQQPRNIQV--NGPTTDIIGEAPAMQDVFRIIGRLSRSSISVLINGESGTGK 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 165 ELVARCLHDYSRRHQHAFVALNCGGLPENLFDSEIFGHEAHAFTGANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLR 244
Cdd:PRK10923  175 ELVAHALHRHSPRAKAPFIALNMAAIPKDLIESELFGHEKGAFTGANTIRQGRFEQADGGTLFLDEIGDMPLDVQTRLLR 254

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 245 VLQEHTLERLGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEHFLQQSSLRFD 324
Cdd:PRK10923  255 VLADGQFYRVGGYAPVKVDVRIIAATHQNLEQRVQEGKFREDLFHRLNVIRVHLPPLRERREDIPRLARHFLQVAARELG 334

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 325 RPAPELDRATVASLMAHDWPGNVRELRNV-------------------AERFALGLPvfNKGGQAVQTGGPR-------- 377
Cdd:PRK10923  335 VEAKLLHPETEAALTRLAWPGNVRQLENTcrwltvmaagqevliqdlpGELFESTVP--ESTSQMQPDSWATllaqwadr 412

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1544283978 378 ---------FAEAVEAFEKALLGDALARHHGNLTQASQDLGMAKTTLFDKVKKYGLQ 425
Cdd:PRK10923  413 alrsghqnlLSEAQPELERTLLTTALRHTQGHKQEAARLLGWGRNTLTRKLKELGME 469
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
102-410 5.52e-99

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 304.79  E-value: 5.52e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 102 RALE-QRGLAREVSALRRQLAGRQDlaqRIIGRSPAIQALRELIANVGDTSANVLILGETGTGKELVARCLHDYSRRHQH 180
Cdd:PRK05022  163 EQLEsQAELPQDVAEFLRQEALKEG---EMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASPRADK 239

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 181 AFVALNCGGLPENLFDSEIFGHEAHAFTGANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLRVLQEHTLERLGSNQSI 260
Cdd:PRK05022  240 PLVYLNCAALPESLAESELFGHVKGAFTGAISNRSGKFELADGGTLFLDEIGELPLALQAKLLRVLQYGEIQRVGSDRSL 319

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 261 PVDCRVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEHFLQQSSLRFDRPAPELDRATVASLMA 340
Cdd:PRK05022  320 RVDVRVIAATNRDLREEVRAGRFRADLYHRLSVFPLSVPPLRERGDDVLLLAGYFLEQNRARLGLRSLRLSPAAQAALLA 399

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 341 HDWPGNVRELRNVAERFAL------------------------GLPVFNKGGQAVQTGGPRFAEAVEAFEKALLGDALAR 396
Cdd:PRK05022  400 YDWPGNVRELEHVISRAALlarargagrivtleaqhldlpaevALPPPEAAAAPAAVVSQNLREATEAFQRQLIRQALAQ 479

                         330
                  ....*....|....
gi 1544283978 397 HHGNLTQASQDLGM 410
Cdd:PRK05022  480 HQGNWAAAARALEL 493
Sigma54_activat pfam00158
Sigma-54 interaction domain;
130-297 6.17e-99

Sigma-54 interaction domain;


Pssm-ID: 425491 [Multi-domain]  Cd Length: 168  Bit Score: 292.38  E-value: 6.17e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 130 IIGRSPAIQALRELIANVGDTSANVLILGETGTGKELVARCLHDYSRRHQHAFVALNCGGLPENLFDSEIFGHEAHAFTG 209
Cdd:pfam00158   1 IIGESPAMQEVLEQAKRVAPTDAPVLITGESGTGKELFARAIHQLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 210 ANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLRVLQEHTLERLGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLYY 289
Cdd:pfam00158  81 ADSDRKGLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTKPIKVDVRIIAATNRDLEEAVAEGRFREDLYY 160


                  ....*...
gi 1544283978 290 RLNVVSLE 297
Cdd:pfam00158 161 RLNVIPIE 168
PRK15424 PRK15424
propionate catabolism operon regulatory protein PrpR; Provisional
 101-421 3.53e-90

propionate catabolism operon regulatory protein PrpR; Provisional


Pssm-ID: 237963 [Multi-domain]  Cd Length: 538  Bit Score: 282.76  E-value: 3.53e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 101 RRALEQR-GLAREVSALRRQLAGRQDLAQR-----IIGRSPAIQALRELIANVGDTSANVLILGETGTGKELVARCLH-- 172
Cdd:PRK15424  186 RQAFEDAlDMTRMTLRHNTHYATRNALRTRyvlgdLLGQSPQMEQVRQTILLYARSSAAVLIQGETGTGKELAAQAIHre 265

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 173 ------DYSRRHQHAFVALNCGGLPENLFDSEIFGHEAHAFTGANKR-RIGKIEHANGGTLFLDEIESMPVNLQIKLLRV 245
Cdd:PRK15424  266 yfarhdARQGKKSHPFVAVNCGAIAESLLEAELFGYEEGAFTGSRRGgRAGLFEIAHGGTLFLDEIGEMPLPLQTRLLRV 345

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 246 LQEHTLERLGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEHFLQQSSLRFDR 325
Cdd:PRK15424  346 LEEKEVTRVGGHQPVPVDVRVISATHCDLEEDVRQGRFRRDLFYRLSILRLQLPPLRERVADILPLAESFLKQSLAALSA 425

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 326 PAPELDRATVAS----LMAHDWPGNVRELRNVAERFALGLPVfnkggQAVQTGGPRFAE------AVEAFEK-------A 388
Cdd:PRK15424  426 PFSAALRQGLQQcetlLLHYDWPGNVRELRNLMERLALFLSV-----EPTPDLTPQFLQlllpelARESAKTpaprllaA 500

                         330       340       350
                  ....*....|....*....|....*....|...
gi 1544283978 389 LLGDALARHHGNLTQASQDLGMAKTTLFDKVKK 421
Cdd:PRK15424  501 TLQQALERFNGDKTAAANYLGISRTTLWRRLKA 533
TyrR COG3283
Transcriptional regulator TyrR of aromatic amino acids metabolism [Transcription, Amino acid ...
 129-424 3.76e-87

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


Pssm-ID: 442513 [Multi-domain]  Cd Length: 514  Bit Score: 274.37  E-value: 3.76e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 129 RIIGRSPAIQALRELIANVGDTSANVLILGETGTGKELVARCLHDYSRRHQHAFVALNCGGLPENLFDSEIFGHEAHAFT 208
Cdd:COG3283   205 HIVASSPKMRQVIRQAKKMAMLDAPLLIQGETGTGKELLARACHLASPRGDKPFLALNCAALPDDVAESELFGYAPGAFG 284

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 209 GANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLRVLQEHTLERLGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLY 288
Cdd:COG3283   285 NAREGKKGLFEQANGGTVFLDEIGEMSPQLQAKLLRFLQDGTFRRVGEEQEVKVDVRVICATQKDLAELVQEGEFREDLY 364

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 289 YRLNVVSLELPALRDRREDILLLFEHFLQQSSLRFDRPAPELDRATVASLMAHDWPGNVRELRNV-------AERFALG- 360
Cdd:COG3283   365 YRLNVLTLTLPPLRERKSDILPLAEHFVARFSQQLGRPRPRLSPDLVDFLQSYPWPGNVRQLENAlyravslLEGDELTp 444

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1544283978 361 ----LPVFNKG-GQAVQTGGPRFAEAVEAFEKALLgDALARHHGNLTQASQDLGMAKTTLFDKVKKYGL 424
Cdd:COG3283   445 edlqLPEYAASaGLLDDLLEGSLDEIVKRFERSLL-RRLYPSYPSTRKLAKRLGVSHTAIANKLREYGI 512
phageshock_pspF TIGR02974
psp operon transcriptional activator PspF; Members of this protein family are PspF, the ...
 130-422 3.99e-85

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


Pssm-ID: 274371 [Multi-domain]  Cd Length: 329  Bit Score: 263.00  E-value: 3.99e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 130 IIGRSPAIQALRELIANVGDTSANVLILGETGTGKELVARCLHDYSRRHQHAFVALNCGGLPENLFDSEIFGHEAHAFTG 209
Cdd:TIGR02974   1 LIGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAALSENLLDSELFGHEAGAFTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 210 ANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLRVLQEHTLERLGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLYY 289
Cdd:TIGR02974  81 AQKRHQGRFERADGGTLFLDELATASLLVQEKLLRVIEYGEFERVGGSQTLQVDVRLVCATNADLPALAAEGRFRADLLD 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 290 RLNVVSLELPALRDRREDILLLFEHFLQQSSLRFDRPA-PELDRATVASLMAHDWPGNVRELRNVAER--FALGLP---- 362
Cdd:TIGR02974 161 RLAFDVITLPPLRERQEDIMLLAEHFAIRMARELGLPLfPGFTPQAREQLLEYHWPGNVRELKNVVERsvYRHGLEeapi 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 363 ---VFN-----------------KGGQAVQTGGPR---------FAEAVEAFEKALLGDALARHHGNLTQASQDLGMAKT 413
Cdd:TIGR02974 241 deiIIDpfaspwrpkqaapavdeVNSTPTDLPSPSsiaaafpldLKQAQQDYEIELLQQALAEAQFNQRKAAELLGLTYH 320


                  ....*....
gi 1544283978 414 TLFDKVKKY 422
Cdd:TIGR02974 321 QLRGLLRKH 329
nifA TIGR01817
Nif-specific regulatory protein; This model represents NifA, a DNA-binding regulatory protein ...
 94-358 5.90e-85

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: 269.28  E-value: 5.90e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  94 ERLVEVARRalEQRGLAREVSALRRQLAGRQDLaqrIIGRSPAIQALRELIANVGDTSANVLILGETGTGKELVARCLHD 173
Cdd:TIGR01817 167 ERLIAEAVQ--LSKQLRDKAPEIARRRSGKEDG---IIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHY 241

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 174 YSRRHQHAFVALNCGGLPENLFDSEIFGHEAHAFTGANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLRVLQEHTLER 253
Cdd:TIGR01817 242 LSPRAKRPFVKVNCAALSETLLESELFGHEKGAFTGAIAQRKGRFELADGGTLFLDEIGEISPAFQAKLLRVLQEGEFER 321

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 254 LGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEHFL------QQSSLRFDRPA 327
Cdd:TIGR01817 322 VGGNRTLKVDVRLVAATNRDLEEAVAKGEFRADLYYRINVVPIFLPPLRERREDIPLLAEAFLekfnreNGRPLTITPSA 401

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1544283978 328 PELdratvasLMAHDWPGNVRELRNVAERFA 358
Cdd:TIGR01817 402 IRV-------LMSCKWPGNVRELENCLERTA 425
propionate_PrpR TIGR02329
propionate catabolism operon regulatory protein PrpR; At least five distinct pathways exists ...
 114-421 6.94e-85

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: 269.04  E-value: 6.94e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 114 SALRRQLAGRQDLAQrIIGRSPAIQALRELIANVGDTSANVLILGETGTGKELVARCLHDYSRRHQHAFVALNCGGLPEN 193
Cdd:TIGR02329 199 SATRNQLRTRYRLDD-LLGASAPMEQVRALVRLYARSDATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIAES 277

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 194 LFDSEIFGHEAHAFTGANK-RRIGKIEHANGGTLFLDEIESMPVNLQIKLLRVLQEHTLERLGSNQSIPVDCRVIAATKA 272
Cdd:TIGR02329 278 LLEAELFGYEEGAFTGARRgGRTGLIEAAHRGTLFLDEIGEMPLPLQTRLLRVLEEREVVRVGGTEPVPVDVRVVAATHC 357

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 273 DLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEHFLQQSSLRFDRPAPELDRATVAS----LMAHDWPGNVR 348
Cdd:TIGR02329 358 ALTTAVQQGRFRRDLFYRLSILRIALPPLRERPGDILPLAAEYLVQAAAALRLPDSEAAAQVLAGvadpLQRYPWPGNVR 437

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 349 ELRNVAERFALGLPVFNKGG---QAVQTGGPRFAE--------AVEAFEKALLG-----DALARHHGNLTQASQDLGMAK 412
Cdd:TIGR02329 438 ELRNLVERLALELSAMPAGAltpDVLRALAPELAEasgkgktsALSLRERSRVEalavrAALERFGGDRDAAAKALGISR 517


                  ....*....
gi 1544283978 413 TTLFDKVKK 421
Cdd:TIGR02329 518 TTLWRRLKA 526
PRK15429 PRK15429
formate hydrogenlyase transcriptional activator FlhA;
98-424 3.42e-77

formate hydrogenlyase transcriptional activator FlhA;


Pssm-ID: 237965 [Multi-domain]  Cd Length: 686  Bit Score: 252.83  E-value: 3.42e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  98 EVARraLEQRgLAREVSALRRQLAGRQDLAQRIIGRSPAIQALRELIANVGDTSANVLILGETGTGKELVARCLHDYSRR 177
Cdd:PRK15429  349 EIHR--LKER-LVDENLALTEQLNNVDSEFGEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLSGR 425

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 178 HQHAFVALNCGGLPENLFDSEIFGHEAHAFTGANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLRVLQEHTLERLGSN 257
Cdd:PRK15429  426 NNRRMVKMNCAAMPAGLLESDLFGHERGAFTGASAQRIGRFELADKSSLFLDEVGDMPLELQPKLLRVLQEQEFERLGSN 505

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 258 QSIPVDCRVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEHFLQQSSLRFDRPAPELDRATVAS 337
Cdd:PRK15429  506 KIIQTDVRLIAATNRDLKKMVADREFRSDLYYRLNVFPIHLPPLRERPEDIPLLVKAFTFKIARRMGRNIDSIPAETLRT 585

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 338 LMAHDWPGNVRELRNVAER---------FALGLPVFNKGGQAVQTGGPRFAEAVEAfEKALLGDALARHHGNLT---QAS 405
Cdd:PRK15429  586 LSNMEWPGNVRELENVIERavlltrgnvLQLSLPDITLPEPETPPAATVVAQEGED-EYQLIVRVLKETNGVVAgpkGAA 664

                         330
                  ....*....|....*....
gi 1544283978 406 QDLGMAKTTLFDKVKKYGL 424
Cdd:PRK15429  665 QRLGLKRTTLLSRMKRLGI 683
pspF PRK11608
phage shock protein operon transcriptional activator; Provisional
 154-356 5.60e-75

phage shock protein operon transcriptional activator; Provisional


Pssm-ID: 236936 [Multi-domain]  Cd Length: 326  Bit Score: 236.88  E-value: 5.60e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 154 VLILGETGTGKELVARCLHDYSRRHQHAFVALNCGGLPENLFDSEIFGHEAHAFTGANKRRIGKIEHANGGTLFLDEIES 233
Cdd:PRK11608   32 VLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELAT 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 234 MPVNLQIKLLRVLQEHTLERLGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFE 313
Cdd:PRK11608  112 APMLVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVAEGKFRADLLDRLAFDVVQLPPLRERQSDIMLMAE 191

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1544283978 314 HFLQQSSLRFDRPA-PELDRATVASLMAHDWPGNVRELRNVAER 356
Cdd:PRK11608  192 HFAIQMCRELGLPLfPGFTERARETLLNYRWPGNIRELKNVVER 235
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 134-425 1.29e-73

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: 233.97  E-value: 1.29e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 134 SPAIQALRELIANVgdtsANVLILGETGTGKELVARCLHDYSRRHQHAFVALNCGGLPENLFDSeifgheahaftgankr 213
Cdd:COG3604   102 SEEDLRLLETLASL----AAVAILGETGTGKELVANAIHELSPRADKPFVKVNCAALPESLLES---------------- 161

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 214 rigkiehanggtlfldeiesmpvnlqikllrvLQEHTLERLGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLYYRLNV 293
Cdd:COG3604   162 --------------------------------LQEGEFERVGGDETIKVDVRIIAATNRDLEEEVAEGRFREDLYYRLNV 209

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 294 VSLELPALRDRREDILLLFEHFLQQSSLRFDRPAPELDRATVASLMAHDWPGNVRELRNVAERFALglpVFNKGGQAVQT 373
Cdd:COG3604   210 FPIRLPPLRERREDIPLLAEHFLEKFSRRLGKPILRLSPEALEALMAYPWPGNVRELENVIERAVI---LAEGGVLDADD 286

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1544283978 374 GGPRFAEAVEAFEKALLGDALARHHGNLTQASQDLGMAKTTLFDKVKKYGLQ 425
Cdd:COG3604   287 LAPGSREALEEVEREHILEALERTGGNIAGAARLLGLTPSTLRSRMKKLGIK 338
REC_DctD-like cd17549
phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and ...
 4-120 8.05e-62

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: 196.17  E-value: 8.05e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   4 CQQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGA 83
Cdd:cd17549    14 LQQTLELAGFRVRAFADAEEALAALSPDFPGVVISDIRMPGMDGLELLAQIRELDPDLPVILITGHGDVPMAVEAMRAGA 93

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1544283978  84 YDFMEKPFSPERLVEVARRALEQRGLAREVSALRRQL 120
Cdd:cd17549    94 YDFLEKPFDPERLLDVVRRALEKRRLVLENRRLRQQL 130
PRK10820 PRK10820
transcriptional regulator TyrR;
114-424 1.83e-61

transcriptional regulator TyrR;


Pssm-ID: 236769 [Multi-domain]  Cd Length: 520  Bit Score: 207.62  E-value: 1.83e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 114 SALR--RQLagrQDLA-------QRIIGRSPAIQALRELIANVGDTSANVLILGETGTGKELVARCLHDYSRRHQHAFVA 184
Cdd:PRK10820  184 STARmgRQL---QNLAvnddsafSQIVAVSPKMRQVVEQARKLAMLDAPLLITGDTGTGKDLLAYACHLRSPRGKKPFLA 260

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 185 LNCGGLPENLFDSEIFGHEAHAFTGANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLRVLQEHTLERLGSNQSIPVDC 264
Cdd:PRK10820  261 LNCASIPDDVVESELFGHAPGAYPNALEGKKGFFEQANGGSVLLDEIGEMSPRMQAKLLRFLNDGTFRRVGEDHEVHVDV 340

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 265 RVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEHFLQQSSLRFDRPAPELDRATVASLMAHDWP 344
Cdd:PRK10820  341 RVICATQKNLVELVQKGEFREDLYYRLNVLTLNLPPLRDRPQDIMPLTELFVARFADEQGVPRPKLAADLNTVLTRYGWP 420

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 345 GNVRELRNVAERfALG-------------LPVFNKG---GQAVQTGGprFAEAVEAFEKALLgDALARHHGNLTQASQDL 408
Cdd:PRK10820  421 GNVRQLKNAIYR-ALTqlegyelrpqdilLPDYDAAvavGEDAMEGS--LDEITSRFERSVL-TRLYRNYPSTRKLAKRL 496

                         330
                  ....*....|....*.
gi 1544283978 409 GMAKTTLFDKVKKYGL 424
Cdd:PRK10820  497 GVSHTAIANKLREYGL 512
PRK11388 PRK11388
DNA-binding transcriptional regulator DhaR; Provisional
 154-425 1.47e-53

DNA-binding transcriptional regulator DhaR; Provisional


Pssm-ID: 183114 [Multi-domain]  Cd Length: 638  Bit Score: 188.73  E-value: 1.47e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 154 VLILGETGTGKELVARCLHDYSRRHQHAFVALNCGGLPENLFDSEIFGHEAhafTGANKRRIGKIEHANGGTLFLDEIES 233
Cdd:PRK11388  351 VLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPDEALAEEFLGSDR---TDSENGRLSKFELAHGGTLFLEKVEY 427

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 234 MPVNLQIKLLRVLQEHTLERLGSNQSIPVDCRVIAATKADLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFE 313
Cdd:PRK11388  428 LSPELQSALLQVLKTGVITRLDSRRLIPVDVRVIATTTADLAMLVEQNRFSRQLYYALHAFEITIPPLRMRREDIPALVN 507

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 314 HFLQQSSLRFDRPApELDRATVASLMAHDWPGNVRELRNVAERFAL----------GLPVF----NKGGQAVQTGGPRFA 379
Cdd:PRK11388  508 NKLRSLEKRFSTRL-KIDDDALARLVSYRWPGNDFELRSVIENLALssdngrirlsDLPEHlfteQATDDVSATRLSTSL 586

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*.
gi 1544283978 380 EAVEAFEKALLGDALARhHGNLTQASQDLGMAKTTLFDKVKKYGLQ 425
Cdd:PRK11388  587 SLAELEKEAIINAAQVC-GGRIQEMAALLGIGRTTLWRKMKQHGID 631
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 8-123 1.35e-37

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 135.23  E-value: 1.35e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   8 LELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFM 87
Cdd:COG4566    19 LESAGLRVETFASAEAFLAALDPDRPGCLLLDVRMPGMSGLELQEELAARGSPLPVIFLTGHGDVPMAVRAMKAGAVDFL 98

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1544283978  88 EKPFSPERLVEVARRALEQRGLAREVSALRRQLAGR 123
Cdd:COG4566    99 EKPFDDQALLDAVRRALARDRARRAERARRAELRAR 134
REC_NtrX-like cd17550
phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and ...
 18-105 4.13e-32

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: 117.98  E-value: 4.13e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  18 VGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLV 97
Cdd:cd17550    28 AADGEEALKLIKERRPDLVLLDIWLPDMDGLELLKEIKEKYPDLPVIMISGHGTIETAVKATKLGAYDFIEKPLSLDRLL 107


                  ....*...
gi 1544283978  98 EVARRALE 105
Cdd:cd17550   108 LTIERALE 115
RtcR COG4650
Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a ...
 117-350 7.63e-32

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: 126.87  E-value: 7.63e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 117 RRQLAGRQDLAQRIIGRSPAIQALRELIANVGDTS-ANVLILGETGTGKELVARCLHDYSR-RHQ--HAFVALNCGGLPE 192
Cdd:COG4650   173 QEQQEAVSFLKSGIATRNAAFNRLIEQIERVAIRSrAPILLTGPTGAGKSQLARRIYELKKaRHQvsGRFVEVNCATLRG 252

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 193 NLFDSEIFGHEAHAFTGANKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLRVLQEHTLERLGSNQSIPVDCRVIAATKA 272
Cdd:COG4650   253 DGAMSALFGHVKGAFTGAVSDRAGLLRSADGGVLFLDEIGELGLDEQAMLLRAIEEKRFLPVGSDKEVSSDFQLIAGTNR 332

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 273 DLAAMGKSGQFRSDLYYRLNVVSLELPALRDRREDILLLFEHFLQQSS------LRFDRPAPELDRATVASLMAHdWPGN 346
Cdd:COG4650   333 DLRQEVAEGRFREDLLARINLWTFRLPGLAERREDIEPNLDYELARFAreqgrrVRFNKEARARYLAFATSPEAL-WSGN 411


                  ....
gi 1544283978 347 VREL 350
Cdd:COG4650   412 FRDL 415
fixJ PRK09390
response regulator FixJ; Provisional
 34-145 1.26e-30

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 116.64  E-value: 1.26e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  34 GIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLVEVARRALEQRGLAREV 113
Cdd:PRK09390   49 GCVVTDVRMPGIDGIELLRRLKARGSPLPVIVMTGHGDVPLAVEAMKLGAVDFIEKPFEDERLIGAIERALAQAPEAAKS 128

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1544283978 114 SALrrqlagRQDLAQRIIGRSP-AIQALRELIA 145
Cdd:PRK09390  129 EAV------AADIRARIASLSErERQVMDGLVA 155
REC_FixJ cd17537
phosphoacceptor receiver (REC) domain of FixJ family response regulators; FixJ family response ...
 20-104 2.25e-28

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: 107.68  E-value: 2.25e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  20 SAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLVEV 99
Cdd:cd17537    32 SASAFLAAAPPDQPGCLVLDVRMPGMSGLELQDELLARGSNIPIIFITGHGDVPMAVEAMKAGAVDFLEKPFRDQVLLDA 111


                  ....*
gi 1544283978 100 ARRAL 104
Cdd:cd17537   112 IEQAL 116
PspF COG1221
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain ...
 153-353 1.99e-27

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: 115.20  E-value: 1.99e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 153 NVLILGETGTGKELVARCLHDYS----RRHQHA-FVALNCGGLPEN--LFDSEIFGHEAHAFTGANKRRIGKIEHANGGT 225
Cdd:COG1221   132 HTLILGPTGVGKSFFAELMYEYAieigVLPEDApFVVFNCADYANNpqLLMSQLFGYVKGAFTGADKDKEGLIEKADGGI 211

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 226 LFLDEIESMPVNLQIKLLRVLQEHTLERLG-SNQSIPVDCRVIAATKADLaamgksgqfRSDLyyrLNV------VSLEL 298
Cdd:COG1221   212 LFLDEVHRLPPEGQEMLFTFMDKGIYRRLGeTEKTRKANVRIIFATTEDP---------ESSL---LKTflrripMVIKL 279

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1544283978 299 PALRDR-REDILLLFEHFLQQSSLRFDRPApELDRATVASLMAHDWPGNVRELRNV 353
Cdd:COG1221   280 PSLEERsLEERLELIKHFFKEEAKRLNKPI-KVSKEVLKALLLYDCPGNIGQLKSD 334
Response_reg pfam00072
Response regulator receiver domain; This domain receives the signal from the sensor partner in ...
 3-101 2.35e-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: 104.93  E-value: 2.35e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   3 GCQQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAG 82
Cdd:pfam00072  13 LLRQLLEKEGYVVAEADDGKEALELLKEERPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTAHGDEDDAVEALEAG 92

                          90
                  ....*....|....*....
gi 1544283978  83 AYDFMEKPFSPERLVEVAR 101
Cdd:pfam00072  93 ADDFLSKPFDPDELLAAIR 111
REC_NtrC1-like cd17572
phosphoacceptor receiver (REC) domain of nitrogen regulatory protein C 1 (NtrC1) from Aquifex ...
 5-109 6.91e-25

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: 98.42  E-value: 6.91e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAY 84
Cdd:cd17572    15 QEYLSDEGYKVTHVETGKEALAFLSDQPPDVVLLDLKLPDMSGMEILKWIQERSLPTSVIVITAHGSVDIAVEAMRLGAY 94

                          90       100
                  ....*....|....*....|....*
gi 1544283978  85 DFMEKPFSPERLVEVARRALEQRGL 109
Cdd:cd17572    95 DFLEKPFDADRLRVTVRNALKHRKL 119
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 131-294 1.22e-24

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: 98.76  E-value: 1.22e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 131 IGRSPAIQALRELIANvgDTSANVLILGETGTGKELVARCLHDYSRRHQHAFVALNCGGLPENLFDSEIFGHEahaftgA 210
Cdd:cd00009     1 VGQEEAIEALREALEL--PPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHF------L 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 211 NKRRIGKIEHANGGTLFLDEIESMPVNLQIKLLRVLQEHTLERLgsnqsIPVDCRVIAATKADLaamgkSGQFRSDLYYR 290
Cdd:cd00009    73 VRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRI-----DRENVRVIGATNRPL-----LGDLDRALYDR 142


                  ....
gi 1544283978 291 LNVV 294
Cdd:cd00009   143 LDIR 146
REC_NtrC cd19919
phosphoacceptor receiver (REC) domain of DNA-binding transcriptional regulator NtrC; ...
 5-104 3.09e-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: 96.57  E-value: 3.09e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAY 84
Cdd:cd19919    17 ERALAGAGLTVTSFENAQEALAALASSQPDVLISDIRMPGMDGLALLAQIKQRHPDLPVIIMTAHSDLDSAVSAYQGGAF 96

                          90       100
                  ....*....|....*....|
gi 1544283978  85 DFMEKPFSPERLVEVARRAL 104
Cdd:cd19919    97 EYLPKPFDIDEAVALVERAI 116
Sigma54_activ_2 pfam14532
Sigma-54 interaction domain;
131-301 4.38e-23

Sigma-54 interaction domain;


Pssm-ID: 434021 [Multi-domain]  Cd Length: 138  Bit Score: 94.33  E-value: 4.38e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 131 IGRSPAIQALRELIANVGDTSANVLILGETGTGKELVARCLHDYSRRHQHAFVALNCGGLPENLFDSeifgheahaftga 210
Cdd:pfam14532   1 LGASAAIQEIKRRLEQAAQSTLPVFLTGEPGSGKEFCARYLHNPSTPWVQPFDIEYLAHAPLELLEQ------------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 211 nkrrigkiehANGGTLFLDEIESMPVNLQIKLlrvlqehtLERLGSNQsiPVDCRVIAATKADLAAMGKSGQFRSDLYYR 290
Cdd:pfam14532  68 ----------AKGGTLYLKDIADLSKALQKGL--------LLLLAKAE--GYRVRLVCTSSKDLPQLAAAGLFDEQLYFE 127

                         170
                  ....*....|.
gi 1544283978 291 LNVVSLELPAL 301
Cdd:pfam14532 128 LSALRLHVPPL 138
RpfG COG3437
Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains ...
 5-121 6.43e-22

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: 93.69  E-value: 6.43e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPS--LPVVLITGHGDISMAVQAMHAG 82
Cdd:COG3437    23 RQLLRTLGYDVVTAESGEEALELLLEAPPDLILLDVRMPGMDGFELLRLLRADPSTrdIPVIFLTALADPEDRERALEAG 102

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1544283978  83 AYDFMEKPFSPERLVEVARRALEQRGLAREVSALRRQLA 121
Cdd:COG3437   103 ADDYLTKPFDPEELLARVRNALELRRLQRELDDLVLYLK 141
REC cd00156
phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response ...
 5-90 7.13e-22

phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response regulators (PRRs); Two-component systems (TCSs) involving a sensor and a response regulator are used by bacteria to adapt to changing environments. Processes regulated by two-component systems in bacteria include sporulation, pathogenicity, virulence, chemotaxis, and membrane transport. Response regulators (RRs) share the common phosphoacceptor REC domain and different effector/output domains such as DNA, RNA, ligand-binding, protein-binding, or enzymatic domains. Response regulators regulate transcription, post-transcription or post-translation, or have functions such as methylesterases, adenylate or diguanylate cyclase, c-di-GMP-specific phosphodiesterases, histidine kinases, serine/threonine protein kinases, and protein phosphatases, depending on their output domains. The function of some output domains are still unknown. TCSs are found in all three domains of life - bacteria, archaea, and eukaryotes, however, the presence and abundance of particular RRs vary between the lineages. Archaea encode very few RRs with DNA-binding output domains; most are stand-alone REC domains. Among eukaryotes, TCSs are found primarily in protozoa, fungi, algae, and green plants. REC domains function as phosphorylation-mediated switches within RRs, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381085 [Multi-domain]  Cd Length: 99  Bit Score: 89.59  E-value: 7.13e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAY 84
Cdd:cd00156    14 KSLLEREGYEVDTAADGEEALELLREERPDLVLLDLMMPGMDGLELLRKLRELPPDIPVIVLTAKADEEDAVRALELGAD 93


                  ....*.
gi 1544283978  85 DFMEKP 90
Cdd:cd00156    94 DYLVKP 99
REC_YesN-like cd17536
phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response ...
 2-106 8.63e-22

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: 90.09  E-value: 8.63e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   2 LGCQQALELEDipcigvgsAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHA 81
Cdd:cd17536    23 LGFEVVGEAEN--------GEEALELIEEHKPDIVITDIRMPGMDGLELIEKIRELYPDIKIIILSGYDDFEYAQKAIRL 94

                          90       100
                  ....*....|....*....|....*
gi 1544283978  82 GAYDFMEKPFSPERLVEVARRALEQ 106
Cdd:cd17536    95 GVVDYLLKPVDEEELEEALEKAKEE 119
CheY COG0784
CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator ...
 5-107 5.60e-21

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: 87.98  E-value: 5.60e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLD--PSLPVVLITGHGDISMAVQAMHAG 82
Cdd:COG0784    22 RRLLERLGYEVTTAEDGAEALELLRAGPPDLILLDINMPGMDGLELLRRIRALPrlPDIPIIALTAYADEEDRERALEAG 101

                          90       100
                  ....*....|....*....|....*
gi 1544283978  83 AYDFMEKPFSPERLVEVARRALEQR 107
Cdd:COG0784   102 ADDYLTKPVDPEELLEALRRLLARA 126
YesN COG4753
Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding ...
 9-90 1.81e-20

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: 85.60  E-value: 1.81e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   9 ELEDIPCIGV-GSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFM 87
Cdd:COG4753    21 WEAGFEVVGEaENGEEALELLEEHKPDLVITDINMPGMDGLELLEAIRELDPDTKIIILSGYSDFEYAQEAIKLGADDYL 100


                  ...
gi 1544283978  88 EKP 90
Cdd:COG4753   101 LKP 103
CitB COG4565
DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal ...
 18-112 2.37e-20

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


Pssm-ID: 443622 [Multi-domain]  Cd Length: 138  Bit Score: 86.56  E-value: 2.37e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  18 VGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLV 97
Cdd:COG4565    35 ASSGEEALALLAEHRPDLILLDIYLPDGDGLELLRELRARGPDVDVIVITAARDPETVREALRAGVVDYLIKPFTFERLR 114

                          90
                  ....*....|....*
gi 1544283978  98 EVARRALEQRGLARE 112
Cdd:COG4565   115 EALERYLEYRRLLRE 129
OmpR COG0745
DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain ...
 5-111 3.68e-20

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: 88.09  E-value: 3.68e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAY 84
Cdd:COG0745    18 ADALEREGYEVDTAADGEEALELLEEERPDLILLDLMLPGMDGLEVCRRLRARPSDIPIIMLTARDDEEDRVRGLEAGAD 97

                          90       100
                  ....*....|....*....|....*..
gi 1544283978  85 DFMEKPFSPERLVEVARRALEQRGLAR 111
Cdd:COG0745    98 DYLTKPFDPEELLARIRALLRRRAAEV 124
PleD COG3706
Two-component response regulator, PleD family, consists of two REC domains and a diguanylate ...
 5-101 3.54e-18

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: 81.88  E-value: 3.54e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLD--PSLPVVLITGHGDISMAVQAMHAG 82
Cdd:COG3706    18 RRLLEAAGYEVVEAADGEEALELLQEHRPDLILLDLEMPDMDGLELCRRLRADPrtADIPIIFLTALDDEEDRARALEAG 97

                          90       100
                  ....*....|....*....|...
gi 1544283978  83 AYDFMEKPFSPERLVE----VAR 101
Cdd:COG3706    98 ADDYLTKPFDPEELLArvdlVAR 120
REC_HupR-like cd17569
phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR) and similar ...
 20-105 9.22e-18

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: 78.60  E-value: 9.22e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  20 SAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGA-YDFMEKPFSPERLVE 98
Cdd:cd17569    32 SGEEALEILKQEPVDVVISDQRMPGMDGAELLKRVRERYPDTVRILLTGYADLDAAIEAINEGEiYRFLTKPWDDEELKE 111


                  ....*..
gi 1544283978  99 VARRALE 105
Cdd:cd17569   112 TIRQALE 118
LytT COG3279
DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction ...
 9-120 1.61e-17

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


Pssm-ID: 442510 [Multi-domain]  Cd Length: 235  Bit Score: 81.40  E-value: 1.61e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   9 ELEDIPCIGV-GSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDisMAVQAMHAGAYDFM 87
Cdd:COG3279    23 KYPDLEVVGEaSNGEEALELLEEHKPDLVFLDIQMPGLDGFELARQLRELDPPPPIIFTTAYDE--YALEAFEVNAVDYL 100

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1544283978  88 EKPFSPERLVEVARRALEQRGLAREVSALRRQL 120
Cdd:COG3279   101 LKPIDEERLAKALEKAKERLEAKAAAEASPEEK 133
COG4567 COG4567
DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains ...
 5-106 1.98e-17

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: 79.58  E-value: 1.98e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAY 84
Cdd:COG4567    21 ARALERRGFEVTTAASVEEALALLEQAPPDYAVLDLRLGDGSGLDLIEALRERDPDARIVVLTGYASIATAVEAIKLGAD 100

                          90       100
                  ....*....|....*....|..
gi 1544283978  85 DFMEKPFSPERLVEVARRALEQ 106
Cdd:COG4567   101 DYLAKPADADDLLAALERAEGD 122
REC_NarL-like cd17535
phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family ...
 19-105 3.73e-16

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: 74.09  E-value: 3.73e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  19 GSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLVE 98
Cdd:cd17535    31 ADGEEALALLRELRPDVVLMDLSMPGMDGIEALRRLRRRYPDLKVIVLTAHDDPEYVLRALKAGAAGYLLKDSSPEELIE 110


                  ....*..
gi 1544283978  99 VARRALE 105
Cdd:cd17535   111 AIRAVAA 117
REC_RegA-like cd17563
phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA; ...
 5-90 3.69e-15

phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA; Rhodobacter sphaeroides RegA, also called response regulator PrrA, is the DNA binding regulatory protein of a redox-responsive two-component regulatory system RegB/RegA that is involved in transactivating anaerobic expression of the photosynthetic apparatus. It contains a REC domain and a DNA-binding helix-turn-helix output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381111 [Multi-domain]  Cd Length: 112  Bit Score: 71.32  E-value: 3.69e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRD-FAGIVVsDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGA 83
Cdd:cd17563    17 ARALERRGFEVETAHSVEEALALAREEkPDYAVL-DLRLGGDSGLDLIPPLRALQPDARIVVLTGYASIATAVEAIKLGA 95


                  ....*..
gi 1544283978  84 YDFMEKP 90
Cdd:cd17563    96 DDYLAKP 102
REC_CheY cd17542
phosphoacceptor receiver (REC) domain of chemotaxis protein CheY; The chemotaxis response ...
 18-104 5.28e-15

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: 70.77  E-value: 5.28e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  18 VGSA---EEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPE 94
Cdd:cd17542    28 VGEAangEEAVEKYKELKPDLVTMDITMPEMDGIEALKEIKKIDPNAKVIMCSAMGQEEMVKEAIKAGAKDFIVKPFQPE 107

                          90
                  ....*....|
gi 1544283978  95 RLVEVARRAL 104
Cdd:cd17542   108 RVLEAVEKVL 117
AmiR COG3707
Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding ...
 18-124 1.04e-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: 72.30  E-value: 1.04e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  18 VGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSlDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERL- 96
Cdd:COG3707    34 AADGEDAVELVRELKPDLVIVDIDMPDRDGLEAARQISE-ERPAPVILLTAYSDPELIERALEAGVSAYLVKPLDPEDLl 112

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1544283978  97 --VEVAR-RALEQRGLAREVSALRRQLAGRQ 124
Cdd:COG3707   113 paLELALaRFRELRALRRELAKLREALEERK 143
REC_OmpR_MtPhoP-like cd17615
phosphoacceptor receiver (REC) domain of MtPhoP-like OmpR family response regulators; ...
 19-107 1.63e-14

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


Pssm-ID: 381131 [Multi-domain]  Cd Length: 118  Bit Score: 69.69  E-value: 1.63e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  19 GSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLve 98
Cdd:cd17615    30 ADGAEALAAAREFRPDAVVLDIMLPDMDGLEVLRRLRADGPDVPVLFLTAKDSVEDRIAGLTAGGDDYVTKPFSLEEV-- 107

                          90
                  ....*....|
gi 1544283978  99 VAR-RALEQR 107
Cdd:cd17615   108 VARlRALLRR 117
REC_typeB_ARR-like cd17584
phosphoacceptor receiver (REC) domain of type B Arabidopsis response regulators (ARRs) and ...
 15-104 3.63e-14

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: 68.42  E-value: 3.63e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  15 CIGVGSAEEALQ--RVDRDFAGIVVSDIRLPGIDGLTLLERLKSLdPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFS 92
Cdd:cd17584    25 VTTCTDAEEALSmlRENKDEFDLVITDVHMPDMDGFEFLELIRLE-MDLPVIMMSADGSTSTVMKGLAHGACDYLLKPVS 103

                          90
                  ....*....|..
gi 1544283978  93 PERLVEVARRAL 104
Cdd:cd17584   104 IEDLKNIWQHVV 115
REC_RssB-like cd17555
phosphoacceptor receiver (REC) domain of Pseudomonas aeruginosa RssB and similar domains; ...
 19-90 3.84e-14

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: 68.38  E-value: 3.84e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1544283978  19 GSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKP 90
Cdd:cd17555    31 ADGRQGLELFRSEQPDLVLCDLRMPEMDGLEVLKQITKESPDTPVIVVSGAGVMSDAVEALRLGAWDYLTKP 102
REC_HupR cd17596
phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR); Members of ...
 11-120 3.13e-13

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: 66.24  E-value: 3.13e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  11 EDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMH-AGAYDFMEK 89
Cdd:cd17596    22 EDFDVLTAASAEEALAILEEEWVQVILCDQRMPGTTGVEFLKEVRERWPEVVRIIISGYTDSEDIIAGINeAGIYQYLTK 101

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1544283978  90 PFSPERLVEVARRALEQRGLAREVSALRRQL 120
Cdd:cd17596   102 PWHPDQLLLTVRNAARLFELQRENERLSLEL 132
REC_LytTR_AlgR-like cd17532
phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR; ...
 10-108 3.10e-12

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: 62.94  E-value: 3.10e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  10 LEDIPCIG-VGSAE---EALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDisMAVQAMHAGAYD 85
Cdd:cd17532    18 LEEHPDIEiVGEAEngeEALEAIEELKPDVVFLDIQMPGLDGLELAKKLSKLAKPPLIVFVTAYDE--YAVEAFELNAVD 95

                          90       100
                  ....*....|....*....|...
gi 1544283978  86 FMEKPFSPERLVEVARRALEQRG 108
Cdd:cd17532    96 YLLKPFSEERLAEALAKLRKRLS 118
REC_TrrA-like cd17554
phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator TrrA and ...
 9-92 1.33e-11

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: 61.08  E-value: 1.33e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   9 ELED--IPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDF 86
Cdd:cd17554    19 ELEDegYEVVTAGNGEEALEKLESEDPDLVILDIKMPGMDGLETLRKIREKKPDLPVIICTAYSEYKSDFSSWAADAYVV 98


                  ....*.
gi 1544283978  87 MEKPFS 92
Cdd:cd17554    99 KSSDLT 104
REC_OmpR cd17574
phosphoacceptor receiver (REC) domain of OmpR family response regulators; OmpR-like proteins ...
 5-90 1.38e-11

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: 60.50  E-value: 1.38e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAY 84
Cdd:cd17574    14 SDYLEKEGYEVDTAADGEEALELAREEQPDLIILDVMLPGMDGFEVCRRLREKGSDIPIIMLTAKDEEEDKVLGLELGAD 93


                  ....*.
gi 1544283978  85 DFMEKP 90
Cdd:cd17574    94 DYITKP 99
REC_RpfG-like cd17551
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator ...
 9-103 1.60e-11

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: 60.92  E-value: 1.60e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   9 ELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPS--LPVVLITGHGDISMAVQAMHAGAYDF 86
Cdd:cd17551    22 SAGYLEVVSFTDPREALAWCRENPPDLILLDYMMPGMDGLEFIRRLRALPGLedVPIVMITADTDREVRLRALEAGATDF 101

                          90
                  ....*....|....*..
gi 1544283978  87 MEKPFSPerlVEVARRA 103
Cdd:cd17551   102 LTKPFDP---VELLARV 115
REC_CheB-like cd17541
phosphoacceptor receiver (REC) domain of chemotaxis response regulator protein-glutamate ...
 10-93 1.62e-11

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: 61.25  E-value: 1.62e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  10 LEDIPCIGV-GSA---EEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPsLPVVLITGH--GDISMAVQAMHAGA 83
Cdd:cd17541    20 LESDPDIEVvGTArdgEEALEKIKELKPDVITLDIEMPVMDGLEALRRIMAERP-TPVVMVSSLteEGAEITLEALELGA 98

                          90
                  ....*....|
gi 1544283978  84 YDFMEKPFSP 93
Cdd:cd17541    99 VDFIAKPSGG 108
REC_hyHK_CKI1_RcsC-like cd17546
phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinases/response regulators ...
 18-99 1.79e-11

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


Pssm-ID: 381099 [Multi-domain]  Cd Length: 113  Bit Score: 60.56  E-value: 1.79e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  18 VGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLD---PSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPE 94
Cdd:cd17546    28 AENGQEALELLKEEPFDLVLMDLQMPVMDGLEATRRIRELEgggRRTPIIALTANALEEDREKCLEAGMDDYLSKPVKLD 107


                  ....*
gi 1544283978  95 RLVEV 99
Cdd:cd17546   108 QLKEV 112
REC_OmpR_PhoB cd17618
phosphoacceptor receiver (REC) domain of PhoB response regulator from the OmpR family; The ...
 7-97 1.90e-11

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: 60.73  E-value: 1.90e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   7 ALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSlDPSL---PVVLITGHGDISMAVQAMHAGA 83
Cdd:cd17618    19 NLERAGFDVVEAEDAESAVNLIVEPRPDLILLDWMLPGGSGIQFIRRLKR-DEMTrdiPIIMLTARGEEEDKVRGLEAGA 97

                          90
                  ....*....|....
gi 1544283978  84 YDFMEKPFSPERLV 97
Cdd:cd17618    98 DDYITKPFSPRELV 111
REC_OmpR_EcPhoP-like cd19934
phosphoacceptor receiver (REC) domain of EcPhoP-like OmpR family response regulators; ...
 21-108 2.44e-11

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: 60.37  E-value: 2.44e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  21 AEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLveVA 100
Cdd:cd19934    31 GEEALFQGEEEPYDLVVLDLGLPGMDGLSVLRRWRSEGRATPVLILTARDSWQDKVEGLDAGADDYLTKPFHIEEL--LA 108


                  ....*....
gi 1544283978 101 R-RALEQRG 108
Cdd:cd19934   109 RlRALIRRA 117
REC_CheY4-like cd17562
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY4 and similar CheY ...
 22-104 2.47e-11

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: 60.39  E-value: 2.47e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  22 EEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLdPS---LPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLVE 98
Cdd:cd17562    34 RDALSKAQSKKFDLIITDQNMPNMDGIELIKELRKL-PAykfTPILMLTTESSDEKKQEGKAAGATGWLVKPFDPEQLLE 112


                  ....*.
gi 1544283978  99 VARRAL 104
Cdd:cd17562   113 VVKKVL 118
REC_Spo0F-like cd17553
phosphoacceptor receiver (REC) domain of Spo0F and similar domains; Spo0F, a stand-alone ...
 23-91 2.71e-11

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: 60.26  E-value: 2.71e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1544283978  23 EALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPF 91
Cdd:cd17553    35 QALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPF 103
PRK10643 PRK10643
two-component system response regulator PmrA;
3-107 2.92e-11

two-component system response regulator PmrA;


Pssm-ID: 182612 [Multi-domain]  Cd Length: 222  Bit Score: 62.75  E-value: 2.92e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   3 GCQQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAG 82
Cdd:PRK10643   15 GLILALQTEGYACDCASTAREAEALLESGHYSLVVLDLGLPDEDGLHLLRRWRQKKYTLPVLILTARDTLEDRVAGLDVG 94

                          90       100
                  ....*....|....*....|....*.
gi 1544283978  83 AYDFMEKPFSPERLveVAR-RALEQR 107
Cdd:PRK10643   95 ADDYLVKPFALEEL--HARiRALIRR 118
REC_PA4781-like cd19920
phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase PA4781 and similar ...
 20-91 6.39e-11

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


Pssm-ID: 381147 [Multi-domain]  Cd Length: 103  Bit Score: 58.68  E-value: 6.39e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1544283978  20 SAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSlDPS---LPVVLITGHGDISMAVQAMHAGAYDFMEKPF 91
Cdd:cd19920    30 DGQQALQRAQAEPPDLILLDVMMPGMDGFEVCRRLKA-DPAtrhIPVIFLTALTDTEDKVKGFELGAVDYITKPF 103
REC_CheY_CheY3 cd19923
phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY ...
 2-98 1.30e-10

phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY family proteins; CheY family chemotaxis response regulators (RRs) comprise about 17% of bacterial RRs and almost half of all RRs in archaea. This subfamily contains Vibrio cholerae CheY3, Escherichia coli CheY, and similar CheY family RRs. CheY proteins control bacterial motility and participate in signaling phosphorelays and in protein-protein interactions. CheY RRs contain only the REC domain with no output/effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381150 [Multi-domain]  Cd Length: 119  Bit Score: 58.50  E-value: 1.30e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   2 LGCQQALELEDipciGVgsaeEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSlDPSL---PVVLITGHGDISMAVQA 78
Cdd:cd19923    23 LGFNNVEEAED----GV----DALEKLKAGGFDFVITDWNMPNMDGLELLKTIRA-DGALshlPVLMVTAEAKKENVIAA 93

                          90       100
                  ....*....|....*....|
gi 1544283978  79 MHAGAYDFMEKPFSPERLVE 98
Cdd:cd19923    94 AQAGVNNYIVKPFTAATLKE 113
REC_OmpR_BsPhoP-like cd19937
phosphoacceptor receiver (REC) domain of BsPhoP-like OmpR family response regulators; Bacillus ...
 20-101 2.04e-10

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: 57.67  E-value: 2.04e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  20 SAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDP--SLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLv 97
Cdd:cd19937    29 DGEEALKRAKDEKPDLIILDLMLPGIDGLEVCRILRSDPKtsSIPIIMLTAKGEEFDKVLGLELGADDYITKPFSPREL- 107


                  ....
gi 1544283978  98 eVAR 101
Cdd:cd19937   108 -LAR 110
REC_OmpR_DrrD-like cd17625
phosphoacceptor receiver (REC) domain of DrrD-like OmpR family response regulators; DrrD is a ...
 21-107 2.06e-10

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: 57.62  E-value: 2.06e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  21 AEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLveVA 100
Cdd:cd17625    30 GEEGLEYALSGIYDLIILDIMLPGMDGLEVLKSLREEGIETPVLLLTALDAVEDRVKGLDLGADDYLPKPFSLAEL--LA 107


                  ....*...
gi 1544283978 101 R-RALEQR 107
Cdd:cd17625   108 RiRALLRR 115
REC_OmpR_PrrA-like cd17627
phosphoacceptor receiver (REC) domain of PrrA-like OmpR family response regulators; The ...
 5-107 2.48e-10

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: 57.78  E-value: 2.48e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAY 84
Cdd:cd17627    15 RRSLRFEGYEVETAVDGAEALRVISGNRPDAVVLDVMMPRLDGLEVCRRLRAAGNDLPILVLTARDSVSDRVAGLDAGAD 94

                          90       100
                  ....*....|....*....|....
gi 1544283978  85 DFMEKPFSPERLveVAR-RALEQR 107
Cdd:cd17627    95 DYLVKPFALEEL--LARvRALLRR 116
PRK15479 PRK15479
transcriptional regulator TctD;
35-117 2.78e-10

transcriptional regulator TctD;


Pssm-ID: 185376 [Multi-domain]  Cd Length: 221  Bit Score: 60.12  E-value: 2.78e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  35 IVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLvEVARRALEQRGLAREVS 114
Cdd:PRK15479   47 LAVLDINMPGMDGLEVLQRLRKRGQTLPVLLLTARSAVADRVKGLNVGADDYLPKPFELEEL-DARLRALLRRSAGQVQE 125


                  ...
gi 1544283978 115 ALR 117
Cdd:PRK15479  126 VQQ 128
REC_D1_PleD-like cd17538
first (D1) phosphoacceptor receiver (REC) domain of response regulator PleD and similar ...
 8-91 2.94e-10

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


Pssm-ID: 381093 [Multi-domain]  Cd Length: 104  Bit Score: 57.12  E-value: 2.94e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   8 LELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSlDPS---LPVVLITGHGDISMAVQAMHAGAY 84
Cdd:cd17538    19 LSAEGYEVLTADSGQEALALAEEELPDLILLDVMMPGMDGFEVCRRLKE-DPEtrhIPVIMITALDDREDRIRGLEAGAD 97


                  ....*..
gi 1544283978  85 DFMEKPF 91
Cdd:cd17538    98 DFLSKPI 104
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 153-270 5.56e-10

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 57.38  E-value: 5.56e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  153 NVLILGETGTGKELVARCLHDYSRRHQHAFVALNCGGLPENLFDS---EIFGHEAHAFTGANKRRIG--KIEHANGGTLF 227
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQlllIIVGGKKASGSGELRLRLAlaLARKLKPDVLI 83

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 1544283978  228 LDEIESMPVNLQIKLLRVLQEhtlERLGSNQSIPVDCRVIAAT 270
Cdd:smart00382  84 LDEITSLLDAEQEALLLLLEE---LRLLLLLKSEKNLTVILTT 123
REC_PilR cd19926
phosphoacceptor receiver (REC) domain of type 4 fimbriae expression regulatory protein PilR ...
 23-90 5.84e-10

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


Pssm-ID: 381153 [Multi-domain]  Cd Length: 100  Bit Score: 56.01  E-value: 5.84e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1544283978  23 EALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKP 90
Cdd:cd19926    33 EARELLASEPYDLCLTDMRLPDGSGLELVQHIQQRLPQTPVAVITAYGSLDTAIEALKAGAFDFLTKP 100
REC_OmpR_PmrA-like cd17624
phosphoacceptor receiver (REC) domain of PmrA-like OmpR family response regulators; This ...
 3-104 6.93e-10

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: 56.34  E-value: 6.93e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   3 GCQQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAG 82
Cdd:cd17624    13 GLKTGLRKAGYAVDWVRTGAEAEAALASGPYDLVILDLGLPDGDGLDLLRRWRRQGQSLPVLILTARDGVDDRVAGLDAG 92

                          90       100
                  ....*....|....*....|...
gi 1544283978  83 AYDFMEKPFSPERLveVAR-RAL 104
Cdd:cd17624    93 ADDYLVKPFALEEL--LARlRAL 113
REC_2_DhkD-like cd17580
second phosphoacceptor receiver (REC) domain of Dictyostelium discoideum hybrid signal ...
 18-99 1.07e-09

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: 55.54  E-value: 1.07e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  18 VGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDP--SLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPER 95
Cdd:cd17580    28 AHSGEEALEAAQRFRPDVILSDIGMPGMDGYELARRLRELPWlaNTPAIALTGYGQPEDRERALEAGFDAHLVKPVDPDE 107


                  ....
gi 1544283978  96 LVEV 99
Cdd:cd17580   108 LIEL 111
REC_OmpR_CpxR cd17623
phosphoacceptor receiver (REC) domain of CpxR-like OmpR family response regulators; CpxR is ...
 5-107 1.36e-09

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: 55.39  E-value: 1.36e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSlDPSLPVVLITGHGDISMAVQAMHAGAY 84
Cdd:cd17623    15 TEYLEMEGFNVRAAHDGEQGLAALLEGSPDLVVLDVMLPKMNGLDVLKELRK-TSQVPVLMLTARGDDIDRILGLELGAD 93

                          90       100
                  ....*....|....*....|....
gi 1544283978  85 DFMEKPFSPERLveVAR-RALEQR 107
Cdd:cd17623    94 DYLPKPFNPREL--VARiRAILRR 115
REC_CpdR_CckA-like cd18160
phosphoacceptor receiver (REC) domain of Brucella abortus CpdR and CckA, and similar domains; ...
 2-91 1.46e-09

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: 55.20  E-value: 1.46e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   2 LGCQQALELEDIPCIGVGSAEEALQRVDRDFA-GIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMH 80
Cdd:cd18160    13 KFIVTTLKKAGYAVTEAESGAEALEKLQQGKDiDIVVTDIVMPEMDGIELAREARKIDPDVKILFISGGAAAAPELLSDA 92

                          90
                  ....*....|.
gi 1544283978  81 AGAYDFMEKPF 91
Cdd:cd18160    93 VGDNATLKKPF 103
orf27 CHL00148
Ycf27; Reviewed
 20-118 4.16e-09

Ycf27; Reviewed


Pssm-ID: 214376 [Multi-domain]  Cd Length: 240  Bit Score: 56.65  E-value: 4.16e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  20 SAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSlDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPerlvev 99
Cdd:CHL00148   38 DGEEALKLFRKEQPDLVILDVMMPKLDGYGVCQEIRK-ESDVPIIMLTALGDVSDRITGLELGADDYVVKPFSP------ 110

                          90
                  ....*....|....*....
gi 1544283978 100 arRALEqrglAREVSALRR 118
Cdd:CHL00148  111 --KELE----ARIRSVLRR 123
ompR PRK09468
osmolarity response regulator; Provisional
 18-119 5.88e-09

osmolarity response regulator; Provisional


Pssm-ID: 181883 [Multi-domain]  Cd Length: 239  Bit Score: 56.14  E-value: 5.88e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  18 VGSAE--EALQRV-DRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPE 94
Cdd:PRK09468   32 VRSAAnaEQMDRLlTRESFHLMVLDLMLPGEDGLSICRRLRSQNNPTPIIMLTAKGEEVDRIVGLEIGADDYLPKPFNPR 111

                          90       100
                  ....*....|....*....|....*
gi 1544283978  95 RLvevarraleqrgLAREVSALRRQ 119
Cdd:PRK09468  112 EL------------LARIRAVLRRQ 124
REC_DesR-like cd19930
phosphoacceptor receiver (REC) domain of DesR and similar proteins; This group is composed of ...
 6-105 1.32e-08

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: 52.66  E-value: 1.32e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   6 QALELE-DIPCIG-VGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGA 83
Cdd:cd19930    16 ALLELEdDLEVVAqASNGQEALRLVLKHSPDVAILDIEMPGRTGLEVAAELREELPDTKVLIVTTFGRPGYFRRALAAGV 95

                          90       100
                  ....*....|....*....|..
gi 1544283978  84 YDFMEKPFSPERLVEVARRALE 105
Cdd:cd19930    96 DGYVLKDRPIEELADAIRTVHA 117
REC_OmpR_ArcA_TorR-like cd17619
phosphoacceptor receiver (REC) domain of ArcA- and TorR-like OmpR family response regulators; ...
 19-101 2.17e-08

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: 52.00  E-value: 2.17e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  19 GSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSlDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLVE 98
Cdd:cd17619    31 GDGEEMRQILARQDIDLVLLDINLPGKDGLSLTRELRE-QSEVGIILVTGRDDEVDRIVGLEIGADDYVTKPFNPRELLV 109


                  ...
gi 1544283978  99 VAR 101
Cdd:cd17619   110 RAK 112
REC_Ycf29 cd19927
phosphoacceptor receiver (REC) domain of probable transcriptional regulator Ycf29; Ycf29 is a ...
 5-90 2.26e-08

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: 51.61  E-value: 2.26e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDP--SLPVVLITGHGDISMAVQAMHAG 82
Cdd:cd19927    15 KDYLEDQGFTVIAASNGLEALDLLNQYIPDLIISDIIMPGVDGYSLLGKLRKNADfdTIPVIFLTAKGMTSDRIKGYNAG 94


                  ....*...
gi 1544283978  83 AYDFMEKP 90
Cdd:cd19927    95 CDGYLSKP 102
REC_DivK-like cd17548
phosphoacceptor receiver (REC) domain of DivK and similar proteins; Caulobacter crescentus ...
 19-102 2.29e-08

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


Pssm-ID: 381100 [Multi-domain]  Cd Length: 115  Bit Score: 51.77  E-value: 2.29e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  19 GSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSlDPSL---PVVLITGH---GDismAVQAMHAGAYDFMEKPFS 92
Cdd:cd17548    30 ADGEEALEIARKEKPDLILMDIQLPGMDGLEATRLLKE-DPATrdiPVIALTAYamkGD---REKILEAGCDGYISKPID 105

                          90
                  ....*....|
gi 1544283978  93 PERLVEVARR 102
Cdd:cd17548   106 TREFLETVAK 115
REC_2_GGDEF cd17544
second phosphoacceptor receiver (REC) domain of uncharacterized GGDEF domain proteins; This ...
 18-96 2.30e-08

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: 52.14  E-value: 2.30e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  18 VGSAEEALQRVDRDFA-GIVVSDIRLPGIDGLTLLERLKSLDPS--LPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPE 94
Cdd:cd17544    30 AANGQEALEVLEQHPDiKLVITDYNMPEMDGFELVREIRKKYSRdqLAIIGISASGDNALSARFIKAGANDFLTKPFLPE 109


                  ..
gi 1544283978  95 RL 96
Cdd:cd17544   110 EF 111
REC_citrate_TCS cd19925
phosphoacceptor receiver (REC) domain of citrate family two-component system response ...
 10-106 2.46e-08

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: 51.86  E-value: 2.46e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  10 LEDIP---CIG-VGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYD 85
Cdd:cd19925    20 VEQVPgftVIGtAGTGEEALKLLKERQPDLILLDIYLPDGNGLDLLRELRAAGHDVDVIVVTAANDVETVREALRLGVVD 99

                          90       100
                  ....*....|....*....|.
gi 1544283978  86 FMEKPFSPERLvevaRRALEQ 106
Cdd:cd19925   100 YLIKPFTFERL----RQRLER 116
REC_OmpR_MtrA-like cd17626
phosphoacceptor receiver (REC) domain of MtrA-like OmpR family response regulators; MtrA is ...
 20-104 2.51e-08

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: 51.70  E-value: 2.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  20 SAEEALQRVDRDfagIVVSDIRLPGIDGLTLLERLKsLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLVEV 99
Cdd:cd17626    35 QALAAFREVRPD---LVLLDLMLPGIDGIEVCRQIR-AESGVPIVMLTAKSDTVDVVLGLESGADDYVAKPFKPKELVAR 110


                  ....*
gi 1544283978 100 ARRAL 104
Cdd:cd17626   111 IRARL 115
pleD PRK09581
response regulator PleD; Reviewed
 20-90 3.09e-08

response regulator PleD; Reviewed


Pssm-ID: 236577 [Multi-domain]  Cd Length: 457  Bit Score: 55.29  E-value: 3.09e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1544283978  20 SAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSlDPS---LPVVLITGHGDISMAVQAMHAGAYDFMEKP 90
Cdd:PRK09581   34 SGAEAIAICEREQPDIILLDVMMPGMDGFEVCRRLKS-DPAtthIPVVMVTALDDPEDRVRGLEAGADDFLTKP 106
REC_RcNtrC-like cd19928
phosphoacceptor receiver (REC) domain of Rhodobacter capsulatus nitrogen regulatory protein C ...
 6-90 3.28e-08

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: 50.97  E-value: 3.28e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   6 QALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYD 85
Cdd:cd19928    16 QALGRAGYEVRTTGNAATLWRWVEEGEGDLVITDVVMPDENGLDLIPRIKKARPDLPIIVMSAQNTLMTAVKAAERGAFE 95


                  ....*
gi 1544283978  86 FMEKP 90
Cdd:cd19928    96 YLPKP 100
PRK10360 PRK10360
transcriptional regulator UhpA;
3-125 5.27e-08

transcriptional regulator UhpA;


Pssm-ID: 182408 [Multi-domain]  Cd Length: 196  Bit Score: 52.67  E-value: 5.27e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   3 GCQQALELE-DIPCIG-VGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSldpSLPVVLITGHGDISMAVQAMH 80
Cdd:PRK10360   16 GFAQLLGLEpDLQVVAeFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPK---GMATIMLSVHDSPALVEQALN 92

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1544283978  81 AGAYDFMEKPFSPERLVeVARRALEQRGLAREVSALRRQLAGRQD 125
Cdd:PRK10360   93 AGARGFLSKRCSPDELI-AAVHTVATGGCYLTPDIAIKLASGRQD 136
REC_DC-like cd17534
phosphoacceptor receiver (REC) domain of modulated diguanylate cyclase and similar domains; ...
 5-100 9.81e-08

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: 50.10  E-value: 9.81e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIG-VGSAEEALQRVDRDFAGIVVSDIRLPG-IDGLTLLERLKSLDPsLPVVLITGHGDISMAVQAMHAG 82
Cdd:cd17534    17 KEILESLGYEVVGiADSGEEAIELAEENKPDLILMDINLKGdMDGIEAAREIREKFD-IPVIFLTAYSDEETLERAKETN 95

                          90       100
                  ....*....|....*....|.
gi 1544283978  83 AYDFMEKPFSPERL---VEVA 100
Cdd:cd17534    96 PYGYLVKPFNERELkaaIELA 116
REC_RR468-like cd17552
phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator RR468 and ...
 19-104 1.01e-07

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: 50.24  E-value: 1.01e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  19 GSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSlDP---SLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPER 95
Cdd:cd17552    33 SSGQEGLEKAATEQPDAILLDVMMPDMDGLATLKKLQA-NPetqSIPVILLTAKAQPSDRQRFASLGVAGVIAKPFDPLT 111


                  ....*....
gi 1544283978  96 LVEVARRAL 104
Cdd:cd17552   112 LAEQIAKLL 120
dpiA PRK10046
two-component response regulator DpiA; Provisional
 19-131 1.06e-07

two-component response regulator DpiA; Provisional


Pssm-ID: 182208 [Multi-domain]  Cd Length: 225  Bit Score: 52.33  E-value: 1.06e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  19 GSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLVE 98
Cdd:PRK10046   37 GNLAQARMMIERFKPGLILLDNYLPDGRGINLLHELVQAHYPGDVVFTTAASDMETVSEAVRCGVFDYLIKPIAYERLGQ 116

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1544283978  99 VARRaLEQRglarevsalRRQLAGRQDLAQRII 131
Cdd:PRK10046  117 TLTR-FRQR---------KHMLESIDSASQKQI 139
PRK11083 PRK11083
DNA-binding response regulator CreB; Provisional
 21-107 1.24e-07

DNA-binding response regulator CreB; Provisional


Pssm-ID: 236838 [Multi-domain]  Cd Length: 228  Bit Score: 52.27  E-value: 1.24e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  21 AEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLveVA 100
Cdd:PRK11083   36 GLPALDKLRQQPPDLVILDVGLPDISGFELCRQLLAFHPALPVIFLTARSDEVDRLVGLEIGADDYVAKPFSPREV--AA 113


                  ....*...
gi 1544283978 101 R-RALEQR 107
Cdd:PRK11083  114 RvRTILRR 121
PRK10161 PRK10161
phosphate response regulator transcription factor PhoB;
6-117 1.62e-07

phosphate response regulator transcription factor PhoB;


Pssm-ID: 182277 [Multi-domain]  Cd Length: 229  Bit Score: 52.03  E-value: 1.62e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   6 QALELEDIpcigvgsaEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLK--SLDPSLPVVLITGHGDISMAVQAMHAGA 83
Cdd:PRK10161   28 QPVEAEDY--------DSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKreSMTRDIPVVMLTARGEEEDRVRGLETGA 99

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1544283978  84 YDFMEKPFSPERLV----EVARR--------ALEQRGLAREVSALR 117
Cdd:PRK10161  100 DDYITKPFSPKELVarikAVMRRispmaveeVIEMQGLSLDPTSHR 145
REC_hyHK cd17598
phosphoacceptor receiver (REC) domain of uncharacterized hybrid sensor histidine kinase ...
 23-97 1.70e-07

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: 49.63  E-value: 1.70e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1544283978  23 EALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSlDPSL---PVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLV 97
Cdd:cd17598    33 EALAMLAEHRPTLVISDIVMPEMDGYELCRKIKS-DPDLkdiPVILLTTLSDPRDVIRGLECGADNFITKPYDEKYLL 109
REC_OmpR_CtrA cd17616
phosphoacceptor receiver (REC) domain of CtrA-like OmpR family response regulators; CtrA is ...
 8-97 2.23e-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: 2.23e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   8 LELEDIPCIGVGSAEEAL---QRVDRDfagIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAY 84
Cdd:cd17616    18 LKSEGFNVYTTDLGEEGLdlgKLYDYD---IILLDLNLPDMSGYEVLRTLRLAKVKTPILILSGLADIEDKVKGLGFGAD 94

                          90
                  ....*....|...
gi 1544283978  85 DFMEKPFSPERLV 97
Cdd:cd17616    95 DYMTKPFHKDELV 107
PRK10816 PRK10816
two-component system response regulator PhoP;
35-116 4.19e-07

two-component system response regulator PhoP;


Pssm-ID: 182755 [Multi-domain]  Cd Length: 223  Bit Score: 50.51  E-value: 4.19e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  35 IVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLveVAR-RALEQR--GLAR 111
Cdd:PRK10816   47 IAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEV--MARmQALMRRnsGLAS 124


                  ....*
gi 1544283978 112 EVSAL 116
Cdd:PRK10816  125 QVISL 129
PRK00742 PRK00742
chemotaxis-specific protein-glutamate methyltransferase CheB;
18-136 4.69e-07

chemotaxis-specific protein-glutamate methyltransferase CheB;


Pssm-ID: 234828 [Multi-domain]  Cd Length: 354  Bit Score: 51.30  E-value: 4.69e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  18 VGSA---EEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPsLPVVLI---TGHG-DISMavQAMHAGAYDFMEKP 90
Cdd:PRK00742   32 VGTApdgLEAREKIKKLNPDVITLDVEMPVMDGLDALEKIMRLRP-TPVVMVsslTERGaEITL--RALELGAVDFVTKP 108

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1544283978  91 FSPERL-VEVARRALEQ--RGLARevsALRRQLAGRQDLAQRIIGRSPA 136
Cdd:PRK00742  109 FLGISLgMDEYKEELAEkvRAAAR---ARVRALPPRAAAAARAAAAAPA 154
PRK10610 PRK10610
chemotaxis protein CheY;
23-109 4.85e-07

chemotaxis protein CheY;


Pssm-ID: 170568 [Multi-domain]  Cd Length: 129  Bit Score: 48.43  E-value: 4.85e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  23 EALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLD--PSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLVEVA 100
Cdd:PRK10610   41 DALNKLQAGGFGFVISDWNMPNMDGLELLKTIRADGamSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKL 120


                  ....*....
gi 1544283978 101 RRALEQRGL 109
Cdd:PRK10610  121 NKIFEKLGM 129
REC_Rcp-like cd17557
phosphoacceptor receiver (REC) domain of cyanobacterial phytochrome response regulator Rcp and ...
 5-102 6.34e-07

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: 48.18  E-value: 6.34e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPC--IGVGSAEEALQRVDR--DFAG-----IVVSDIRLPGIDGLTLLERLKSlDPSL---PVVLIT---GH 69
Cdd:cd17557    16 QEAFKEAGVPNelHVVRDGEEALDFLRGegEYADaprpdLILLDLNMPRMDGFEVLREIKA-DPDLrriPVVVLTtsdAE 94

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1544283978  70 GDIsmaVQAMHAGAYDFMEKPFSPERLVEVARR 102
Cdd:cd17557    95 EDI---ERAYELGANSYIVKPVDFEEFVEAIRS 124
REC_OmpR_CusR-like cd19935
phosphoacceptor receiver (REC) domain of CusR-like OmpR family response regulators; ...
 35-90 6.52e-07

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: 47.43  E-value: 6.52e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1544283978  35 IVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKP 90
Cdd:cd19935    45 LIILDVMLPGLDGLEVLRRLRAAGKQTPVLMLTARDSVEDRVKGLDLGADDYLVKP 100
PRK10336 PRK10336
two-component system response regulator QseB;
36-117 6.71e-07

two-component system response regulator QseB;


Pssm-ID: 182387 [Multi-domain]  Cd Length: 219  Bit Score: 49.89  E-value: 6.71e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  36 VVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSperLVEVARR--ALEQRGLAREV 113
Cdd:PRK10336   48 VILDLTLPGMDGRDILREWREKGQREPVLILTARDALAERVEGLRLGADDYLCKPFA---LIEVAARleALMRRTNGQAS 124


                  ....
gi 1544283978 114 SALR 117
Cdd:PRK10336  125 NELR 128
REC_Spo0A cd17561
phosphoacceptor receiver (REC) domain of Spo0A; Spo0A is a response regulator of the ...
 9-91 1.62e-06

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: 46.45  E-value: 1.62e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   9 ELEDIPCIGVGS-AEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKS--LDPSLPVVLITGHGDISMAVQAMHAGAYD 85
Cdd:cd17561    23 SQPDMEVVGVAHnGQEALELIEEKEPDVLLLDIIMPHLDGIGVLEKLRRmrLEKRPKIIMLTAFGQEDITQRAVELGASY 102


                  ....*.
gi 1544283978  86 FMEKPF 91
Cdd:cd17561   103 YILKPF 108
PRK09836 PRK09836
DNA-binding transcriptional activator CusR; Provisional
 35-108 3.07e-06

DNA-binding transcriptional activator CusR; Provisional


Pssm-ID: 182102 [Multi-domain]  Cd Length: 227  Bit Score: 48.00  E-value: 3.07e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1544283978  35 IVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLveVAR-RALEQRG 108
Cdd:PRK09836   47 LIILDIMLPDVNGWDIVRMLRSANKGMPILLLTALGTIEHRVKGLELGADDYLVKPFAFAEL--LARvRTLLRRG 119
REC_HP-RR-like cd17573
phosphoacceptor receiver (REC) domain of orphan response regulator HP-RR and similar proteins; ...
 35-97 3.74e-06

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


Pssm-ID: 381115 [Multi-domain]  Cd Length: 110  Bit Score: 45.50  E-value: 3.74e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1544283978  35 IVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLV 97
Cdd:cd17573    45 LVLVSDKLPDGNGLSIVSRIKEKHPSIVVIVLSDNPKTEQEIEAFKEGADDYIAKPFDFKVLV 107
PRK11517 PRK11517
DNA-binding response regulator HprR;
31-106 3.83e-06

DNA-binding response regulator HprR;


Pssm-ID: 183172 [Multi-domain]  Cd Length: 223  Bit Score: 47.59  E-value: 3.83e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1544283978  31 DFAGIVVsDIRLPGIDGLTLLERLKSLDPSlPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLVEVARRALEQ 106
Cdd:PRK11517   44 DYALIIL-DIMLPGMDGWQILQTLRTAKQT-PVICLTARDSVDDRVRGLDSGANDYLVKPFSFSELLARVRAQLRQ 117
REC_NarL cd19931
phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL); Nitrate ...
 3-104 4.37e-06

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: 45.42  E-value: 4.37e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   3 GCQQALELE-DIPCIG-VGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMH 80
Cdd:cd19931    13 GIKQLIELDpDFTVVGeASSGEEGIELAERLDPDLILLDLNMKGMSGLDTLKALREEGVSARIVILTVSDAEDDVVTALR 92

                          90       100
                  ....*....|....*....|....
gi 1544283978  81 AGAYDFMEKPFSPERLVEVARRAL 104
Cdd:cd19931    93 AGADGYLLKDMEPEDLLEALKQAA 116
REC_CheC-like cd17593
phosphoacceptor receiver (REC) domain of uncharacterized response regulators containing a CheC ...
 22-108 4.68e-06

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


Pssm-ID: 381124 [Multi-domain]  Cd Length: 117  Bit Score: 45.22  E-value: 4.68e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  22 EEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGhgDI-SMAVQ-AMHAGAYDFMEKPFSPERLvev 99
Cdd:cd17593    35 EEALEILREGRIDVLFLDLTMPVMDGYEVLEALPVEQLETKVIVVSG--DVqPEAKErVLELGALAFLKKPFDPEKL--- 109


                  ....*....
gi 1544283978 100 aRRALEQRG 108
Cdd:cd17593   110 -AQLLEELG 117
PRK09935 PRK09935
fimbriae biosynthesis transcriptional regulator FimZ;
35-89 5.01e-06

fimbriae biosynthesis transcriptional regulator FimZ;


Pssm-ID: 182154 [Multi-domain]  Cd Length: 210  Bit Score: 47.18  E-value: 5.01e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1544283978  35 IVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEK 89
Cdd:PRK09935   52 LIIMDIDLPGTDGFTFLKRIKQIQSTVKVLFLSSKSECFYAGRAIQAGANGFVSK 106
REC_OmpR_VirG cd17594
phosphoacceptor receiver (REC) domain of VirG-like OmpR family response regulators; VirG is ...
 19-101 5.12e-06

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: 45.13  E-value: 5.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  19 GSAEEALQRVDRdfAGIVVSDIRLPGIDGLTLLERLKSlDPSLPVVLITGHGDISMA-VQAMHAGAYDFMEKPFSPERLV 97
Cdd:cd17594    32 GAEEARLMLHRR--VDLVLLDLRLGQESGLDLLRTIRA-RSDVPIIIISGDRRDEIDrVVGLELGADDYLAKPFGLRELL 108


                  ....
gi 1544283978  98 EVAR 101
Cdd:cd17594   109 ARVR 112
REC_OmpR_kpRstA-like cd17622
phosphoacceptor receiver (REC) domain of kpRstA-like OmpR family response regulators; ...
 21-104 5.40e-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: 45.06  E-value: 5.40e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  21 AEEALQRVDRDfagIVVSDIRLPGIDGLTLLERLKSLdPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLveVA 100
Cdd:cd17622    36 ALEVIAREKPD---AVLLDIMLPGIDGLTLCRDLRPK-YQGPILLLTALDSDIDHILGLELGADDYVVKPVEPAVL--LA 109


                  ....*
gi 1544283978 101 R-RAL 104
Cdd:cd17622   110 RlRAL 114
REC_OmpR_KdpE-like cd17620
phosphoacceptor receiver (REC) domain of KdpE-like OmpR family response regulators; KdpE is a ...
 7-90 8.86e-06

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: 44.08  E-value: 8.86e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   7 ALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDpSLPVVLITGHGDISMAVQAMHAGAYDF 86
Cdd:cd17620    17 ALEAHGYRVFEAETGQEGLLEAATRKPDLIILDLGLPDMDGLEVIRRLREWS-AVPVIVLSARDEESDKIAALDAGADDY 95


                  ....
gi 1544283978  87 MEKP 90
Cdd:cd17620    96 LTKP 99
REC_OmpR_BaeR-like cd19938
phosphoacceptor receiver (REC) domain of BaeR-like OmpR family response regulators; BaeR is ...
 22-97 9.44e-06

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: 44.29  E-value: 9.44e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1544283978  22 EEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLdPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLV 97
Cdd:cd19938    33 DQVLPYVRHTPPDLILLDLMLPGTDGLTLCREIRRF-SDVPIIMVTARVEEIDRLLGLELGADDYICKPYSPREVV 107
HTH_8 pfam02954
Bacterial regulatory protein, Fis family;
382-421 1.33e-05

Bacterial regulatory protein, Fis family;


Pssm-ID: 427077 [Multi-domain]  Cd Length: 40  Bit Score: 42.00  E-value: 1.33e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1544283978 382 VEAFEKALLGDALARHHGNLTQASQDLGMAKTTLFDKVKK 421
Cdd:pfam02954   1 LEEVEKELIEAALERTGGNKSKAARLLGISRRTLYRKLKK 40
REC_OmpR_BfmR-like cd19939
phosphoacceptor receiver (REC) domain of BfmR-like OmpR family response regulators; ...
 18-118 1.43e-05

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


Pssm-ID: 381166 [Multi-domain]  Cd Length: 116  Bit Score: 43.90  E-value: 1.43e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  18 VGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSlDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLV 97
Cdd:cd19939    29 FTDGQRAVRRIIDEQPSLVVLDIMLPGMDGLTVCREVRE-HSHVPILMLTARTEEMDRVLGLEMGADDYLCKPFSPRELL 107

                          90       100
                  ....*....|....*....|.
gi 1544283978  98 evarraleqrglAREVSALRR 118
Cdd:cd19939   108 ------------ARVRALLRR 116
PRK11697 PRK11697
two-component system response regulator BtsR;
12-128 2.30e-05

two-component system response regulator BtsR;


Pssm-ID: 236956 [Multi-domain]  Cd Length: 238  Bit Score: 45.61  E-value: 2.30e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  12 DIPCIG-VGSAEEALQRVDRDFAGIVVSDIRLPGIDGLtllERLKSLDP-SLP-VVLITGHGDisMAVQAMHAGAYDFME 88
Cdd:PRK11697   26 DIEIVGeCSNAIEAIGAIHRLKPDVVFLDIQMPRISGL---ELVGMLDPeHMPyIVFVTAFDE--YAIKAFEEHAFDYLL 100

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1544283978  89 KPFSPERLvevarraleQRGLARevsaLRRQLAGrQDLAQ 128
Cdd:PRK11697  101 KPIDPARL---------AKTLAR----LRQERSP-QDVLL 126
PRK13558 PRK13558
bacterio-opsin activator; Provisional
 7-135 2.63e-05

bacterio-opsin activator; Provisional


Pssm-ID: 237426 [Multi-domain]  Cd Length: 665  Bit Score: 46.37  E-value: 2.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   7 ALELEDIPcigvgSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDF 86
Cdd:PRK13558   31 RLDVTQIR-----DFVAARDRVEAGEIDCVVADHEPDGFDGLALLEAVRQTTAVPPVVVVPTAGDEAVARRAVDADAAAY 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1544283978  87 MekPFSPERLVEVARRALEQRGLAREVSALRRQ------LAGRQDLAQRIIGRSP 135
Cdd:PRK13558  106 V--PAVSDDATAAIAERIESAVPEHSRDTEARMpisdltVESDRRLKERALDEAP 158
RecA-like_ClpB_Hsp104-like cd19499
Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and ...
 123-252 2.78e-05

Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and eukaryotic Heat shock protein 104 (Hsp104) are ATP-dependent molecular chaperones and essential proteins of the heat-shock response. ClpB/Hsp104 ATPases, in concert with the DnaK/Hsp70 chaperone system, disaggregate and reactivate aggregated proteins. This RecA-like_ClpB_Hsp104_like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410907 [Multi-domain]  Cd Length: 178  Bit Score: 44.48  E-value: 2.78e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 123 RQDLAQRIIGRSPAIQALRELI----ANVGDTS---ANVLILGETGTGKELVARCLHDYSRRHQHAFVALNCGGLPEnlf 195
Cdd:cd19499     6 EERLHERVVGQDEAVKAVSDAIrrarAGLSDPNrpiGSFLFLGPTGVGKTELAKALAELLFGDEDNLIRIDMSEYME--- 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1544283978 196 dseifGHEAHAFTGANKRRIGKIEhanGGTL------------FLDEIESMPVNLQIKLLRVLQEHTLE 252
Cdd:cd19499    83 -----KHSVSRLIGAPPGYVGYTE---GGQLteavrrkpysvvLLDEIEKAHPDVQNLLLQVLDDGRLT 143
PRK09483 PRK09483
response regulator; Provisional
 10-124 4.05e-05

response regulator; Provisional


Pssm-ID: 236538 [Multi-domain]  Cd Length: 217  Bit Score: 44.71  E-value: 4.05e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  10 LEDIPCIGV----GSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYD 85
Cdd:PRK09483   21 LEDIKGIKVvgeaCCGEDAVKWCRTNAVDVVLMDMNMPGIGGLEATRKILRYTPDVKIIMLTVHTENPLPAKVMQAGAAG 100

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1544283978  86 FMEKPFSPERLVEVARR-ALEQRGLAREVSalrRQLAGRQ 124
Cdd:PRK09483  101 YLSKGAAPQEVVSAIRSvHSGQRYIASDIA---QQMALSQ 137
PRK10693 PRK10693
two-component system response regulator RssB;
22-119 7.97e-05

two-component system response regulator RssB;


Pssm-ID: 182652 [Multi-domain]  Cd Length: 303  Bit Score: 44.21  E-value: 7.97e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  22 EEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSP-ERLVEVA 100
Cdd:PRK10693    7 VDALELLGGFTPDLIICDLAMPRMNGIEFVEHLRNRGDQTPVLVISATENMADIAKALRLGVQDVLLKPVKDlNRLREMV 86

                          90       100
                  ....*....|....*....|....*....
gi 1544283978 101 ----------RRALEQRGLAREVSALRRQ 119
Cdd:PRK10693   87 faclypsmfnSRVEEEERLFRDWDALVDN 115
REC_GlnL-like cd17565
phosphoacceptor receiver (REC) domain of transcriptional regulatory protein GlnL and similar ...
 21-90 9.76e-05

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: 41.10  E-value: 9.76e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  21 AEEALQRVDRDfagIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKP 90
Cdd:cd17565    36 AYDEILFLQPD---IVLIDLLMPGMDGIQLVRKLKDTGSNGKFIMISQVSDKEMIGKAYQAGIEFFINKP 102
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 3-54 9.79e-05

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: 41.80  E-value: 9.79e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1544283978   3 GCQQALELE-DIPCIG-VGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERL 54
Cdd:COG2197    16 GLRALLEAEpDIEVVGeAADGEEALELLEELRPDVVLLDIRMPGMDGLEALRRL 69
PRK10529 PRK10529
DNA-binding transcriptional activator KdpE; Provisional
 35-148 1.41e-04

DNA-binding transcriptional activator KdpE; Provisional


Pssm-ID: 182522 [Multi-domain]  Cd Length: 225  Bit Score: 42.87  E-value: 1.41e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  35 IVVSDIRLPGIDGLTLLERLKSLDpSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLVEVARRALEQRGLAREVS 114
Cdd:PRK10529   48 LIILDLGLPDGDGIEFIRDLRQWS-AIPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRHSATPAPD 126

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1544283978 115 ALRRQLAGRQDLAQRIIGRSPA--------IQALRELIANVG 148
Cdd:PRK10529  127 PLVKFSDVTVDLAARVIHRGEEevhltpieFRLLAVLLNNAG 168
PRK10430 PRK10430
two-component system response regulator DcuR;
15-143 1.49e-04

two-component system response regulator DcuR;


Pssm-ID: 182454 [Multi-domain]  Cd Length: 239  Bit Score: 43.17  E-value: 1.49e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  15 CIGVGS----AEEALQRVDRDFaGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKP 90
Cdd:PRK10430   29 CCGTAStleqAKEIIFNSDTPI-DLILLDIYMQQENGLDLLPVLHEAGCKSDVIVISSAADAATIKDSLHYGVVDYLIKP 107

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1544283978  91 FSPERLVEVARRALEQRGLARevsalRRQLAGRQDLAQRIIGRSPAIQALREL 143
Cdd:PRK10430  108 FQASRFEEALTGWRQKKMALE-----KHQYYDQAELDQLIHGSSSNEQDPRRL 155
PRK15369 PRK15369
two component system response regulator;
18-83 1.70e-04

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 42.76  E-value: 1.70e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1544283978  18 VGSAE------EALQRVDRDfagIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGA 83
Cdd:PRK15369   32 VGQVDnglevyNACRQLEPD---IVILDLGLPGMNGLDVIPQLHQRWPAMNILVLTARQEEHMASRTLAAGA 100
REC_OmpR_RegX3-like cd17621
phosphoacceptor receiver (REC) domain of RegX3-like OmpR family response regulators; RegX3 is ...
 23-90 2.35e-04

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: 40.26  E-value: 2.35e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1544283978  23 EALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSlDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKP 90
Cdd:cd17621    33 AALAEFDRAGADIVLLDLMLPGLSGTEVCRQLRA-RSNVPVIMVTAKDSEIDKVVGLELGADDYVTKP 99
REC_CheV-like cd19924
phosphoacceptor receiver (REC) domain of chemotaxis protein CheV and similar proteins; This ...
 35-90 2.35e-04

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: 40.44  E-value: 2.35e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1544283978  35 IVVSDIRLPGIDGLTLLERLKSlDP---SLPVVLITGHGDISMAVQAMHAGAYDFMEKP 90
Cdd:cd19924    54 LIITDIEMPKMDGYELTFELRD-DPrlaNIPVILNSSLSGEFSRARGKKVGADAYLAKF 111
REC_PdtaR-like cd19932
phosphoacceptor receiver (REC) domain of PdtaR and similar proteins; This subfamily includes ...
 18-101 2.39e-04

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: 40.47  E-value: 2.39e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  18 VGSA---EEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSlPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPE 94
Cdd:cd19932    28 VGEAsdgEEAVELAKKHKPDLVIMDVKMPRLDGIEAAKIITSENIA-PIVLLTAYSQQDLVERAKEAGAMAYLVKPFSES 106

                          90
                  ....*....|
gi 1544283978  95 RL---VEVAR 101
Cdd:cd19932   107 DLipaIEMAI 116
REC_TrxB cd17595
phosphoacceptor receiver (REC) domain a fused response regulator with a thioredoxin reductase ...
 19-99 2.59e-04

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: 40.78  E-value: 2.59e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  19 GSAEEALQ-----RVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDF-MEKPFS 92
Cdd:cd17595    34 DSGAEALDalkelKLRGEAVALFLVDQRMPEMDGVEFLEKAMELFPEAKRVLLTAYADTDAAIRAINDVQLDYyLLKPWD 113


                  ....*....
gi 1544283978  93 P--ERLVEV 99
Cdd:cd17595   114 PpeEKLYPV 122
PRK09959 PRK09959
acid-sensing system histidine kinase EvgS;
23-265 2.93e-04

acid-sensing system histidine kinase EvgS;


Pssm-ID: 182169 [Multi-domain]  Cd Length: 1197  Bit Score: 43.18  E-value: 2.93e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   23 EALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSperlVEVARR 102
Cdd:PRK09959   993 QALHKVSMQHYDLLITDVNMPNMDGFELTRKLREQNSSLPIWGLTANAQANEREKGLSCGMNLCLFKPLT----LDVLKT 1068

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  103 ALEQRGLAREVSALRRQLagrqdlaqriigrspAIQALRELIANVGDTSANVLILGETGTGKELVArclhdysrrhqhAF 182
Cdd:PRK09959  1069 HLSQLHQVAHIAPQYRHL---------------DIEALKNNTANDLQLMQEILMTFQHETHKDLPA------------AF 1121

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  183 VALNCGglpenlfDSEIFGHEAHAFTGA----NKRRIGKIEHANGGTLFLDeiESMPVNLQikLLRVLQEHTLERlgsNQ 258
Cdd:PRK09959  1122 HALEAG-------DNRTFHQCIHRIHGAanilNLQKLINISHQLEITPVSD--DSKPEILQ--LLNSVKEHIAEL---DQ 1187


                   ....*..
gi 1544283978  259 SIPVDCR 265
Cdd:PRK09959  1188 EIAVFCQ 1194
psREC-like_D2_PleD cd17539
REC-like adaptor domain (D2) of response regulator PleD; PleD contains a REC domain (D1) with ...
 1-119 3.31e-04

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


Pssm-ID: 381094 [Multi-domain]  Cd Length: 124  Bit Score: 40.37  E-value: 3.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   1 MLGCQQALELEDIPcigvgsaEEALQR-VDRDFAGIVVSdIRLPGIDGLTLLERLKSLDPS--LPVVLITGHGDISMAVQ 77
Cdd:cd17539    17 MLSSEHEVVVEADP-------DEALFRaAEGPFDLVIVS-LALEDFDGLRLCSQLRSLERTrqLPILAVADPGDRGRLIR 88

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1544283978  78 AMHAGAYDFMEKPFSPERLvevarraleqrgLAREVSALRRQ 119
Cdd:cd17539    89 ALEIGVNDYLVRPIDPNEL------------LARVRTQIRRK 118
REC_OmpR_ChvI-like cd19936
phosphoacceptor receiver (REC) domain of ChvI-like OmpR family response regulators; ...
 7-90 4.12e-04

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: 39.35  E-value: 4.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   7 ALELEDIPCIGVGSAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDpSLPVVLITGHGDISMAVQAMHAGAYDF 86
Cdd:cd19936    17 ALEAEGFSVETYTDGASALDGLNARPPDLAILDIKMPRMDGMELLQRLRQKS-TLPVIFLTSKDDEIDEVFGLRMGADDY 95


                  ....
gi 1544283978  87 MEKP 90
Cdd:cd19936    96 ITKP 99
PRK10710 PRK10710
DNA-binding transcriptional regulator BaeR; Provisional
 22-137 4.38e-04

DNA-binding transcriptional regulator BaeR; Provisional


Pssm-ID: 182665 [Multi-domain]  Cd Length: 240  Bit Score: 41.59  E-value: 4.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  22 EEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDpSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLVevar 101
Cdd:PRK10710   44 DEVLPYVRQTPPDLILLDLMLPGTDGLTLCREIRRFS-DIPIVMVTAKIEEIDRLLGLEIGADDYICKPYSPREVV---- 118

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1544283978 102 raleqrglAREVSALRRqlAGRQDLAQRIIGRSPAI 137
Cdd:PRK10710  119 --------ARVKTILRR--CKPQRELQQQDAESPLI 144
Fis COG2901
DNA-binding protein Fis (factor for inversion stimulation) [Transcription];
382-424 5.73e-04

DNA-binding protein Fis (factor for inversion stimulation) [Transcription];


Pssm-ID: 442146 [Multi-domain]  Cd Length: 83  Bit Score: 38.64  E-value: 5.73e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1544283978 382 VEAFEKALLGDALARHHGNLTQASQDLGMAKTTLFDKVKKYGL 424
Cdd:COG2901    40 LAEVEKPLLETVLEHTRGNQSRAAEMLGINRNTLRKKLKQYGL 82
PRK10955 PRK10955
envelope stress response regulator transcription factor CpxR;
5-107 6.63e-04

envelope stress response regulator transcription factor CpxR;


Pssm-ID: 182864 [Multi-domain]  Cd Length: 232  Bit Score: 40.94  E-value: 6.63e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELEDIPCIGVGSAEEALQRVDrDFAGIVVSDIRLPGIDGLTLLERLKSlDPSLPVVLITGHGDISMAVQAMHAGAY 84
Cdd:PRK10955   18 KELLEMEGFNVIVAHDGEQALDLLD-DSIDLLLLDVMMPKKNGIDTLKELRQ-THQTPVIMLTARGSELDRVLGLELGAD 95

                          90       100
                  ....*....|....*....|....
gi 1544283978  85 DFMEKPFSPERLveVAR-RALEQR 107
Cdd:PRK10955   96 DYLPKPFNDREL--VARiRAILRR 117
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 153-304 6.90e-04

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: 39.58  E-value: 6.90e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 153 NVLILGETGTGK-ELVARCLHDYSRRHQHAfVALNCGGLPENLFDSEIFGHEAHAFTGANKRRIGKiehaNGGTLFLDEI 231
Cdd:pfam07728   1 GVLLVGPPGTGKtELAERLAAALSNRPVFY-VQLTRDTTEEDLFGRRNIDPGGASWVDGPLVRAAR----EGEIAVLDEI 75

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1544283978 232 ESMPVNLQIKLLRVLQE---HTLERLGSNQSIPVDCRVIAATkadlaamgksgqfrSDLYYRLNVVSlelPALRDR 304
Cdd:pfam07728  76 NRANPDVLNSLLSLLDErrlLLPDGGELVKAAPDGFRLIATM--------------NPLDRGLNELS---PALRSR 134
REC_TPR cd17589
phosphoacceptor receiver (REC) domain of uncharacterized tetratricopeptide repeat (TPR) ...
 20-98 6.93e-04

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


Pssm-ID: 381123 [Multi-domain]  Cd Length: 115  Bit Score: 39.17  E-value: 6.93e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  20 SAEEALQRVDRDFAGIVVSDIRL-PGIDGLTLLERLKS---LDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPER 95
Cdd:cd17589    31 SGEEALRMCENKTYDIVLCDYNLgKGKNGQQLLEELRHkklISPSTVFIMVTGESSRAMVLSALELEPDDYLLKPFTVSE 110


                  ...
gi 1544283978  96 LVE 98
Cdd:cd17589   111 LRE 113
HTH_50 pfam18024
Helix-turn-helix domain; The TyrR protein of Haemophilus influenzae is a 36-kD transcription ...
 380-425 7.54e-04

Helix-turn-helix domain; The TyrR protein of Haemophilus influenzae is a 36-kD transcription factor whose major function is to control the expression of genes important in the biosynthesis and transport of aromatic amino acids. This entry represents the C-terminal helix-turn-helix DNA-binding domain of TyrR and related proteins.


Pssm-ID: 407862 [Multi-domain]  Cd Length: 50  Bit Score: 37.39  E-value: 7.54e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1544283978 380 EAVEAFEKALLGDALaRHHGNLTQASQDLGMAKTTLFDKVKKYGLQ 425
Cdd:pfam18024   6 EYVSYIERELIGAAY-ENYKSARKVAKALGLSHTTIANKMKRYGIS 50
PRK12555 PRK12555
chemotaxis-specific protein-glutamate methyltransferase CheB;
5-143 8.65e-04

chemotaxis-specific protein-glutamate methyltransferase CheB;


Pssm-ID: 237135 [Multi-domain]  Cd Length: 337  Bit Score: 41.02  E-value: 8.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   5 QQALELE-DIPCIGVGS-AEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPsLPVVLITGhgDISMAV----QA 78
Cdd:PRK12555   17 RRALARDpDHEVVWVATdGAQAVERCAAQPPDVILMDLEMPRMDGVEATRRIMAERP-CPILIVTS--LTERNAsrvfEA 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  79 MHAGAYDFMEKPF---------SPERL---VEVARRALEQRGLARevSALRRQLAGRQDLAQRI--IGRS---PAiqALR 141
Cdd:PRK12555   94 MGAGALDAVDTPTlgigagleeYAAELlakIDQIGRLLGRRLAPA--AAPAAASAAPFRTTPRLvaIGASaggPA--ALA 169


                  ..
gi 1544283978 142 EL 143
Cdd:PRK12555  170 VL 171
REC_hyHK_blue-like cd18161
phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinase/response regulators ...
 15-91 1.07e-03

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: 38.48  E-value: 1.07e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1544283978  15 CIGVGSAEEALQRVDRDFA-GIVVSDIRLPG-IDGLTLLERLKSLDPSLPVVLITGHGDISmAVQAMHAGAYDFMEKPF 91
Cdd:cd18161    25 VLEAASGDEALDLLESGPDiDLLVTDVIMPGgMNGSQLAEEARRRRPDLKVLLTSGYAENA-IEGGDLAPGVDVLSKPF 102
PRK11173 PRK11173
two-component response regulator; Provisional
 35-119 1.27e-03

two-component response regulator; Provisional


Pssm-ID: 183013 [Multi-domain]  Cd Length: 237  Bit Score: 40.00  E-value: 1.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  35 IVVSDIRLPGIDGLTLLERLKSlDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLVEVARRALEQRGLAREVS 114
Cdd:PRK11173   50 LVIMDINLPGKNGLLLARELRE-QANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSRTMNLGTVS 128


                  ....*
gi 1544283978 115 ALRRQ 119
Cdd:PRK11173  129 EERRS 133
CDC6 COG1474
Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];
129-187 1.39e-03

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


Pssm-ID: 441083 [Multi-domain]  Cd Length: 389  Bit Score: 40.60  E-value: 1.39e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1544283978 129 RIIGRSPAIQALRELIANV--GDTSANVLILGETGTGKELVARC----LHDYSRRHQH--AFVALNC 187
Cdd:COG1474    27 RLPHREEEIEELASALRPAlrGERPSNVLIYGPTGTGKTAVAKYvleeLEEEAEERGVdvRVVYVNC 93
REC_OmpR_NsrR-like cd18159
phosphoacceptor receiver (REC) domain of Streptococcus agalactiae NsrR-like OmpR family ...
 35-104 1.71e-03

phosphoacceptor receiver (REC) domain of Streptococcus agalactiae NsrR-like OmpR family response regulators; Streptococcus agalactiae NsrR is a lantibiotic resistance-associated response regulator and is part of the nisin resistance operon. It is a member of the NsrRK two-component system (TCS) that is involved in the regulation of lantibiotic resistance genes such as a membrane-associated lipoprotein of LanI, and the nsr gene cluster which encodes for the resistance protein NSR and the ABC transporter NsrFP, both conferring resistance against nisin. This subfamily also includes Staphylococcus epidermidis GraR, part of the GraR/GraS TCS involved in resistance against cationic antimicrobial peptides, and Bacillus subtilis BceR, part of the BceS/BceR TCS involved in the regulation of bacitracin resistance. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.


Pssm-ID: 381143 [Multi-domain]  Cd Length: 113  Bit Score: 38.03  E-value: 1.71e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  35 IVVSDIRLPGIDGLTLLERLKSLDPsLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLVEVARRAL 104
Cdd:cd18159    45 LVLLDINLPYFDGFYWCREIRQISN-VPIIFISSRDDNMDQVMAINMGGDDYITKPFDLDVLLAKIKAIL 113
AAA_16 pfam13191
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 129-187 2.03e-03

AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.


Pssm-ID: 433025 [Multi-domain]  Cd Length: 167  Bit Score: 38.64  E-value: 2.03e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978 129 RIIGRSPAIQALRELIANVGDTSA-NVLILGETGTGKELVARCLHDYSRRHQHAFVALNC 187
Cdd:pfam13191   1 RLVGREEELEQLLDALDRVRSGRPpSVLLTGEAGTGKTTLLRELLRALERDGGYFLRGKC 60
PRK09958 PRK09958
acid-sensing system DNA-binding response regulator EvgA;
24-89 2.75e-03

acid-sensing system DNA-binding response regulator EvgA;


Pssm-ID: 182168 [Multi-domain]  Cd Length: 204  Bit Score: 38.72  E-value: 2.75e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1544283978  24 ALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDPSLPVVLITGHGDISMAVQAMHAGAYDFMEK 89
Cdd:PRK09958   37 AVQRVETLKPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSAKNDHFYGKHCADAGANGFVSK 102
psREC_PRR cd17582
pseudo receiver domain of pseudo-response regulators; In Arabidopsis, five pseudo-response ...
 35-90 3.30e-03

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


Pssm-ID: 381120 [Multi-domain]  Cd Length: 104  Bit Score: 36.99  E-value: 3.30e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1544283978  35 IVVSDIRLPGIDGLTLLERLKSLD--PSLPVVLITGHGDISMAVQAMHAGAYDFMEKP 90
Cdd:cd17582    47 LILTEVDLPVSSGFKLLSYIMRHKicKNIPVIMMSSQDSVGVVFKCLSKGAADYLVKP 104
PRK10766 PRK10766
two-component system response regulator TorR;
20-99 4.28e-03

two-component system response regulator TorR;


Pssm-ID: 182711 [Multi-domain]  Cd Length: 221  Bit Score: 38.48  E-value: 4.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  20 SAEEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSlDPSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSP-ERLVE 98
Cdd:PRK10766   34 SGAGMREIMQNQHVDLILLDINLPGEDGLMLTRELRS-RSTVGIILVTGRTDSIDRIVGLEMGADDYVTKPLELrELLVR 112


                  .
gi 1544283978  99 V 99
Cdd:PRK10766  113 V 113
REC_OmpR_YycF-like cd17614
phosphoacceptor receiver (REC) domain of YrcF-like OmpR family response regulators; YycF ...
 22-118 4.76e-03

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: 36.63  E-value: 4.76e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978  22 EEALQRVDRDFAGIVVSDIRLPGIDGLTLLERLKSLDpSLPVVLITGHGDISMAVQAMHAGAYDFMEKPFSPERLvevar 101
Cdd:cd17614    32 REALEKVEEEQPDLILLDLMLPEKDGLEVCREVRKTS-NVPIIMLTAKDSEVDKVLGLELGADDYVTKPFSNREL----- 105

                          90
                  ....*....|....*..
gi 1544283978 102 raleqrgLAREVSALRR 118
Cdd:cd17614   106 -------LARVKANLRR 115
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 3-103 7.34e-03

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 37.70  E-value: 7.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544283978   3 GCQQALELEDIPCIgVGSA---EEALQRVDRDFAGIVVSDIRLPGIDGLTLLERL--KSLDPSLPVVLITGHGDisMAVQ 77
Cdd:PRK10651   21 GVKQLISMAPDITV-VGEAsngEQGIELAESLDPDLILLDLNMPGMNGLETLDKLreKSLSGRIVVFSVSNHEE--DVVT 97

                          90       100
                  ....*....|....*....|....*.
gi 1544283978  78 AMHAGAYDFMEKPFSPERLVEVARRA 103
Cdd:PRK10651   98 ALKRGADGYLLKDMEPEDLLKALQQA 123
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH