NCBI Conserved Domain Search

Conserved domains on [gi|490419162|ref|WP_004291471|]

View

MULTISPECIES: sigma-54 dependent transcriptional regulator [FCB group]

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, ...

2-432

5.86e-160

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: 457.89 E-value: 5.86e-160

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   2 NKTKIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQAtDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFII 81
Cdd:COG2204    1 SMARILVVDDDPDIRRLLKELLERAGYEVETAASGEEALALLREE-PPDLVLLDLRMPGMDGLELLRELRALDPDLPVIL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  82 MTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQAGQRRMPIFAREGS--AFQKIMHRIRLVAATDMSVMI 159
Cdd:COG2204   80 LTGYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERALERRRLRRENAEDSGLIGRspAMQEVRRLIEKVAPSDATVLI 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 160 FGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVKGAFTGADNAKKGYFHEAEGGTLFLDEVGNLAL 239
Cdd:COG2204  160 TGESGTGKELVARAIHRLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTGAVARRIGKFELADGGTLFLDEIGEMPL 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 240 ETQQMLLRAIQERRYRPVGDKADRNFNVRIIAATNEDLEVSVNEKRFRQDLLYRLHDFGITVPPLRDCQEDIMPLAEFFR 319
Cdd:COG2204  240 ALQAKLLRVLQEREFERVGGNKPIPVDVRVIAATNRDLEELVEEGRFREDLYYRLNVFPIELPPLRERREDIPLLARHFL 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 320 DMANRELECSVSgFSSEARKALLTHAWPGNVRELRQKVMGAVLQAQEGVVMKEHLELAvtkptstvsfalRNDAEdKERI 399
Cdd:COG2204  320 ARFAAELGKPVK-LSPEALEALLAYDWPGNVRELENVIERAVILADGEVITAEDLPEA------------LEEVE-RELI 385

                        410       420       430
                 ....*....|....*....|....*....|...
gi 490419162 400 LRALKQANGNRSVAAELLGIGRTTLYSKLEEYG 432
Cdd:COG2204  386 ERALEETGGNVSRAAELLGISRRTLYRKLKKYG 418

Name

Accession

Description

Interval

E-value

AtoC

COG2204

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

2-432

5.86e-160

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: 457.89 E-value: 5.86e-160

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   2 NKTKIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQAtDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFII 81
Cdd:COG2204    1 SMARILVVDDDPDIRRLLKELLERAGYEVETAASGEEALALLREE-PPDLVLLDLRMPGMDGLELLRELRALDPDLPVIL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  82 MTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQAGQRRMPIFAREGS--AFQKIMHRIRLVAATDMSVMI 159
Cdd:COG2204   80 LTGYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERALERRRLRRENAEDSGLIGRspAMQEVRRLIEKVAPSDATVLI 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 160 FGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVKGAFTGADNAKKGYFHEAEGGTLFLDEVGNLAL 239
Cdd:COG2204  160 TGESGTGKELVARAIHRLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTGAVARRIGKFELADGGTLFLDEIGEMPL 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 240 ETQQMLLRAIQERRYRPVGDKADRNFNVRIIAATNEDLEVSVNEKRFRQDLLYRLHDFGITVPPLRDCQEDIMPLAEFFR 319
Cdd:COG2204  240 ALQAKLLRVLQEREFERVGGNKPIPVDVRVIAATNRDLEELVEEGRFREDLYYRLNVFPIELPPLRERREDIPLLARHFL 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 320 DMANRELECSVSgFSSEARKALLTHAWPGNVRELRQKVMGAVLQAQEGVVMKEHLELAvtkptstvsfalRNDAEdKERI 399
Cdd:COG2204  320 ARFAAELGKPVK-LSPEALEALLAYDWPGNVRELENVIERAVILADGEVITAEDLPEA------------LEEVE-RELI 385

                        410       420       430
                 ....*....|....*....|....*....|...
gi 490419162 400 LRALKQANGNRSVAAELLGIGRTTLYSKLEEYG 432
Cdd:COG2204  386 ERALEETGGNVSRAAELLGISRRTLYRKLKKYG 418

PRK10365

sigma-54-dependent response regulator transcription factor ZraR;

2-428

4.25e-99

sigma-54-dependent response regulator transcription factor ZraR;

Pssm-ID: 182412 [Multi-domain] Cd Length: 441 Bit Score: 303.49 E-value: 4.25e-99

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   2 NKTKIIVVEDNIVYCEYVCNMLSREGYRNMKAYhlsTAKKHLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMQPF 79
Cdd:PRK10365   4 DNIDILVVDDDISHCTILQALLRGWGYNVALAN---SGRQALEQVREQvfDLVLCDVRMAEMDGIATLKEIKALNPAIPV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  80 IIMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQAGQRRMPIFAR-------EGSAFQKIMHRIRLVAA 152
Cdd:PRK10365  81 LIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAHTHSIDAETPAVTAsqfgmvgKSPAMQHLLSEIALVAP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 153 TDMSVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVKGAFTGADNAKKGYFHEAEGGTLFLD 232
Cdd:PRK10365 161 SEATVLIHGDSGTGKELVARAIHASSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLD 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 233 EVGNLALETQQMLLRAIQERRYRPVGDKADRNFNVRIIAATNEDLEVSVNEKRFRQDLLYRLHDFGITVPPLRDCQEDIM 312
Cdd:PRK10365 241 EIGDISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNVVAIEVPSLRQRREDIP 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 313 PLAE-FFRDMANRELEcSVSGFSSEARKALLTHAWPGNVRELRQKVMGAVLQAQEGVVMKEHLELAV--TKPTSTVSFAL 389
Cdd:PRK10365 321 LLAGhFLQRFAERNRK-AVKGFTPQAMDLLIHYDWPGNIRELENAVERAVVLLTGEYISERELPLAIasTPIPLGQSQDI 399

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|
gi 490419162 390 RNDAE-DKERILRALKQANGNRSVAAELLGIGRTTLYSKL 428
Cdd:PRK10365 400 QPLVEvEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439

ntrC

TIGR01818

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

23-430

1.50e-95

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: 295.11 E-value: 1.50e-95

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   23 LSREGYRNMKAYHLSTAKKHLQQATDnDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDYAEVNTAVESMKLGSIDY 102
Cdd:TIGR01818  18 LSRAGYEVRTFGNAASVLRALARGQP-DLLITDVRMPGEDGLDLLPQIKKRHPQLPVIVMTAHSDLDTAVAAYQRGAFEY 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  103 IPKQLVEDKLVPLIRSIL---KERQAGQRRMPIFAR------EGSAFQKIMHRIRLVAATDMSVMIFGENGTGKEHIAHL 173
Cdd:TIGR01818  97 LPKPFDLDEAVTLVERALahaQEQVALPADAGEAEDsaeligEAPAMQEVFRAIGRLSRSDITVLINGESGTGKELVARA 176

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  174 LHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVKGAFTGADNAKKGYFHEAEGGTLFLDEVGNLALETQQMLLRAIQERR 253
Cdd:TIGR01818 177 LHRHSPRANGPFIALNMAAIPKDLIESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDEIGDMPLDAQTRLLRVLADGE 256

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  254 YRPVGDKADRNFNVRIIAATNEDLEVSVNEKRFRQDLLYRLHDFGITVPPLRDCQEDIMPLAEFFRDMANRELECSVSGF 333
Cdd:TIGR01818 257 FYRVGGRTPIKVDVRIVAATHQNLEALVRQGKFREDLFHRLNVIRIHLPPLRERREDIPRLARHFLALAARELDVEPKLL 336

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  334 SSEARKALLTHAWPGNVRELRQKVMG-AVLQAQEGVVMKE-HLELAvtkPTSTVSFALRNDAEDK--------------- 396
Cdd:TIGR01818 337 DPEALERLKQLRWPGNVRQLENLCRWlTVMASGDEVLVSDlPAELA---LTGRPASAPDSDGQDSwdealeawakqalsr 413

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*....
gi 490419162  397 -------------ERIL--RALKQANGNRSVAAELLGIGRTTLYSKLEE 430
Cdd:TIGR01818 414 geqglldralpefERPLleAALQHTRGHKQEAAALLGWGRNTLTRKLKE 462

Sigma54_activat

pfam00158

Sigma-54 interaction domain;

139-300

1.57e-87

Sigma-54 interaction domain;

Pssm-ID: 425491 [Multi-domain] Cd Length: 168 Bit Score: 263.88 E-value: 1.57e-87

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  139 AFQKIMHRIRLVAATDMSVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVKGAFTGADNAKK 218
Cdd:pfam00158   7 AMQEVLEQAKRVAPTDAPVLITGESGTGKELFARAIHQLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTGADSDRK 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  219 GYFHEAEGGTLFLDEVGNLALETQQMLLRAIQERRYRPVGDKADRNFNVRIIAATNEDLEVSVNEKRFRQDLLYRLHDFG 298
Cdd:pfam00158  87 GLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTKPIKVDVRIIAATNRDLEEAVAEGRFREDLYYRLNVIP 166


                  ..
gi 490419162  299 IT 300
Cdd:pfam00158 167 IE 168

REC

cd00156

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

8-105

2.22e-21

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: 88.44 E-value: 2.22e-21

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   8 VVEDNIVYCEYVCNMLSREGYRnmkAYHLSTAKKHLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDY 85
Cdd:cd00156    2 IVDDDPAIRELLKSLLEREGYE---VDTAADGEEALELLREErpDLVLLDLMMPGMDGLELLRKLRELPPDIPVIVLTAK 78

                         90       100
                 ....*....|....*....|
gi 490419162  86 AEVNTAVESMKLGSIDYIPK 105
Cdd:cd00156   79 ADEEDAVRALELGADDYLVK 98

AAA

smart00382

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

156-276

1.61e-11

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: 62.01 E-value: 1.61e-11

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   156 SVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSL---SKELAPSAFFGHVKGAFTGADNAKKGyFHEAEG---GTL 229
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDIleeVLDQLLLIIVGGKKASGSGELRLRLA-LALARKlkpDVL 82

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 490419162   230 FLDEVGNLALETQQMLLRAIQERRyrpVGDKADRNFNVRIIAATNED 276
Cdd:smart00382  83 ILDEITSLLDAEQEALLLLLEELR---LLLLLKSEKNLTVILTTNDE 126

Name

Accession

Description

Interval

E-value

AtoC

COG2204

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

2-432

5.86e-160

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: 457.89 E-value: 5.86e-160

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   2 NKTKIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQAtDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFII 81
Cdd:COG2204    1 SMARILVVDDDPDIRRLLKELLERAGYEVETAASGEEALALLREE-PPDLVLLDLRMPGMDGLELLRELRALDPDLPVIL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  82 MTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQAGQRRMPIFAREGS--AFQKIMHRIRLVAATDMSVMI 159
Cdd:COG2204   80 LTGYGDVETAVEAIKAGAFDYLTKPFDLEELLAAVERALERRRLRRENAEDSGLIGRspAMQEVRRLIEKVAPSDATVLI 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 160 FGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVKGAFTGADNAKKGYFHEAEGGTLFLDEVGNLAL 239
Cdd:COG2204  160 TGESGTGKELVARAIHRLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTGAVARRIGKFELADGGTLFLDEIGEMPL 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 240 ETQQMLLRAIQERRYRPVGDKADRNFNVRIIAATNEDLEVSVNEKRFRQDLLYRLHDFGITVPPLRDCQEDIMPLAEFFR 319
Cdd:COG2204  240 ALQAKLLRVLQEREFERVGGNKPIPVDVRVIAATNRDLEELVEEGRFREDLYYRLNVFPIELPPLRERREDIPLLARHFL 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 320 DMANRELECSVSgFSSEARKALLTHAWPGNVRELRQKVMGAVLQAQEGVVMKEHLELAvtkptstvsfalRNDAEdKERI 399
Cdd:COG2204  320 ARFAAELGKPVK-LSPEALEALLAYDWPGNVRELENVIERAVILADGEVITAEDLPEA------------LEEVE-RELI 385

                        410       420       430
                 ....*....|....*....|....*....|...
gi 490419162 400 LRALKQANGNRSVAAELLGIGRTTLYSKLEEYG 432
Cdd:COG2204  386 ERALEETGGNVSRAAELLGISRRTLYRKLKKYG 418

RocR

COG3829

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

136-434

2.45e-126

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: 373.34 E-value: 2.45e-126

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 136 EGSAFQKIMHRIRLVAATDMSVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVKGAFTGADN 215
Cdd:COG3829  143 KSPAMKELLELAKRVAKSDSTVLILGESGTGKELFARAIHNASPRRDGPFVAVNCAAIPENLLESELFGYEKGAFTGAKK 222

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 216 A-KKGYFHEAEGGTLFLDEVGNLALETQQMLLRAIQERRYRPVGDKADRNFNVRIIAATNEDLEVSVNEKRFRQDLLYRL 294
Cdd:COG3829  223 GgKPGLFELADGGTLFLDEIGEMPLSLQAKLLRVLQEKEVRRVGGTKPIPVDVRIIAATNRDLEEMVEEGRFREDLYYRL 302

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 295 HDFGITVPPLRDCQEDIMPLAEFFRDMANRELECSVSGFSSEARKALLTHAWPGNVRELRQKVMGAVLQAQEGVVMKEHL 374
Cdd:COG3829  303 NVIPIHIPPLRERKEDIPLLAEHFLEKFNKKYGKNIKGISPEALELLLAYDWPGNVRELENVIERAVVLSEGDVITPEHL 382

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490419162 375 ELAVTKPTSTVSFALRNDAED------KERILRALKQANGNRSVAAELLGIGRTTLYSKLEEYGLK 434
Cdd:COG3829  383 PEYLLEEAEAASAAEEGSLKEaleeveKELIEEALEKTGGNKSKAAKALGISRSTLYRKLKKYGIK 448

AcoR

COG3284

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

119-432

2.61e-100

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

Pssm-ID: 442514 [Multi-domain] Cd Length: 625 Bit Score: 312.22 E-value: 2.61e-100

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 119 ILKERQAGQRRMPIFAREGSAF----------QKIMHRIRLVAATDMSVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAV 188
Cdd:COG3284  299 RLRPARRAARAAPAGAPAPAALaalaggdpamRRALRRARRLADRDIPVLILGETGTGKELFARAIHAASPRADGPFVAV 378

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 189 DCGSLSKELAPSAFFGHVKGAFTGAD-NAKKGYFHEAEGGTLFLDEVGNLALETQQMLLRAIQERRYRPVGDKADRNFNV 267
Cdd:COG3284  379 NCAAIPEELIESELFGYEPGAFTGARrKGRPGKIEQADGGTLFLDEIGDMPLALQARLLRVLQEREVTPLGGTKPIPVDV 458

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 268 RIIAATNEDLEVSVNEKRFRQDLLYRLHDFGITVPPLRDcQEDIMPLAE-FFRDMANRELECSvsgFSSEARKALLTHAW 346
Cdd:COG3284  459 RLIAATHRDLRELVAAGRFREDLYYRLNGLTLTLPPLRE-REDLPALIEhLLRELAAGRGPLR---LSPEALALLAAYPW 534

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 347 PGNVRELRQKVMGAVLQAQEGVVMKEHL------ELAVTKPTSTVSFALRNDAEdKERILRALKQANGNRSVAAELLGIG 420
Cdd:COG3284  535 PGNVRELRNVLRTALALADGGVITVEDLpdelraELAAAAPAAAAPLTSLEEAE-RDAILRALRACGGNVSAAARALGIS 613

                        330
                 ....*....|..
gi 490419162 421 RTTLYSKLEEYG 432
Cdd:COG3284  614 RSTLYRKLKRYG 625

PRK10365

sigma-54-dependent response regulator transcription factor ZraR;

2-428

4.25e-99

sigma-54-dependent response regulator transcription factor ZraR;

Pssm-ID: 182412 [Multi-domain] Cd Length: 441 Bit Score: 303.49 E-value: 4.25e-99

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   2 NKTKIIVVEDNIVYCEYVCNMLSREGYRNMKAYhlsTAKKHLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMQPF 79
Cdd:PRK10365   4 DNIDILVVDDDISHCTILQALLRGWGYNVALAN---SGRQALEQVREQvfDLVLCDVRMAEMDGIATLKEIKALNPAIPV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  80 IIMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQAGQRRMPIFAR-------EGSAFQKIMHRIRLVAA 152
Cdd:PRK10365  81 LIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKALAHTHSIDAETPAVTAsqfgmvgKSPAMQHLLSEIALVAP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 153 TDMSVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVKGAFTGADNAKKGYFHEAEGGTLFLD 232
Cdd:PRK10365 161 SEATVLIHGDSGTGKELVARAIHASSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLD 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 233 EVGNLALETQQMLLRAIQERRYRPVGDKADRNFNVRIIAATNEDLEVSVNEKRFRQDLLYRLHDFGITVPPLRDCQEDIM 312
Cdd:PRK10365 241 EIGDISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYYRLNVVAIEVPSLRQRREDIP 320

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 313 PLAE-FFRDMANRELEcSVSGFSSEARKALLTHAWPGNVRELRQKVMGAVLQAQEGVVMKEHLELAV--TKPTSTVSFAL 389
Cdd:PRK10365 321 LLAGhFLQRFAERNRK-AVKGFTPQAMDLLIHYDWPGNIRELENAVERAVVLLTGEYISERELPLAIasTPIPLGQSQDI 399

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|
gi 490419162 390 RNDAE-DKERILRALKQANGNRSVAAELLGIGRTTLYSKL 428
Cdd:PRK10365 400 QPLVEvEKEVILAALEKTGGNKTEAARQLGITRKTLLAKL 439

ntrC

TIGR01818

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

23-430

1.50e-95

Pssm-ID: 273818 [Multi-domain] Cd Length: 463 Bit Score: 295.11 E-value: 1.50e-95

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   23 LSREGYRNMKAYHLSTAKKHLQQATDnDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDYAEVNTAVESMKLGSIDY 102
Cdd:TIGR01818  18 LSRAGYEVRTFGNAASVLRALARGQP-DLLITDVRMPGEDGLDLLPQIKKRHPQLPVIVMTAHSDLDTAVAAYQRGAFEY 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  103 IPKQLVEDKLVPLIRSIL---KERQAGQRRMPIFAR------EGSAFQKIMHRIRLVAATDMSVMIFGENGTGKEHIAHL 173
Cdd:TIGR01818  97 LPKPFDLDEAVTLVERALahaQEQVALPADAGEAEDsaeligEAPAMQEVFRAIGRLSRSDITVLINGESGTGKELVARA 176

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  174 LHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVKGAFTGADNAKKGYFHEAEGGTLFLDEVGNLALETQQMLLRAIQERR 253
Cdd:TIGR01818 177 LHRHSPRANGPFIALNMAAIPKDLIESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDEIGDMPLDAQTRLLRVLADGE 256

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  254 YRPVGDKADRNFNVRIIAATNEDLEVSVNEKRFRQDLLYRLHDFGITVPPLRDCQEDIMPLAEFFRDMANRELECSVSGF 333
Cdd:TIGR01818 257 FYRVGGRTPIKVDVRIVAATHQNLEALVRQGKFREDLFHRLNVIRIHLPPLRERREDIPRLARHFLALAARELDVEPKLL 336

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  334 SSEARKALLTHAWPGNVRELRQKVMG-AVLQAQEGVVMKE-HLELAvtkPTSTVSFALRNDAEDK--------------- 396
Cdd:TIGR01818 337 DPEALERLKQLRWPGNVRQLENLCRWlTVMASGDEVLVSDlPAELA---LTGRPASAPDSDGQDSwdealeawakqalsr 413

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*....
gi 490419162  397 -------------ERIL--RALKQANGNRSVAAELLGIGRTTLYSKLEE 430
Cdd:TIGR01818 414 geqglldralpefERPLleAALQHTRGHKQEAAALLGWGRNTLTRKLKE 462

PRK11361

acetoacetate metabolism transcriptional regulator AtoC;

5-433

1.21e-94

acetoacetate metabolism transcriptional regulator AtoC;

Pssm-ID: 183099 [Multi-domain] Cd Length: 457 Bit Score: 292.52 E-value: 1.21e-94

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATdNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTD 84
Cdd:PRK11361   6 RILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADIH-PDVVLMDIRMPEMDGIKALKEMRSHETRTPVILMTA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  85 YAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQAGQRRMPIFAREGSAFQ------------KIMHRIRLVAA 152
Cdd:PRK11361  85 YAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRALQLQSMKKEIRHLHQALSTSWQwghiltnspammDICKDTAKIAL 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 153 TDMSVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVKGAFTGADNAKKGYFHEAEGGTLFLD 232
Cdd:PRK11361 165 SQASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGHEKGAFTGAQTLRQGLFERANEGTLLLD 244

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 233 EVGNLALETQQMLLRAIQERRYRPVGDKADRNFNVRIIAATNEDLEVSVNEKRFRQDLLYRLHDFGITVPPLRDCQEDIM 312
Cdd:PRK11361 245 EIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFREDLFYRLNVIHLILPPLRDRREDIS 324

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 313 PLAEFFRDMANRELECSVSGFSSEARKALLTHAWPGNVRELRQKVMGAVLQAQEGVVMKEHLELAVTKPTSTVSFA---- 388
Cdd:PRK11361 325 LLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWPGNIRELSNVIERAVVMNSGPIIFSEDLPPQIRQPVCNAGEVktap 404

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|..
gi 490419162 389 -----LRNDAEDKER--ILRALKQANGNRSVAAELLGIGRTTLYSKLEEYGL 433
Cdd:PRK11361 405 vgernLKEEIKRVEKriIMEVLEQQEGNRTRTALMLGISRRALMYKLQEYGI 456

PEP_resp_reg

TIGR02915

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

51-434

1.74e-88

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: 276.24 E-value: 1.74e-88

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   51 IVVADLRLP---DGSGIDLLCwMRKEGKMQPF---IIMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLI-RSI-LKE 122
Cdd:TIGR02915  43 VVTLDLGLPpdaDGASEGLAA-LQQILAIAPDtkvIVITGNDDRENAVKAIGLGAYDFYQKPIDPDVLKLIVdRAFhLYT 121

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  123 RQAGQRRMpIFAREGSAF----------QKIMHRIRLVAATDMSVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGS 192
Cdd:TIGR02915 122 LETENRRL-QSALGGTALrglitsspgmQKICRTIEKIAPSDITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAA 200

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  193 LSKELAPSAFFGHVKGAFTGADNAKKGYFHEAEGGTLFLDEVGNLALETQQMLLRAIQERRYRPVGDKADRNFNVRIIAA 272
Cdd:TIGR02915 201 IPENLLESELFGYEKGAFTGAVKQTLGKIEYAHGGTLFLDEIGDLPLNLQAKLLRFLQERVIERLGGREEIPVDVRIVCA 280

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  273 TNEDLEVSVNEKRFRQDLLYRLHDFGITVPPLRDCQEDIMPLAEFFRDMANRELECSVSGFSSEARKALLTHAWPGNVRE 352
Cdd:TIGR02915 281 TNQDLKRMIAEGTFREDLFYRIAEISITIPPLRSRDGDAVLLANAFLERFARELKRKTKGFTDDALRALEAHAWPGNVRE 360

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  353 LRQKVMGAVLQAQEGVVMKEHLEL-AVTKPTSTVSFALRNDAEDKERIL--RALKQANGNRSVAAELLGIGRTTLYSKLE 429
Cdd:TIGR02915 361 LENKVKRAVIMAEGNQITAEDLGLdARERAETPLEVNLREVRERAEREAvrKAIARVDGNIARAAELLGITRPTLYDLMK 440


                  ....*
gi 490419162  430 EYGLK 434
Cdd:TIGR02915 441 KHGIK 445

PRK05022

nitric oxide reductase transcriptional regulator NorR;

139-425

1.31e-87

nitric oxide reductase transcriptional regulator NorR;

Pssm-ID: 235331 [Multi-domain] Cd Length: 509 Bit Score: 275.90 E-value: 1.31e-87

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 139 AFQKIMHRIRLVAATDMSVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVKGAFTGADNAKK 218
Cdd:PRK05022 195 AMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAALPESLAESELFGHVKGAFTGAISNRS 274

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 219 GYFHEAEGGTLFLDEVGNLALETQQMLLRAIQERRYRPVGDkaDRNF--NVRIIAATNEDLEVSVNEKRFRQDLLYRLHD 296
Cdd:PRK05022 275 GKFELADGGTLFLDEIGELPLALQAKLLRVLQYGEIQRVGS--DRSLrvDVRVIAATNRDLREEVRAGRFRADLYHRLSV 352

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 297 FGITVPPLRDCQEDIMPLAEFFRDMANRELECSVSGFSSEARKALLTHAWPGNVRELRQKVMGAVLQA-QEG-----VVM 370
Cdd:PRK05022 353 FPLSVPPLRERGDDVLLLAGYFLEQNRARLGLRSLRLSPAAQAALLAYDWPGNVRELEHVISRAALLArARGagrivTLE 432

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490419162 371 KEHLEL----------AVTKPTSTVSFALRNDAEDKER--ILRALKQANGNRSVAAELLGIGRTTLY 425
Cdd:PRK05022 433 AQHLDLpaevalpppeAAAAPAAVVSQNLREATEAFQRqlIRQALAQHQGNWAAAARALELDRANLH 499

Sigma54_activat

pfam00158

Sigma-54 interaction domain;

139-300

1.57e-87

Sigma-54 interaction domain;

Pssm-ID: 425491 [Multi-domain] Cd Length: 168 Bit Score: 263.88 E-value: 1.57e-87

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  139 AFQKIMHRIRLVAATDMSVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVKGAFTGADNAKK 218
Cdd:pfam00158   7 AMQEVLEQAKRVAPTDAPVLITGESGTGKELFARAIHQLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTGADSDRK 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  219 GYFHEAEGGTLFLDEVGNLALETQQMLLRAIQERRYRPVGDKADRNFNVRIIAATNEDLEVSVNEKRFRQDLLYRLHDFG 298
Cdd:pfam00158  87 GLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTKPIKVDVRIIAATNRDLEEAVAEGRFREDLYYRLNVIP 166


                  ..
gi 490419162  299 IT 300
Cdd:pfam00158 167 IE 168

glnG

PRK10923

nitrogen regulation protein NR(I); Provisional

1-434

7.03e-86

nitrogen regulation protein NR(I); Provisional

Pssm-ID: 182842 [Multi-domain] Cd Length: 469 Bit Score: 270.20 E-value: 7.03e-86

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   1 MNKTKIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATDnDIVVADLRLPDGSGIDLLCWMRKEGKMQPFI 80
Cdd:PRK10923   1 MQRGIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLEALASKTP-DVLLSDIRMPGMDGLALLKQIKQRHPMLPVI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  81 IMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLI-RSILKERQAGQRRMPIFAR-------EGSAFQKIMHRIRLVAA 152
Cdd:PRK10923  80 IMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVeRAISHYQEQQQPRNIQVNGpttdiigEAPAMQDVFRIIGRLSR 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 153 TDMSVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVKGAFTGADNAKKGYFHEAEGGTLFLD 232
Cdd:PRK10923 160 SSISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIPKDLIESELFGHEKGAFTGANTIRQGRFEQADGGTLFLD 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 233 EVGNLALETQQMLLRAIQERRYRPVGDKADRNFNVRIIAATNEDLEVSVNEKRFRQDLLYRLHDFGITVPPLRDCQEDIM 312
Cdd:PRK10923 240 EIGDMPLDVQTRLLRVLADGQFYRVGGYAPVKVDVRIIAATHQNLEQRVQEGKFREDLFHRLNVIRVHLPPLRERREDIP 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 313 PLAEFFRDMANRELECSVSGFSSEARKALLTHAWPGNVRELRQ-----KVMGAvlqAQEGVVMKEHLEL-AVTKPTSTVS 386
Cdd:PRK10923 320 RLARHFLQVAARELGVEAKLLHPETEAALTRLAWPGNVRQLENtcrwlTVMAA---GQEVLIQDLPGELfESTVPESTSQ 396

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490419162 387 F---------------ALRNDAED--------KERIL--RALKQANGNRSVAAELLGIGRTTLYSKLEEYGLK 434
Cdd:PRK10923 397 MqpdswatllaqwadrALRSGHQNllseaqpeLERTLltTALRHTQGHKQEAARLLGWGRNTLTRKLKELGME 469

PRK15115

response regulator GlrR; Provisional

23-433

2.57e-81

response regulator GlrR; Provisional

Pssm-ID: 185070 [Multi-domain] Cd Length: 444 Bit Score: 257.84 E-value: 2.57e-81

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  23 LSREGYRNMKAYHLSTAKKHLQQATdNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDYAEVNTAVESMKLGSIDY 102
Cdd:PRK15115  25 LTSEGYSVVTAESGQEALRVLNREK-VDLVISDLRMDEMDGMQLFAEIQKVQPGMPVIILTAHGSIPDAVAATQQGVFSF 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 103 IPKQLVEDKLVPLIRSILKERQAG---QRRMPIFAREgSAFQKIMHRIRLVAATDMSVMIFGENGTGKEHIAHLLHDKSK 179
Cdd:PRK15115 104 LTKPVDRDALYKAIDDALEQSAPAtdeRWREAIVTRS-PLMLRLLEQARMVAQSDVSVLINGQSGTGKEILAQAIHNASP 182

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 180 RAGKPFVAVDCGSLSKELAPSAFFGHVKGAFTGADNAKKGYFHEAEGGTLFLDEVGNLALETQQMLLRAIQERRYRPVGD 259
Cdd:PRK15115 183 RASKPFIAINCGALPEQLLESELFGHARGAFTGAVSNREGLFQAAEGGTLFLDEIGDMPAPLQVKLLRVLQERKVRPLGS 262

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 260 KADRNFNVRIIAATNEDLEVSVNEKRFRQDLLYRLHDFGITVPPLRDCQEDIMPLA-EFFRDMANRElECSVSGFSSEAR 338
Cdd:PRK15115 263 NRDIDIDVRIISATHRDLPKAMARGEFREDLYYRLNVVSLKIPALAERTEDIPLLAnHLLRQAAERH-KPFVRAFSTDAM 341

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 339 KALLTHAWPGNVRELRQKVMGAVLQAQEGVVMKEHLELAVT-KPTSTVSFA-LRNDAEdkERILRALKQ-ANGNRSVAAE 415
Cdd:PRK15115 342 KRLMTASWPGNVRQLVNVIEQCVALTSSPVISDALVEQALEgENTALPTFVeARNQFE--LNYLRKLLQiTKGNVTHAAR 419

                        410
                 ....*....|....*...
gi 490419162 416 LLGIGRTTLYSKLEEYGL 433
Cdd:PRK15115 420 MAGRNRTEFYKLLSRHEL 437

TyrR

COG3283

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

132-433

7.97e-80

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

Pssm-ID: 442513 [Multi-domain] Cd Length: 514 Bit Score: 255.88 E-value: 7.97e-80

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 132 IFArEGSAFQKIMHRIRLVAATDMSVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVKGAFT 211
Cdd:COG3283  206 IVA-SSPKMRQVIRQAKKMAMLDAPLLIQGETGTGKELLARACHLASPRGDKPFLALNCAALPDDVAESELFGYAPGAFG 284

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 212 GADNAKKGYFHEAEGGTLFLDEVGNLALETQQMLLRAIQERRYRPVGDKADRNFNVRIIAATNEDLEVSVNEKRFRQDLL 291
Cdd:COG3283  285 NAREGKKGLFEQANGGTVFLDEIGEMSPQLQAKLLRFLQDGTFRRVGEEQEVKVDVRVICATQKDLAELVQEGEFREDLY 364

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 292 YRLHDFGITVPPLRDCQEDIMPLAEFFRDMANRELECSVSGFSSEARKALLTHAWPGNVRELRQKVMGAVLQAQEGVVMK 371
Cdd:COG3283  365 YRLNVLTLTLPPLRERKSDILPLAEHFVARFSQQLGRPRPRLSPDLVDFLQSYPWPGNVRQLENALYRAVSLLEGDELTP 444

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490419162 372 EHLELavtkPTSTVSFALRNDAEDK---------ER-ILRALKQANGNRSVAAELLGIGRTTLYSKLEEYGL 433
Cdd:COG3283  445 EDLQL----PEYAASAGLLDDLLEGsldeivkrfERsLLRRLYPSYPSTRKLAKRLGVSHTAIANKLREYGI 512

nifA

TIGR01817

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

106-419

2.69e-72

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: 236.92 E-value: 2.69e-72

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  106 QLVEDKLVPLIRSILKERQAGQRRMPIFAREGS-----------AFQKIMHRIRLVAATDMSVMIFGENGTGKEHIAHLL 174
Cdd:TIGR01817 160 RLVAQRRERLIAEAVQLSKQLRDKAPEIARRRSgkedgiigkspAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAI 239

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  175 HDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVKGAFTGADNAKKGYFHEAEGGTLFLDEVGNLALETQQMLLRAIQERRY 254
Cdd:TIGR01817 240 HYLSPRAKRPFVKVNCAALSETLLESELFGHEKGAFTGAIAQRKGRFELADGGTLFLDEIGEISPAFQAKLLRVLQEGEF 319

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  255 RPVGDKADRNFNVRIIAATNEDLEVSVNEKRFRQDLLYRLHDFGITVPPLRDCQEDIMPLAEFFRDMANRELECSVSgFS 334
Cdd:TIGR01817 320 ERVGGNRTLKVDVRLVAATNRDLEEAVAKGEFRADLYYRINVVPIFLPPLRERREDIPLLAEAFLEKFNRENGRPLT-IT 398

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  335 SEARKALLTHAWPGNVRELRQKVMGAVLQAQEGVVMKEHLE----------LAVTKPTSTVSF----------------- 387
Cdd:TIGR01817 399 PSAIRVLMSCKWPGNVRELENCLERTATLSRSGTITRSDFScqsgqclspmLAKTCPHGHISIdplagttpphspasaal 478

                         330       340       350
                  ....*....|....*....|....*....|....*..
gi 490419162  388 -----ALRNDAEDKERILRALKQANGNRSVAAELLGI 419
Cdd:TIGR01817 479 pgepgLSGPTLSERERLIAALEQAGWVQAKAARLLGM 515

FhlA

COG3604

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

132-434

3.72e-69

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: 222.80 E-value: 3.72e-69

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 132 IFAREGSAFQKIMHRIRLVAATDMSVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELapsaffghvkgaft 211
Cdd:COG3604   93 LDSRRPGAFSEEDLRLLETLASLAAVAILGETGTGKELVANAIHELSPRADKPFVKVNCAALPESL-------------- 158

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 212 gadnakkgyfheaeggtlfldevgnlaletqqmlLRAIQERRYRPVGDKADRNFNVRIIAATNEDLEVSVNEKRFRQDLL 291
Cdd:COG3604  159 ----------------------------------LESLQEGEFERVGGDETIKVDVRIIAATNRDLEEEVAEGRFREDLY 204

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 292 YRLHDFGITVPPLRDCQEDIMPLAEFFRDMANRELECSVSGFSSEARKALLTHAWPGNVRELRQKVMGAVLQAQEGVVMK 371
Cdd:COG3604  205 YRLNVFPIRLPPLRERREDIPLLAEHFLEKFSRRLGKPILRLSPEALEALMAYPWPGNVRELENVIERAVILAEGGVLDA 284

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490419162 372 EHLELAVTKPTstvsfalrnDAEDKERILRALKQANGNRSVAAELLGIGRTTLYSKLEEYGLK 434
Cdd:COG3604  285 DDLAPGSREAL---------EEVEREHILEALERTGGNIAGAARLLGLTPSTLRSRMKKLGIK 338

PRK15429

formate hydrogenlyase transcriptional activator FlhA;

139-433

7.70e-66

formate hydrogenlyase transcriptional activator FlhA;

Pssm-ID: 237965 [Multi-domain] Cd Length: 686 Bit Score: 223.17 E-value: 7.70e-66

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 139 AFQKIMHRIRLVAATDMSVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVKGAFTGADNAKK 218
Cdd:PRK15429 384 AMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPAGLLESDLFGHERGAFTGASAQRI 463

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 219 GYFHEAEGGTLFLDEVGNLALETQQMLLRAIQERRYRPVGDKADRNFNVRIIAATNEDLEVSVNEKRFRQDLLYRLHDFG 298
Cdd:PRK15429 464 GRFELADKSSLFLDEVGDMPLELQPKLLRVLQEQEFERLGSNKIIQTDVRLIAATNRDLKKMVADREFRSDLYYRLNVFP 543

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 299 ITVPPLRDCQEDIMPLAEFFRDMANRELECSVSGFSSEARKALLTHAWPGNVRELRQKVMGAVLQAQEGVVMKEHLELA- 377
Cdd:PRK15429 544 IHLPPLRERPEDIPLLVKAFTFKIARRMGRNIDSIPAETLRTLSNMEWPGNVRELENVIERAVLLTRGNVLQLSLPDITl 623

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 378 VTKPTSTVSFALRNDAEDK-ERILRALKQANG---NRSVAAELLGIGRTTLYSKLEEYGL 433
Cdd:PRK15429 624 PEPETPPAATVVAQEGEDEyQLIVRVLKETNGvvaGPKGAAQRLGLKRTTLLSRMKRLGI 683

PRK15424

propionate catabolism operon regulatory protein PrpR; Provisional

136-434

7.37e-65

propionate catabolism operon regulatory protein PrpR; Provisional

Pssm-ID: 237963 [Multi-domain] Cd Length: 538 Bit Score: 217.28 E-value: 7.37e-65

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 136 EGSAFQKIMHRIRLVAATDMSVMIFGENGTGKEHIAHLLH---------DKSKRAGkPFVAVDCGSLSKELAPSAFFGHV 206
Cdd:PRK15424 224 QSPQMEQVRQTILLYARSSAAVLIQGETGTGKELAAQAIHreyfarhdaRQGKKSH-PFVAVNCGAIAESLLEAELFGYE 302

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 207 KGAFTGAD-NAKKGYFHEAEGGTLFLDEVGNLALETQQMLLRAIQERRYRPVGDKADRNFNVRIIAATNEDLEVSVNEKR 285
Cdd:PRK15424 303 EGAFTGSRrGGRAGLFEIAHGGTLFLDEIGEMPLPLQTRLLRVLEEKEVTRVGGHQPVPVDVRVISATHCDLEEDVRQGR 382

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 286 FRQDLLYRLHDFGITVPPLRDCQEDIMPLAEFFRDMANRELEcsvSGFSSEARKALLTHA-------WPGNVRELRQKV- 357
Cdd:PRK15424 383 FRRDLFYRLSILRLQLPPLRERVADILPLAESFLKQSLAALS---APFSAALRQGLQQCEtlllhydWPGNVRELRNLMe 459

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490419162 358 -MGAVLQAQEGVVMKEHLELAVTKPTSTVSFALRNDAEDKERILRALKQANGNRSVAAELLGIGRTTLYSKLEEYGLK 434
Cdd:PRK15424 460 rLALFLSVEPTPDLTPQFLQLLLPELARESAKTPAPRLLAATLQQALERFNGDKTAAANYLGISRTTLWRRLKAEAKA 537

pspF

PRK11608

phage shock protein operon transcriptional activator; Provisional

136-419

8.50e-64

phage shock protein operon transcriptional activator; Provisional

Pssm-ID: 236936 [Multi-domain] Cd Length: 326 Bit Score: 208.37 E-value: 8.50e-64

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 136 EGSAFQKIMHRIRLVAATDMSVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVKGAFTGADN 215
Cdd:PRK11608  11 EANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHEAGAFTGAQK 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 216 AKKGYFHEAEGGTLFLDEVGNLALETQQMLLRAIQERRYRPVGDKADRNFNVRIIAATNEDLEVSVNEKRFRQDLLYRLH 295
Cdd:PRK11608  91 RHPGRFERADGGTLFLDELATAPMLVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVAEGKFRADLLDRLA 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 296 DFGITVPPLRDCQEDIMPLAEFFRDMANRELECSV-SGFSSEARKALLTHAWPGNVRELRQKVMGAVL------QAQEGV 368
Cdd:PRK11608 171 FDVVQLPPLRERQSDIMLMAEHFAIQMCRELGLPLfPGFTERARETLLNYRWPGNIRELKNVVERSVYrhgtseYPLDNI 250

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490419162 369 VMK--------EHLELAVTKPTSTVSFALRNDAEDKER--ILRALKQANGNRSVAAELLGI 419
Cdd:PRK11608 251 IIDpfkrrpaeEAIAVSETTSLPTLPLDLREWQHQQEKelLQRSLQQAKFNQKRAAELLGL 311

propionate_PrpR

TIGR02329

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

136-429

8.20e-63

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: 211.64 E-value: 8.20e-63

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  136 EGSAFQKIMHRIRLVAATDMSVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVKGAFTGA-D 214
Cdd:TIGR02329 217 ASAPMEQVRALVRLYARSDATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIAESLLEAELFGYEEGAFTGArR 296

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  215 NAKKGYFHEAEGGTLFLDEVGNLALETQQMLLRAIQERRYRPVGDKADRNFNVRIIAATNEDLEVSVNEKRFRQDLLYRL 294
Cdd:TIGR02329 297 GGRTGLIEAAHRGTLFLDEIGEMPLPLQTRLLRVLEEREVVRVGGTEPVPVDVRVVAATHCALTTAVQQGRFRRDLFYRL 376

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  295 HDFGITVPPLRDCQEDIMPLAEFFRDMANRELECSVSGFSSE----ARKALLTHAWPGNVRELRQKV--MGAVLQAQ-EG 367
Cdd:TIGR02329 377 SILRIALPPLRERPGDILPLAAEYLVQAAAALRLPDSEAAAQvlagVADPLQRYPWPGNVRELRNLVerLALELSAMpAG 456

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 490419162  368 VVMKEHLELAVTK------PTSTVSFALRNDAE-DKERILRALKQANGNRSVAAELLGIGRTTLYSKLE 429
Cdd:TIGR02329 457 ALTPDVLRALAPElaeasgKGKTSALSLRERSRvEALAVRAALERFGGDRDAAAKALGISRTTLWRRLK 525

PRK10820

transcriptional regulator TyrR;

138-436

7.63e-58

transcriptional regulator TyrR;

Pssm-ID: 236769 [Multi-domain] Cd Length: 520 Bit Score: 198.37 E-value: 7.63e-58

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 138 SAFQKIM----------HRIRLVAATDMSVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVK 207
Cdd:PRK10820 201 SAFSQIVavspkmrqvvEQARKLAMLDAPLLITGDTGTGKDLLAYACHLRSPRGKKPFLALNCASIPDDVVESELFGHAP 280

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 208 GAFTGADNAKKGYFHEAEGGTLFLDEVGNLALETQQMLLRAIQERRYRPVGDKADRNFNVRIIAATNEDLEVSVNEKRFR 287
Cdd:PRK10820 281 GAYPNALEGKKGFFEQANGGSVLLDEIGEMSPRMQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQKNLVELVQKGEFR 360

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 288 QDLLYRLHDFGITVPPLRDCQEDIMPLAEFFRDMANRELECSVSGFSSEARKALLTHAWPGNVRELRQKVMGAVLQAqEG 367
Cdd:PRK10820 361 EDLYYRLNVLTLNLPPLRDRPQDIMPLTELFVARFADEQGVPRPKLAADLNTVLTRYGWPGNVRQLKNAIYRALTQL-EG 439

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490419162 368 -------VVMKEHlELAVTKPTSTVSFALRNDAEDKER-ILRALKQANGNRSVAAELLGIGRTTLYSKLEEYGLKYK 436
Cdd:PRK10820 440 yelrpqdILLPDY-DAAVAVGEDAMEGSLDEITSRFERsVLTRLYRNYPSTRKLAKRLGVSHTAIANKLREYGLSQK 515

PRK11388

DNA-binding transcriptional regulator DhaR; Provisional

136-433

8.20e-51

DNA-binding transcriptional regulator DhaR; Provisional

Pssm-ID: 183114 [Multi-domain] Cd Length: 638 Bit Score: 181.80 E-value: 8.20e-51

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 136 EGSAFQKIMHRIRLVAATDMSVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELAPSAFFGhvkGAFTGADN 215
Cdd:PRK11388 330 DSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPDEALAEEFLG---SDRTDSEN 406

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 216 AKKGYFHEAEGGTLFLDEVGNLALETQQMLLRAIQE--------RRYRPVgdkadrnfNVRIIAATNEDLEVSVNEKRFR 287
Cdd:PRK11388 407 GRLSKFELAHGGTLFLEKVEYLSPELQSALLQVLKTgvitrldsRRLIPV--------DVRVIATTTADLAMLVEQNRFS 478

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 288 QDLLYRLHDFGITVPPLRDCQEDIMPLAEFFRDMANRELECSVSgFSSEARKALLTHAWPGNVRELRQKVMGAVLQAQEG 367
Cdd:PRK11388 479 RQLYYALHAFEITIPPLRMRREDIPALVNNKLRSLEKRFSTRLK-IDDDALARLVSYRWPGNDFELRSVIENLALSSDNG 557

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490419162 368 VV-----------MKEHLELAVTKPTSTVSFAlrnDAEdKERILRALKQANGNRSVAAELLGIGRTTLYSKLEEYGL 433
Cdd:PRK11388 558 RIrlsdlpehlftEQATDDVSATRLSTSLSLA---ELE-KEAIINAAQVCGGRIQEMAALLGIGRTTLWRKMKQHGI 630

RtcR

COG4650

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

139-353

8.98e-48

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: 171.55 E-value: 8.98e-48

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 139 AFQKIMHRIRLVA-ATDMSVMIFGENGTGKEHIAHLLHD-KSKR---AGkPFVAVDCGSLSKELAPSAFFGHVKGAFTGA 213
Cdd:COG4650  192 AFNRLIEQIERVAiRSRAPILLTGPTGAGKSQLARRIYElKKARhqvSG-RFVEVNCATLRGDGAMSALFGHVKGAFTGA 270

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 214 DNAKKGYFHEAEGGTLFLDEVGNLALETQQMLLRAIQERRYRPVGdkADR----NFnvRIIAATNEDLEVSVNEKRFRQD 289
Cdd:COG4650  271 VSDRAGLLRSADGGVLFLDEIGELGLDEQAMLLRAIEEKRFLPVG--SDKevssDF--QLIAGTNRDLRQEVAEGRFRED 346

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 290 LLYRLHDFGITVPPLRDCQEDIMPLAEFFRDMANRELECSVSgFSSEARKALLTHA------WPGNVREL 353
Cdd:COG4650  347 LLARINLWTFRLPGLAERREDIEPNLDYELARFAREQGRRVR-FNKEARARYLAFAtspealWSGNFRDL 415

PspF

COG1221

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

155-354

3.68e-29

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: 120.60 E-value: 3.68e-29

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 155 MSVMIFGENGTGKEHIAHLLHDKSKRAGK-----PFVAVDCGSLS--KELAPSAFFGHVKGAFTGADNAKKGYFHEAEGG 227
Cdd:COG1221  131 LHTLILGPTGVGKSFFAELMYEYAIEIGVlpedaPFVVFNCADYAnnPQLLMSQLFGYVKGAFTGADKDKEGLIEKADGG 210

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 228 TLFLDEVGNLALETQQMLLRAIQERRYRPVGDKA-DRNFNVRIIAATNEDLEVSVnekrfrqdllyrLHDF------GIT 300
Cdd:COG1221  211 ILFLDEVHRLPPEGQEMLFTFMDKGIYRRLGETEkTRKANVRIIFATTEDPESSL------------LKTFlrripmVIK 278

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 490419162 301 VPPLRD--CQEDIMPLAEFFRDMANR-ELECSVsgfSSEARKALLTHAWPGNVRELR 354
Cdd:COG1221  279 LPSLEErsLEERLELIKHFFKEEAKRlNKPIKV---SKEVLKALLLYDCPGNIGQLK 332

REC

cd00156

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

8-105

2.22e-21

Pssm-ID: 381085 [Multi-domain] Cd Length: 99 Bit Score: 88.44 E-value: 2.22e-21

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   8 VVEDNIVYCEYVCNMLSREGYRnmkAYHLSTAKKHLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDY 85
Cdd:cd00156    2 IVDDDPAIRELLKSLLEREGYE---VDTAADGEEALELLREErpDLVLLDLMMPGMDGLELLRKLRELPPDIPVIVLTAK 78

                         90       100
                 ....*....|....*....|
gi 490419162  86 AEVNTAVESMKLGSIDYIPK 105
Cdd:cd00156   79 ADEEDAVRALELGADDYLVK 98

REC_NtrC1-like

cd17572

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

6-124

1.40e-20

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: 86.87 E-value: 1.40e-20

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDN----IVYCEYvcnmLSREGYrnmKAYHLSTAKKHLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMQPF 79
Cdd:cd17572    1 VLLVEDSpslaALYQEY----LSDEGY---KVTHVETGKEALAFLSDQppDVVLLDLKLPDMSGMEILKWIQERSLPTSV 73

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 490419162  80 IIMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQ 124
Cdd:cd17572   74 IVITAHGSVDIAVEAMRLGAYDFLEKPFDADRLRVTVRNALKHRK 118

AAA

cd00009

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

156-294

3.55e-19

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: 83.73 E-value: 3.55e-19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162 156 SVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELAPSAFFGHVkgaftgADNAKKGYFHEAEGGTLFLDEVG 235
Cdd:cd00009   21 NLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHF------LVRLLFELAEKAKPGVLFIDEID 94

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 490419162 236 NLALETQQMLLRAIQERRYRPVGDKadrnfNVRIIAATNEDLEVsvnekRFRQDLLYRL 294
Cdd:cd00009   95 SLSRGAQNALLRVLETLNDLRIDRE-----NVRVIGATNRPLLG-----DLDRALYDRL 143

OmpR

COG0745

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

3-129

6.20e-18

DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain [Signal transduction mechanisms, Transcription];

Pssm-ID: 440508 [Multi-domain] Cd Length: 204 Bit Score: 81.93 E-value: 6.20e-18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   3 KTKIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAkkhLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMQPFI 80
Cdd:COG0745    1 MPRILVVEDDPDIRELLADALEREGYEVDTAADGEEA---LELLEEErpDLILLDLMLPGMDGLEVCRRLRARPSDIPII 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 490419162  81 IMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQAGQRR 129
Cdd:COG0745   78 MLTARDDEEDRVRGLEAGADDYLTKPFDPEELLARIRALLRRRAAEVLR 126

CitB

COG4565

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

1-125

2.47e-17

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

Pssm-ID: 443622 [Multi-domain] Cd Length: 138 Bit Score: 78.09 E-value: 2.47e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   1 MNKTKIIVVEDNIVYCEYVCNMLSR-EGYRNM-KAYHLSTAKKHLQQaTDNDIVVADLRLPDGSGIDLLCWMRKEGKMQP 78
Cdd:COG4565    1 MKMIRVLIVEDDPMVAELLRRYLERlPGFEVVgVASSGEEALALLAE-HRPDLILLDIYLPDGDGLELLRELRARGPDVD 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 490419162  79 FIIMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQA 125
Cdd:COG4565   80 VIVITAARDPETVREALRAGVVDYLIKPFTFERLREALERYLEYRRL 126

REC_RegA-like

cd17563

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

5-105

4.39e-16

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: 74.02 E-value: 4.39e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATDNDIVVaDLRLPDGSGIDLLCWMRKegkMQP---FII 81
Cdd:cd17563    2 SLLLVDDDEVFAERLARALERRGFEVETAHSVEEALALAREEKPDYAVL-DLRLGGDSGLDLIPPLRA---LQPdarIVV 77

                         90       100
                 ....*....|....*....|....
gi 490419162  82 MTDYAEVNTAVESMKLGSIDYIPK 105
Cdd:cd17563   78 LTGYASIATAVEAIKLGADDYLAK 101

fixJ

PRK09390

response regulator FixJ; Provisional

52-132

5.24e-16

response regulator FixJ; Provisional

Pssm-ID: 181815 [Multi-domain] Cd Length: 202 Bit Score: 76.19 E-value: 5.24e-16

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  52 VVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQAGQRRMP 131
Cdd:PRK09390  51 VVTDVRMPGIDGIELLRRLKARGSPLPVIVMTGHGDVPLAVEAMKLGAVDFIEKPFEDERLIGAIERALAQAPEAAKSEA 130


                 .
gi 490419162 132 I 132
Cdd:PRK09390 131 V 131

Response_reg

pfam00072

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

6-117

5.28e-16

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: 73.72 E-value: 5.28e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162    6 IIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQAtDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDY 85
Cdd:pfam00072   1 VLIVDDDPLIRELLRQLLEKEGYVVAEADDGKEALELLKEE-RPDLILLDINMPGMDGLELLKRIRRRDPTTPVIILTAH 79

                          90       100       110
                  ....*....|....*....|....*....|..
gi 490419162   86 AEVNTAVESMKLGSIDYIPKQLVEDKLVPLIR 117
Cdd:pfam00072  80 GDEDDAVEALEAGADDFLSKPFDPDELLAAIR 111

REC_NtrX-like

cd17550

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

6-121

1.02e-15

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: 72.91 E-value: 1.02e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATDnDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDY 85
Cdd:cd17550    1 ILIVDDEEDIRESLSGILEDEGYEVDTAADGEEALKLIKERRP-DLVLLDIWLPDMDGLELLKEIKEKYPDLPVIMISGH 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 490419162  86 AEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILK 121
Cdd:cd17550   80 GTIETAVKATKLGAYDFIEKPLSLDRLLLTIERALE 115

PleD

COG3706

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

3-113

1.21e-15

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: 74.56 E-value: 1.21e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   3 KTKIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQaTDNDIVVADLRLPDGSGIDLLCWMRKEGKMQ--PFI 80
Cdd:COG3706    1 PARILVVDDDPTNRKLLRRLLEAAGYEVVEAADGEEALELLQE-HRPDLILLDLEMPDMDGLELCRRLRADPRTAdiPII 79

                         90       100       110
                 ....*....|....*....|....*....|...
gi 490419162  81 IMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLV 113
Cdd:COG3706   80 FLTALDDEEDRARALEAGADDYLTKPFDPEELL 112

CheY

COG0784

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

1-125

1.98e-15

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: 72.58 E-value: 1.98e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   1 MNKTKIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQaTDNDIVVADLRLPDGSGIDLLCWMRKEGKMQ--P 78
Cdd:COG0784    3 LGGKRILVVDDNPDNRELLRRLLERLGYEVTTAEDGAEALELLRA-GPPDLILLDINMPGMDGLELLRRIRALPRLPdiP 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 490419162  79 FIIMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQA 125
Cdd:COG0784   82 IIALTAYADEEDRERALEAGADDYLTKPVDPEELLEALRRLLARASA 128

COG4567

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

5-105

2.31e-15

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: 73.80 E-value: 2.31e-15

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATDnDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTD 84
Cdd:COG4567    6 SLLLVDDDEAFARVLARALERRGFEVTTAASVEEALALLEQAPP-DYAVLDLRLGDGSGLDLIEALRERDPDARIVVLTG 84

                         90       100
                 ....*....|....*....|.
gi 490419162  85 YAEVNTAVESMKLGSIDYIPK 105
Cdd:COG4567   85 YASIATAVEAIKLGADDYLAK 105

REC_DctD-like

cd17549

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

6-124

2.16e-14

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: 69.44 E-value: 2.16e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATdNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDY 85
Cdd:cd17549    1 VLLVDDDADVREALQQTLELAGFRVRAFADAEEALAALSPDF-PGVVISDIRMPGMDGLELLAQIRELDPDLPVILITGH 79

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 490419162  86 AEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQ 124
Cdd:cd17549   80 GDVPMAVEAMRAGAYDFLEKPFDPERLLDVVRRALEKRR 118

REC_OmpR

cd17574

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

8-105

1.19e-13

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

Pssm-ID: 381116 [Multi-domain] Cd Length: 99 Bit Score: 66.66 E-value: 1.19e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   8 VVEDNIVYCEYVCNMLSREGYRnmkAYHLSTAKKHLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDY 85
Cdd:cd17574    2 VVEDDEEIAELLSDYLEKEGYE---VDTAADGEEALELAREEqpDLIILDVMLPGMDGFEVCRRLREKGSDIPIIMLTAK 78

                         90       100
                 ....*....|....*....|
gi 490419162  86 AEVNTAVESMKLGSIDYIPK 105
Cdd:cd17574   79 DEEEDKVLGLELGADDYITK 98

FixJ

COG4566

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

6-135

1.36e-13

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: 68.97 E-value: 1.36e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRnMKAYhlSTAKKHLQQATDNDI--VVADLRLPDGSGIDLLCWMRKEGKMQPFIIMT 83
Cdd:COG4566    2 VYIVDDDEAVRDSLAFLLESAGLR-VETF--ASAEAFLAALDPDRPgcLLLDVRMPGMSGLELQEELAARGSPLPVIFLT 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 490419162  84 DYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKE----RQAGQRRMPIFAR 135
Cdd:COG4566   79 GHGDVPMAVRAMKAGAVDFLEKPFDDQALLDAVRRALARdrarRAERARRAELRAR 134

RpfG

COG3437

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

3-154

2.03e-13

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: 69.42 E-value: 2.03e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   3 KTKIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATDnDIVVADLRLPDGSGIDLLCWMRKEGKMQ--PFI 80
Cdd:COG3437    6 APTVLIVDDDPENLELLRQLLRTLGYDVVTAESGEEALELLLEAPP-DLILLDVRMPGMDGFELLRLLRADPSTRdiPVI 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490419162  81 IMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQAGQRRMPIFAREGSAFQkiMHRIRLVAATD 154
Cdd:COG3437   85 FLTALADPEDRERALEAGADDYLTKPFDPEELLARVRNALELRRLQRELDDLVLYLKLAAP--LHDIGKIGIPD 156

Sigma54_activ_2

pfam14532

Sigma-54 interaction domain;

137-304

4.61e-13

Sigma-54 interaction domain;

Pssm-ID: 434021 [Multi-domain] Cd Length: 138 Bit Score: 66.21 E-value: 4.61e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  137 GSAFQKIMHRIRLVAATDMSVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSLSKELapsaffghvkgaftgadna 216
Cdd:pfam14532   4 SAAIQEIKRRLEQAAQSTLPVFLTGEPGSGKEFCARYLHNPSTPWVQPFDIEYLAHAPLEL------------------- 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  217 kkgyFHEAEGGTLFLDEVGNLALETQQMLLRAIQerryrpvgdKADRNfNVRIIAATNEDLEVSVNEKRFRQDLLYRLHD 296
Cdd:pfam14532  65 ----LEQAKGGTLYLKDIADLSKALQKGLLLLLA---------KAEGY-RVRLVCTSSKDLPQLAAAGLFDEQLYFELSA 130


                  ....*...
gi 490419162  297 FGITVPPL 304
Cdd:pfam14532 131 LRLHVPPL 138

YesN

COG4753

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

5-105

1.69e-12

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: 63.25 E-value: 1.69e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSRE-GYRNM-KAYHLSTAKKHLQQaTDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIM 82
Cdd:COG4753    1 KVLIVDDEPLIREGLKRILEWEaGFEVVgEAENGEEALELLEE-HKPDLVITDINMPGMDGLELLEAIRELDPDTKIIIL 79

                         90       100
                 ....*....|....*....|...
gi 490419162  83 TDYAEVNTAVESMKLGSIDYIPK 105
Cdd:COG4753   80 SGYSDFEYAQEAIKLGADDYLLK 102

REC_FixJ

cd17537

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

6-120

3.61e-12

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: 63.00 E-value: 3.61e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYrNMKAYhlSTAKKHLQQATDND--IVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMT 83
Cdd:cd17537    3 VYVVDDDEAVRDSLAFLLRSVGL-AVKTF--TSASAFLAAAPPDQpgCLVLDVRMPGMSGLELQDELLARGSNIPIIFIT 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 490419162  84 DYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSIL 120
Cdd:cd17537   80 GHGDVPMAVEAMKAGAVDFLEKPFRDQVLLDAIEQAL 116

AAA

smart00382

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

156-276

1.61e-11

Pssm-ID: 214640 [Multi-domain] Cd Length: 148 Bit Score: 62.01 E-value: 1.61e-11

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   156 SVMIFGENGTGKEHIAHLLHDKSKRAGKPFVAVDCGSL---SKELAPSAFFGHVKGAFTGADNAKKGyFHEAEG---GTL 229
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDIleeVLDQLLLIIVGGKKASGSGELRLRLA-LALARKlkpDVL 82

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 490419162   230 FLDEVGNLALETQQMLLRAIQERRyrpVGDKADRNFNVRIIAATNED 276
Cdd:smart00382  83 ILDEITSLLDAEQEALLLLLEELR---LLLLLKSEKNLTVILTTNDE 126

REC_OmpR_PmrA-like

cd17624

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

6-105

2.12e-11

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: 60.58 E-value: 2.12e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYrnmKAYHLSTAK--KHLQQATDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMT 83
Cdd:cd17624    1 ILLVEDDALLGDGLKTGLRKAGY---AVDWVRTGAeaEAALASGPYDLVILDLGLPDGDGLDLLRRWRRQGQSLPVLILT 77

                         90       100
                 ....*....|....*....|..
gi 490419162  84 DYAEVNTAVESMKLGSIDYIPK 105
Cdd:cd17624   78 ARDGVDDRVAGLDAGADDYLVK 99

REC_OmpR_DrrD-like

cd17625

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

8-121

6.83e-11

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: 59.16 E-value: 6.83e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   8 VVEDNIVYCEYVCNMLSREGYRNMKAYHlstAKKHLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDY 85
Cdd:cd17625    2 VVEDEKDLSEAITKHLKKEGYTVDVCFD---GEEGLEYALSGiyDLIILDIMLPGMDGLEVLKSLREEGIETPVLLLTAL 78

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 490419162  86 AEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILK 121
Cdd:cd17625   79 DAVEDRVKGLDLGADDYLPKPFSLAELLARIRALLR 114

PRK09836

DNA-binding transcriptional activator CusR; Provisional

5-121

7.69e-11

DNA-binding transcriptional activator CusR; Provisional

Pssm-ID: 182102 [Multi-domain] Cd Length: 227 Bit Score: 61.86 E-value: 7.69e-11

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGY------RNMKAYHLStakkhlqQATDNDIVVADLRLPDGSGIDLLCWMRKEGKMQP 78
Cdd:PRK09836   2 KLLIVEDEKKTGEYLTKGLTEAGFvvdladNGLNGYHLA-------MTGDYDLIILDIMLPDVNGWDIVRMLRSANKGMP 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 490419162  79 FIIMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILK 121
Cdd:PRK09836  75 ILLLTALGTIEHRVKGLELGADDYLVKPFAFAELLARVRTLLR 117

PRK10643

two-component system response regulator PmrA;

5-124

1.51e-10

two-component system response regulator PmrA;

Pssm-ID: 182612 [Multi-domain] Cd Length: 222 Bit Score: 60.82 E-value: 1.51e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQqATDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTD 84
Cdd:PRK10643   2 KILIVEDDTLLLQGLILALQTEGYACDCASTAREAEALLE-SGHYSLVVLDLGLPDEDGLHLLRRWRQKKYTLPVLILTA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 490419162  85 YAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQ 124
Cdd:PRK10643  81 RDTLEDRVAGLDVGADDYLVKPFALEELHARIRALIRRHQ 120

REC_OmpR_CpxR

cd17623

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

6-121

5.51e-10

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: 56.54 E-value: 5.51e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYrNMKAYHlsTAKKHLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMqPFIIMT 83
Cdd:cd17623    1 ILLIDDDRELTELLTEYLEMEGF-NVRAAH--DGEQGLAALLEGspDLVVLDVMLPKMNGLDVLKELRKTSQV-PVLMLT 76

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 490419162  84 DYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILK 121
Cdd:cd17623   77 ARGDDIDRILGLELGADDYLPKPFNPRELVARIRAILR 114

REC_NtrC

cd19919

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

50-117

8.68e-10

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: 56.13 E-value: 8.68e-10

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490419162  50 DIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIR 117
Cdd:cd19919   46 DVLISDIRMPGMDGLALLAQIKQRHPDLPVIIMTAHSDLDSAVSAYQGGAFEYLPKPFDIDEAVALVE 113

REC_OmpR_PhoB

cd17618

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

4-120

1.43e-09

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

Pssm-ID: 381133 [Multi-domain] Cd Length: 118 Bit Score: 55.33 E-value: 1.43e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   4 TKIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATDnDIVVADLRLPDGSGIDLLCWMRKEGKMQ--PFII 81
Cdd:cd17618    1 RTILIVEDEPAIREMIAFNLERAGFDVVEAEDAESAVNLIVEPRP-DLILLDWMLPGGSGIQFIRRLKRDEMTRdiPIIM 79

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 490419162  82 MTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSIL 120
Cdd:cd17618   80 LTARGEEEDKVRGLEAGADDYITKPFSPRELVARIKAVL 118

REC_YesN-like

cd17536

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

6-124

1.63e-09

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: 55.42 E-value: 1.63e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMT 83
Cdd:cd17536    1 VLIVDDEPLIREGLKKLIDWEELGFEVVGEAENGEEALELIEEHkpDIVITDIRMPGMDGLELIEKIRELYPDIKIIILS 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 490419162  84 DYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQ 124
Cdd:cd17536   81 GYDDFEYAQKAIRLGVVDYLLKPVDEEELEEALEKAKEELD 121

PRK10161

phosphate response regulator transcription factor PhoB;

5-147

2.76e-09

phosphate response regulator transcription factor PhoB;

Pssm-ID: 182277 [Multi-domain] Cd Length: 229 Bit Score: 57.42 E-value: 2.76e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATDnDIVVADLRLPDGSGIDLLCWMRKEGKMQ--PFIIM 82
Cdd:PRK10161   4 RILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWP-DLILLDWMLPGGSGIQFIKHLKRESMTRdiPVVML 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490419162  83 TDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKeRQAGQRRMPIFAREGSAFQKIMHRI 147
Cdd:PRK10161  83 TARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMR-RISPMAVEEVIEMQGLSLDPTSHRV 146

REC_PilR

cd19926

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

6-106

6.23e-09

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

Pssm-ID: 381153 [Multi-domain] Cd Length: 100 Bit Score: 53.31 E-value: 6.23e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATdNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDY 85
Cdd:cd19926    1 VLVVDDEPDIRELLEITLGRMGLDVRSARNVKEARELLASEP-YDLCLTDMRLPDGSGLELVQHIQQRLPQTPVAVITAY 79

                         90       100
                 ....*....|....*....|.
gi 490419162  86 AEVNTAVESMKLGSIDYIPKQ 106
Cdd:cd19926   80 GSLDTAIEALKAGAFDFLTKP 100

AmiR

COG3707

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

1-128

7.66e-09

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: 55.35 E-value: 7.66e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   1 MNKTKIIVVEDNIVYCEYVCNMLSREGYRNmkAYHLSTAKKHLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMqP 78
Cdd:COG3707    1 MRGLRVLVVDDEPLRRADLREGLREAGYEV--VAEAADGEDAVELVRELkpDLVIVDIDMPDRDGLEAARQISEERPA-P 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 490419162  79 FIIMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQAGQR 128
Cdd:COG3707   78 VILLTAYSDPELIERALEAGVSAYLVKPLDPEDLLPALELALARFRELRA 127

REC_typeB_ARR-like

cd17584

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

6-112

1.04e-08

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: 53.02 E-value: 1.04e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATDN-DIVVADLRLPDGSGIDLLCWMRKEgKMQPFIIMTD 84
Cdd:cd17584    1 VLVVDDDPTCLAILKRMLLRCGYQVTTCTDAEEALSMLRENKDEfDLVITDVHMPDMDGFEFLELIRLE-MDLPVIMMSA 79

                         90       100
                 ....*....|....*....|....*...
gi 490419162  85 YAEVNTAVESMKLGSIDYIPKQLVEDKL 112
Cdd:cd17584   80 DGSTSTVMKGLAHGACDYLLKPVSIEDL 107

HTH_8

pfam02954

Bacterial regulatory protein, Fis family;

395-430

1.26e-08

Bacterial regulatory protein, Fis family;

Pssm-ID: 427077 [Multi-domain] Cd Length: 40 Bit Score: 50.47 E-value: 1.26e-08

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 490419162  395 DKERILRALKQANGNRSVAAELLGIGRTTLYSKLEE 430
Cdd:pfam02954   5 EKELIEAALERTGGNKSKAARLLGISRRTLYRKLKK 40

REC_OmpR_CtrA

cd17616

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

6-120

1.27e-08

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: 52.80 E-value: 1.27e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYrNMKAYHLSTAKKHLQQATDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDY 85
Cdd:cd17616    1 VLLIEDDSATAQSIELMLKSEGF-NVYTTDLGEEGLDLGKLYDYDIILLDLNLPDMSGYEVLRTLRLAKVKTPILILSGL 79

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 490419162  86 AEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSIL 120
Cdd:cd17616   80 ADIEDKVKGLGFGADDYMTKPFHKDELVARIHAIV 114

Fis

COG2901

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

402-433

1.46e-08

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

Pssm-ID: 442146 [Multi-domain] Cd Length: 83 Bit Score: 51.74 E-value: 1.46e-08

                         10        20        30
                 ....*....|....*....|....*....|..
gi 490419162 402 ALKQANGNRSVAAELLGIGRTTLYSKLEEYGL 433
Cdd:COG2901   51 VLEHTRGNQSRAAEMLGINRNTLRKKLKQYGL 82

REC_RcNtrC-like

cd19928

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

6-105

2.78e-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: 51.35 E-value: 2.78e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQAtDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDY 85
Cdd:cd19928    1 ILVADDDRAIRTVLTQALGRAGYEVRTTGNAATLWRWVEEG-EGDLVITDVVMPDENGLDLIPRIKKARPDLPIIVMSAQ 79

                         90       100
                 ....*....|....*....|
gi 490419162  86 AEVNTAVESMKLGSIDYIPK 105
Cdd:cd19928   80 NTLMTAVKAAERGAFEYLPK 99

REC_OmpR_CusR-like

cd19935

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

6-105

4.56e-08

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: 50.52 E-value: 4.56e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAkKHLQQATDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDY 85
Cdd:cd19935    1 ILVVEDEKKLAEYLKKGLTEEGYAVDVAYDGEDG-LHLALTNEYDLIILDVMLPGLDGLEVLRRLRAAGKQTPVLMLTAR 79

                         90       100
                 ....*....|....*....|
gi 490419162  86 AEVNTAVESMKLGSIDYIPK 105
Cdd:cd19935   80 DSVEDRVKGLDLGADDYLVK 99

LytT

COG3279

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

5-203

9.32e-08

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

Pssm-ID: 442510 [Multi-domain] Cd Length: 235 Bit Score: 52.51 E-value: 9.32e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSRegYRNMK----AYHLSTAKKHLQQaTDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFI 80
Cdd:COG3279    3 KILIVDDEPLARERLERLLEK--YPDLEvvgeASNGEEALELLEE-HKPDLVFLDIQMPGLDGFELARQLRELDPPPPII 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  81 IMTDYAEVntAVESMKLGSIDYIPK-----QLVE--DKLVPLIRSILKERQAGQRRMPIFAREGSAFQKIMHR-IRLVAA 152
Cdd:COG3279   80 FTTAYDEY--ALEAFEVNAVDYLLKpideeRLAKalEKAKERLEAKAAAEASPEEKDRIFVKSGGKLVKIPLDdILYIEA 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 490419162 153 TDMSVMIFGENGTgkehiaHLLHDKSKragkpfvavdcgSLSKELAPSAFF 203
Cdd:COG3279  158 EGNYVKIHTKDKK------YLVRKTLK------------ELEEKLPPKQFF 190

REC_CheY_CheY3

cd19923

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

5-120

2.80e-07

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: 48.87 E-value: 2.80e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGYRNM-KAYHLSTAKKHLQQAtDNDIVVADLRLPDGSGIDLLCWMRKEGKMQ--PFII 81
Cdd:cd19923    2 KVLVVDDFSTMRRIIKNLLKELGFNNVeEAEDGVDALEKLKAG-GFDFVITDWNMPNMDGLELLKTIRADGALShlPVLM 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 490419162  82 MTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSIL 120
Cdd:cd19923   81 VTAEAKKENVIAAAQAGVNNYIVKPFTAATLKEKLEKIF 119

REC_OmpR_EcPhoP-like

cd19934

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

6-121

3.13e-07

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: 48.82 E-value: 3.13e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAkkHLQQATDN-DIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTD 84
Cdd:cd19934    1 LLLVEDDALLAAQLKEQLSDAGYVVDVAEDGEEA--LFQGEEEPyDLVVLDLGLPGMDGLSVLRRWRSEGRATPVLILTA 78

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 490419162  85 YAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILK 121
Cdd:cd19934   79 RDSWQDKVEGLDAGADDYLTKPFHIEELLARLRALIR 115

AAA_5

pfam07728

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

156-283

4.79e-07

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: 48.83 E-value: 4.79e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  156 SVMIFGENGTGK----EHIAHLLhdkskrAGKPFVAVdcgSLSKELAPSAFFG----------HVKGAFTGADNakkgyf 221
Cdd:pfam07728   1 GVLLVGPPGTGKtelaERLAAAL------SNRPVFYV---QLTRDTTEEDLFGrrnidpggasWVDGPLVRAAR------ 65

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490419162  222 heaEGGTLFLDEVGNLALETQQMLLRAIQERRYRPV-GDKADR--NFNVRIIAATNeDLEVSVNE 283
Cdd:pfam07728  66 ---EGEIAVLDEINRANPDVLNSLLSLLDERRLLLPdGGELVKaaPDGFRLIATMN-PLDRGLNE 126

PRK10529

DNA-binding transcriptional activator KdpE; Provisional

4-132

5.94e-07

DNA-binding transcriptional activator KdpE; Provisional

Pssm-ID: 182522 [Multi-domain] Cd Length: 225 Bit Score: 50.19 E-value: 5.94e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   4 TKIIVVEDNIVYCEYVCNMLSREGYRnmkAYHLSTAKKHLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMqPFII 81
Cdd:PRK10529   2 TNVLIVEDEQAIRRFLRTALEGDGMR---VFEAETLQRGLLEAATRkpDLIILDLGLPDGDGIEFIRDLRQWSAI-PVIV 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 490419162  82 MTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQAGQRRMPI 132
Cdd:PRK10529  78 LSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRHSATPAPDPL 128

PRK15479

transcriptional regulator TctD;

39-127

6.75e-07

transcriptional regulator TctD;

Pssm-ID: 185376 [Multi-domain] Cd Length: 221 Bit Score: 50.11 E-value: 6.75e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  39 AKKHLQQATDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRS 118
Cdd:PRK15479  35 AADHLLQSEMYALAVLDINMPGMDGLEVLQRLRKRGQTLPVLLLTARSAVADRVKGLNVGADDYLPKPFELEELDARLRA 114


                 ....*....
gi 490419162 119 ILKeRQAGQ 127
Cdd:PRK15479 115 LLR-RSAGQ 122

REC_HupR-like

cd17569

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

5-121

7.57e-07

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: 47.78 E-value: 7.57e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQaTDNDIVVADLRLPDGSGIDLLCWMRKEgkmQPF---II 81
Cdd:cd17569    2 TILLVDDEPNILKALKRLLRREGYEVLTATSGEEALEILKQ-EPVDVVISDQRMPGMDGAELLKRVRER---YPDtvrIL 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 490419162  82 MTDYAEVNTAVESMKLGSID-YIPKQLVEDKLVPLIRSILK 121
Cdd:cd17569   78 LTGYADLDAAIEAINEGEIYrFLTKPWDDEELKETIRQALE 118

PRK10336

two-component system response regulator QseB;

5-129

1.16e-06

two-component system response regulator QseB;

Pssm-ID: 182387 [Multi-domain] Cd Length: 219 Bit Score: 49.12 E-value: 1.16e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATdNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTD 84
Cdd:PRK10336   2 RILLIEDDMLIGDGIKTGLSKMGFSVDWFTQGRQGKEALYSAP-YDAVILDLTLPGMDGRDILREWREKGQREPVLILTA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 490419162  85 YAEVNTAVESMKLGSIDYI--PKQLVE--DKLVPLIRsilkeRQAGQRR 129
Cdd:PRK10336  81 RDALAERVEGLRLGADDYLckPFALIEvaARLEALMR-----RTNGQAS 124

REC_1_GGDEF

cd19921

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

5-106

1.17e-06

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

Pssm-ID: 381148 [Multi-domain] Cd Length: 115 Bit Score: 47.17 E-value: 1.17e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSRE-GYRNMKAYHLSTAKKHLQQATDNDIVVADLRLPD---GSGIDLLCwmrkeGKMQPFI 80
Cdd:cd19921    1 KVLIVEDSKTFSKVLKHLIAQElGLEVDVAETLAEAKALLEEGDDYFAALVDLNLPDapnGEAVDLVL-----EKGIPVI 75

                         90       100
                 ....*....|....*....|....*...
gi 490419162  81 IMTdyAEVNTAV-ESM-KLGSIDYIPKQ 106
Cdd:cd19921   76 VLT--GSFDEDKrETLlSKGVVDYVLKD 101

PRK10955

envelope stress response regulator transcription factor CpxR;

1-121

1.25e-06

envelope stress response regulator transcription factor CpxR;

Pssm-ID: 182864 [Multi-domain] Cd Length: 232 Bit Score: 49.42 E-value: 1.25e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   1 MNKtkIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATDndIVVADLRLPDGSGIDLLCWMRKEgKMQPFI 80
Cdd:PRK10955   1 MNK--ILLVDDDRELTSLLKELLEMEGFNVIVAHDGEQALDLLDDSID--LLLLDVMMPKKNGIDTLKELRQT-HQTPVI 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 490419162  81 IMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILK 121
Cdd:PRK10955  76 MLTARGSELDRVLGLELGADDYLPKPFNDRELVARIRAILR 116

REC_TrrA-like

cd17554

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

5-87

2.55e-06

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: 46.06 E-value: 2.55e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVED--NI--VYCEyvcnMLSREGYRNMKAyhlSTAKKHLQ--QATDNDIVVADLRLPDGSGIDLLCWMRKEGKMQP 78
Cdd:cd17554    2 KILVVDDeeNIreLYKE----ELEDEGYEVVTA---GNGEEALEklESEDPDLVILDIKMPGMDGLETLRKIREKKPDLP 74


                 ....*....
gi 490419162  79 FIIMTDYAE 87
Cdd:cd17554   75 VIICTAYSE 83

REC_RssB-like

cd17555

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

50-109

2.84e-06

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: 46.04 E-value: 2.84e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  50 DIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDYAEVNTAVESMKLGSIDYIPKQLVE 109
Cdd:cd17555   46 DLVLCDLRMPEMDGLEVLKQITKESPDTPVIVVSGAGVMSDAVEALRLGAWDYLTKPIED 105

REC_OmpR_MtPhoP-like

cd17615

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

5-121

4.25e-06

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: 45.42 E-value: 4.25e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQaTDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTD 84
Cdd:cd17615    1 RVLVVDDEPNITELLSMALRYEGWDVETAADGAEALAAARE-FRPDAVVLDIMLPDMDGLEVLRRLRADGPDVPVLFLTA 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 490419162  85 YAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILK 121
Cdd:cd17615   80 KDSVEDRIAGLTAGGDDYVTKPFSLEEVVARLRALLR 116

REC_citrate_TCS

cd19925

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

4-112

4.45e-06

phosphoacceptor receiver (REC) domain of citrate family two-component system response regulators; This family includes Lactobacillus paracasei MaeR, Escherichia coli DcuR and DpiA, Klebsiella pneumoniae CitB, as well as Bacillus DctR, MalR, and CitT. These are all response regulators of two-component systems (TCSs) from the citrate family, and are involved in the transcriptional regulation of genes associated with L-malate catabolism (MaeRK), citrate-specific fermentation (DpiAB, CitAB), plasmid inheritance (DpiAB), anaerobic fumarate respiratory system (DcuRS), and malate transport/utilization (MalKR). REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays.

Pssm-ID: 381152 [Multi-domain] Cd Length: 118 Bit Score: 45.70 E-value: 4.45e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   4 TKIIVVEDNIVYCEYVCNMLSR-EGYRNMKAYHLSTAKKHLQQATDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIM 82
Cdd:cd19925    1 INVLIVEDDPMVAEIHRAYVEQvPGFTVIGTAGTGEEALKLLKERQPDLILLDIYLPDGNGLDLLRELRAAGHDVDVIVV 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 490419162  83 TDYAEVNTAVESMKLGSIDYIPKQLVEDKL 112
Cdd:cd19925   81 TAANDVETVREALRLGVVDYLIKPFTFERL 110

REC_OmpR_KdpE-like

cd17620

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

6-105

7.08e-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: 44.46 E-value: 7.08e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRNMKAyhlSTAKKHLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMqPFIIMT 83
Cdd:cd17620    1 ILVIEDEPQIRRFLRTALEAHGYRVFEA---ETGQEGLLEAATRkpDLIILDLGLPDMDGLEVIRRLREWSAV-PVIVLS 76

                         90       100
                 ....*....|....*....|..
gi 490419162  84 DYAEVNTAVESMKLGSIDYIPK 105
Cdd:cd17620   77 ARDEESDKIAALDAGADDYLTK 98

REC_Spo0F-like

cd17553

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

5-112

8.40e-06

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: 44.85 E-value: 8.40e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGYRNMKAyhlSTAKKHLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIM 82
Cdd:cd17553    2 KILIVDDQYGIRILLNEVFNKEGYQTFQA---ANGLQALDIVTKErpDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIM 78

                         90       100       110
                 ....*....|....*....|....*....|
gi 490419162  83 TDYAEVNTAVESMKLGSIDYIPKQLVEDKL 112
Cdd:cd17553   79 TAYGELDMIQESKELGALTHFAKPFDIDEI 108

REC_hyHK_CKI1_RcsC-like

cd17546

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

6-116

1.39e-05

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: 44.00 E-value: 1.39e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRNMKAyhlSTAKKHLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMQ---PFI 80
Cdd:cd17546    1 VLVVDDNPVNRKVLKKLLEKLGYEVDVA---ENGQEALELLKEEpfDLVLMDLQMPVMDGLEATRRIRELEGGGrrtPII 77

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 490419162  81 IMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLI 116
Cdd:cd17546   78 ALTANALEEDREKCLEAGMDDYLSKPVKLDQLKEVL 113

PRK11083

DNA-binding response regulator CreB; Provisional

1-141

2.19e-05

DNA-binding response regulator CreB; Provisional

Pssm-ID: 236838 [Multi-domain] Cd Length: 228 Bit Score: 45.34 E-value: 2.19e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   1 MNKTKIIVVEDNIVYCEYVCNMLSREGYrNMKAYHLSTAKKHLQQATDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFI 80
Cdd:PRK11083   1 MQQPTILLVEDEQAIADTLVYALQSEGF-TVEWFERGLPALDKLRQQPPDLVILDVGLPDISGFELCRQLLAFHPALPVI 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490419162  81 IMT-DYAEVNTAVeSMKLGSIDYIPKQLVEDKLVPLIRSILKERQAGQRRMPifAREGSAFQ 141
Cdd:PRK11083  80 FLTaRSDEVDRLV-GLEIGADDYVAKPFSPREVAARVRTILRRVKKFAAPSP--VIRIGHFE 138

psREC_PRR

cd17582

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

50-105

2.41e-05

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

Pssm-ID: 381120 [Multi-domain] Cd Length: 104 Bit Score: 43.16 E-value: 2.41e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 490419162  50 DIVVADLRLPDGSGIDLLCW-MR-KEGKMQPFIIMTDYAEVNTAVESMKLGSIDYIPK 105
Cdd:cd17582   46 DLILTEVDLPVSSGFKLLSYiMRhKICKNIPVIMMSSQDSVGVVFKCLSKGAADYLVK 103

REC_OmpR_BsPhoP-like

cd19937

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

8-121

2.85e-05

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: 43.03 E-value: 2.85e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   8 VVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAkkhLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMQ--PFIIMT 83
Cdd:cd19937    2 VVDDEEDIVELLKYNLEKEGYEVVTAYDGEEA---LKRAKDEkpDLIILDLMLPGIDGLEVCRILRSDPKTSsiPIIMLT 78

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 490419162  84 DYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILK 121
Cdd:cd19937   79 AKGEEFDKVLGLELGADDYITKPFSPRELLARVKAVLR 116

REC

smart00448

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

5-59

3.15e-05

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

Pssm-ID: 214668 [Multi-domain] Cd Length: 55 Bit Score: 41.40 E-value: 3.15e-05

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 490419162     5 KIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQaTDNDIVVADLRLP 59
Cdd:smart00448   2 RILVVDDDPLLRELLKALLEKEGYEVDEATDGEEALELLKE-EKPDLILLDIMMP 55

REC_NarL-like

cd17535

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

50-120

3.58e-05

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: 42.88 E-value: 3.58e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490419162  50 DIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSIL 120
Cdd:cd17535   46 DVVLMDLSMPGMDGIEALRRLRRRYPDLKVIVLTAHDDPEYVLRALKAGAAGYLLKDSSPEELIEAIRAVA 116

REC_hyHK_blue-like

cd18161

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

6-88

4.09e-05

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: 42.33 E-value: 4.09e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATDNDIVVADLRLPDG-SGIDLLCWMRKEGKMQPFIIMTD 84
Cdd:cd18161    1 VLVVEDDPDVRRLTAEVLEDLGYTVLEAASGDEALDLLESGPDIDLLVTDVIMPGGmNGSQLAEEARRRRPDLKVLLTSG 80


                 ....
gi 490419162  85 YAEV 88
Cdd:cd18161   81 YAEN 84

PRK01905

Fis family transcriptional regulator;

403-433

4.64e-05

Fis family transcriptional regulator;

Pssm-ID: 179348 [Multi-domain] Cd Length: 77 Bit Score: 41.72 E-value: 4.64e-05

                         10        20        30
                 ....*....|....*....|....*....|.
gi 490419162 403 LKQANGNRSVAAELLGIGRTTLYSKLEEYGL 433
Cdd:PRK01905  46 MEQAGGNQSLAAEYLGINRNTLRKKLQQHGL 76

orf27

CHL00148

Ycf27; Reviewed

2-121

7.23e-05

Ycf27; Reviewed

Pssm-ID: 214376 [Multi-domain] Cd Length: 240 Bit Score: 43.94 E-value: 7.23e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   2 NKTKIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATDnDIVVADLRLP--DGSGIdllC-WMRKEGKMqP 78
Cdd:CHL00148   5 SKEKILVVDDEAYIRKILETRLSIIGYEVITASDGEEALKLFRKEQP-DLVILDVMMPklDGYGV---CqEIRKESDV-P 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 490419162  79 FIIMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILK 121
Cdd:CHL00148  80 IIMLTALGDVSDRITGLELGADDYVVKPFSPKELEARIRSVLR 122

REC_OmpR_MtrA-like

cd17626

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

5-120

8.09e-05

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: 42.07 E-value: 8.09e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQqATDNDIVVADLRLPDGSGIDLLCWMRKEGKMqPFIIMTD 84
Cdd:cd17626    2 RILVVDDDAALAEMIGIVLRGEGFDPAFCGDGTQALAAFR-EVRPDLVLLDLMLPGIDGIEVCRQIRAESGV-PIVMLTA 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 490419162  85 YAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSIL 120
Cdd:cd17626   80 KSDTVDVVLGLESGADDYVAKPFKPKELVARIRARL 115

REC_CpdR_CckA-like

cd18160

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

5-105

1.02e-04

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: 41.33 E-value: 1.02e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTD 84
Cdd:cd18160    1 TILLADDEPSVRKFIVTTLKKAGYAVTEAESGAEALEKLQQGKDIDIVVTDIVMPEMDGIELAREARKIDPDVKILFISG 80

                         90       100
                 ....*....|....*....|.
gi 490419162  85 YAEVNTAVESMKLGSIDYIPK 105
Cdd:cd18160   81 GAAAAPELLSDAVGDNATLKK 101

REC_HP-RR-like

cd17573

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

6-116

1.54e-04

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: 40.88 E-value: 1.54e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQqATDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDY 85
Cdd:cd17573    1 ILLIEDDSTLGKEISKGLNEKGYQADVAESLKDGEYYID-IRNYDLVLVSDKLPDGNGLSIVSRIKEKHPSIVVIVLSDN 79

                         90       100       110
                 ....*....|....*....|....*....|.
gi 490419162  86 AEVNTAVESMKLGSIDYIPKQLVEDKLVPLI 116
Cdd:cd17573   80 PKTEQEIEAFKEGADDYIAKPFDFKVLVARI 110

REC_OmpR_VirG

cd17594

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

5-117

1.78e-04

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: 40.89 E-value: 1.78e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATdNDIVVADLRLPDGSGIDLLCWMRKEGKMqPFIIMTD 84
Cdd:cd17594    1 HVLVVDDDAAMRHLLILYLRERGFDVTAAADGAEEARLMLHRR-VDLVLLDLRLGQESGLDLLRTIRARSDV-PIIIISG 78

                         90       100       110
                 ....*....|....*....|....*....|....
gi 490419162  85 YAEVNTA-VESMKLGSIDYIPKQLVEDKLVPLIR 117
Cdd:cd17594   79 DRRDEIDrVVGLELGADDYLAKPFGLRELLARVR 112

fis

PRK00430

DNA-binding transcriptional regulator Fis;

408-433

1.84e-04

DNA-binding transcriptional regulator Fis;

Pssm-ID: 179020 [Multi-domain] Cd Length: 95 Bit Score: 40.43 E-value: 1.84e-04

                         10        20
                 ....*....|....*....|....*.
gi 490419162 408 GNRSVAAELLGIGRTTLYSKLEEYGL 433
Cdd:PRK00430  69 GNQTRAALMLGINRGTLRKKLKKYGM 94

REC_DivK-like

cd17548

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

5-105

2.86e-04

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: 40.22 E-value: 2.86e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGYRNMKAyhlSTAKKHLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMQ--PFI 80
Cdd:cd17548    1 KILIVEDNPLNMKLARDLLESAGYEVLEA---ADGEEALEIARKEkpDLILMDIQLPGMDGLEATRLLKEDPATRdiPVI 77

                         90       100
                 ....*....|....*....|....*
gi 490419162  81 IMTDYAEVNTAVESMKLGSIDYIPK 105
Cdd:cd17548   78 ALTAYAMKGDREKILEAGCDGYISK 102

REC_OmpR_RegX3-like

cd17621

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

6-105

5.92e-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: 39.10 E-value: 5.92e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRNMKAyhlSTAKKHLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMT 83
Cdd:cd17621    1 VLVVEDEESFSDPLAYLLRKEGFEVTVA---TDGPAALAEFDRAgaDIVLLDLMLPGLSGTEVCRQLRARSNVPVIMVTA 77

                         90       100
                 ....*....|....*....|..
gi 490419162  84 DYAEVNTAVeSMKLGSIDYIPK 105
Cdd:cd17621   78 KDSEIDKVV-GLELGADDYVTK 98

REC_OmpR_YycF-like

cd17614

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

6-121

6.02e-04

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

Pssm-ID: 381130 [Multi-domain] Cd Length: 115 Bit Score: 39.33 E-value: 6.02e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQaTDNDIVVADLRLPDGSGIDLLCWMRKEGKMqPFIIMTDY 85
Cdd:cd17614    1 ILVVDDEKPISDILKFNLTKEGYEVVTAYDGREALEKVEE-EQPDLILLDLMLPEKDGLEVCREVRKTSNV-PIIMLTAK 78

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 490419162  86 AEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILK 121
Cdd:cd17614   79 DSEVDKVLGLELGADDYVTKPFSNRELLARVKANLR 114

REC_PA4781-like

cd19920

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

6-105

7.07e-04

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: 39.03 E-value: 7.07e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRNMKAyhlSTAKKHLQQATDN--DIVVADLRLPDGSGIDLlCWMRKEGKMQ---PFI 80
Cdd:cd19920    1 ILIVDDVPDNLRLLSELLRAAGYRVLVA---TDGQQALQRAQAEppDLILLDVMMPGMDGFEV-CRRLKADPATrhiPVI 76

                         90       100
                 ....*....|....*....|....*
gi 490419162  81 IMTDYAEVNTAVESMKLGSIDYIPK 105
Cdd:cd19920   77 FLTALTDTEDKVKGFELGAVDYITK 101

PRK10610

chemotaxis protein CheY;

5-112

7.37e-04

chemotaxis protein CheY;

Pssm-ID: 170568 [Multi-domain] Cd Length: 129 Bit Score: 39.57 E-value: 7.37e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATDNDIVVADLRLPDGSGIDLLCWMRKEGKMQ--PFIIM 82
Cdd:PRK10610   7 KFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGFGFVISDWNMPNMDGLELLKTIRADGAMSalPVLMV 86

                         90       100       110
                 ....*....|....*....|....*....|....
gi 490419162  83 TDYAEVNTAVESMKLGSIDYIPKQL----VEDKL 112
Cdd:PRK10610  87 TAEAKKENIIAAAQAGASGYVVKPFtaatLEEKL 120

REC_2_GGDEF

cd17544

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

4-105

8.00e-04

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: 39.04 E-value: 8.00e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   4 TKIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIM- 82
Cdd:cd17544    1 IKVLVVDDSATSRNHLRALLRRHNFQVLEAANGQEALEVLEQHPDIKLVITDYNMPEMDGFELVREIRKKYSRDQLAIIg 80

                         90       100
                 ....*....|....*....|....
gi 490419162  83 -TDYAEVNTAVESMKLGSIDYIPK 105
Cdd:cd17544   81 iSASGDNALSARFIKAGANDFLTK 104

ompR

PRK09468

osmolarity response regulator; Provisional

4-125

8.49e-04

osmolarity response regulator; Provisional

Pssm-ID: 181883 [Multi-domain] Cd Length: 239 Bit Score: 40.73 E-value: 8.49e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   4 TKIIVVEDNIVYCEYVCNMLSREGYRnMKAYHLSTAKKHLQQATDNDIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMT 83
Cdd:PRK09468   6 YKILVVDDDMRLRALLERYLTEQGFQ-VRSAANAEQMDRLLTRESFHLMVLDLMLPGEDGLSICRRLRSQNNPTPIIMLT 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 490419162  84 DYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKeRQA 125
Cdd:PRK09468  85 AKGEEVDRIVGLEIGADDYLPKPFNPRELLARIRAVLR-RQA 125

REC_OmpR_ArcA_TorR-like

cd17619

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

6-117

9.37e-04

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: 38.91 E-value: 9.37e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQAtDNDIVVADLRLPDGSGIDLLCWMRKEGKMqPFIIMTDY 85
Cdd:cd17619    3 ILIVEDEPVTRATLKSYFEQEGYDVSEAGDGEEMRQILARQ-DIDLVLLDINLPGKDGLSLTRELREQSEV-GIILVTGR 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 490419162  86 AEVNTAVESMKLGSIDYIPKQLVEDKLVPLIR 117
Cdd:cd17619   81 DDEVDRIVGLEIGADDYVTKPFNPRELLVRAK 112

REC_OmpR_kpRstA-like

cd17622

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

4-121

1.05e-03

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: 38.90 E-value: 1.05e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   4 TKIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQaTDNDIVVADLRLPdgsGIDLLCWMRK-EGKMQ-PFII 81
Cdd:cd17622    1 TRILLVEDDPKLARLIADFLESHGFNVVVEHRGDRALEVIAR-EKPDAVLLDIMLP---GIDGLTLCRDlRPKYQgPILL 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 490419162  82 MTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILK 121
Cdd:cd17622   77 LTALDSDIDHILGLELGADDYVVKPVEPAVLLARLRALLR 116

REC_RpfG-like

cd17551

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

5-105

1.14e-03

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: 38.58 E-value: 1.14e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQATDNDIVVADLRLPDGSGIDLLCWMRKEGKMQ--PFIIM 82
Cdd:cd17551    2 RILIVDDNPTNLLLLEALLRSAGYLEVVSFTDPREALAWCRENPPDLILLDYMMPGMDGLEFIRRLRALPGLEdvPIVMI 81

                         90       100
                 ....*....|....*....|...
gi 490419162  83 TDYAEVNTAVESMKLGSIDYIPK 105
Cdd:cd17551   82 TADTDREVRLRALEAGATDFLTK 104

REC_hyHK

cd17598

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

6-120

2.22e-03

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: 37.69 E-value: 2.22e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRNMKAYHLSTAKKHLQQaTDNDIVVADLRLPDGSGIDLLCWMRKEGKMQ--PFIIMT 83
Cdd:cd17598    1 ILIVEDSPTQAEQLKHILEEQGYKVQVARNGREALAMLAE-HRPTLVISDIVMPEMDGYELCRKIKSDPDLKdiPVILLT 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 490419162  84 DYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSIL 120
Cdd:cd17598   80 TLSDPRDVIRGLECGADNFITKPYDEKYLLSRIKYIL 116

PRK10430

two-component system response regulator DcuR;

36-105

3.77e-03

two-component system response regulator DcuR;

Pssm-ID: 182454 [Multi-domain] Cd Length: 239 Bit Score: 38.94 E-value: 3.77e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490419162  36 LSTAKKHLQQATDN-DIVVADLRLPDGSGIDLLCWMRKEGKMQPFIIMTDYAEVNTAVESMKLGSIDYIPK 105
Cdd:PRK10430  36 LEQAKEIIFNSDTPiDLILLDIYMQQENGLDLLPVLHEAGCKSDVIVISSAADAATIKDSLHYGVVDYLIK 106

AAA

pfam00004

ATPase family associated with various cellular activities (AAA); AAA family proteins often ...

157-275

3.80e-03

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.

Pssm-ID: 459627 [Multi-domain] Cd Length: 130 Bit Score: 37.57 E-value: 3.80e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162  157 VMIFGENGTGKEHIAHLLhdkSKRAGKPFVAVDCGSL-SKELAPSAffGHVKGAFTGADNAKKGyfheaeggTLFLDEVG 235
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAV---AKELGAPFIEISGSELvSKYVGESE--KRLRELFEAAKKLAPC--------VIFIDEID 67

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 490419162  236 NLAL-----------ETQQMLLRAIQERRyrpvgdkaDRNFNVRIIAATNE 275
Cdd:pfam00004  68 ALAGsrgsggdsesrRVVNQLLTELDGFT--------SSNSKVIVIAATNR 110

CitB

COG2197

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

3-67

3.84e-03

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: 37.56 E-value: 3.84e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490419162   3 KTKIIVVEDNIVYCEYVCNMLSRE-GYRNMKAYHLSTAKKHLQQATDNDIVVADLRLPDGSGIDLL 67
Cdd:COG2197    1 MIRVLIVDDHPLVREGLRALLEAEpDIEVVGEAADGEEALELLEELRPDVVLLDIRMPGMDGLEAL 66

REC_2_DhkD-like

cd17580

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

6-86

4.10e-03

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: 37.05 E-value: 4.10e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   6 IIVVEDNIVYCEYVCNMLSREGYRNMKAYhlsTAKKHLQQATDN--DIVVADLRLPDGSGIDLLCWMRKEGKMQ--PFII 81
Cdd:cd17580    1 ILVVDDNEDAAEMLALLLELEGAEVTTAH---SGEEALEAAQRFrpDVILSDIGMPGMDGYELARRLRELPWLAntPAIA 77


                 ....*
gi 490419162  82 MTDYA 86
Cdd:cd17580   78 LTGYG 82

PRK11517

DNA-binding response regulator HprR;

5-132

4.35e-03

DNA-binding response regulator HprR;

Pssm-ID: 183172 [Multi-domain] Cd Length: 223 Bit Score: 38.34 E-value: 4.35e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGYRNMKAyhlSTAKKHLQQATDND--IVVADLRLPDGSGIDLLCWMRKeGKMQPFIIM 82
Cdd:PRK11517   2 KILLIEDNQRTQEWVTQGLSEAGYVIDAV---SDGRDGLYLALKDDyaLIILDIMLPGMDGWQILQTLRT-AKQTPVICL 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 490419162  83 TDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQAGQRRMPI 132
Cdd:PRK11517  78 TARDSVDDRVRGLDSGANDYLVKPFSFSELLARVRAQLRQHHALNSTLEI 127

PRK15369

two component system response regulator;

1-124

6.93e-03

two component system response regulator;

Pssm-ID: 185267 [Multi-domain] Cd Length: 211 Bit Score: 37.75 E-value: 6.93e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   1 MNKTKIIVVEDNivycEYVCNmlsreGYRNMKA----YHLSTAKK------HLQQATDNDIVVADLRLPDGSGIDLLCWM 70
Cdd:PRK15369   1 MKNYKILLVDDH----ELIIN-----GIKNMLApyprYKIVGQVDnglevyNACRQLEPDIVILDLGLPGMNGLDVIPQL 71

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 490419162  71 RKEGKMQPFIIMTDYAEVNTAVESMKLGSIDYIPKQLVEDKLVPLIRSILKERQ 124
Cdd:PRK15369  72 HQRWPAMNILVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTVAVGKR 125

REC_DC-like

cd17534

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

5-87

8.64e-03

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: 36.23 E-value: 8.64e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490419162   5 KIIVVEDNIVYCEYVCNMLSREGYRNMKayHLSTAKKHLQQATDN--DIVVADLRLPDG-SGIDLLCWMRKEGKMqPFII 81
Cdd:cd17534    2 KILIVEDEAIIALDLKEILESLGYEVVG--IADSGEEAIELAEENkpDLILMDINLKGDmDGIEAAREIREKFDI-PVIF 78


                 ....*.
gi 490419162  82 MTDYAE 87
Cdd:cd17534   79 LTAYSD 84

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