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Conserved domains on  [gi|503772589|ref|WP_014006665|]
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sigma-54-dependent Fis family transcriptional regulator [Collimonas fungivorans]

Protein Classification

sigma-54 interaction domain-containing protein( domain architecture ID 11467367)

sigma-54 interaction domain-containing protein may be a sigma-54 dependent transcriptional regulator similar to FisR, NtrC, NifA, and RocR

CATH:  1.10.8.60
Gene Ontology:  GO:0005524|GO:0006355|GO:0008134
PubMed:  12618438|8407777

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 1-466 9.96e-162

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: 464.63  E-value: 9.96e-162
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589   1 MDTELASALAIFSQLFDAMPQPVAIIDSEGNYVYYNQESAKIDAYPAERAVGHPLLDIYPamdaeSSTLLQALHHGKRYT 80
Cdd:COG3829    2 EELELKELEEELEAILDSLDDGIIVVDADGRITYVNRAAERILGLPREEVIGKNVTELIP-----NSPLLEVLKTGKPVT 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  81 GAFQafiNAQGRLVQQIHTTLPLLnRRGAVVGAVEIARDL----AAAGSDDGASAIAPNKQEACRHGIVSQDPAMQVLIR 156
Cdd:COG3829   77 GVIQ---KTGGKGKTVIVTAIPIF-EDGEVIGAVETFRDItelkRLERKLREEELERGLSAKYTFDDIIGKSPAMKELLE 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 157 QAEALGKAGVNVLLCGETGTGKELFARLLHQSSQRAGAPspslspFVVLNCAAIPETLFESTLFGTARGAFTGA--QERQ 234
Cdd:COG3829  153 LAKRVAKSDSTVLILGESGTGKELFARAIHNASPRRDGP------FVAVNCAAIPENLLESELFGYEKGAFTGAkkGGKP 226

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 235 GLIETANSGTLFLDELNSLPWSVQGKLLRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAARKLRPDLLYRLNIGQ 314
Cdd:COG3829  227 GLFELADGGTLFLDEIGEMPLSLQAKLLRVLQEKEVRRVGGTKPIPVDVRIIAATNRDLEEMVEEGRFREDLYYRLNVIP 306

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 315 LSIPPLRERCGDIPLLAEAFLHKHRGVAGGRVKRIAPAAMRQLQACRWPGNVRMLENVMQRSLIFCEtGDELQAIWIGED 394
Cdd:COG3829  307 IHIPPLRERKEDIPLLAEHFLEKFNKKYGKNIKGISPEALELLLAYDWPGNVRELENVIERAVVLSE-GDVITPEHLPEY 385

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503772589 395 AADTRSHDAPAEPvadtqgqgsgLSLEEQMSSYEKTLLIGLLKEHAS-LSEVARRCAIPRATLQYKLKKHNIT 466
Cdd:COG3829  386 LLEEAEAASAAEE----------GSLKEALEEVEKELIEEALEKTGGnKSKAAKALGISRSTLYRKLKKYGIK 448
 
Name Accession Description Interval E-value
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 1-466 9.96e-162

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: 464.63  E-value: 9.96e-162
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589   1 MDTELASALAIFSQLFDAMPQPVAIIDSEGNYVYYNQESAKIDAYPAERAVGHPLLDIYPamdaeSSTLLQALHHGKRYT 80
Cdd:COG3829    2 EELELKELEEELEAILDSLDDGIIVVDADGRITYVNRAAERILGLPREEVIGKNVTELIP-----NSPLLEVLKTGKPVT 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  81 GAFQafiNAQGRLVQQIHTTLPLLnRRGAVVGAVEIARDL----AAAGSDDGASAIAPNKQEACRHGIVSQDPAMQVLIR 156
Cdd:COG3829   77 GVIQ---KTGGKGKTVIVTAIPIF-EDGEVIGAVETFRDItelkRLERKLREEELERGLSAKYTFDDIIGKSPAMKELLE 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 157 QAEALGKAGVNVLLCGETGTGKELFARLLHQSSQRAGAPspslspFVVLNCAAIPETLFESTLFGTARGAFTGA--QERQ 234
Cdd:COG3829  153 LAKRVAKSDSTVLILGESGTGKELFARAIHNASPRRDGP------FVAVNCAAIPENLLESELFGYEKGAFTGAkkGGKP 226

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 235 GLIETANSGTLFLDELNSLPWSVQGKLLRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAARKLRPDLLYRLNIGQ 314
Cdd:COG3829  227 GLFELADGGTLFLDEIGEMPLSLQAKLLRVLQEKEVRRVGGTKPIPVDVRIIAATNRDLEEMVEEGRFREDLYYRLNVIP 306

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 315 LSIPPLRERCGDIPLLAEAFLHKHRGVAGGRVKRIAPAAMRQLQACRWPGNVRMLENVMQRSLIFCEtGDELQAIWIGED 394
Cdd:COG3829  307 IHIPPLRERKEDIPLLAEHFLEKFNKKYGKNIKGISPEALELLLAYDWPGNVRELENVIERAVVLSE-GDVITPEHLPEY 385

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503772589 395 AADTRSHDAPAEPvadtqgqgsgLSLEEQMSSYEKTLLIGLLKEHAS-LSEVARRCAIPRATLQYKLKKHNIT 466
Cdd:COG3829  386 LLEEAEAASAAEE----------GSLKEALEEVEKELIEEALEKTGGnKSKAAKALGISRSTLYRKLKKYGIK 448
nifA TIGR01817
Nif-specific regulatory protein; This model represents NifA, a DNA-binding regulatory protein ...
 104-469 7.74e-85

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


Pssm-ID: 273817 [Multi-domain]  Cd Length: 534  Bit Score: 270.43  E-value: 7.74e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  104 LNRRGAVVGAVEI--ARDLAAAGSDDGASAiaPNKQEACRHGIVSQDPAMQVLIRQAEALGKAGVNVLLCGETGTGKELF 181
Cdd:TIGR01817 158 LHRLVAQRRERLIaeAVQLSKQLRDKAPEI--ARRRSGKEDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELI 235

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  182 ARLLHQSSQRAGAPspslspFVVLNCAAIPETLFESTLFGTARGAFTGAQ-ERQGLIETANSGTLFLDELNSLPWSVQGK 260
Cdd:TIGR01817 236 AKAIHYLSPRAKRP------FVKVNCAALSETLLESELFGHEKGAFTGAIaQRKGRFELADGGTLFLDEIGEISPAFQAK 309

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  261 LLRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAARKLRPDLLYRLNIGQLSIPPLRERCGDIPLLAEAFLHKHRg 340
Cdd:TIGR01817 310 LLRVLQEGEFERVGGNRTLKVDVRLVAATNRDLEEAVAKGEFRADLYYRINVVPIFLPPLRERREDIPLLAEAFLEKFN- 388

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  341 VAGGRVKRIAPAAMRQLQACRWPGNVRMLENVMQR------------SLIFCETGDELQA-IWIGED--------AADTR 399
Cdd:TIGR01817 389 RENGRPLTITPSAIRVLMSCKWPGNVRELENCLERtatlsrsgtitrSDFSCQSGQCLSPmLAKTCPhghisidpLAGTT 468

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503772589  400 SHDAPAEPVADTQGQGSGLSLEeqmssyEKTLLIGLLKEHASLSEVARRC--AIPRaTLQYKLKKHNITLHR 469
Cdd:TIGR01817 469 PPHSPASAALPGEPGLSGPTLS------ERERLIAALEQAGWVQAKAARLlgMTPR-QVGYALRKLNIEMKK 533
Sigma54_activat pfam00158
Sigma-54 interaction domain;
144-315 2.44e-82

Sigma-54 interaction domain;


Pssm-ID: 425491 [Multi-domain]  Cd Length: 168  Bit Score: 251.55  E-value: 2.44e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  144 IVSQDPAMQVLIRQAEALGKAGVNVLLCGETGTGKELFARLLHQSSQRAGAPspslspFVVLNCAAIPETLFESTLFGTA 223
Cdd:pfam00158   1 IIGESPAMQEVLEQAKRVAPTDAPVLITGESGTGKELFARAIHQLSPRADGP------FVAVNCAAIPEELLESELFGHE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  224 RGAFTGA-QERQGLIETANSGTLFLDELNSLPWSVQGKLLRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAARKL 302
Cdd:pfam00158  75 KGAFTGAdSDRKGLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTKPIKVDVRIIAATNRDLEEAVAEGRF 154

                         170
                  ....*....|...
gi 503772589  303 RPDLLYRLNIGQL 315
Cdd:pfam00158 155 REDLYYRLNVIPI 167
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
109-462 4.00e-82

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 262.80  E-value: 4.00e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 109 AVVGAVEIARDLAAAGSDDGASAiAPNKQEACRHG-IVSQDPAMQVLIRQAEALGKAGVNVLLCGETGTGKELFARLLHQ 187
Cdd:PRK05022 154 ATLRNALLIEQLESQAELPQDVA-EFLRQEALKEGeMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHA 232

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 188 SSQRAGAPspslspFVVLNCAAIPETLFESTLFGTARGAFTGA-QERQGLIETANSGTLFLDELNSLPWSVQGKLLRVLQ 266
Cdd:PRK05022 233 ASPRADKP------LVYLNCAALPESLAESELFGHVKGAFTGAiSNRSGKFELADGGTLFLDEIGELPLALQAKLLRVLQ 306

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 267 DGMFSRVGSNKEIRADLRVIAAAN-ETQQEMLAARkLRPDLLYRLNIGQLSIPPLRERCGDIPLLAEAFLHKHRGVAGGR 345
Cdd:PRK05022 307 YGEIQRVGSDRSLRVDVRVIAATNrDLREEVRAGR-FRADLYHRLSVFPLSVPPLRERGDDVLLLAGYFLEQNRARLGLR 385

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 346 VKRIAPAAMRQLQACRWPGNVRMLENVMQRSLIFCETGDELQAIWIGEDAADTRSHDA-PAEPVADTQGQGSGLSLEEQM 424
Cdd:PRK05022 386 SLRLSPAAQAALLAYDWPGNVRELEHVISRAALLARARGAGRIVTLEAQHLDLPAEVAlPPPEAAAAPAAVVSQNLREAT 465

                        330       340       350
                 ....*....|....*....|....*....|....*....
gi 503772589 425 SSYEKTLLIGLLKEHA-SLSEVARRCAIPRATLqYKLKK 462
Cdd:PRK05022 466 EAFQRQLIRQALAQHQgNWAAAARALELDRANL-HRLAK 503
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 149-312 1.15e-20

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: 88.36  E-value: 1.15e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 149 PAMQVLIRQAE--ALGKAGVNVLLCGETGTGKELFARLLHQSSQRAGApspslsPFVVLNCAAIPETLFESTLFGtarga 226
Cdd:cd00009    1 VGQEEAIEALReaLELPPPKNLLLYGPPGTGKTTLARAIANELFRPGA------PFLYLNASDLLEGLVVAELFG----- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 227 FTGAQERQGLIETANSGTLFLDELNSLPWSVQGKLLRVLQDGMFSRvgsnkEIRADLRVIAAANETQqemlaARKLRPDL 306
Cdd:cd00009   70 HFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLR-----IDRENVRVIGATNRPL-----LGDLDRAL 139


                 ....*.
gi 503772589 307 LYRLNI 312
Cdd:cd00009  140 YDRLDI 145
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 165-310 2.02e-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: 2.02e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589   165 GVNVLLCGETGTGKELFARLLHQSSQRAGApspslsPFVVLNCAAIPETLFES---TLFGTARGAFTGAQERQGLIETAN 241
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPGG------GVIYIDGEDILEEVLDQlllIIVGGKKASGSGELRLRLALALAR 75

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 503772589   242 S---GTLFLDELNSLPWSVQGKLLRVLQDgmfSRVGSNKEIRADLRVIAAANETQ--QEMLAARKLRPDLLYRL 310
Cdd:smart00382  76 KlkpDVLILDEITSLLDAEQEALLLLLEE---LRLLLLLKSEKNLTVILTTNDEKdlGPALLRRRFDRRIVLLL 146
 
Name Accession Description Interval E-value
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 1-466 9.96e-162

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: 464.63  E-value: 9.96e-162
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589   1 MDTELASALAIFSQLFDAMPQPVAIIDSEGNYVYYNQESAKIDAYPAERAVGHPLLDIYPamdaeSSTLLQALHHGKRYT 80
Cdd:COG3829    2 EELELKELEEELEAILDSLDDGIIVVDADGRITYVNRAAERILGLPREEVIGKNVTELIP-----NSPLLEVLKTGKPVT 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  81 GAFQafiNAQGRLVQQIHTTLPLLnRRGAVVGAVEIARDL----AAAGSDDGASAIAPNKQEACRHGIVSQDPAMQVLIR 156
Cdd:COG3829   77 GVIQ---KTGGKGKTVIVTAIPIF-EDGEVIGAVETFRDItelkRLERKLREEELERGLSAKYTFDDIIGKSPAMKELLE 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 157 QAEALGKAGVNVLLCGETGTGKELFARLLHQSSQRAGAPspslspFVVLNCAAIPETLFESTLFGTARGAFTGA--QERQ 234
Cdd:COG3829  153 LAKRVAKSDSTVLILGESGTGKELFARAIHNASPRRDGP------FVAVNCAAIPENLLESELFGYEKGAFTGAkkGGKP 226

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 235 GLIETANSGTLFLDELNSLPWSVQGKLLRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAARKLRPDLLYRLNIGQ 314
Cdd:COG3829  227 GLFELADGGTLFLDEIGEMPLSLQAKLLRVLQEKEVRRVGGTKPIPVDVRIIAATNRDLEEMVEEGRFREDLYYRLNVIP 306

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 315 LSIPPLRERCGDIPLLAEAFLHKHRGVAGGRVKRIAPAAMRQLQACRWPGNVRMLENVMQRSLIFCEtGDELQAIWIGED 394
Cdd:COG3829  307 IHIPPLRERKEDIPLLAEHFLEKFNKKYGKNIKGISPEALELLLAYDWPGNVRELENVIERAVVLSE-GDVITPEHLPEY 385

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503772589 395 AADTRSHDAPAEPvadtqgqgsgLSLEEQMSSYEKTLLIGLLKEHAS-LSEVARRCAIPRATLQYKLKKHNIT 466
Cdd:COG3829  386 LLEEAEAASAAEE----------GSLKEALEEVEKELIEEALEKTGGnKSKAAKALGISRSTLYRKLKKYGIK 448
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 136-464 7.67e-107

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: 323.45  E-value: 7.67e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 136 KQEACRHGIVSQDPAMQVLIRQAEALGKAGVNVLLCGETGTGKELFARLLHQSSQRAGAPspslspFVVLNCAAIPETLF 215
Cdd:COG2204  125 RENAEDSGLIGRSPAMQEVRRLIEKVAPSDATVLITGESGTGKELVARAIHRLSPRADGP------FVAVNCAAIPEELL 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 216 ESTLFGTARGAFTGAQE-RQGLIETANSGTLFLDELNSLPWSVQGKLLRVLQDGMFSRVGSNKEIRADLRVIAAANETQQ 294
Cdd:COG2204  199 ESELFGHEKGAFTGAVArRIGKFELADGGTLFLDEIGEMPLALQAKLLRVLQEREFERVGGNKPIPVDVRVIAATNRDLE 278

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 295 EMLAARKLRPDLLYRLNIGQLSIPPLRERCGDIPLLAEAFLHKHrGVAGGRVKRIAPAAMRQLQACRWPGNVRMLENVMQ 374
Cdd:COG2204  279 ELVEEGRFREDLYYRLNVFPIELPPLRERREDIPLLARHFLARF-AAELGKPVKLSPEALEALLAYDWPGNVRELENVIE 357

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 375 RSLIFCEtGDELQAiwigEDaadtrshdapaepvadtqgqgsglsLEEQMSSYEKTLLIGLLKEHA-SLSEVARRCAIPR 453
Cdd:COG2204  358 RAVILAD-GEVITA----ED-------------------------LPEALEEVERELIERALEETGgNVSRAAELLGISR 407

                        330
                 ....*....|.
gi 503772589 454 ATLQYKLKKHN 464
Cdd:COG2204  408 RTLYRKLKKYG 418
AcoR COG3284
Transcriptional regulator DhaR of acetoin/glycerol metabolism [Transcription];
15-464 7.53e-98

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


Pssm-ID: 442514 [Multi-domain]  Cd Length: 625  Bit Score: 306.83  E-value: 7.53e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  15 LFDAMPQPVAIIDSEGNYVYYNQESAKIDAYPAERAVGHPLLDIypaMDAESSTLLQALHHgkrytgafqafinaqgrlv 94
Cdd:COG3284  221 FLGSLSEGLLAFDEDGRIVAANRAARRLLGLADAALLGRPLEEL---FGLDLEALPDGARR------------------- 278

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  95 qQIHTTLPLLNRRGAVVGAVEIARDLAAAGSDDGASAIAPnkqeACRHGIVSQDPAMQVLIRQAEALGKAGVNVLLCGET 174
Cdd:COG3284  279 -APASPRPLRLRDGRRLGALLRLRPARRAARAAPAGAPAP----AALAALAGGDPAMRRALRRARRLADRDIPVLILGET 353

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 175 GTGKELFARLLHQSSQRAGAPspslspFVVLNCAAIPETLFESTLFGTARGAFTGAQE--RQGLIETANSGTLFLDELNS 252
Cdd:COG3284  354 GTGKELFARAIHAASPRADGP------FVAVNCAAIPEELIESELFGYEPGAFTGARRkgRPGKIEQADGGTLFLDEIGD 427

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 253 LPWSVQGKLLRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAARKLRPDLLYRLNIGQLSIPPLRERcGDIPLLAE 332
Cdd:COG3284  428 MPLALQARLLRVLQEREVTPLGGTKPIPVDVRLIAATHRDLRELVAAGRFREDLYYRLNGLTLTLPPLRER-EDLPALIE 506

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 333 AFLHKHRGVAGGRvkRIAPAAMRQLQACRWPGNVRMLENVMQRSLIFCETGDelqaiwIGEDA--ADTRSHDAPAEPVAD 410
Cdd:COG3284  507 HLLRELAAGRGPL--RLSPEALALLAAYPWPGNVRELRNVLRTALALADGGV------ITVEDlpDELRAELAAAAPAAA 578

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 503772589 411 tqgqGSGLSLEEQmssyEKTLLIGLLKEHA-SLSEVARRCAIPRATLQYKLKKHN 464
Cdd:COG3284  579 ----APLTSLEEA----ERDAILRALRACGgNVSAAARALGISRSTLYRKLKRYG 625
nifA TIGR01817
Nif-specific regulatory protein; This model represents NifA, a DNA-binding regulatory protein ...
 104-469 7.74e-85

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


Pssm-ID: 273817 [Multi-domain]  Cd Length: 534  Bit Score: 270.43  E-value: 7.74e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  104 LNRRGAVVGAVEI--ARDLAAAGSDDGASAiaPNKQEACRHGIVSQDPAMQVLIRQAEALGKAGVNVLLCGETGTGKELF 181
Cdd:TIGR01817 158 LHRLVAQRRERLIaeAVQLSKQLRDKAPEI--ARRRSGKEDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELI 235

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  182 ARLLHQSSQRAGAPspslspFVVLNCAAIPETLFESTLFGTARGAFTGAQ-ERQGLIETANSGTLFLDELNSLPWSVQGK 260
Cdd:TIGR01817 236 AKAIHYLSPRAKRP------FVKVNCAALSETLLESELFGHEKGAFTGAIaQRKGRFELADGGTLFLDEIGEISPAFQAK 309

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  261 LLRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAARKLRPDLLYRLNIGQLSIPPLRERCGDIPLLAEAFLHKHRg 340
Cdd:TIGR01817 310 LLRVLQEGEFERVGGNRTLKVDVRLVAATNRDLEEAVAKGEFRADLYYRINVVPIFLPPLRERREDIPLLAEAFLEKFN- 388

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  341 VAGGRVKRIAPAAMRQLQACRWPGNVRMLENVMQR------------SLIFCETGDELQA-IWIGED--------AADTR 399
Cdd:TIGR01817 389 RENGRPLTITPSAIRVLMSCKWPGNVRELENCLERtatlsrsgtitrSDFSCQSGQCLSPmLAKTCPhghisidpLAGTT 468

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503772589  400 SHDAPAEPVADTQGQGSGLSLEeqmssyEKTLLIGLLKEHASLSEVARRC--AIPRaTLQYKLKKHNITLHR 469
Cdd:TIGR01817 469 PPHSPASAALPGEPGLSGPTLS------ERERLIAALEQAGWVQAKAARLlgMTPR-QVGYALRKLNIEMKK 533
TyrR COG3283
Transcriptional regulator TyrR of aromatic amino acids metabolism [Transcription, Amino acid ...
 15-466 6.98e-83

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


Pssm-ID: 442513 [Multi-domain]  Cd Length: 514  Bit Score: 264.74  E-value: 6.98e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  15 LFDAMPQPVAIIDSEGNYVYYNQESAKIDAYPAERAVGHPLLDIYPAMD----AESSTLLQALHHGKrytgafqafINAQ 90
Cdd:COG3283   85 LLEALPDPVFSIDLKGKIELANPAALSLLGLSEEELIGQPLSELLKGFNfsrwLESNEPRPQSERVV---------INGQ 155

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  91 GRLVQQIHTTLPLLNRRGAVVGAVEIARDLAAAGSDdgASAIAPNKQEACRHgIVSQDPAMQVLIRQAEALGKAGVNVLL 170
Cdd:COG3283  156 DYLADILPIYLPDEEGKSILAGAVVTLKSAARLGEQ--LQALQVNDDSGFDH-IVASSPKMRQVIRQAKKMAMLDAPLLI 232

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 171 CGETGTGKELFARLLHQSSQRAGAPspslspFVVLNCAAIPETLFESTLFGTARGAFTGAQERQ-GLIETANSGTLFLDE 249
Cdd:COG3283  233 QGETGTGKELLARACHLASPRGDKP------FLALNCAALPDDVAESELFGYAPGAFGNAREGKkGLFEQANGGTVFLDE 306

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 250 LNSLPWSVQGKLLRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAARKLRPDLLYRLNIGQLSIPPLRERCGDIPL 329
Cdd:COG3283  307 IGEMSPQLQAKLLRFLQDGTFRRVGEEQEVKVDVRVICATQKDLAELVQEGEFREDLYYRLNVLTLTLPPLRERKSDILP 386

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 330 LAEAFLHKHRGVAGGRVKRIAPAAMRQLQACRWPGNVRMLENVMQRSLIFCEtGDELqaiwigeDAADTRSHD-APAEPV 408
Cdd:COG3283  387 LAEHFVARFSQQLGRPRPRLSPDLVDFLQSYPWPGNVRQLENALYRAVSLLE-GDEL-------TPEDLQLPEyAASAGL 458

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 503772589 409 ADTQGQGsglSLEEQMSSYEKTLLIGLLKEHASLSEVARRCAIPRATLQYKLKKHNIT 466
Cdd:COG3283  459 LDDLLEG---SLDEIVKRFERSLLRRLYPSYPSTRKLAKRLGVSHTAIANKLREYGIG 513
Sigma54_activat pfam00158
Sigma-54 interaction domain;
144-315 2.44e-82

Sigma-54 interaction domain;


Pssm-ID: 425491 [Multi-domain]  Cd Length: 168  Bit Score: 251.55  E-value: 2.44e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  144 IVSQDPAMQVLIRQAEALGKAGVNVLLCGETGTGKELFARLLHQSSQRAGAPspslspFVVLNCAAIPETLFESTLFGTA 223
Cdd:pfam00158   1 IIGESPAMQEVLEQAKRVAPTDAPVLITGESGTGKELFARAIHQLSPRADGP------FVAVNCAAIPEELLESELFGHE 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  224 RGAFTGA-QERQGLIETANSGTLFLDELNSLPWSVQGKLLRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAARKL 302
Cdd:pfam00158  75 KGAFTGAdSDRKGLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTKPIKVDVRIIAATNRDLEEAVAEGRF 154

                         170
                  ....*....|...
gi 503772589  303 RPDLLYRLNIGQL 315
Cdd:pfam00158 155 REDLYYRLNVIPI 167
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
109-462 4.00e-82

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 262.80  E-value: 4.00e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 109 AVVGAVEIARDLAAAGSDDGASAiAPNKQEACRHG-IVSQDPAMQVLIRQAEALGKAGVNVLLCGETGTGKELFARLLHQ 187
Cdd:PRK05022 154 ATLRNALLIEQLESQAELPQDVA-EFLRQEALKEGeMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHA 232

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 188 SSQRAGAPspslspFVVLNCAAIPETLFESTLFGTARGAFTGA-QERQGLIETANSGTLFLDELNSLPWSVQGKLLRVLQ 266
Cdd:PRK05022 233 ASPRADKP------LVYLNCAALPESLAESELFGHVKGAFTGAiSNRSGKFELADGGTLFLDEIGELPLALQAKLLRVLQ 306

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 267 DGMFSRVGSNKEIRADLRVIAAAN-ETQQEMLAARkLRPDLLYRLNIGQLSIPPLRERCGDIPLLAEAFLHKHRGVAGGR 345
Cdd:PRK05022 307 YGEIQRVGSDRSLRVDVRVIAATNrDLREEVRAGR-FRADLYHRLSVFPLSVPPLRERGDDVLLLAGYFLEQNRARLGLR 385

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 346 VKRIAPAAMRQLQACRWPGNVRMLENVMQRSLIFCETGDELQAIWIGEDAADTRSHDA-PAEPVADTQGQGSGLSLEEQM 424
Cdd:PRK05022 386 SLRLSPAAQAALLAYDWPGNVRELEHVISRAALLARARGAGRIVTLEAQHLDLPAEVAlPPPEAAAAPAAVVSQNLREAT 465

                        330       340       350
                 ....*....|....*....|....*....|....*....
gi 503772589 425 SSYEKTLLIGLLKEHA-SLSEVARRCAIPRATLqYKLKK 462
Cdd:PRK05022 466 EAFQRQLIRQALAQHQgNWAAAARALELDRANL-HRLAK 503
PRK11361 PRK11361
acetoacetate metabolism transcriptional regulator AtoC;
142-466 1.23e-76

acetoacetate metabolism transcriptional regulator AtoC;


Pssm-ID: 183099 [Multi-domain]  Cd Length: 457  Bit Score: 247.07  E-value: 1.23e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 142 HGIVSQDPAMQVLIRQAEALGKAGVNVLLCGETGTGKELFARLLHQSSQRAGAPspslspFVVLNCAAIPETLFESTLFG 221
Cdd:PRK11361 143 GHILTNSPAMMDICKDTAKIALSQASVLISGESGTGKELIARAIHYNSRRAKGP------FIKVNCAALPESLLESELFG 216

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 222 TARGAFTGAQ-ERQGLIETANSGTLFLDELNSLPWSVQGKLLRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAAR 300
Cdd:PRK11361 217 HEKGAFTGAQtLRQGLFERANEGTLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEG 296

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 301 KLRPDLLYRLNIGQLSIPPLRERCGDIPLLAEAFLHKHRGVAGGRVKRIAPAAMRQLQACRWPGNVRMLENVMQRSLIFc 380
Cdd:PRK11361 297 TFREDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWPGNIRELSNVIERAVVM- 375

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 381 ETGDELQAIWIGEDAADTRSHDAPAEPVADTQgqgsgLSLEEQMSSYEKTLLIGLLKEHA-SLSEVARRCAIPRATLQYK 459
Cdd:PRK11361 376 NSGPIIFSEDLPPQIRQPVCNAGEVKTAPVGE-----RNLKEEIKRVEKRIIMEVLEQQEgNRTRTALMLGISRRALMYK 450


                 ....*..
gi 503772589 460 LKKHNIT 466
Cdd:PRK11361 451 LQEYGID 457
PEP_resp_reg TIGR02915
PEP-CTERM-box response regulator transcription factor; Members of this protein family share ...
 140-465 1.73e-72

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: 235.80  E-value: 1.73e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  140 CRHGIVSQDPAMQVLIRQAEALGKAGVNVLLCGETGTGKELFARLLHQSSQRagapspSLSPFVVLNCAAIPETLFESTL 219
Cdd:TIGR02915 137 ALRGLITSSPGMQKICRTIEKIAPSDITVLLLGESGTGKEVLARALHQLSDR------KDKRFVAINCAAIPENLLESEL 210

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  220 FGTARGAFTGAQERQ-GLIETANSGTLFLDELNSLPWSVQGKLLRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLA 298
Cdd:TIGR02915 211 FGYEKGAFTGAVKQTlGKIEYAHGGTLFLDEIGDLPLNLQAKLLRFLQERVIERLGGREEIPVDVRIVCATNQDLKRMIA 290

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  299 ARKLRPDLLYRLNIGQLSIPPLRERCGDIPLLAEAFLHKHRGVAGGRVKRIAPAAMRQLQACRWPGNVRMLENVMQRSLI 378
Cdd:TIGR02915 291 EGTFREDLFYRIAEISITIPPLRSRDGDAVLLANAFLERFARELKRKTKGFTDDALRALEAHAWPGNVRELENKVKRAVI 370

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  379 FCEtGDELQAIWIGEDAADtrshDAPAEpvadtqgqgSGLSLEEQMSSYEKTLLI-GLLKEHASLSEVARRCAIPRATLQ 457
Cdd:TIGR02915 371 MAE-GNQITAEDLGLDARE----RAETP---------LEVNLREVRERAEREAVRkAIARVDGNIARAAELLGITRPTLY 436


                  ....*...
gi 503772589  458 YKLKKHNI 465
Cdd:TIGR02915 437 DLMKKHGI 444
PRK15429 PRK15429
formate hydrogenlyase transcriptional activator FlhA;
144-465 2.43e-68

formate hydrogenlyase transcriptional activator FlhA;


Pssm-ID: 237965 [Multi-domain]  Cd Length: 686  Bit Score: 230.87  E-value: 2.43e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 144 IVSQDPAMQVLIRQAEALGKAGVNVLLCGETGTGKELFARLLHQSSQRAGapspslSPFVVLNCAAIPETLFESTLFGTA 223
Cdd:PRK15429 378 IIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLSGRNN------RRMVKMNCAAMPAGLLESDLFGHE 451

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 224 RGAFTGAQ-ERQGLIETANSGTLFLDELNSLPWSVQGKLLRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAARKL 302
Cdd:PRK15429 452 RGAFTGASaQRIGRFELADKSSLFLDEVGDMPLELQPKLLRVLQEQEFERLGSNKIIQTDVRLIAATNRDLKKMVADREF 531

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 303 RPDLLYRLNIGQLSIPPLRERCGDIPLLAEAFLHKHRGVAGGRVKRIAPAAMRQLQACRWPGNVRMLENVMQRSLIFCEt 382
Cdd:PRK15429 532 RSDLYYRLNVFPIHLPPLRERPEDIPLLVKAFTFKIARRMGRNIDSIPAETLRTLSNMEWPGNVRELENVIERAVLLTR- 610

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 383 GDELQaIWIGEDAADTRSHdAPAEPVADTQGQGsglsleeqmssyEKTLLIGLLKEH----ASLSEVARRCAIPRATLQY 458
Cdd:PRK15429 611 GNVLQ-LSLPDITLPEPET-PPAATVVAQEGED------------EYQLIVRVLKETngvvAGPKGAAQRLGLKRTTLLS 676


                 ....*..
gi 503772589 459 KLKKHNI 465
Cdd:PRK15429 677 RMKRLGI 683
PRK10365 PRK10365
sigma-54-dependent response regulator transcription factor ZraR;
130-462 3.42e-66

sigma-54-dependent response regulator transcription factor ZraR;


Pssm-ID: 182412 [Multi-domain]  Cd Length: 441  Bit Score: 219.13  E-value: 3.42e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 130 SAIAPNKQEACRHGIVSQDPAMQVLIRQAEALGKAGVNVLLCGETGTGKELFARLLHQSSQRagapspSLSPFVVLNCAA 209
Cdd:PRK10365 127 IDAETPAVTASQFGMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHASSAR------SEKPLVTLNCAA 200

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 210 IPETLFESTLFGTARGAFTGA-QERQGLIETANSGTLFLDELNSLPWSVQGKLLRVLQDGMFSRVGSNKEIRADLRVIAA 288
Cdd:PRK10365 201 LNESLLESELFGHEKGAFTGAdKRREGRFVEADGGTLFLDEIGDISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAA 280

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 289 ANETQQEMLAARKLRPDLLYRLNIGQLSIPPLRERCGDIPLLAEAFLHKHRGVAGGRVKRIAPAAMRQLQACRWPGNVRM 368
Cdd:PRK10365 281 THRDLAAEVNAGRFRQDLYYRLNVVAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRE 360

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 369 LENVMQRSLIFCeTGDELQAIWIGEDAADTrshDAPAEPVADTQgqgsglsleeQMSSYEK-TLLIGLLKEHASLSEVAR 447
Cdd:PRK10365 361 LENAVERAVVLL-TGEYISERELPLAIAST---PIPLGQSQDIQ----------PLVEVEKeVILAALEKTGGNKTEAAR 426

                        330
                 ....*....|....*
gi 503772589 448 RCAIPRATLQYKLKK 462
Cdd:PRK10365 427 QLGITRKTLLAKLSR 441
PRK15115 PRK15115
response regulator GlrR; Provisional
 118-375 5.06e-66

response regulator GlrR; Provisional


Pssm-ID: 185070 [Multi-domain]  Cd Length: 444  Bit Score: 218.94  E-value: 5.06e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 118 RDLAAAGSDDGASAIAPNKQEACRHGIVSQDPAMQVLIRQAEALGKAGVNVLLCGETGTGKELFARLLHQSSQRAGapsp 197
Cdd:PRK15115 110 RDALYKAIDDALEQSAPATDERWREAIVTRSPLMLRLLEQARMVAQSDVSVLINGQSGTGKEILAQAIHNASPRAS---- 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 198 slSPFVVLNCAAIPETLFESTLFGTARGAFTGA-QERQGLIETANSGTLFLDELNSLPWSVQGKLLRVLQDGMFSRVGSN 276
Cdd:PRK15115 186 --KPFIAINCGALPEQLLESELFGHARGAFTGAvSNREGLFQAAEGGTLFLDEIGDMPAPLQVKLLRVLQERKVRPLGSN 263

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 277 KEIRADLRVIAAANETQQEMLAARKLRPDLLYRLNIGQLSIPPLRERCGDIPLLAEAFLHKHRGVAGGRVKRIAPAAMRQ 356
Cdd:PRK15115 264 RDIDIDVRIISATHRDLPKAMARGEFREDLYYRLNVVSLKIPALAERTEDIPLLANHLLRQAAERHKPFVRAFSTDAMKR 343

                        250
                 ....*....|....*....
gi 503772589 357 LQACRWPGNVRMLENVMQR 375
Cdd:PRK15115 344 LMTASWPGNVRQLVNVIEQ 362
glnG PRK10923
nitrogen regulation protein NR(I); Provisional
 144-462 1.05e-63

nitrogen regulation protein NR(I); Provisional


Pssm-ID: 182842 [Multi-domain]  Cd Length: 469  Bit Score: 213.58  E-value: 1.05e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 144 IVSQDPAMQVLIRQAEALGKAGVNVLLCGETGTGKELFARLLHQSSQRAGAPspslspFVVLNCAAIPETLFESTLFGTA 223
Cdd:PRK10923 140 IIGEAPAMQDVFRIIGRLSRSSISVLINGESGTGKELVAHALHRHSPRAKAP------FIALNMAAIPKDLIESELFGHE 213

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 224 RGAFTGA-QERQGLIETANSGTLFLDELNSLPWSVQGKLLRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAARKL 302
Cdd:PRK10923 214 KGAFTGAnTIRQGRFEQADGGTLFLDEIGDMPLDVQTRLLRVLADGQFYRVGGYAPVKVDVRIIAATHQNLEQRVQEGKF 293

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 303 RPDLLYRLNIGQLSIPPLRERCGDIPLLAEAFLHKHRGVAGGRVKRIAPAAMRQLQACRWPGNVRMLENVMqRSLIFCET 382
Cdd:PRK10923 294 REDLFHRLNVIRVHLPPLRERREDIPRLARHFLQVAARELGVEAKLLHPETEAALTRLAWPGNVRQLENTC-RWLTVMAA 372

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 383 GDE-----LQAIWIGEDAADTRSHDAP-------AEPVADTQGQGSGLSLEEQMSSYEKTLLIGLLKE-HASLSEVARRC 449
Cdd:PRK10923 373 GQEvliqdLPGELFESTVPESTSQMQPdswatllAQWADRALRSGHQNLLSEAQPELERTLLTTALRHtQGHKQEAARLL 452

                        330
                 ....*....|...
gi 503772589 450 AIPRATLQYKLKK 462
Cdd:PRK10923 453 GWGRNTLTRKLKE 465
PRK10820 PRK10820
transcriptional regulator TyrR;
13-472 2.53e-63

transcriptional regulator TyrR;


Pssm-ID: 236769 [Multi-domain]  Cd Length: 520  Bit Score: 213.78  E-value: 2.53e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  13 SQLFDAMPQPVAIIDSEGNYVYYNQESAKIDAYPAERAVGHPLLDIYPAMDaesstLLQALHHGKRYTGAFQAFINAQGR 92
Cdd:PRK10820  83 SALLEALPEPVLSIDMKGKVELANPASCQLFGQSEEKLRNHTAAQLINGFN-----FLRWLESEPQDSHNEHVVINGQDF 157

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  93 LVQQIHTTLPLLNRRGAVVGAVEIARDLAAAGSDdgASAIAPNKQEACRHgIVSQDPAMQVLIRQAEALGKAGVNVLLCG 172
Cdd:PRK10820 158 LMEITPVYLQDENDQHVLVGAVVMLRSTARMGRQ--LQNLAVNDDSAFSQ-IVAVSPKMRQVVEQARKLAMLDAPLLITG 234

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 173 ETGTGKELFARLLHQSSQRAGapspslSPFVVLNCAAIPETLFESTLFGTARGAFTGAQE-RQGLIETANSGTLFLDELN 251
Cdd:PRK10820 235 DTGTGKDLLAYACHLRSPRGK------KPFLALNCASIPDDVVESELFGHAPGAYPNALEgKKGFFEQANGGSVLLDEIG 308

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 252 SLPWSVQGKLLRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAARKLRPDLLYRLNIGQLSIPPLRERCGDIPLLA 331
Cdd:PRK10820 309 EMSPRMQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQKNLVELVQKGEFREDLYYRLNVLTLNLPPLRDRPQDIMPLT 388

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 332 EAFLHKHRGVAGGRVKRIAPAAMRQLQACRWPGNVRMLENVMQRSLIFCEtGDEL--QAIWIGEDAADTrshdapaePVA 409
Cdd:PRK10820 389 ELFVARFADEQGVPRPKLAADLNTVLTRYGWPGNVRQLKNAIYRALTQLE-GYELrpQDILLPDYDAAV--------AVG 459

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503772589 410 DTQGQGsglSLEEQMSSYEKTLLIGLLKEHASLSEVARRCAIPRATLQYKLKKHNITLHRSAS 472
Cdd:PRK10820 460 EDAMEG---SLDEITSRFERSVLTRLYRNYPSTRKLAKRLGVSHTAIANKLREYGLSQKKGEE 519
PRK15424 PRK15424
propionate catabolism operon regulatory protein PrpR; Provisional
 113-379 4.72e-63

propionate catabolism operon regulatory protein PrpR; Provisional


Pssm-ID: 237963 [Multi-domain]  Cd Length: 538  Bit Score: 213.43  E-value: 4.72e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 113 AVEIARDLAAAGSDDGAsAIAPNKQEACRHG---IVSQDPAMQVlIRQAEAL-GKAGVNVLLCGETGTGKELFARLLHQ- 187
Cdd:PRK15424 188 AFEDALDMTRMTLRHNT-HYATRNALRTRYVlgdLLGQSPQMEQ-VRQTILLyARSSAAVLIQGETGTGKELAAQAIHRe 265

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 188 ----SSQRAGAPSPslsPFVVLNCAAIPETLFESTLFGTARGAFTGAQE--RQGLIETANSGTLFLDELNSLPWSVQGKL 261
Cdd:PRK15424 266 yfarHDARQGKKSH---PFVAVNCGAIAESLLEAELFGYEEGAFTGSRRggRAGLFEIAHGGTLFLDEIGEMPLPLQTRL 342

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 262 LRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAARKLRPDLLYRLNIGQLSIPPLRERCGDIPLLAEAFLhkHRGV 341
Cdd:PRK15424 343 LRVLEEKEVTRVGGHQPVPVDVRVISATHCDLEEDVRQGRFRRDLFYRLSILRLQLPPLRERVADILPLAESFL--KQSL 420

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*
gi 503772589 342 AGGRVkRIAPAAMRQLQAC-------RWPGNVRMLENVMQRSLIF 379
Cdd:PRK15424 421 AALSA-PFSAALRQGLQQCetlllhyDWPGNVRELRNLMERLALF 464
pspF PRK11608
phage shock protein operon transcriptional activator; Provisional
 157-465 3.71e-61

phage shock protein operon transcriptional activator; Provisional


Pssm-ID: 236936 [Multi-domain]  Cd Length: 326  Bit Score: 202.59  E-value: 3.71e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 157 QAEALGKAGVNVLLCGETGTGKELFARLLHQSSQRAGAPspslspFVVLNCAAIPETLFESTLFGTARGAFTGAQER-QG 235
Cdd:PRK11608  21 QVSRLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGP------FISLNCAALNENLLDSELFGHEAGAFTGAQKRhPG 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 236 LIETANSGTLFLDELNSLPWSVQGKLLRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAARKLRPDLLYRLNIGQL 315
Cdd:PRK11608  95 RFERADGGTLFLDELATAPMLVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVAEGKFRADLLDRLAFDVV 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 316 SIPPLRERCGDIPLLAEAF-LHKHRGVAGGRVKRIAPAAMRQLQACRWPGNVRMLENVMQRSLIFCETGD-ELQAIWIge 393
Cdd:PRK11608 175 QLPPLRERQSDIMLMAEHFaIQMCRELGLPLFPGFTERARETLLNYRWPGNIRELKNVVERSVYRHGTSEyPLDNIII-- 252

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503772589 394 DAADTRSHDAPAEPVADTQGQGSGLSLEEQMSSYEKTLLIGLLKEhaslSEVARRCAIPRATLQYK-----LKKHNI 465
Cdd:PRK11608 253 DPFKRRPAEEAIAVSETTSLPTLPLDLREWQHQQEKELLQRSLQQ----AKFNQKRAAELLGLTYHqlralLKKHQI 325
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 170-466 7.97e-61

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: 202.00  E-value: 7.97e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 170 LCGETGTGKELFARLLHQSSQRAGAPspslspFVVLNCAAIPETLFEStlfgtargaftgaqerqglietansgtlflde 249
Cdd:COG3604  120 ILGETGTGKELVANAIHELSPRADKP------FVKVNCAALPESLLES-------------------------------- 161

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 250 lnslpwsvqgkllrvLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAARKLRPDLLYRLNIGQLSIPPLRERCGDIPL 329
Cdd:COG3604  162 ---------------LQEGEFERVGGDETIKVDVRIIAATNRDLEEEVAEGRFREDLYYRLNVFPIRLPPLRERREDIPL 226

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 330 LAEAFLHKHRGVAGGRVKRIAPAAMRQLQACRWPGNVRMLENVMQRSLIFCETGdelqaiWIGEDAADTRSHDAPAEpva 409
Cdd:COG3604  227 LAEHFLEKFSRRLGKPILRLSPEALEALMAYPWPGNVRELENVIERAVILAEGG------VLDADDLAPGSREALEE--- 297

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 503772589 410 dtqgqgsglsleeqmssYEKTLLIGLLKEHAS-LSEVARRCAIPRATLQYKLKKHNIT 466
Cdd:COG3604  298 -----------------VEREHILEALERTGGnIAGAARLLGLTPSTLRSRMKKLGIK 338
propionate_PrpR TIGR02329
propionate catabolism operon regulatory protein PrpR; At least five distinct pathways exists ...
 107-462 2.63e-58

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: 200.47  E-value: 2.63e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  107 RGAVVGAVEIARdlAAAGSDDGASAIAPNKQEACRH---GIVSQDPAMQVLIRQAEALGKAGVNVLLCGETGTGKELFAR 183
Cdd:TIGR02329 176 RQAFDDALDVAR--ATRLRQAATLRSATRNQLRTRYrldDLLGASAPMEQVRALVRLYARSDATVLILGESGTGKELVAQ 253

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  184 LLHQSSQRAGapspslSPFVVLNCAAIPETLFESTLFGTARGAFTGAQE--RQGLIETANSGTLFLDELNSLPWSVQGKL 261
Cdd:TIGR02329 254 AIHQLSGRRD------FPFVAINCGAIAESLLEAELFGYEEGAFTGARRggRTGLIEAAHRGTLFLDEIGEMPLPLQTRL 327

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  262 LRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAARKLRPDLLYRLNIGQLSIPPLRERCGDIPLLAEAFLhkHRGV 341
Cdd:TIGR02329 328 LRVLEEREVVRVGGTEPVPVDVRVVAATHCALTTAVQQGRFRRDLFYRLSILRIALPPLRERPGDILPLAAEYL--VQAA 405

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  342 AGGRVKrIAPAAMRQLQACR-------WPGNVRMLENVMQRSLIFCE-------TGDELQAIwigedaadtrshdAPAEP 407
Cdd:TIGR02329 406 AALRLP-DSEAAAQVLAGVAdplqrypWPGNVRELRNLVERLALELSampagalTPDVLRAL-------------APELA 471

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 503772589  408 VADTQGQGSGLSLEEQMSSYEKTLLIGLLKEHASLSEVARRCAIPRATLQYKLKK 462
Cdd:TIGR02329 472 EASGKGKTSALSLRERSRVEALAVRAALERFGGDRDAAAKALGISRTTLWRRLKA 526
PRK11388 PRK11388
DNA-binding transcriptional regulator DhaR; Provisional
 1-465 1.26e-49

DNA-binding transcriptional regulator DhaR; Provisional


Pssm-ID: 183114 [Multi-domain]  Cd Length: 638  Bit Score: 179.10  E-value: 1.26e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589   1 MDTELASALAIFSQ---LFDAMPQPVAIIDSEGNYVYYNQESAKIDAYPAERAVGHPLLDI--YPAMdaesstLLQALHH 75
Cdd:PRK11388 191 TDSLLAESNRHLNQlnaLLESMDDGVIAWDEQGNLQFLNAQAARLLRLDATASQGRAITELltLPAV------LQQAIKQ 264

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  76 GKRYTGAfQAFINAQGRLVQQIHTTLPLLNRRG----AVVGAVEIARDLAAagsddgasaiapNKQEACRH---GIVSQD 148
Cdd:PRK11388 265 AHPLKHV-EVTFESQGQFIDAVITLKPIIEGQGtsfiLLLHPVEQMRQLMT------------SQLGKVSHtfdHMPQDS 331

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 149 PAMQVLIRQAEALGKAGVNVLLCGETGTGKELFARLLHQSSQRAGAPspslspFVVLNCAAIPETLFESTLFGTARGAft 228
Cdd:PRK11388 332 PQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNESERAAGP------YIAVNCQLYPDEALAEEFLGSDRTD-- 403

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 229 GAQERQGLIETANSGTLFLDELNSLPWSVQGKLLRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAARKLRPDLLY 308
Cdd:PRK11388 404 SENGRLSKFELAHGGTLFLEKVEYLSPELQSALLQVLKTGVITRLDSRRLIPVDVRVIATTTADLAMLVEQNRFSRQLYY 483

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 309 RLNIGQLSIPPLRERCGDIPLLAEAFLhKHRGVAGGRVKRIAPAAMRQLQACRWPGNVRMLENVMQRSLIFCETGDelqa 388
Cdd:PRK11388 484 ALHAFEITIPPLRMRREDIPALVNNKL-RSLEKRFSTRLKIDDDALARLVSYRWPGNDFELRSVIENLALSSDNGR---- 558

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 389 iwIG-EDAADTRSHDAPAEPVADTQGQGSgLSLEEqmssYEKTLLIgllkeHAS------LSEVARRCAIPRATLQYKLK 461
Cdd:PRK11388 559 --IRlSDLPEHLFTEQATDDVSATRLSTS-LSLAE----LEKEAII-----NAAqvcggrIQEMAALLGIGRTTLWRKMK 626


                 ....
gi 503772589 462 KHNI 465
Cdd:PRK11388 627 QHGI 630
RtcR COG4650
Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a ...
 91-448 6.82e-32

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


Pssm-ID: 443688 [Multi-domain]  Cd Length: 534  Bit Score: 128.03  E-value: 6.82e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  91 GRLVQqihtTLPLLNRRGAVVGAVEIArDLAAAGSDDGASAIAPNKQEAC---RHGIVSQDPAMQVLIRQAE--AL-GKA 164
Cdd:COG4650  135 GRLLQ----TSPPRKRRAGAAGSYTII-DLDLSRYDAIASRFAQEQQEAVsflKSGIATRNAAFNRLIEQIErvAIrSRA 209

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 165 gvNVLLCGETGTGKELFAR----LLHQSSQRAGapspslsPFVVLNCAaipeTL----FESTLFGTARGAFTGAQ-ERQG 235
Cdd:COG4650  210 --PILLTGPTGAGKSQLARriyeLKKARHQVSG-------RFVEVNCA----TLrgdgAMSALFGHVKGAFTGAVsDRAG 276

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 236 LIETANSGTLFLDELNSLPWSVQGKLLRVLQDGMFSRVGSNKEIRADLRVIAAANETQQEMLAARKLRPDLLYRLNIGQL 315
Cdd:COG4650  277 LLRSADGGVLFLDEIGELGLDEQAMLLRAIEEKRFLPVGSDKEVSSDFQLIAGTNRDLRQEVAEGRFREDLLARINLWTF 356

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 316 SIPPLRERCGDIPLLAEAFLHKHRGVAGGRVKRIAPAAMRQLQ-AC----RWPGNVRMLENVMQRSLIFCETG------- 383
Cdd:COG4650  357 RLPGLAERREDIEPNLDYELARFAREQGRRVRFNKEARARYLAfATspeaLWSGNFRDLNASVTRMATLAEGGritvalv 436

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503772589 384 DE----LQAIWigedaadtrsHDAPAEPVADTQGQGSGLSLEEQMSSYEKTLL---IGLLKEHASLSEVARR 448
Cdd:COG4650  437 DEeiarLRRLW----------QRAEAATGDDLLAELLGAEQAAELDLFDRVQLaavIRVCRRSRSLSEAGRT 498
PspF COG1221
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain ...
 144-374 3.03e-31

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: 127.53  E-value: 3.03e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 144 IVSQDPAMQVLIRQAealgKA-------GVNVLLCGETGTGKELFARLLHQSSQRAGAPSPSlSPFVVLNCAAI---PET 213
Cdd:COG1221  106 LIGANGSLKNAIEQA----KAailyppkGLHTLILGPTGVGKSFFAELMYEYAIEIGVLPED-APFVVFNCADYannPQL 180

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 214 LFeSTLFGTARGAFTGAQ-ERQGLIETANSGTLFLDELNSLPWSVQGKLLRVLQDGMFSRVG-SNKEIRADLRVIAAANE 291
Cdd:COG1221  181 LM-SQLFGYVKGAFTGADkDKEGLIEKADGGILFLDEVHRLPPEGQEMLFTFMDKGIYRRLGeTEKTRKANVRIIFATTE 259

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 292 TQQEMLAARKLRpdllyRLNIgQLSIPPLRERcgdiPL-----LAEAFLHKHrgvaGGRVKR---IAPAAMRQLQACRWP 363
Cdd:COG1221  260 DPESSLLKTFLR-----RIPM-VIKLPSLEER----SLeerleLIKHFFKEE----AKRLNKpikVSKEVLKALLLYDCP 325

                        250
                 ....*....|.
gi 503772589 364 GNVRMLENVMQ 374
Cdd:COG1221  326 GNIGQLKSDIQ 336
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 149-312 1.15e-20

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: 88.36  E-value: 1.15e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 149 PAMQVLIRQAE--ALGKAGVNVLLCGETGTGKELFARLLHQSSQRAGApspslsPFVVLNCAAIPETLFESTLFGtarga 226
Cdd:cd00009    1 VGQEEAIEALReaLELPPPKNLLLYGPPGTGKTTLARAIANELFRPGA------PFLYLNASDLLEGLVVAELFG----- 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589 227 FTGAQERQGLIETANSGTLFLDELNSLPWSVQGKLLRVLQDGMFSRvgsnkEIRADLRVIAAANETQqemlaARKLRPDL 306
Cdd:cd00009   70 HFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLR-----IDRENVRVIGATNRPL-----LGDLDRAL 139


                 ....*.
gi 503772589 307 LYRLNI 312
Cdd:cd00009  140 YDRLDI 145
PAS_4 pfam08448
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 16-120 3.22e-15

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. This domain is associated to signalling systems and works as a signal sensor domain. It recognizes differently substituted aromatic hydrocarbons, oxygen, different dodecanoic acids, autoinducers, 3,5-dimethyl-pyrazin-2-ol and N-alanyl-aminoacetone (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 312075 [Multi-domain]  Cd Length: 110  Bit Score: 71.68  E-value: 3.22e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589   16 FDAMPQPVAIIDSEGNYVYYNQESAKIDAYPAERAVGHPLLDIYPAMDAE--SSTLLQALHHGKRYTgaFQAFINAQGRL 93
Cdd:pfam08448   1 LDSLPDALAVLDPDGRVRYANAAAAELFGLPPEELLGKTLAELLPPEDAArlERALRRALEGEEPID--FLEELLLNGEE 78

                          90       100
                  ....*....|....*....|....*..
gi 503772589   94 VQQIHTTLPLLNRRGAVVGAVEIARDL 120
Cdd:pfam08448  79 RHYELRLTPLRDPDGEVIGVLVISRDI 105
Sigma54_activ_2 pfam14532
Sigma-54 interaction domain;
149-320 1.14e-13

Sigma-54 interaction domain;


Pssm-ID: 434021 [Multi-domain]  Cd Length: 138  Bit Score: 68.14  E-value: 1.14e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  149 PAMQVLIRQAEALGKAGVNVLLCGETGTGKELFARLLHQSSqragapSPSLSPFVVLNCAAIPETLFEStlfgtargaft 228
Cdd:pfam14532   5 AAIQEIKRRLEQAAQSTLPVFLTGEPGSGKEFCARYLHNPS------TPWVQPFDIEYLAHAPLELLEQ----------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  229 gaqerqglietANSGTLFLDELNSLPwsvqgkllRVLQDGMFSRVGSNKeiRADLRVIAAANETQQEMLAARKLRPDLLY 308
Cdd:pfam14532  68 -----------AKGGTLYLKDIADLS--------KALQKGLLLLLAKAE--GYRVRLVCTSSKDLPQLAAAGLFDEQLYF 126

                         170
                  ....*....|..
gi 503772589  309 RLNIGQLSIPPL 320
Cdd:pfam14532 127 ELSALRLHVPPL 138
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 165-310 2.02e-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: 2.02e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589   165 GVNVLLCGETGTGKELFARLLHQSSQRAGApspslsPFVVLNCAAIPETLFES---TLFGTARGAFTGAQERQGLIETAN 241
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPGG------GVIYIDGEDILEEVLDQlllIIVGGKKASGSGELRLRLALALAR 75

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 503772589   242 S---GTLFLDELNSLPWSVQGKLLRVLQDgmfSRVGSNKEIRADLRVIAAANETQ--QEMLAARKLRPDLLYRL 310
Cdd:smart00382  76 KlkpDVLILDEITSLLDAEQEALLLLLEE---LRLLLLLKSEKNLTVILTTNDEKdlGPALLRRRFDRRIVLLL 146
PAS COG2202
PAS domain [Signal transduction mechanisms];
4-119 3.74e-10

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 60.42  E-value: 3.74e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589   4 ELASALAIFSQLFDAMPQPVAIIDSEGNYVYYNQESAKIDAYPAERAVGHPLLDIYPAMDAESS--TLLQALHHGKRYTG 81
Cdd:COG2202    5 ALEESERRLRALVESSPDAIIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFleLLRAALAGGGVWRG 84

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 503772589  82 AFQaFINAQGRLVQQIHTTLPLLNRRGAVVGAVEIARD 119
Cdd:COG2202   85 ELR-NRRKDGSLFWVELSISPVRDEDGEITGFVGIARD 121
NtrB COG3852
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];
4-120 1.07e-09

Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];


Pssm-ID: 443061 [Multi-domain]  Cd Length: 361  Bit Score: 59.86  E-value: 1.07e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589   4 ELASALAIFSQLFDAMPQPVAIIDSEGNYVYYNQESAKIDAYPAERAVGHPLLDIYPAMDAESSTLLQALHHGKRYTGAF 83
Cdd:COG3852    1 ALRESEELLRAILDSLPDAVIVLDADGRITYVNPAAERLLGLSAEELLGRPLAELFPEDSPLRELLERALAEGQPVTERE 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 503772589  84 QAFINAQGRLVqQIHTTLPLLNRRGAVVGAVEIARDL 120
Cdd:COG3852   81 VTLRRKDGEER-PVDVSVSPLRDAEGEGGVLLVLRDI 116
PAS COG2202
PAS domain [Signal transduction mechanisms];
4-120 1.67e-08

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 55.42  E-value: 1.67e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589   4 ELASALAIFSQLFDAMPQPVAIIDSEGNYVYYNQESAKIDAYPAERAVGHPLLDIYPAMDAESST-LLQALHHGKRYTGA 82
Cdd:COG2202  131 ALRESEERLRLLVENAPDGIFVLDLDGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERLLeLLRRLLEGGRESYE 210

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 503772589  83 FQAFINAQGRLVQQIHTTLPLLNRRGAVVGAVEIARDL 120
Cdd:COG2202  211 LELRLKDGDGRWVWVEASAVPLRDGGEVIGVLGIVRDI 248
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 167-299 1.23e-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: 50.37  E-value: 1.23e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  167 NVLLCGETGTGKELFARLLhqssqrAGAPSPSlSPFVVLNCAAIPET-LFESTLFGTARGAFTgaqeRQGLIETANSG-T 244
Cdd:pfam07728   1 GVLLVGPPGTGKTELAERL------AAALSNR-PVFYVQLTRDTTEEdLFGRRNIDPGGASWV----DGPLVRAAREGeI 69

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503772589  245 LFLDELNSLPWSVQGKLLRVLQDGMFSRVGSNKEIRADL---RVIAAANETQQ---EMLAA 299
Cdd:pfam07728  70 AVLDEINRANPDVLNSLLSLLDERRLLLPDGGELVKAAPdgfRLIATMNPLDRglnELSPA 130
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 19-120 6.09e-05

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 42.24  E-value: 6.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  19 MPQPVAIIDSEGNYVYYNQESAKIDAYPAERAVGHPLLDIYP--AMDAESSTLLQALHHGKRYTGAFQaFINAQGRLVQQ 96
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHpeDREELRERLENLLSGGEPVTLEVR-LRRKDGSVIWV 79

                         90       100
                 ....*....|....*....|....
gi 503772589  97 IHTTLPLLNRRGAVVGAVEIARDL 120
Cdd:cd00130   80 LVSLTPIRDEGGEVIGLLGVVRDI 103
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 12-119 6.10e-05

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 42.40  E-value: 6.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589   12 FSQLFDAMPQPVAIIDSEGNYVYYNQESAKIDAYPAERAVGHPLLD--IYPAMDAESSTLLQALHHGKRYTGAFQAFINA 89
Cdd:pfam00989   3 LRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDliPEEDDAEVAELLRQALLQGEESRGFEVSFRVP 82

                          90       100       110
                  ....*....|....*....|....*....|.
gi 503772589   90 QGRlVQQIHTTL-PLLNRRGAVVGAVEIARD 119
Cdd:pfam00989  83 DGR-PRHVEVRAsPVRDAGGEILGFLGVLRD 112
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 12-60 1.81e-04

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels.


Pssm-ID: 214512  Cd Length: 67  Bit Score: 39.69  E-value: 1.81e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 503772589    12 FSQLFDAMPQPVAIIDSEGNYVYYNQESAKIDAYPAERAVGHPLLDIYP 60
Cdd:smart00091   3 LRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIH 51
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 9-120 2.46e-04

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. [Regulatory functions, Small molecule interactions]


Pssm-ID: 272971 [Multi-domain]  Cd Length: 124  Bit Score: 40.74  E-value: 2.46e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589    9 LAIFSQLFDAMPQPVAIIDSEGNYVYYNQESAKIDAYPAERAVGHPLLDIYPAMDAESSTLLQALHHGKRY--TGAFQAF 86
Cdd:TIGR00229   2 EERYRAIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERRLEGEPepVSEERRV 81

                          90       100       110
                  ....*....|....*....|....*....|....
gi 503772589   87 INAQGRLVqQIHTTLPLLNRRGAVVGAVEIARDL 120
Cdd:TIGR00229  82 RRKDGSEI-WVEVSVSPIRTNGGELGVVGIVRDI 114
PRK11360 PRK11360
two-component system sensor histidine kinase AtoS;
26-122 6.13e-04

two-component system sensor histidine kinase AtoS;


Pssm-ID: 236901 [Multi-domain]  Cd Length: 607  Bit Score: 42.26  E-value: 6.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  26 IDSEGNYVYYNQESAKIDAYPAERAVGHPLLDIYPAMDAESSTLLQALHHGKRYTGAFQAFiNAQGRLVQQIHTTLPLLN 105
Cdd:PRK11360 278 IDRQGKITTMNPAAEVITGLQRHELVGKPYSELFPPNTPFASPLLDTLEHGTEHVDLEISF-PGRDRTIELSVSTSLLHN 356

                         90
                 ....*....|....*..
gi 503772589 106 RRGAVVGAVEIARDLAA 122
Cdd:PRK11360 357 THGEMIGALVIFSDLTE 373
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 168-324 6.53e-04

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: 39.88  E-value: 6.53e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  168 VLLCGETGTGKELFARLLhqsSQRAGApspslsPFVVLNCAAipetlFESTLFGTA----RGAFTGAQERQGLIetansg 243
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAV---AKELGA------PFIEISGSE-----LVSKYVGESekrlRELFEAAKKLAPCV------ 60

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503772589  244 tLFLDELNSL-----------PWSVQGKLLRVLqDGMFSRVGsnkeiraDLRVIAAANetqqemlaarklRPDLLyrlni 312
Cdd:pfam00004  61 -IFIDEIDALagsrgsggdseSRRVVNQLLTEL-DGFTSSNS-------KVIVIAATN------------RPDKL----- 114

                         170
                  ....*....|..
gi 503772589  313 gqlsIPPLRERC 324
Cdd:pfam00004 115 ----DPALLGRF 122
HTH_50 pfam18024
Helix-turn-helix domain; The TyrR protein of Haemophilus influenzae is a 36-kD transcription ...
 417-465 6.39e-03

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


Pssm-ID: 407862 [Multi-domain]  Cd Length: 50  Bit Score: 34.70  E-value: 6.39e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 503772589  417 GLSLEEQMSSYEKTLLIGLLKEHASLSEVARRCAIPRATLQYKLKKHNI 465
Cdd:pfam18024   1 EMSLKEYVSYIERELIGAAYENYKSARKVAKALGLSHTTIANKMKRYGI 49
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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