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Conserved domains on  [gi|2524691643|ref|WP_286714246|]
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sigma-54-dependent Fis family transcriptional regulator [Marinobacter sp. tcs-11]

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 ...
 15-469 0e+00

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: 515.86  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  15 RDLIEALFPMFEEASAGAIAVDRDANITWINSSYSQLLGLvDPSHAIGKSVRKVIPQTRMPEVVETGKPLLLDIMEHN-- 92
Cdd:COG3829     7 KELEEELEAILDSLDDGIIVVDADGRITYVNRAAERILGL-PREEVIGKNVTELIPNSPLLEVLKTGKPVTGVIQKTGgk 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  93 KQQLVVTRLPYYDDqGGIVGAVAFVlyDDLQPLTPLVSKYRRLHRdlaaarkalaKKSRGTRYSLGDFVGGSPAALEVKR 172
Cdd:COG3829    86 GKTVIVTAIPIFED-GEVIGAVETF--RDITELKRLERKLREEEL----------ERGLSAKYTFDDIIGKSPAMKELLE 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 173 RARLAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAYTGADRRTREGKFQLA 252
Cdd:COG3829   153 LAKRVAKSDSTVLILGESGTGKELFARAIHNASPRRDGPFVAVNCAAIPENLLESELFGYEKGAFTGAKKGGKPGLFELA 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 253 NGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSDLYYRLNVLEINIPPL 332
Cdd:COG3829   233 DGGTLFLDEIGEMPLSLQAKLLRVLQEKEVRRVGGTKPIPVDVRIIAATNRDLEEMVEEGRFREDLYYRLNVIPIHIPPL 312

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 333 RDRLADLGVLCEALLGEICEGQDMRG-EITDAGVAALGSYDWPGNIRELRNVLERALTMSeDGDLLDADAifkvLPRAGQ 411
Cdd:COG3829   313 RERKEDIPLLAEHFLEKFNKKYGKNIkGISPEALELLLAYDWPGNVRELENVIERAVVLS-EGDVITPEH----LPEYLL 387

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2524691643 412 RLVSPVPARSVRPLARIVAEAEAQAIEEALVTCRGNRTKAARLLGISRSVLYEKLARL 469
Cdd:COG3829   388 EEAEAASAAEEGSLKEALEEVEKELIEEALEKTGGNKSKAAKALGISRSTLYRKLKKY 445
 
Name Accession Description Interval E-value
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 15-469 0e+00

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: 515.86  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  15 RDLIEALFPMFEEASAGAIAVDRDANITWINSSYSQLLGLvDPSHAIGKSVRKVIPQTRMPEVVETGKPLLLDIMEHN-- 92
Cdd:COG3829     7 KELEEELEAILDSLDDGIIVVDADGRITYVNRAAERILGL-PREEVIGKNVTELIPNSPLLEVLKTGKPVTGVIQKTGgk 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  93 KQQLVVTRLPYYDDqGGIVGAVAFVlyDDLQPLTPLVSKYRRLHRdlaaarkalaKKSRGTRYSLGDFVGGSPAALEVKR 172
Cdd:COG3829    86 GKTVIVTAIPIFED-GEVIGAVETF--RDITELKRLERKLREEEL----------ERGLSAKYTFDDIIGKSPAMKELLE 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 173 RARLAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAYTGADRRTREGKFQLA 252
Cdd:COG3829   153 LAKRVAKSDSTVLILGESGTGKELFARAIHNASPRRDGPFVAVNCAAIPENLLESELFGYEKGAFTGAKKGGKPGLFELA 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 253 NGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSDLYYRLNVLEINIPPL 332
Cdd:COG3829   233 DGGTLFLDEIGEMPLSLQAKLLRVLQEKEVRRVGGTKPIPVDVRIIAATNRDLEEMVEEGRFREDLYYRLNVIPIHIPPL 312

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 333 RDRLADLGVLCEALLGEICEGQDMRG-EITDAGVAALGSYDWPGNIRELRNVLERALTMSeDGDLLDADAifkvLPRAGQ 411
Cdd:COG3829   313 RERKEDIPLLAEHFLEKFNKKYGKNIkGISPEALELLLAYDWPGNVRELENVIERAVVLS-EGDVITPEH----LPEYLL 387

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2524691643 412 RLVSPVPARSVRPLARIVAEAEAQAIEEALVTCRGNRTKAARLLGISRSVLYEKLARL 469
Cdd:COG3829   388 EEAEAASAAEEGSLKEALEEVEKELIEEALEKTGGNKSKAAKALGISRSTLYRKLKKY 445
Sigma54_activat pfam00158
Sigma-54 interaction domain;
160-327 3.96e-99

Sigma-54 interaction domain;


Pssm-ID: 425491 [Multi-domain]  Cd Length: 168  Bit Score: 294.31  E-value: 3.96e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 160 FVGGSPAALEVKRRARLAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAYTG 239
Cdd:pfam00158   1 IIGESPAMQEVLEQAKRVAPTDAPVLITGESGTGKELFARAIHQLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 240 ADRRtREGKFQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSDLY 319
Cdd:pfam00158  81 ADSD-RKGLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTKPIKVDVRIIAATNRDLEEAVAEGRFREDLY 159


                  ....*...
gi 2524691643 320 YRLNVLEI 327
Cdd:pfam00158 160 YRLNVIPI 167
PEP_resp_reg TIGR02915
PEP-CTERM-box response regulator transcription factor; Members of this protein family share ...
 105-469 8.79e-96

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: 295.89  E-value: 8.79e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 105 DDQGGIVGAVAFVLYD------DLQPLTPLVSKYRRLHRdlaAARKALAKKSRGTRYSLGDFVGGSPAALEVKRRARLAA 178
Cdd:TIGR02915  83 DDRENAVKAIGLGAYDfyqkpiDPDVLKLIVDRAFHLYT---LETENRRLQSALGGTALRGLITSSPGMQKICRTIEKIA 159

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 179 GRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAYTGADRRTReGKFQLANGGTLF 258
Cdd:TIGR02915 160 PSDITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIPENLLESELFGYEKGAFTGAVKQTL-GKIEYAHGGTLF 238

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 259 LDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSDLYYRLNVLEINIPPLRDRLAD 338
Cdd:TIGR02915 239 LDEIGDLPLNLQAKLLRFLQERVIERLGGREEIPVDVRIVCATNQDLKRMIAEGTFREDLFYRIAEISITIPPLRSRDGD 318

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 339 LGVLCEALLGE--ICEGQDMRGeITDAGVAALGSYDWPGNIRELRNVLERALTMSEDGDLLDADAIFKVLPRAGQRLvsP 416
Cdd:TIGR02915 319 AVLLANAFLERfaRELKRKTKG-FTDDALRALEAHAWPGNVRELENKVKRAVIMAEGNQITAEDLGLDARERAETPL--E 395

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2524691643 417 VPARSVRPLARivaeaeAQAIEEALVTCRGNRTKAARLLGISRSVLYEKLARL 469
Cdd:TIGR02915 396 VNLREVRERAE------REAVRKAIARVDGNIARAAELLGITRPTLYDLMKKH 442
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
158-468 1.27e-94

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 295.16  E-value: 1.27e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 158 GDFVGGSPAALEVKRRARLAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAY 237
Cdd:PRK05022  187 GEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAALPESLAESELFGHVKGAF 266

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 238 TGADRRtREGKFQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSD 317
Cdd:PRK05022  267 TGAISN-RSGKFELADGGTLFLDEIGELPLALQAKLLRVLQYGEIQRVGSDRSLRVDVRVIAATNRDLREEVRAGRFRAD 345

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 318 LYYRLNVLEINIPPLRDRLADLGVLCeallGEICE------G-QDMRgeITDAGVAALGSYDWPGNIRELRNVLERA--- 387
Cdd:PRK05022  346 LYHRLSVFPLSVPPLRERGDDVLLLA----GYFLEqnrarlGlRSLR--LSPAAQAALLAYDWPGNVRELEHVISRAall 419

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 388 ---------LTMS-EDGDLLDADAifkvLPRAGQRLVSPVPArsVRPLARIVAEAEAQAIEEALVTCRGNRTKAARLLGI 457
Cdd:PRK05022  420 arargagriVTLEaQHLDLPAEVA----LPPPEAAAAPAAVV--SQNLREATEAFQRQLIRQALAQHQGNWAAAARALEL 493

                         330
                  ....*....|.
gi 2524691643 458 SRSVLYeKLAR 468
Cdd:PRK05022  494 DRANLH-RLAK 503
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 161-331 6.93e-23

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: 94.52  E-value: 6.93e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 161 VGGSPAALEVKRRARLAAGRdmPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVapgaytgA 240
Cdd:cd00009     1 VGQEEAIEALREALELPPPK--NLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGH-------F 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 241 DRRTREGKFQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEalgsnKVTTVDVRVIAATSRNLeamiaEGSFRSDLYY 320
Cdd:cd00009    72 LVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDL-----RIDRENVRVIGATNRPL-----LGDLDRALYD 141

                         170
                  ....*....|.
gi 2524691643 321 RLNvLEINIPP 331
Cdd:cd00009   142 RLD-IRIVIPL 151
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 183-322 9.50e-09

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: 54.30  E-value: 9.50e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  183 PVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLE-AEFFGVAPGAYTGADRRTREGKFQLA---NGGTLF 258
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDqLLLIIVGGKKASGSGELRLRLALALArklKPDVLI 83

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2524691643  259 LDEVGDMPLPLQAKLLRALQEgeiEALGSNKVTTVDVRVIAATSR--NLEAMIAEGSFRSDLYYRL 322
Cdd:smart00382  84 LDEITSLLDAEQEALLLLLEE---LRLLLLLKSEKNLTVILTTNDekDLGPALLRRRFDRRIVLLL 146
 
Name Accession Description Interval E-value
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 15-469 0e+00

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: 515.86  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  15 RDLIEALFPMFEEASAGAIAVDRDANITWINSSYSQLLGLvDPSHAIGKSVRKVIPQTRMPEVVETGKPLLLDIMEHN-- 92
Cdd:COG3829     7 KELEEELEAILDSLDDGIIVVDADGRITYVNRAAERILGL-PREEVIGKNVTELIPNSPLLEVLKTGKPVTGVIQKTGgk 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  93 KQQLVVTRLPYYDDqGGIVGAVAFVlyDDLQPLTPLVSKYRRLHRdlaaarkalaKKSRGTRYSLGDFVGGSPAALEVKR 172
Cdd:COG3829    86 GKTVIVTAIPIFED-GEVIGAVETF--RDITELKRLERKLREEEL----------ERGLSAKYTFDDIIGKSPAMKELLE 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 173 RARLAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAYTGADRRTREGKFQLA 252
Cdd:COG3829   153 LAKRVAKSDSTVLILGESGTGKELFARAIHNASPRRDGPFVAVNCAAIPENLLESELFGYEKGAFTGAKKGGKPGLFELA 232

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 253 NGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSDLYYRLNVLEINIPPL 332
Cdd:COG3829   233 DGGTLFLDEIGEMPLSLQAKLLRVLQEKEVRRVGGTKPIPVDVRIIAATNRDLEEMVEEGRFREDLYYRLNVIPIHIPPL 312

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 333 RDRLADLGVLCEALLGEICEGQDMRG-EITDAGVAALGSYDWPGNIRELRNVLERALTMSeDGDLLDADAifkvLPRAGQ 411
Cdd:COG3829   313 RERKEDIPLLAEHFLEKFNKKYGKNIkGISPEALELLLAYDWPGNVRELENVIERAVVLS-EGDVITPEH----LPEYLL 387

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2524691643 412 RLVSPVPARSVRPLARIVAEAEAQAIEEALVTCRGNRTKAARLLGISRSVLYEKLARL 469
Cdd:COG3829   388 EEAEAASAAEEGSLKEALEEVEKELIEEALEKTGGNKSKAAKALGISRSTLYRKLKKY 445
AcoR COG3284
Transcriptional regulator DhaR of acetoin/glycerol metabolism [Transcription];
28-469 1.78e-130

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


Pssm-ID: 442514 [Multi-domain]  Cd Length: 625  Bit Score: 391.19  E-value: 1.78e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  28 ASAGAIAVDRDANITWINSSYSQLLGLvDPSHAIGKSVRKVIPQTrmpevvetgkpllLDIMEHNKQQLVVTRLPYYDDQ 107
Cdd:COG3284   225 LSEGLLAFDEDGRIVAANRAARRLLGL-ADAALLGRPLEELFGLD-------------LEALPDGARRAPASPRPLRLRD 290

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 108 GGIVGAVAFvlyddLQPLTPLVSKyrrlhrdlaaarkalAKKSRGTRYSLGDFVGGSPAALEVKRRARLAAGRDMPVLLL 187
Cdd:COG3284   291 GRRLGALLR-----LRPARRAARA---------------APAGAPAPAALAALAGGDPAMRRALRRARRLADRDIPVLIL 350

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 188 GETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAYTGADRRTREGKFQLANGGTLFLDEVGDMPL 267
Cdd:COG3284   351 GETGTGKELFARAIHAASPRADGPFVAVNCAAIPEELIESELFGYEPGAFTGARRKGRPGKIEQADGGTLFLDEIGDMPL 430

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 268 PLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSDLYYRLNVLEINIPPLRDRlADLGVLCEALL 347
Cdd:COG3284   431 ALQARLLRVLQEREVTPLGGTKPIPVDVRLIAATHRDLRELVAAGRFREDLYYRLNGLTLTLPPLRER-EDLPALIEHLL 509

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 348 GEICEGQDmRGEITDAGVAALGSYDWPGNIRELRNVLERALTMSEDGDLLDADaifkvLP---RAGQRLVSPVPARSVRP 424
Cdd:COG3284   510 RELAAGRG-PLRLSPEALALLAAYPWPGNVRELRNVLRTALALADGGVITVED-----LPdelRAELAAAAPAAAAPLTS 583

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*
gi 2524691643 425 LARIvaeaEAQAIEEALVTCRGNRTKAARLLGISRSVLYEKLARL 469
Cdd:COG3284   584 LEEA----ERDAILRALRACGGNVSAAARALGISRSTLYRKLKRY 624
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 156-469 1.15e-123

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: 366.60  E-value: 1.15e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 156 SLGDFVGGSPAALEVKRRARLAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPG 235
Cdd:COG2204   129 EDSGLIGRSPAMQEVRRLIEKVAPSDATVLITGESGTGKELVARAIHRLSPRADGPFVAVNCAAIPEELLESELFGHEKG 208

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 236 AYTGADRRtREGKFQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFR 315
Cdd:COG2204   209 AFTGAVAR-RIGKFELADGGTLFLDEIGEMPLALQAKLLRVLQEREFERVGGNKPIPVDVRVIAATNRDLEELVEEGRFR 287

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 316 SDLYYRLNVLEINIPPLRDRLADLGVLCEALLGEICEGQDMRGEITDAGVAALGSYDWPGNIRELRNVLERALTMSeDGD 395
Cdd:COG2204   288 EDLYYRLNVFPIELPPLRERREDIPLLARHFLARFAAELGKPVKLSPEALEALLAYDWPGNVRELENVIERAVILA-DGE 366

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2524691643 396 LLDADAIFKVLPRAGQRLVspvparsVRPLARivaeaeaqaieealvtCRGNRTKAARLLGISRSVLYEKLARL 469
Cdd:COG2204   367 VITAEDLPEALEEVERELI-------ERALEE----------------TGGNVSRAAELLGISRRTLYRKLKKY 417
Sigma54_activat pfam00158
Sigma-54 interaction domain;
160-327 3.96e-99

Sigma-54 interaction domain;


Pssm-ID: 425491 [Multi-domain]  Cd Length: 168  Bit Score: 294.31  E-value: 3.96e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 160 FVGGSPAALEVKRRARLAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAYTG 239
Cdd:pfam00158   1 IIGESPAMQEVLEQAKRVAPTDAPVLITGESGTGKELFARAIHQLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 240 ADRRtREGKFQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSDLY 319
Cdd:pfam00158  81 ADSD-RKGLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTKPIKVDVRIIAATNRDLEEAVAEGRFREDLY 159


                  ....*...
gi 2524691643 320 YRLNVLEI 327
Cdd:pfam00158 160 YRLNVIPI 167
TyrR COG3283
Transcriptional regulator TyrR of aromatic amino acids metabolism [Transcription, Amino acid ...
 33-407 5.66e-96

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


Pssm-ID: 442513 [Multi-domain]  Cd Length: 514  Bit Score: 298.64  E-value: 5.66e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  33 IAVDRDANITWINSSYSQLLGLvDPSHAIGKSVRKVI-------------PQTRMPEVVETGKPLLLDIMehnkqqlvvt 99
Cdd:COG3283    94 FSIDLKGKIELANPAALSLLGL-SEEELIGQPLSELLkgfnfsrwlesnePRPQSERVVINGQDYLADIL---------- 162

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 100 rlPYY---DDQGGI-VGAVafVLyddLQPLTPLVSKYRRLHRDLAAarkalakksrgtrySLGDFVGGSPAALEVKRRAR 175
Cdd:COG3283   163 --PIYlpdEEGKSIlAGAV--VT---LKSAARLGEQLQALQVNDDS--------------GFDHIVASSPKMRQVIRQAK 221

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 176 LAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAYtGADRRTREGKFQLANGG 255
Cdd:COG3283   222 KMAMLDAPLLIQGETGTGKELLARACHLASPRGDKPFLALNCAALPDDVAESELFGYAPGAF-GNAREGKKGLFEQANGG 300

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 256 TLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSDLYYRLNVLEINIPPLRDR 335
Cdd:COG3283   301 TVFLDEIGEMSPQLQAKLLRFLQDGTFRRVGEEQEVKVDVRVICATQKDLAELVQEGEFREDLYYRLNVLTLTLPPLRER 380

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2524691643 336 LADLGVLCEALLGEICEGQDM-RGEITDAGVAALGSYDWPGNIRELRNVLERALTMSEdGDLLDADAIfkVLP 407
Cdd:COG3283   381 KSDILPLAEHFVARFSQQLGRpRPRLSPDLVDFLQSYPWPGNVRQLENALYRAVSLLE-GDELTPEDL--QLP 450
PEP_resp_reg TIGR02915
PEP-CTERM-box response regulator transcription factor; Members of this protein family share ...
 105-469 8.79e-96

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: 295.89  E-value: 8.79e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 105 DDQGGIVGAVAFVLYD------DLQPLTPLVSKYRRLHRdlaAARKALAKKSRGTRYSLGDFVGGSPAALEVKRRARLAA 178
Cdd:TIGR02915  83 DDRENAVKAIGLGAYDfyqkpiDPDVLKLIVDRAFHLYT---LETENRRLQSALGGTALRGLITSSPGMQKICRTIEKIA 159

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 179 GRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAYTGADRRTReGKFQLANGGTLF 258
Cdd:TIGR02915 160 PSDITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIPENLLESELFGYEKGAFTGAVKQTL-GKIEYAHGGTLF 238

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 259 LDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSDLYYRLNVLEINIPPLRDRLAD 338
Cdd:TIGR02915 239 LDEIGDLPLNLQAKLLRFLQERVIERLGGREEIPVDVRIVCATNQDLKRMIAEGTFREDLFYRIAEISITIPPLRSRDGD 318

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 339 LGVLCEALLGE--ICEGQDMRGeITDAGVAALGSYDWPGNIRELRNVLERALTMSEDGDLLDADAIFKVLPRAGQRLvsP 416
Cdd:TIGR02915 319 AVLLANAFLERfaRELKRKTKG-FTDDALRALEAHAWPGNVRELENKVKRAVIMAEGNQITAEDLGLDARERAETPL--E 395

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2524691643 417 VPARSVRPLARivaeaeAQAIEEALVTCRGNRTKAARLLGISRSVLYEKLARL 469
Cdd:TIGR02915 396 VNLREVRERAE------REAVRKAIARVDGNIARAAELLGITRPTLYDLMKKH 442
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
158-468 1.27e-94

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 295.16  E-value: 1.27e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 158 GDFVGGSPAALEVKRRARLAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAY 237
Cdd:PRK05022  187 GEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAALPESLAESELFGHVKGAF 266

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 238 TGADRRtREGKFQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSD 317
Cdd:PRK05022  267 TGAISN-RSGKFELADGGTLFLDEIGELPLALQAKLLRVLQYGEIQRVGSDRSLRVDVRVIAATNRDLREEVRAGRFRAD 345

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 318 LYYRLNVLEINIPPLRDRLADLGVLCeallGEICE------G-QDMRgeITDAGVAALGSYDWPGNIRELRNVLERA--- 387
Cdd:PRK05022  346 LYHRLSVFPLSVPPLRERGDDVLLLA----GYFLEqnrarlGlRSLR--LSPAAQAALLAYDWPGNVRELEHVISRAall 419

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 388 ---------LTMS-EDGDLLDADAifkvLPRAGQRLVSPVPArsVRPLARIVAEAEAQAIEEALVTCRGNRTKAARLLGI 457
Cdd:PRK05022  420 arargagriVTLEaQHLDLPAEVA----LPPPEAAAAPAAVV--SQNLREATEAFQRQLIRQALAQHQGNWAAAARALEL 493

                         330
                  ....*....|.
gi 2524691643 458 SRSVLYeKLAR 468
Cdd:PRK05022  494 DRANLH-RLAK 503
nifA TIGR01817
Nif-specific regulatory protein; This model represents NifA, a DNA-binding regulatory protein ...
 161-463 1.12e-93

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: 293.55  E-value: 1.12e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 161 VGGSPAALEVKRRARLAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAYTGA 240
Cdd:TIGR01817 199 IGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYLSPRAKRPFVKVNCAALSETLLESELFGHEKGAFTGA 278

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 241 dRRTREGKFQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSDLYY 320
Cdd:TIGR01817 279 -IAQRKGRFELADGGTLFLDEIGEISPAFQAKLLRVLQEGEFERVGGNRTLKVDVRLVAATNRDLEEAVAKGEFRADLYY 357

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 321 RLNVLEINIPPLRDRLADLGVLCEALLGEICEGQDMRGEITDAGVAALGSYDWPGNIRELRNVLERALTMSEDGDLLDAD 400
Cdd:TIGR01817 358 RINVVPIFLPPLRERREDIPLLAEAFLEKFNRENGRPLTITPSAIRVLMSCKWPGNVRELENCLERTATLSRSGTITRSD 437

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 401 AIFKvlprAGQRLVS------PVPARSVRPLARIVAEAEAQAIEEAL-VTCRGNRT------------------KAARLL 455
Cdd:TIGR01817 438 FSCQ----SGQCLSPmlaktcPHGHISIDPLAGTTPPHSPASAALPGePGLSGPTLsererliaaleqagwvqaKAARLL 513


                  ....*....
gi 2524691643 456 GIS-RSVLY 463
Cdd:TIGR01817 514 GMTpRQVGY 522
PRK11361 PRK11361
acetoacetate metabolism transcriptional regulator AtoC;
153-466 1.50e-87

acetoacetate metabolism transcriptional regulator AtoC;


Pssm-ID: 183099 [Multi-domain]  Cd Length: 457  Bit Score: 275.19  E-value: 1.50e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 153 TRYSLGDFVGGSPAALEVKRRARLAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGV 232
Cdd:PRK11361  138 TSWQWGHILTNSPAMMDICKDTAKIALSQASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGH 217

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 233 APGAYTGADRRtREGKFQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEG 312
Cdd:PRK11361  218 EKGAFTGAQTL-RQGLFERANEGTLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEG 296

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 313 SFRSDLYYRLNVLEINIPPLRDRLADLGVLCEALLGEI-CEGQDMRGEITDAGVAALGSYDWPGNIRELRNVLERALTMS 391
Cdd:PRK11361  297 TFREDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFsSENQRDIIDIDPMAMSLLTAWSWPGNIRELSNVIERAVVMN 376

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 392 EDGDLLDADaifkvLP---RAGQRLVSPVPARSV--RPLARIVAEAEAQAIEEALVTCRGNRTKAARLLGISRSVLYEKL 466
Cdd:PRK11361  377 SGPIIFSED-----LPpqiRQPVCNAGEVKTAPVgeRNLKEEIKRVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKL 451
propionate_PrpR TIGR02329
propionate catabolism operon regulatory protein PrpR; At least five distinct pathways exists ...
 153-466 4.87e-85

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


Pssm-ID: 274079 [Multi-domain]  Cd Length: 526  Bit Score: 270.96  E-value: 4.87e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 153 TRYSLGDFVGGSPAALEVKRRARLAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGV 232
Cdd:TIGR02329 207 TRYRLDDLLGASAPMEQVRALVRLYARSDATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIAESLLEAELFGY 286

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 233 APGAYTGADRRTREGKFQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEG 312
Cdd:TIGR02329 287 EEGAFTGARRGGRTGLIEAAHRGTLFLDEIGEMPLPLQTRLLRVLEEREVVRVGGTEPVPVDVRVVAATHCALTTAVQQG 366

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 313 SFRSDLYYRLNVLEINIPPLRDRLADLGVLCEALLGEICEGQDM-----RGEITDAGVAALGSYDWPGNIRELRNVLER- 386
Cdd:TIGR02329 367 RFRRDLFYRLSILRIALPPLRERPGDILPLAAEYLVQAAAALRLpdseaAAQVLAGVADPLQRYPWPGNVRELRNLVERl 446

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 387 ALTMS-EDGDLLDADAIFKVLPR-AGQRLVSPVPARSVRPLARIVaeaeAQAIEEALVTCRGNRTKAARLLGISRSVLYE 464
Cdd:TIGR02329 447 ALELSaMPAGALTPDVLRALAPElAEASGKGKTSALSLRERSRVE----ALAVRAALERFGGDRDAAAKALGISRTTLWR 522


                  ..
gi 2524691643 465 KL 466
Cdd:TIGR02329 523 RL 524
PRK15424 PRK15424
propionate catabolism operon regulatory protein PrpR; Provisional
 153-466 1.17e-84

propionate catabolism operon regulatory protein PrpR; Provisional


Pssm-ID: 237963 [Multi-domain]  Cd Length: 538  Bit Score: 270.05  E-value: 1.17e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 153 TRYSLGDFVGGSPAALEVKRRARLAAGRDMPVLLLGETGTGKEVLAQAIHA--------VSPRVDKPFVGVNVAAVPENL 224
Cdd:PRK15424  214 TRYVLGDLLGQSPQMEQVRQTILLYARSSAAVLIQGETGTGKELAAQAIHReyfarhdaRQGKKSHPFVAVNCGAIAESL 293

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 225 LEAEFFGVAPGAYTGADRRTREGKFQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRN 304
Cdd:PRK15424  294 LEAELFGYEEGAFTGSRRGGRAGLFEIAHGGTLFLDEIGEMPLPLQTRLLRVLEEKEVTRVGGHQPVPVDVRVISATHCD 373

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 305 LEAMIAEGSFRSDLYYRLNVLEINIPPLRDRLADLGVLCEALLG------EICEGQDMRGEITdAGVAALGSYDWPGNIR 378
Cdd:PRK15424  374 LEEDVRQGRFRRDLFYRLSILRLQLPPLRERVADILPLAESFLKqslaalSAPFSAALRQGLQ-QCETLLLHYDWPGNVR 452

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 379 ELRNVLER-ALTMS-EDGDLLDADAIFKVLPRAGQRLVSPVPARSVRPLARIVaeaeaqaieeaLVTCRGNRTKAARLLG 456
Cdd:PRK15424  453 ELRNLMERlALFLSvEPTPDLTPQFLQLLLPELARESAKTPAPRLLAATLQQA-----------LERFNGDKTAAANYLG 521

                         330
                  ....*....|
gi 2524691643 457 ISRSVLYEKL 466
Cdd:PRK15424  522 ISRTTLWRRL 531
PRK15115 PRK15115
response regulator GlrR; Provisional
 159-468 2.83e-81

response regulator GlrR; Provisional


Pssm-ID: 185070 [Multi-domain]  Cd Length: 444  Bit Score: 258.61  E-value: 2.83e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 159 DFVGGSPAALEVKRRARLAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAYT 238
Cdd:PRK15115  135 AIVTRSPLMLRLLEQARMVAQSDVSVLINGQSGTGKEILAQAIHNASPRASKPFIAINCGALPEQLLESELFGHARGAFT 214

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 239 GAdRRTREGKFQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSDL 318
Cdd:PRK15115  215 GA-VSNREGLFQAAEGGTLFLDEIGDMPAPLQVKLLRVLQERKVRPLGSNRDIDIDVRIISATHRDLPKAMARGEFREDL 293

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 319 YYRLNVLEINIPPLRDRLADLGVLCEALLGEICEGQD--MRGEITDAgVAALGSYDWPGNIRELRNVLER--ALTMSE-D 393
Cdd:PRK15115  294 YYRLNVVSLKIPALAERTEDIPLLANHLLRQAAERHKpfVRAFSTDA-MKRLMTASWPGNVRQLVNVIEQcvALTSSPvI 372

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2524691643 394 GDLLDADAIfkvlprAGQRLVSP--VPARSVRPLARIVaeaeaqaieEALVTCRGNRTKAARLLGISRSVLYEKLAR 468
Cdd:PRK15115  373 SDALVEQAL------EGENTALPtfVEARNQFELNYLR---------KLLQITKGNVTHAARMAGRNRTEFYKLLSR 434
ntrC TIGR01818
nitrogen regulation protein NR(I); This model represents NtrC, a DNA-binding response ...
 159-469 9.00e-81

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: 257.74  E-value: 9.00e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 159 DFVGGSPAALEVKRR-ARLAaGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAY 237
Cdd:TIGR01818 135 ELIGEAPAMQEVFRAiGRLS-RSDITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPKDLIESELFGHEKGAF 213

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 238 TGADRRtREGKFQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSD 317
Cdd:TIGR01818 214 TGANTR-RQGRFEQADGGTLFLDEIGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQNLEALVRQGKFRED 292

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 318 LYYRLNVLEINIPPLRDRLADLGVLCEALLGEICEGQDMRGEITDA-GVAALGSYDWPGNIRELRNVLeRALTMSEDGDL 396
Cdd:TIGR01818 293 LFHRLNVIRIHLPPLRERREDIPRLARHFLALAARELDVEPKLLDPeALERLKQLRWPGNVRQLENLC-RWLTVMASGDE 371

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 397 LDADAIFKVLPRAGQRLVSPVP-------------ARSVRP------LARIVAEAEAQAIEEALVTCRGNRTKAARLLGI 457
Cdd:TIGR01818 372 VLVSDLPAELALTGRPASAPDSdgqdswdealeawAKQALSrgeqglLDRALPEFERPLLEAALQHTRGHKQEAAALLGW 451

                         330
                  ....*....|..
gi 2524691643 458 SRSVLYEKLARL 469
Cdd:TIGR01818 452 GRNTLTRKLKEL 463
PRK10365 PRK10365
sigma-54-dependent response regulator transcription factor ZraR;
161-468 1.63e-80

sigma-54-dependent response regulator transcription factor ZraR;


Pssm-ID: 182412 [Multi-domain]  Cd Length: 441  Bit Score: 256.50  E-value: 1.63e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 161 VGGSPAALEVKRRARLAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAYTGA 240
Cdd:PRK10365  142 VGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHASSARSEKPLVTLNCAALNESLLESELFGHEKGAFTGA 221

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 241 DRRtREGKFQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSDLYY 320
Cdd:PRK10365  222 DKR-REGRFVEADGGTLFLDEIGDISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLYY 300

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 321 RLNVLEINIPPLRDRLADLGVLCEALLGEICE--GQDMRGeITDAGVAALGSYDWPGNIRELRNVLERALTmsedgdLLD 398
Cdd:PRK10365  301 RLNVVAIEVPSLRQRREDIPLLAGHFLQRFAErnRKAVKG-FTPQAMDLLIHYDWPGNIRELENAVERAVV------LLT 373

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2524691643 399 ADAIF-KVLPRAGQRLVSPV-PARSVRPLARIvaeaEAQAIEEALVTCRGNRTKAARLLGISRSVLYEKLAR 468
Cdd:PRK10365  374 GEYISeRELPLAIASTPIPLgQSQDIQPLVEV----EKEVILAALEKTGGNKTEAARQLGITRKTLLAKLSR 441
phageshock_pspF TIGR02974
psp operon transcriptional activator PspF; Members of this protein family are PspF, the ...
 161-458 7.29e-78

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


Pssm-ID: 274371 [Multi-domain]  Cd Length: 329  Bit Score: 246.05  E-value: 7.29e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 161 VGGSPAALEVKRRARLAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAYTGA 240
Cdd:TIGR02974   2 IGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAALSENLLDSELFGHEAGAFTGA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 241 DRRtREGKFQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSDLYY 320
Cdd:TIGR02974  82 QKR-HQGRFERADGGTLFLDELATASLLVQEKLLRVIEYGEFERVGGSQTLQVDVRLVCATNADLPALAAEGRFRADLLD 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 321 RLNVLEINIPPLRDRLADLGVLCEALLGEICE--GQDMRGEITDAGVAALGSYDWPGNIRELRNVLERAL-TMSEDGDLL 397
Cdd:TIGR02974 161 RLAFDVITLPPLRERQEDIMLLAEHFAIRMARelGLPLFPGFTPQAREQLLEYHWPGNVRELKNVVERSVyRHGLEEAPI 240

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2524691643 398 DADAI--F---------------KVLPRAGQRLVSPVPARSVRPLARIVAEAEAQAIEEALVTCRGNRTKAARLLGIS 458
Cdd:TIGR02974 241 DEIIIdpFaspwrpkqaapavdeVNSTPTDLPSPSSIAAAFPLDLKQAQQDYEIELLQQALAEAQFNQRKAAELLGLT 318
PRK15429 PRK15429
formate hydrogenlyase transcriptional activator FlhA;
158-469 3.25e-73

formate hydrogenlyase transcriptional activator FlhA;


Pssm-ID: 237965 [Multi-domain]  Cd Length: 686  Bit Score: 243.97  E-value: 3.25e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 158 GDFVGGSPAALEVKRRARLAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAY 237
Cdd:PRK15429  376 GEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPAGLLESDLFGHERGAF 455

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 238 TGADRRtREGKFQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSD 317
Cdd:PRK15429  456 TGASAQ-RIGRFELADKSSLFLDEVGDMPLELQPKLLRVLQEQEFERLGSNKIIQTDVRLIAATNRDLKKMVADREFRSD 534

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 318 LYYRLNVLEINIPPLRDRLADLGVLCEALLGEICE--GQDMrGEITDAGVAALGSYDWPGNIRELRNVLERALTMSEdGD 395
Cdd:PRK15429  535 LYYRLNVFPIHLPPLRERPEDIPLLVKAFTFKIARrmGRNI-DSIPAETLRTLSNMEWPGNVRELENVIERAVLLTR-GN 612

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 396 LLDADaifkvLPRAGQRLVSPVPARSVRP------LARIVAEAEAQAIEEAlvtcrGNRTKAARlLGISRSVLYEKLARL 469
Cdd:PRK15429  613 VLQLS-----LPDITLPEPETPPAATVVAqegedeYQLIVRVLKETNGVVA-----GPKGAAQR-LGLKRTTLLSRMKRL 681
PRK11388 PRK11388
DNA-binding transcriptional regulator DhaR; Provisional
 31-466 9.48e-73

DNA-binding transcriptional regulator DhaR; Provisional


Pssm-ID: 183114 [Multi-domain]  Cd Length: 638  Bit Score: 241.51  E-value: 9.48e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  31 GAIAVDRDANITWINSSYSQLLGLvDPSHAIGKSVRKVI--PQtRMPEVVETGKPL-LLDIMEHNKQQ---LVVTRLPYY 104
Cdd:PRK11388  215 GVIAWDEQGNLQFLNAQAARLLRL-DATASQGRAITELLtlPA-VLQQAIKQAHPLkHVEVTFESQGQfidAVITLKPII 292

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 105 DDQGgivgaVAFVLYddLQPltplVSKYRRLHRDLAaarkalakksRGTRYSLGDFVGGSPAALEVKRRARLAAGRDMPV 184
Cdd:PRK11388  293 EGQG-----TSFILL--LHP----VEQMRQLMTSQL----------GKVSHTFDHMPQDSPQMRRLIHFGRQAAKSSFPV 351

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 185 LLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAytgaDRRTREGKFQLANGGTLFLDEVGD 264
Cdd:PRK11388  352 LLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPDEALAEEFLGSDRTD----SENGRLSKFELAHGGTLFLEKVEY 427

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 265 MPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSDLYYRLNVLEINIPPLRDRLADLGVLCE 344
Cdd:PRK11388  428 LSPELQSALLQVLKTGVITRLDSRRLIPVDVRVIATTTADLAMLVEQNRFSRQLYYALHAFEITIPPLRMRREDIPALVN 507

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 345 ALLGEICEGQDMRGEITDAGVAALGSYDWPGNIRELRNVLERALTMSEDGDLLDAD---AIFKVLPrAGQRLVSPVPAR- 420
Cdd:PRK11388  508 NKLRSLEKRFSTRLKIDDDALARLVSYRWPGNDFELRSVIENLALSSDNGRIRLSDlpeHLFTEQA-TDDVSATRLSTSl 586

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*...
gi 2524691643 421 SVRPLAR--IVAEAEAqaieealvtCRGNRTKAARLLGISRSVLYEKL 466
Cdd:PRK11388  587 SLAELEKeaIINAAQV---------CGGRIQEMAALLGIGRTTLWRKM 625
PRK10820 PRK10820
transcriptional regulator TyrR;
161-400 6.38e-71

transcriptional regulator TyrR;


Pssm-ID: 236769 [Multi-domain]  Cd Length: 520  Bit Score: 233.81  E-value: 6.38e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 161 VGGSPAALEVKRRARLAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAYTGA 240
Cdd:PRK10820  207 VAVSPKMRQVVEQARKLAMLDAPLLITGDTGTGKDLLAYACHLRSPRGKKPFLALNCASIPDDVVESELFGHAPGAYPNA 286

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 241 drrtREGK---FQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSD 317
Cdd:PRK10820  287 ----LEGKkgfFEQANGGSVLLDEIGEMSPRMQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQKNLVELVQKGEFRED 362

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 318 LYYRLNVLEINIPPLRDRLADLGVLCEALLGEICEGQDM-RGEITDAGVAALGSYDWPGNIRELRNVLERALTMSEDGDL 396
Cdd:PRK10820  363 LYYRLNVLTLNLPPLRDRPQDIMPLTELFVARFADEQGVpRPKLAADLNTVLTRYGWPGNVRQLKNAIYRALTQLEGYEL 442


                  ....
gi 2524691643 397 LDAD 400
Cdd:PRK10820  443 RPQD 446
glnG PRK10923
nitrogen regulation protein NR(I); Provisional
 156-469 1.59e-67

nitrogen regulation protein NR(I); Provisional


Pssm-ID: 182842 [Multi-domain]  Cd Length: 469  Bit Score: 223.59  E-value: 1.59e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 156 SLGDFVGGSPAALEVKRRARLAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPG 235
Cdd:PRK10923  136 PTTDIIGEAPAMQDVFRIIGRLSRSSISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIPKDLIESELFGHEKG 215

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 236 AYTGADRrTREGKFQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFR 315
Cdd:PRK10923  216 AFTGANT-IRQGRFEQADGGTLFLDEIGDMPLDVQTRLLRVLADGQFYRVGGYAPVKVDVRIIAATHQNLEQRVQEGKFR 294

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 316 SDLYYRLNVLEINIPPLRDRLADLGVLCEALLGEICEGQDMRGEITDAGV-AALGSYDWPGNIRELRNVLeRALT----- 389
Cdd:PRK10923  295 EDLFHRLNVIRVHLPPLRERREDIPRLARHFLQVAARELGVEAKLLHPETeAALTRLAWPGNVRQLENTC-RWLTvmaag 373

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 390 ---MSED--GDLLDADA---IFKVLPRAGQRLVSPVPARSVRPLARIVAEAEAQAIEEALVTC-----RGNRTKAARLLG 456
Cdd:PRK10923  374 qevLIQDlpGELFESTVpesTSQMQPDSWATLLAQWADRALRSGHQNLLSEAQPELERTLLTTalrhtQGHKQEAARLLG 453

                         330
                  ....*....|...
gi 2524691643 457 ISRSVLYEKLARL 469
Cdd:PRK10923  454 WGRNTLTRKLKEL 466
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 174-469 3.09e-66

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


Pssm-ID: 442823 [Multi-domain]  Cd Length: 338  Bit Score: 216.25  E-value: 3.09e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 174 ARLAAgrdmpVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAeffgvapgaytgadrrtregkfqlan 253
Cdd:COG3604   113 ASLAA-----VAILGETGTGKELVANAIHELSPRADKPFVKVNCAALPESLLES-------------------------- 161

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 254 ggtlfldevgdmplplqakllraLQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSDLYYRLNVLEINIPPLR 333
Cdd:COG3604   162 -----------------------LQEGEFERVGGDETIKVDVRIIAATNRDLEEEVAEGRFREDLYYRLNVFPIRLPPLR 218

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 334 DRLADLGVLCEALLGEICEGQDMRGE-ITDAGVAALGSYDWPGNIRELRNVLERALTMSEDGDLLDADaifkvlpragqr 412
Cdd:COG3604   219 ERREDIPLLAEHFLEKFSRRLGKPILrLSPEALEALMAYPWPGNVRELENVIERAVILAEGGVLDADD------------ 286

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2524691643 413 lVSPVPARSVRPLARivaeaeaQAIEEALVTCRGNRTKAARLLGISRSVLYEKLARL 469
Cdd:COG3604   287 -LAPGSREALEEVER-------EHILEALERTGGNIAGAARLLGLTPSTLRSRMKKL 335
pspF PRK11608
phage shock protein operon transcriptional activator; Provisional
 169-458 1.73e-64

phage shock protein operon transcriptional activator; Provisional


Pssm-ID: 236936 [Multi-domain]  Cd Length: 326  Bit Score: 211.07  E-value: 1.73e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 169 EVKRRARLaagrDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVAPGAYTGADRRtREGK 248
Cdd:PRK11608   21 QVSRLAPL----DKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHEAGAFTGAQKR-HPGR 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 249 FQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVRVIAATSRNLEAMIAEGSFRSDLYYRLNVLEIN 328
Cdd:PRK11608   96 FERADGGTLFLDELATAPMLVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVAEGKFRADLLDRLAFDVVQ 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 329 IPPLRDRLADLGVLCEALLGEICE--GQDMRGEITDAGVAALGSYDWPGNIRELRNVLERALTMSEDGDLLDADAIFKVL 406
Cdd:PRK11608  176 LPPLRERQSDIMLMAEHFAIQMCRelGLPLFPGFTERARETLLNYRWPGNIRELKNVVERSVYRHGTSEYPLDNIIIDPF 255

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2524691643 407 PRAGQRLVSPVPARSVRP-----LARIVAEAEAQAIEEALVTCRGNRTKAARLLGIS 458
Cdd:PRK11608  256 KRRPAEEAIAVSETTSLPtlpldLREWQHQQEKELLQRSLQQAKFNQKRAAELLGLT 312
PspF COG1221
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain ...
 182-383 1.13e-26

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: 113.66  E-value: 1.13e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 182 MPVLLLGETGTGKEVLAQAIH--AVSPRV---DKPFVGVNVAAVPEN--LLEAEFFGVAPGAYTGADRrTREGKFQLANG 254
Cdd:COG1221   131 LHTLILGPTGVGKSFFAELMYeyAIEIGVlpeDAPFVVFNCADYANNpqLLMSQLFGYVKGAFTGADK-DKEGLIEKADG 209

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 255 GTLFLDEVGDMPLPLQAKLLRALQEGEIEALG-SNKVTTVDVRVIAATSRNLEAmiaegSF-----RsdlyyRLNVLeIN 328
Cdd:COG1221   210 GILFLDEVHRLPPEGQEMLFTFMDKGIYRRLGeTEKTRKANVRIIFATTEDPES-----SLlktflR-----RIPMV-IK 278

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2524691643 329 IPPLRDRLAD--LGVLCEALLGE-ICEGQDMRgeITDAGVAALGSYDWPGNIRELRNV 383
Cdd:COG1221   279 LPSLEERSLEerLELIKHFFKEEaKRLNKPIK--VSKEVLKALLLYDCPGNIGQLKSD 334
Sigma54_activ_2 pfam14532
Sigma-54 interaction domain;
161-332 2.57e-24

Sigma-54 interaction domain;


Pssm-ID: 434021 [Multi-domain]  Cd Length: 138  Bit Score: 98.18  E-value: 2.57e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 161 VGGSPAALEVKRRARLAAGRDMPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAeffgvapgaytga 240
Cdd:pfam14532   1 LGASAAIQEIKRRLEQAAQSTLPVFLTGEPGSGKEFCARYLHNPSTPWVQPFDIEYLAHAPLELLEQ------------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 241 drrtregkfqlANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEalgsnkvttvDVRVIAATSRNLEAMIAEGSFRSDLYY 320
Cdd:pfam14532  68 -----------AKGGTLYLKDIADLSKALQKGLLLLLAKAEGY----------RVRLVCTSSKDLPQLAAAGLFDEQLYF 126

                         170
                  ....*....|..
gi 2524691643 321 RLNVLEINIPPL 332
Cdd:pfam14532 127 ELSALRLHVPPL 138
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 161-331 6.93e-23

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: 94.52  E-value: 6.93e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 161 VGGSPAALEVKRRARLAAGRdmPVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLEAEFFGVapgaytgA 240
Cdd:cd00009     1 VGQEEAIEALREALELPPPK--NLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGH-------F 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 241 DRRTREGKFQLANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEalgsnKVTTVDVRVIAATSRNLeamiaEGSFRSDLYY 320
Cdd:cd00009    72 LVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDL-----RIDRENVRVIGATNRPL-----LGDLDRALYD 141

                         170
                  ....*....|.
gi 2524691643 321 RLNvLEINIPP 331
Cdd:cd00009   142 RLD-IRIVIPL 151
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 183-322 9.50e-09

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: 54.30  E-value: 9.50e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  183 PVLLLGETGTGKEVLAQAIHAVSPRVDKPFVGVNVAAVPENLLE-AEFFGVAPGAYTGADRRTREGKFQLA---NGGTLF 258
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDqLLLIIVGGKKASGSGELRLRLALALArklKPDVLI 83

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2524691643  259 LDEVGDMPLPLQAKLLRALQEgeiEALGSNKVTTVDVRVIAATSR--NLEAMIAEGSFRSDLYYRL 322
Cdd:smart00382  84 LDEITSLLDAEQEALLLLLEE---LRLLLLLKSEKNLTVILTTNDekDLGPALLRRRFDRRIVLLL 146
HTH_8 pfam02954
Bacterial regulatory protein, Fis family;
444-468 2.31e-06

Bacterial regulatory protein, Fis family;


Pssm-ID: 427077 [Multi-domain]  Cd Length: 40  Bit Score: 44.31  E-value: 2.31e-06
                          10        20
                  ....*....|....*....|....*
gi 2524691643 444 CRGNRTKAARLLGISRSVLYEKLAR 468
Cdd:pfam02954  16 TGGNKSKAARLLGISRRTLYRKLKK 40
PAS_4 pfam08448
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 25-117 4.19e-06

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: 45.48  E-value: 4.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  25 FEEASAGAIAVDRDANITWINSSYSQLLGlVDPSHAIGKSVRKVIP-------QTRMPEVVETGKPL-LLDIMEHNKQQL 96
Cdd:pfam08448   1 LDSLPDALAVLDPDGRVRYANAAAAELFG-LPPEELLGKTLAELLPpedaarlERALRRALEGEEPIdFLEELLLNGEER 79

                          90       100
                  ....*....|....*....|...
gi 2524691643  97 VVTR--LPYYDDQGGIVGAVAFV 117
Cdd:pfam08448  80 HYELrlTPLRDPDGEVIGVLVIS 102
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 24-117 9.25e-06

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: 44.72  E-value: 9.25e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  24 MFEEASAGAIAVDRDANITWINSSYSQLLGLvDPSHAIGKSVRKVIPQTRMPEVVE------------TGKPLLLDIMEH 91
Cdd:pfam00989   6 ILESLPDGIFVVDEDGRILYVNAAAEELLGL-SREEVIGKSLLDLIPEEDDAEVAEllrqallqgeesRGFEVSFRVPDG 84

                          90       100
                  ....*....|....*....|....*.
gi 2524691643  92 NKQQLVVTRLPYYDDQGGIVGAVAFV 117
Cdd:pfam00989  85 RPRHVEVRASPVRDAGGEILGFLGVL 110
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 24-80 1.20e-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.


Pssm-ID: 214512  Cd Length: 67  Bit Score: 42.77  E-value: 1.20e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2524691643   24 MFEEASAGAIAVDRDANITWINSSYSQLLGLvDPSHAIGKSVRKVIPQTRMPEVVET 80
Cdd:smart00091   6 ILESLPDGIFVLDLDGRILYANPAAEELLGY-SPEELIGKSLLELIHPEDRERVQEA 61
Fis COG2901
DNA-binding protein Fis (factor for inversion stimulation) [Transcription];
444-469 2.20e-05

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


Pssm-ID: 442146 [Multi-domain]  Cd Length: 83  Bit Score: 42.49  E-value: 2.20e-05
                          10        20
                  ....*....|....*....|....*.
gi 2524691643 444 CRGNRTKAARLLGISRSVLYEKLARL 469
Cdd:COG2901    55 TRGNQSRAAEMLGINRNTLRKKLKQY 80
CitA COG3290
Sensor histidine kinase DipB regulating citrate/malate metabolism [Signal transduction ...
 24-115 4.67e-05

Sensor histidine kinase DipB regulating citrate/malate metabolism [Signal transduction mechanisms];


Pssm-ID: 442519 [Multi-domain]  Cd Length: 389  Bit Score: 45.61  E-value: 4.67e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  24 MFEEASAGAIAVDRDANITWINSSYSQLLGLvdpsHAIGKSVRKVIpqtrmPEVVETGKplLLDIMEHNKQQLVVTRLPY 103
Cdd:COG3290    89 VLESIREGVIAVDRDGRITLINDAARRLLGL----DAIGRPIDEVL-----AEVLETGE--RDEEILLNGRVLVVNRVPI 157

                          90
                  ....*....|..
gi 2524691643 104 YDDqGGIVGAVA 115
Cdd:COG3290   158 RDD-GRVVGAVA 168
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 28-135 1.22e-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. 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: 41.08  E-value: 1.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  28 ASAGAIAVDRDANITWINSSYSQLLGLvDPSHAIGKSVRKVIPQTRMPEVVETgkplLLDIMEHNKQQLVVTRLPYYDDQ 107
Cdd:cd00130     1 LPDGVIVLDLDGRILYANPAAEQLLGY-SPEELIGKSLLDLIHPEDREELRER----LENLLSGGEPVTLEVRLRRKDGS 75

                          90       100
                  ....*....|....*....|....*...
gi 2524691643 108 GGIVGAVAFVLYDDLQPLTPLVSKYRRL 135
Cdd:cd00130    76 VIWVLVSLTPIRDEGGEVIGLLGVVRDI 103
NtrY COG5000
Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism ...
 15-125 1.77e-04

Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms];


Pssm-ID: 444024 [Multi-domain]  Cd Length: 422  Bit Score: 43.80  E-value: 1.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  15 RDLIEALFpmfEEASAGAIAVDRDANITWINSSYSQLLGlVDPSHAIGKSVRKVIPQTRMPEVV----ETGKPLLLDIME 90
Cdd:COG5000    89 RRYLETIL---ENLPAGVIVLDADGRITLANPAAERLLG-IPLEELIGKPLEELLPELDLAELLrealERGWQEEIELTR 164

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2524691643  91 HNKQQLVVTRLPYYDDqggivGAVafVLYDDLQPL 125
Cdd:COG5000   165 DGRRTLLVRASPLRDD-----GYV--IVFDDITEL 192
MCM cd17706
MCM helicase family; MCM helicases are a family of helicases that play an important role in ...
 161-301 2.02e-04

MCM helicase family; MCM helicases are a family of helicases that play an important role in replication and homologous recombination repair. The heterohexameric ring-shaped Mcm2-7 complex is part of the replicative helicase that unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. Mcm8 and Mcm9, form a complex required for homologous recombination (HR) repair induced by DNA interstrand crosslinks (ICLs).


Pssm-ID: 350658 [Multi-domain]  Cd Length: 311  Bit Score: 43.10  E-value: 2.02e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 161 VGGSPAALEVKRRARlaagRDMPVLLLGETGTGKEVLAQAIHAVSPRVdkpfVGVNVAAVPenlleaeffgvAPGAYTGA 240
Cdd:cd17706    25 FGGVQKILEDGTRIR----GDIHILLVGDPGTAKSQILKYVLKIAPRG----VYTSGKGSS-----------GAGLTAAV 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 241 DRRTREGKFQL-------ANGGTLFLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTVDVR--VIAAT 301
Cdd:cd17706    86 VRDSETGEWYLeagalvlADGGVCCIDEFDKMKELDRTALHEAMEQQTISIAKAGIVTTLNARcsILAAA 155
NtrB COG3852
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];
15-111 4.72e-04

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


Pssm-ID: 443061 [Multi-domain]  Cd Length: 361  Bit Score: 42.14  E-value: 4.72e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  15 RDLIEALFPMFEEASAGAIAVDRDANITWINSSYSQLLGlVDPSHAIGKSVRKVIPQT-----RMPEVVETGKPLL---L 86
Cdd:COG3852     3 RESEELLRAILDSLPDAVIVLDADGRITYVNPAAERLLG-LSAEELLGRPLAELFPEDsplreLLERALAEGQPVTereV 81

                          90       100
                  ....*....|....*....|....*....
gi 2524691643  87 DIMEHNKQQLVV----TRLPYYDDQGGIV 111
Cdd:COG3852    82 TLRRKDGEERPVdvsvSPLRDAEGEGGVL 110
PRK11360 PRK11360
two-component system sensor histidine kinase AtoS;
24-137 1.78e-03

two-component system sensor histidine kinase AtoS;


Pssm-ID: 236901 [Multi-domain]  Cd Length: 607  Bit Score: 40.72  E-value: 1.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  24 MFEEASAGAIAVDRDANITWINSSYSQLLGLvDPSHAIGKSVRKVIPQTrmPEVVEtgkpLLLDIMEHNKQ--------- 94
Cdd:PRK11360  267 ILESIADGVIAIDRQGKITTMNPAAEVITGL-QRHELVGKPYSELFPPN--TPFAS----PLLDTLEHGTEhvdleisfp 339

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 2524691643  95 ------QLVVTRLPYYDDQGGIVGAVafVLYDDLQPLTPLVSKYRRLHR 137
Cdd:PRK11360  340 grdrtiELSVSTSLLHNTHGEMIGAL--VIFSDLTERKRLQRRVARQER 386
fis PRK00430
DNA-binding transcriptional regulator Fis;
444-466 2.27e-03

DNA-binding transcriptional regulator Fis;


Pssm-ID: 179020 [Multi-domain]  Cd Length: 95  Bit Score: 37.35  E-value: 2.27e-03
                          10        20
                  ....*....|....*....|...
gi 2524691643 444 CRGNRTKAARLLGISRSVLYEKL 466
Cdd:PRK00430   67 TRGNQTRAALMLGINRGTLRKKL 89
PAS COG2202
PAS domain [Signal transduction mechanisms];
15-117 5.52e-03

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 38.47  E-value: 5.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643  15 RDLIEALFPMFEEASAGAIAVDRDANITWINSSYSQLLGLvDPSHAIGKSVRKVIP-------QTRMPEVVETGKPLLLD 87
Cdd:COG2202     7 EESERRLRALVESSPDAIIITDLDGRILYVNPAFERLTGY-SAEELLGKTLRDLLPpedddefLELLRAALAGGGVWRGE 85

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2524691643  88 IMEHNKQQ----LVVTRLPYYDDQGGIVGAVAFV 117
Cdd:COG2202    86 LRNRRKDGslfwVELSISPVRDEDGEITGFVGIA 119
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 183-336 7.80e-03

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: 36.50  E-value: 7.80e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 183 PVLLLGETGTGKEVLAQAI-HAVSPRVdkpfvgVNVAAVPENLLEAEFFG---VAPGAYTGADRR-TREGKfqlaNGGTL 257
Cdd:pfam07728   1 GVLLVGPPGTGKTELAERLaAALSNRP------VFYVQLTRDTTEEDLFGrrnIDPGGASWVDGPlVRAAR----EGEIA 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2524691643 258 FLDEVGDMPLPLQAKLLRALQEGEIEALGSNKVTTV---DVRVIAATsrnleamiaegsfrSDLYYRLNVLEiniPPLRD 334
Cdd:pfam07728  71 VLDEINRANPDVLNSLLSLLDERRLLLPDGGELVKAapdGFRLIATM--------------NPLDRGLNELS---PALRS 133


                  ..
gi 2524691643 335 RL 336
Cdd:pfam07728 134 RF 135
 
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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