|
Name |
Accession |
Description |
Interval |
E-value |
| nifA |
TIGR01817 |
Nif-specific regulatory protein; This model represents NifA, a DNA-binding regulatory protein ... |
17-524 |
0e+00 |
|
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: 784.29 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 17 SQQFTAMQRISVVLSRATEASKTLQEVLSVLHNDAFMQHGMICLYDSEQEILSIEALQQTGqqplPGSTQIRYRPGEGLV 96
Cdd:TIGR01817 1 DLQLAALYEISKILSAPTRLEKTLANVLNVLSNDLGMRHGLITLSDSEGEPLLVAAIGWSE----EGFAPIRYRVGEGAI 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 97 GTVLAQGQSLVLPRVADDQRFLDRLSLYDYD-LPFIAVPLMgPNARPIGVLAAQPMARQEERLPACTRFLETVANLVAQT 175
Cdd:TIGR01817 77 GQIVATGNSLVVPDVAAEPLFLDRLSLYDPGpVPFIGVPIK-ADSETIGVLAADRDFRSRERLEEEVRFLEMVANLIGQT 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 176 IRL-----MILPASPALSSRQPPKVERPPACSSSRGVGLDNMV-GKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELI 249
Cdd:TIGR01817 156 VRLhrlvaQRRERLIAEAVQLSKQLRDKAPEIARRRSGKEDGIiGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELI 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 250 ANAIHHHSPRAGAAFVKFNCAALPDTLLESELFGHEKGAFTGAVRQRKGRFELADGGTLFLDEIGESSASFQAKLLRILQ 329
Cdd:TIGR01817 236 AKAIHYLSPRAKRPFVKVNCAALSETLLESELFGHEKGAFTGAIAQRKGRFELADGGTLFLDEIGEISPAFQAKLLRVLQ 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 330 EGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHFREDLYYRLNVMPIALPPLRERQEDIAELAHFLVRKIGQHQGRTL 409
Cdd:TIGR01817 316 EGEFERVGGNRTLKVDVRLVAATNRDLEEAVAKGEFRADLYYRINVVPIFLPPLRERREDIPLLAEAFLEKFNRENGRPL 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 410 RISEGAIRLLMEYSWPGNVRELENCLERSAVMSESGLIDRDVILFTHQDRPAKAL------------------------P 465
Cdd:TIGR01817 396 TITPSAIRVLMSCKWPGNVRELENCLERTATLSRSGTITRSDFSCQSGQCLSPMLaktcphghisidplagttpphspaS 475
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*....
gi 1709668812 466 ASGPAEDSWLDNSLDERQRLIAALEKAGWVQAKAARLLGMTPRQVAYRIQIMDITLPRL 524
Cdd:TIGR01817 476 AALPGEPGLSGPTLSERERLIAALEQAGWVQAKAARLLGMTPRQVGYALRKLNIEMKKL 534
|
|
| RocR |
COG3829 |
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ... |
209-515 |
6.00e-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: 467.33 E-value: 6.00e-162
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 209 LDNMVGKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLESELFGHEKGA 288
Cdd:COG3829 137 FDDIIGKSPAMKELLELAKRVAKSDSTVLILGESGTGKELFARAIHNASPRRDGPFVAVNCAAIPENLLESELFGYEKGA 216
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 289 FTGAVRQ-RKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHFRE 367
Cdd:COG3829 217 FTGAKKGgKPGLFELADGGTLFLDEIGEMPLSLQAKLLRVLQEKEVRRVGGTKPIPVDVRIIAATNRDLEEMVEEGRFRE 296
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 368 DLYYRLNVMPIALPPLRERQEDIAELAHFLVRKIGQHQGRTL-RISEGAIRLLMEYSWPGNVRELENCLERSAVMSESGL 446
Cdd:COG3829 297 DLYYRLNVIPIHIPPLRERKEDIPLLAEHFLEKFNKKYGKNIkGISPEALELLLAYDWPGNVRELENVIERAVVLSEGDV 376
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1709668812 447 IDRDVILFTHQDRPAKALPASGPAEDSWLDNSldERQRLIAALEKAGWVQAKAARLLGMTPRQVAYRIQ 515
Cdd:COG3829 377 ITPEHLPEYLLEEAEAASAAEEGSLKEALEEV--EKELIEEALEKTGGNKSKAAKALGISRSTLYRKLK 443
|
|
| AtoC |
COG2204 |
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ... |
210-515 |
8.64e-139 |
|
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: 407.04 E-value: 8.64e-139
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 210 DNMVGKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLESELFGHEKGAF 289
Cdd:COG2204 131 SGLIGRSPAMQEVRRLIEKVAPSDATVLITGESGTGKELVARAIHRLSPRADGPFVAVNCAAIPEELLESELFGHEKGAF 210
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 290 TGAVRQRKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHFREDL 369
Cdd:COG2204 211 TGAVARRIGKFELADGGTLFLDEIGEMPLALQAKLLRVLQEREFERVGGNKPIPVDVRVIAATNRDLEELVEEGRFREDL 290
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 370 YYRLNVMPIALPPLRERQEDIAELAHFLVRKIGQHQGRTLRISEGAIRLLMEYSWPGNVRELENCLERSAVMSESGLIDr 449
Cdd:COG2204 291 YYRLNVFPIELPPLRERREDIPLLARHFLARFAAELGKPVKLSPEALEALLAYDWPGNVRELENVIERAVILADGEVIT- 369
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1709668812 450 dvilfthqdrpakalpasgpAEDswLDNSLD--ERQRLIAALEKAGWVQAKAARLLGMTPRQVAYRIQ 515
Cdd:COG2204 370 --------------------AED--LPEALEevERELIERALEETGGNVSRAAELLGISRRTLYRKLK 415
|
|
| PRK05022 |
PRK05022 |
nitric oxide reductase transcriptional regulator NorR; |
141-505 |
1.44e-126 |
|
nitric oxide reductase transcriptional regulator NorR;
Pssm-ID: 235331 [Multi-domain] Cd Length: 509 Bit Score: 379.13 E-value: 1.44e-126
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 141 RPIGVL---AAQPmaRQEERLPACTrfLETVANLVAQTIRLMILP---ASPALSSRQPPKVERPPACSSSRgvgldnMVG 214
Cdd:PRK05022 122 RLIGALtldALDP--GQFDAFSDEE--LRALAALAAATLRNALLIeqlESQAELPQDVAEFLRQEALKEGE------MIG 191
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 215 KSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLESELFGHEKGAFTGAVR 294
Cdd:PRK05022 192 QSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAALPESLAESELFGHVKGAFTGAIS 271
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 295 QRKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHFREDLYYRLN 374
Cdd:PRK05022 272 NRSGKFELADGGTLFLDEIGELPLALQAKLLRVLQYGEIQRVGSDRSLRVDVRVIAATNRDLREEVRAGRFRADLYHRLS 351
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 375 VMPIALPPLRERQEDIAELA-HFLVRKIGQHQGRTLRISEGAIRLLMEYSWPGNVRELENCLERSAVMSESGLIDRDVIL 453
Cdd:PRK05022 352 VFPLSVPPLRERGDDVLLLAgYFLEQNRARLGLRSLRLSPAAQAALLAYDWPGNVRELEHVISRAALLARARGAGRIVTL 431
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1709668812 454 ----FTHQDRPAKALPASGPAEDSWLDNSLDE------RQRLIAALEKAGWVQAKAARLLGM 505
Cdd:PRK05022 432 eaqhLDLPAEVALPPPEAAAAPAAVVSQNLREateafqRQLIRQALAQHQGNWAAAARALEL 493
|
|
| AcoR |
COG3284 |
Transcriptional regulator DhaR of acetoin/glycerol metabolism [Transcription]; |
177-505 |
3.96e-114 |
|
Transcriptional regulator DhaR of acetoin/glycerol metabolism [Transcription];
Pssm-ID: 442514 [Multi-domain] Cd Length: 625 Bit Score: 351.12 E-value: 3.96e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 177 RLMILPASPALSSRqPPKVERPPAcsssrgvgLDNMVGKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHH 256
Cdd:COG3284 297 LLRLRPARRAARAA-PAGAPAPAA--------LAALAGGDPAMRRALRRARRLADRDIPVLILGETGTGKELFARAIHAA 367
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 257 SPRAGAAFVKFNCAALPDTLLESELFGHEKGAFTGAVRQ-RKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMER 335
Cdd:COG3284 368 SPRADGPFVAVNCAAIPEELIESELFGYEPGAFTGARRKgRPGKIEQADGGTLFLDEIGDMPLALQARLLRVLQEREVTP 447
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 336 VGGDETLRVNVRIIAATNRHLEEEVRLGHFREDLYYRLNVMPIALPPLRERqEDIAELAHFLVRKIGQHQGRtLRISEGA 415
Cdd:COG3284 448 LGGTKPIPVDVRLIAATHRDLRELVAAGRFREDLYYRLNGLTLTLPPLRER-EDLPALIEHLLRELAAGRGP-LRLSPEA 525
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 416 IRLLMEYSWPGNVRELENCLERSAVMSESGLIDRDVILFTHQDRPAKALPASGPAEDSWLDnslDERQRLIAALEKAGWV 495
Cdd:COG3284 526 LALLAAYPWPGNVRELRNVLRTALALADGGVITVEDLPDELRAELAAAAPAAAAPLTSLEE---AERDAILRALRACGGN 602
|
330
....*....|
gi 1709668812 496 QAKAARLLGM 505
Cdd:COG3284 603 VSAAARALGI 612
|
|
| RNA_repair_RtcR |
NF038308 |
RNA repair transcriptional activator RtcR; |
211-509 |
5.04e-111 |
|
RNA repair transcriptional activator RtcR;
Pssm-ID: 468466 [Multi-domain] Cd Length: 527 Bit Score: 339.93 E-value: 5.04e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 211 NMVGKSPAMRQIVEVIRQVSRWDT-TVLVRGESGTGKELIANAIHHHSPRAG---AAFVKFNCAALPDTLLESELFGHEK 286
Cdd:NF038308 180 GIATRNAAFNRLIEQIERVALRSRaPILLTGPTGAGKSFLARRIYELKKRRHqvsGPFVEVNCATLRGDLAMSELFGHVK 259
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 287 GAFTGAVRQRKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHFR 366
Cdd:NF038308 260 GAFTGAQADRAGLLRAADGGTLFLDEIGELGLDEQAMLLRAIEEKRFLPVGSDKEVSSDFQLIAGTNRDLRQEVAEGRFR 339
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 367 EDLYYRLNVMPIALPPLRERQEDIAELAHFLVRKIGQHQGRTL------RISEGAIRLLMEYSWPGNVRELENCLERSAV 440
Cdd:NF038308 340 EDLYARINLWTFRLPGLRERREDIEPNLDYELDRFARELGRQVrfnkeaRFRYLAFATSPEALWPGNFRELSASVTRMAT 419
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 441 MSESGLIDRDVI-----LFTHQDRPAKALPASGPAEDSWLDNSLD--------ERQRLIAALEKAGWVQAKAARLLGMTP 507
Cdd:NF038308 420 LADGGRITEELVeeeiaRLRAAWQSAPAAADDDALADLLGGEQLAeldlfdrvQLAAVLRVCRQSRSLSAAGRRLFGVSR 499
|
..
gi 1709668812 508 RQ 509
Cdd:NF038308 500 QQ 501
|
|
| Sigma54_activat |
pfam00158 |
Sigma-54 interaction domain; |
212-378 |
8.80e-109 |
|
Sigma-54 interaction domain;
Pssm-ID: 425491 [Multi-domain] Cd Length: 168 Bit Score: 320.89 E-value: 8.80e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 212 MVGKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLESELFGHEKGAFTG 291
Cdd:pfam00158 1 IIGESPAMQEVLEQAKRVAPTDAPVLITGESGTGKELFARAIHQLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 292 AVRQRKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHFREDLYY 371
Cdd:pfam00158 81 ADSDRKGLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTKPIKVDVRIIAATNRDLEEAVAEGRFREDLYY 160
|
....*..
gi 1709668812 372 RLNVMPI 378
Cdd:pfam00158 161 RLNVIPI 167
|
|
| PRK11361 |
PRK11361 |
acetoacetate metabolism transcriptional regulator AtoC; |
216-520 |
6.70e-107 |
|
acetoacetate metabolism transcriptional regulator AtoC;
Pssm-ID: 183099 [Multi-domain] Cd Length: 457 Bit Score: 326.81 E-value: 6.70e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 216 SPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLESELFGHEKGAFTGAVRQ 295
Cdd:PRK11361 149 SPAMMDICKDTAKIALSQASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGHEKGAFTGAQTL 228
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 296 RKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHFREDLYYRLNV 375
Cdd:PRK11361 229 RQGLFERANEGTLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFREDLFYRLNV 308
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 376 MPIALPPLRERQEDIAELA-HFLVRKIGQHQGRTLRISEGAIRLLMEYSWPGNVRELENCLERSAVMSESGLIDRDVI-- 452
Cdd:PRK11361 309 IHLILPPLRDRREDISLLAnHFLQKFSSENQRDIIDIDPMAMSLLTAWSWPGNIRELSNVIERAVVMNSGPIIFSEDLpp 388
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1709668812 453 LFTHQDRPAKALPASGPAEDSWLDNSLDERQRLIA-ALEKAGWVQAKAARLLGMTPRQVAYRIQIMDIT 520
Cdd:PRK11361 389 QIRQPVCNAGEVKTAPVGERNLKEEIKRVEKRIIMeVLEQQEGNRTRTALMLGISRRALMYKLQEYGID 457
|
|
| TF_PrdR |
NF041552 |
sigma-54 dependent transcriptional regulator PrdR; |
209-512 |
2.09e-105 |
|
sigma-54 dependent transcriptional regulator PrdR;
Pssm-ID: 469437 [Multi-domain] Cd Length: 577 Bit Score: 326.85 E-value: 2.09e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 209 LDNMVGKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHHSPRAGAaFVKFNCAALPDTLLESELFGHEKGA 288
Cdd:NF041552 266 FGKIIGKSKKIIKKIEIAKQVAKTNSSVLITGESGTGKEVFARAIHQASGRKGP-FVPVNCSAIPEELFESEFFGYEEGA 344
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 289 FTGAVRQRK-GRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHFRE 367
Cdd:NF041552 345 FTGALKKGKiGKFELANNGTLFLDEIGDMPLSMQAKLLRVLQEKQVRRVGGEKYIKINVRIISATNKDLKKMVKEGKFRE 424
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 368 DLYYRLNVMPIALPPLRERQEDIAELAHFLVRKIGQHQG-RTLRISEGAIRLLMEYSWPGNVRELENCLERSAVMSESGL 446
Cdd:NF041552 425 DLYYRLNVVEIELPPLRERKEDIPLLINYFLKEICKENNkEIPKIDKEVYDILQNYKWKGNIRELKNTIEHLVVLSKNGT 504
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1709668812 447 IDRDVIlfthqdrPAKALPASGPAEDSWLDNSLD--------ERQRLIAALEKAGWVQAKAARLLGMtPRQVAY 512
Cdd:NF041552 505 ITKDSI-------PEYILESVKKKEDEEGDYPLDlnkaveklEIDTIKKALEMSNGNKAKAAKLLNI-PRSTLY 570
|
|
| TyrR |
COG3283 |
Transcriptional regulator TyrR of aromatic amino acids metabolism [Transcription, Amino acid ... |
208-481 |
2.75e-102 |
|
Transcriptional regulator TyrR of aromatic amino acids metabolism [Transcription, Amino acid transport and metabolism];
Pssm-ID: 442513 [Multi-domain] Cd Length: 514 Bit Score: 316.75 E-value: 2.75e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 208 GLDNMVGKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLESELFGHEKG 287
Cdd:COG3283 202 GFDHIVASSPKMRQVIRQAKKMAMLDAPLLIQGETGTGKELLARACHLASPRGDKPFLALNCAALPDDVAESELFGYAPG 281
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 288 AFTGAVRQRKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHFRE 367
Cdd:COG3283 282 AFGNAREGKKGLFEQANGGTVFLDEIGEMSPQLQAKLLRFLQDGTFRRVGEEQEVKVDVRVICATQKDLAELVQEGEFRE 361
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 368 DLYYRLNVMPIALPPLRERQEDIAELAHFLVRKIGQHQGRTL-RISEGAIRLLMEYSWPGNVRELENCLERSAVMSESGL 446
Cdd:COG3283 362 DLYYRLNVLTLTLPPLRERKSDILPLAEHFVARFSQQLGRPRpRLSPDLVDFLQSYPWPGNVRQLENALYRAVSLLEGDE 441
|
250 260 270
....*....|....*....|....*....|....*...
gi 1709668812 447 IDRDVIlfthqdrpakALPASGPAE---DSWLDNSLDE 481
Cdd:COG3283 442 LTPEDL----------QLPEYAASAgllDDLLEGSLDE 469
|
|
| ntrC |
TIGR01818 |
nitrogen regulation protein NR(I); This model represents NtrC, a DNA-binding response ... |
186-504 |
4.24e-99 |
|
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: 307.05 E-value: 4.24e-99
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 186 ALSSRQPPKVERPPACSSSRGVgldNMVGKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHHSPRAGAAFV 265
Cdd:TIGR01818 113 ALAHAQEQVALPADAGEAEDSA---ELIGEAPAMQEVFRAIGRLSRSDITVLINGESGTGKELVARALHRHSPRANGPFI 189
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 266 KFNCAALPDTLLESELFGHEKGAFTGAVRQRKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVN 345
Cdd:TIGR01818 190 ALNMAAIPKDLIESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDEIGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVD 269
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 346 VRIIAATNRHLEEEVRLGHFREDLYYRLNVMPIALPPLRERQEDIAELA-HFLVRKIGQHQGRTLRISEGAIRLLMEYSW 424
Cdd:TIGR01818 270 VRIVAATHQNLEALVRQGKFREDLFHRLNVIRIHLPPLRERREDIPRLArHFLALAARELDVEPKLLDPEALERLKQLRW 349
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 425 PGNVRELENCLERSAVMSESGLIDRDVI--LFTHQDRPAKAlPASGPAED------SWLDNSLD--------------ER 482
Cdd:TIGR01818 350 PGNVRQLENLCRWLTVMASGDEVLVSDLpaELALTGRPASA-PDSDGQDSwdealeAWAKQALSrgeqglldralpefER 428
|
330 340
....*....|....*....|..
gi 1709668812 483 QRLIAALEKAGWVQAKAARLLG 504
Cdd:TIGR01818 429 PLLEAALQHTRGHKQEAAALLG 450
|
|
| PRK10365 |
PRK10365 |
sigma-54-dependent response regulator transcription factor ZraR; |
186-506 |
5.77e-98 |
|
sigma-54-dependent response regulator transcription factor ZraR;
Pssm-ID: 182412 [Multi-domain] Cd Length: 441 Bit Score: 303.49 E-value: 5.77e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 186 ALSSRQPPKVERPPACSSSRGvgldnMVGKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHHSPRAGAAFV 265
Cdd:PRK10365 120 ALAHTHSIDAETPAVTASQFG-----MVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHASSARSEKPLV 194
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 266 KFNCAALPDTLLESELFGHEKGAFTGAVRQRKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVN 345
Cdd:PRK10365 195 TLNCAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPMMQVRLLRAIQEREVQRVGSNQTISVD 274
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 346 VRIIAATNRHLEEEVRLGHFREDLYYRLNVMPIALPPLRERQEDIAELA-HFLVRKIGQHQGRTLRISEGAIRLLMEYSW 424
Cdd:PRK10365 275 VRLIAATHRDLAAEVNAGRFRQDLYYRLNVVAIEVPSLRQRREDIPLLAgHFLQRFAERNRKAVKGFTPQAMDLLIHYDW 354
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 425 PGNVRELENCLERSAVMSESGLI-DRDVILFThqdrPAKALPASGPAEDSWLDNSldERQRLIAALEKAGWVQAKAARLL 503
Cdd:PRK10365 355 PGNIRELENAVERAVVLLTGEYIsERELPLAI----ASTPIPLGQSQDIQPLVEV--EKEVILAALEKTGGNKTEAARQL 428
|
...
gi 1709668812 504 GMT 506
Cdd:PRK10365 429 GIT 431
|
|
| FhlA |
COG3604 |
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ... |
86-520 |
4.44e-97 |
|
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: 297.53 E-value: 4.44e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 86 QIRYRPGEGLVGTVLAQGQSLVLPRVADDQRFLDRLSLYDYDLPFIAVPLMGPNaRPIGVLAAQPMaRQEERLPACTRFL 165
Cdd:COG3604 32 LRGDLLASALVLEESLELLALALSEALLAAQARQAALAARERQLFLGVPLRVGG-EVLGVLTLDSR-RPGAFSEEDLRLL 109
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 166 ETVANLVAQTIRlmilpaspalssrqppkverppacsssrgvgldnmvgkspamrqivevirqvsrwdttvlvrGESGTG 245
Cdd:COG3604 110 ETLASLAAVAIL--------------------------------------------------------------GETGTG 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 246 KELIANAIHHHSPRAGAAFVKFNCAALPDTLLESelfghekgaftgavrqrkgrfeladggtlfldeigessasfqakll 325
Cdd:COG3604 128 KELVANAIHELSPRADKPFVKVNCAALPESLLES---------------------------------------------- 161
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 326 riLQEGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHFREDLYYRLNVMPIALPPLRERQEDIAELAHFLVRKIGQHQ 405
Cdd:COG3604 162 --LQEGEFERVGGDETIKVDVRIIAATNRDLEEEVAEGRFREDLYYRLNVFPIRLPPLRERREDIPLLAEHFLEKFSRRL 239
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 406 GRT-LRISEGAIRLLMEYSWPGNVRELENCLERSAVMSESGLIDRDviLFTHQDRPAKAlpasgpaedswldnsLDERQR 484
Cdd:COG3604 240 GKPiLRLSPEALEALMAYPWPGNVRELENVIERAVILAEGGVLDAD--DLAPGSREALE---------------EVEREH 302
|
410 420 430
....*....|....*....|....*....|....*.
gi 1709668812 485 LIAALEKAGWVQAKAARLLGMTPRQVAYRIQIMDIT 520
Cdd:COG3604 303 ILEALERTGGNIAGAARLLGLTPSTLRSRMKKLGIK 338
|
|
| phageshock_pspF |
TIGR02974 |
psp operon transcriptional activator PspF; Members of this protein family are PspF, the ... |
213-509 |
2.74e-96 |
|
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: 294.97 E-value: 2.74e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 213 VGKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLESELFGHEKGAFTGA 292
Cdd:TIGR02974 2 IGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAALSENLLDSELFGHEAGAFTGA 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 293 VRQRKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHFREDLYYR 372
Cdd:TIGR02974 82 QKRHQGRFERADGGTLFLDELATASLLVQEKLLRVIEYGEFERVGGSQTLQVDVRLVCATNADLPALAAEGRFRADLLDR 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 373 LNVMPIALPPLRERQEDIAELAHFLVRKIGQHQGRTL--RISEGAIRLLMEYSWPGNVRELENCLERSAV-MSESGLIDR 449
Cdd:TIGR02974 162 LAFDVITLPPLRERQEDIMLLAEHFAIRMARELGLPLfpGFTPQAREQLLEYHWPGNVRELKNVVERSVYrHGLEEAPID 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 450 DVIL--FTHQDRPAKALPASGPAEDSWLDNSLD------------------ERQRLIAALEKAGWVQAKAARLLGMTPRQ 509
Cdd:TIGR02974 242 EIIIdpFASPWRPKQAAPAVDEVNSTPTDLPSPssiaaafpldlkqaqqdyEIELLQQALAEAQFNQRKAAELLGLTYHQ 321
|
|
| PEP_resp_reg |
TIGR02915 |
PEP-CTERM-box response regulator transcription factor; Members of this protein family share ... |
202-506 |
5.32e-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: 298.59 E-value: 5.32e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 202 SSSRGVGLDNMVGKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLESEL 281
Cdd:TIGR02915 131 SALGGTALRGLITSSPGMQKICRTIEKIAPSDITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIPENLLESEL 210
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 282 FGHEKGAFTGAVRQRKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEEVR 361
Cdd:TIGR02915 211 FGYEKGAFTGAVKQTLGKIEYAHGGTLFLDEIGDLPLNLQAKLLRFLQERVIERLGGREEIPVDVRIVCATNQDLKRMIA 290
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 362 LGHFREDLYYRLNVMPIALPPLRERQEDIAELAHFLVRKIGQHQGRTLR-ISEGAIRLLMEYSWPGNVRELENCLERSAV 440
Cdd:TIGR02915 291 EGTFREDLFYRIAEISITIPPLRSRDGDAVLLANAFLERFARELKRKTKgFTDDALRALEAHAWPGNVRELENKVKRAVI 370
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1709668812 441 MSESGLIDRDVILFTHQDRPAKALPASgpaedswLDNSLD--ERQRLIAALEKAGWVQAKAARLLGMT 506
Cdd:TIGR02915 371 MAEGNQITAEDLGLDARERAETPLEVN-------LREVREraEREAVRKAIARVDGNIARAAELLGIT 431
|
|
| PRK15429 |
PRK15429 |
formate hydrogenlyase transcriptional activator FlhA; |
212-505 |
3.55e-88 |
|
formate hydrogenlyase transcriptional activator FlhA;
Pssm-ID: 237965 [Multi-domain] Cd Length: 686 Bit Score: 285.19 E-value: 3.55e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 212 MVGKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLESELFGHEKGAFTG 291
Cdd:PRK15429 378 IIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPAGLLESDLFGHERGAFTG 457
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 292 AVRQRKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHFREDLYY 371
Cdd:PRK15429 458 ASAQRIGRFELADKSSLFLDEVGDMPLELQPKLLRVLQEQEFERLGSNKIIQTDVRLIAATNRDLKKMVADREFRSDLYY 537
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 372 RLNVMPIALPPLRERQEDIAELAHFLVRKIGQHQGRTL-RISEGAIRLLMEYSWPGNVRELENCLERSAvmsesgLIDRD 450
Cdd:PRK15429 538 RLNVFPIHLPPLRERPEDIPLLVKAFTFKIARRMGRNIdSIPAETLRTLSNMEWPGNVRELENVIERAV------LLTRG 611
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*...
gi 1709668812 451 VILFTHQDRPAKALPASGPAEDSWLDNSLDERQRLIAALEKAGWVQA---KAARLLGM 505
Cdd:PRK15429 612 NVLQLSLPDITLPEPETPPAATVVAQEGEDEYQLIVRVLKETNGVVAgpkGAAQRLGL 669
|
|
| glnG |
PRK10923 |
nitrogen regulation protein NR(I); Provisional |
186-504 |
2.78e-87 |
|
nitrogen regulation protein NR(I); Provisional
Pssm-ID: 182842 [Multi-domain] Cd Length: 469 Bit Score: 276.75 E-value: 2.78e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 186 ALSSRQPPKVERPPACSSSrgvgLDNMVGKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHHSPRAGAAFV 265
Cdd:PRK10923 118 AISHYQEQQQPRNIQVNGP----TTDIIGEAPAMQDVFRIIGRLSRSSISVLINGESGTGKELVAHALHRHSPRAKAPFI 193
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 266 KFNCAALPDTLLESELFGHEKGAFTGAVRQRKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVN 345
Cdd:PRK10923 194 ALNMAAIPKDLIESELFGHEKGAFTGANTIRQGRFEQADGGTLFLDEIGDMPLDVQTRLLRVLADGQFYRVGGYAPVKVD 273
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 346 VRIIAATNRHLEEEVRLGHFREDLYYRLNVMPIALPPLRERQEDIAELAHFLVRKIGQHQGRTLRI-SEGAIRLLMEYSW 424
Cdd:PRK10923 274 VRIIAATHQNLEQRVQEGKFREDLFHRLNVIRVHLPPLRERREDIPRLARHFLQVAARELGVEAKLlHPETEAALTRLAW 353
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 425 PGNVRELENCLERSAVMSESGLI---DRDVILF--THQDRPAKALPASGPAEDS-WLDNSLD--------------ERQR 484
Cdd:PRK10923 354 PGNVRQLENTCRWLTVMAAGQEVliqDLPGELFesTVPESTSQMQPDSWATLLAqWADRALRsghqnllseaqpelERTL 433
|
330 340
....*....|....*....|
gi 1709668812 485 LIAALEKAGWVQAKAARLLG 504
Cdd:PRK10923 434 LTTALRHTQGHKQEAARLLG 453
|
|
| pspF |
PRK11608 |
phage shock protein operon transcriptional activator; Provisional |
209-509 |
3.19e-86 |
|
phage shock protein operon transcriptional activator; Provisional
Pssm-ID: 236936 [Multi-domain] Cd Length: 326 Bit Score: 269.23 E-value: 3.19e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 209 LDNMVGKSPAMrqiVEVIRQVSRW---DTTVLVRGESGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLESELFGHE 285
Cdd:PRK11608 5 KDNLLGEANSF---LEVLEQVSRLaplDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 286 KGAFTGAVRQRKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHF 365
Cdd:PRK11608 82 AGAFTGAQKRHPGRFERADGGTLFLDELATAPMLVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVAEGKF 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 366 REDLYYRLNVMPIALPPLRERQEDIAELA-HFLVrKIGQHQGRTL--RISEGAIRLLMEYSWPGNVRELENCLERSAVM- 441
Cdd:PRK11608 162 RADLLDRLAFDVVQLPPLRERQSDIMLMAeHFAI-QMCRELGLPLfpGFTERARETLLNYRWPGNIRELKNVVERSVYRh 240
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1709668812 442 --SESGLidrDVILFTHQDRPAKALPASGPAEDSWLDNSLD--------ERQRLIAALEKAGWVQAKAARLLGMTPRQ 509
Cdd:PRK11608 241 gtSEYPL---DNIIIDPFKRRPAEEAIAVSETTSLPTLPLDlrewqhqqEKELLQRSLQQAKFNQKRAAELLGLTYHQ 315
|
|
| PRK15115 |
PRK15115 |
response regulator GlrR; Provisional |
210-447 |
4.57e-82 |
|
response regulator GlrR; Provisional
Pssm-ID: 185070 [Multi-domain] Cd Length: 444 Bit Score: 262.47 E-value: 4.57e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 210 DNMVGKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLESELFGHEKGAF 289
Cdd:PRK15115 134 EAIVTRSPLMLRLLEQARMVAQSDVSVLINGQSGTGKEILAQAIHNASPRASKPFIAINCGALPEQLLESELFGHARGAF 213
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 290 TGAVRQRKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHFREDL 369
Cdd:PRK15115 214 TGAVSNREGLFQAAEGGTLFLDEIGDMPAPLQVKLLRVLQERKVRPLGSNRDIDIDVRIISATHRDLPKAMARGEFREDL 293
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1709668812 370 YYRLNVMPIALPPLRERQEDIAELAHFLVRKIGQ-HQGRTLRISEGAIRLLMEYSWPGNVRELENCLERSAVMSESGLI 447
Cdd:PRK15115 294 YYRLNVVSLKIPALAERTEDIPLLANHLLRQAAErHKPFVRAFSTDAMKRLMTASWPGNVRQLVNVIEQCVALTSSPVI 372
|
|
| PRK10820 |
PRK10820 |
transcriptional regulator TyrR; |
210-481 |
1.24e-81 |
|
transcriptional regulator TyrR;
Pssm-ID: 236769 [Multi-domain] Cd Length: 520 Bit Score: 263.47 E-value: 1.24e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 210 DNMVGKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLESELFGHEKGAF 289
Cdd:PRK10820 204 SQIVAVSPKMRQVVEQARKLAMLDAPLLITGDTGTGKDLLAYACHLRSPRGKKPFLALNCASIPDDVVESELFGHAPGAY 283
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 290 TGAVRQRKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHFREDL 369
Cdd:PRK10820 284 PNALEGKKGFFEQANGGSVLLDEIGEMSPRMQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQKNLVELVQKGEFREDL 363
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 370 YYRLNVMPIALPPLRERQEDIAELAHFLVRKIGQHQGRTL-RISEGAIRLLMEYSWPGNVRELENCLERSAVMSESG-LI 447
Cdd:PRK10820 364 YYRLNVLTLNLPPLRDRPQDIMPLTELFVARFADEQGVPRpKLAADLNTVLTRYGWPGNVRQLKNAIYRALTQLEGYeLR 443
|
250 260 270
....*....|....*....|....*....|....
gi 1709668812 448 DRDVILFTHQdrpakalpASGPAEDSWLDNSLDE 481
Cdd:PRK10820 444 PQDILLPDYD--------AAVAVGEDAMEGSLDE 469
|
|
| PRK15424 |
PRK15424 |
propionate catabolism operon regulatory protein PrpR; Provisional |
209-506 |
1.21e-78 |
|
propionate catabolism operon regulatory protein PrpR; Provisional
Pssm-ID: 237963 [Multi-domain] Cd Length: 538 Bit Score: 256.18 E-value: 1.21e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 209 LDNMVGKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHH-HSPRAGAA-------FVKFNCAALPDTLLESE 280
Cdd:PRK15424 218 LGDLLGQSPQMEQVRQTILLYARSSAAVLIQGETGTGKELAAQAIHReYFARHDARqgkkshpFVAVNCGAIAESLLEAE 297
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 281 LFGHEKGAFTGAVRQ-RKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEE 359
Cdd:PRK15424 298 LFGYEEGAFTGSRRGgRAGLFEIAHGGTLFLDEIGEMPLPLQTRLLRVLEEKEVTRVGGHQPVPVDVRVISATHCDLEED 377
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 360 VRLGHFREDLYYRLNVMPIALPPLRERQEDIAELA-HFLVRKIGqhqGRTLRISEGAIR-------LLMEYSWPGNVREL 431
Cdd:PRK15424 378 VRQGRFRRDLFYRLSILRLQLPPLRERVADILPLAeSFLKQSLA---ALSAPFSAALRQglqqcetLLLHYDWPGNVREL 454
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1709668812 432 ENCLERSAVMSESGLIDRDVILFTHQDRPAKALPASGPAEdswldnSLDERQRLIAALEKAGWVQAKAARLLGMT 506
Cdd:PRK15424 455 RNLMERLALFLSVEPTPDLTPQFLQLLLPELARESAKTPA------PRLLAATLQQALERFNGDKTAAANYLGIS 523
|
|
| propionate_PrpR |
TIGR02329 |
propionate catabolism operon regulatory protein PrpR; At least five distinct pathways exists ... |
209-506 |
2.27e-75 |
|
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: 247.47 E-value: 2.27e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 209 LDNMVGKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLESELFGHEKGA 288
Cdd:TIGR02329 211 LDDLLGASAPMEQVRALVRLYARSDATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIAESLLEAELFGYEEGA 290
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 289 FTGAVRQ-RKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHFRE 367
Cdd:TIGR02329 291 FTGARRGgRTGLIEAAHRGTLFLDEIGEMPLPLQTRLLRVLEEREVVRVGGTEPVPVDVRVVAATHCALTTAVQQGRFRR 370
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 368 DLYYRLNVMPIALPPLRERQEDIAELA-HFLVRKIGQhqgRTLRISEGAIR-------LLMEYSWPGNVRELENCLERSA 439
Cdd:TIGR02329 371 DLFYRLSILRIALPPLRERPGDILPLAaEYLVQAAAA---LRLPDSEAAAQvlagvadPLQRYPWPGNVRELRNLVERLA 447
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 440 V---MSESGLIDRDVILFTHQDRPAKALPASGPAeDSWLDNSLDERQRLIAALEKAGWVQAKAARLLGMT 506
Cdd:TIGR02329 448 LelsAMPAGALTPDVLRALAPELAEASGKGKTSA-LSLRERSRVEALAVRAALERFGGDRDAAAKALGIS 516
|
|
| PRK11388 |
PRK11388 |
DNA-binding transcriptional regulator DhaR; Provisional |
209-504 |
6.97e-64 |
|
DNA-binding transcriptional regulator DhaR; Provisional
Pssm-ID: 183114 [Multi-domain] Cd Length: 638 Bit Score: 219.55 E-value: 6.97e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 209 LDNMVGKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLESELFGhekGA 288
Cdd:PRK11388 324 FDHMPQDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPDEALAEEFLG---SD 400
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 289 FTGAVRQRKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHFRED 368
Cdd:PRK11388 401 RTDSENGRLSKFELAHGGTLFLEKVEYLSPELQSALLQVLKTGVITRLDSRRLIPVDVRVIATTTADLAMLVEQNRFSRQ 480
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 369 LYYRLNVMPIALPPLRERQEDIAELAHFLVRKIGQHQGRTLRISEGAIRLLMEYSWPGNVRELENCLERSAVMSESGLI- 447
Cdd:PRK11388 481 LYYALHAFEITIPPLRMRREDIPALVNNKLRSLEKRFSTRLKIDDDALARLVSYRWPGNDFELRSVIENLALSSDNGRIr 560
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1709668812 448 --DRDVILFTHQ---DRPAKALPASGPAEDSwldnsldERQRLIAALEKAGWVQAKAARLLG 504
Cdd:PRK11388 561 lsDLPEHLFTEQatdDVSATRLSTSLSLAEL-------EKEAIINAAQVCGGRIQEMAALLG 615
|
|
| RtcR |
COG4650 |
Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a ... |
215-452 |
2.83e-44 |
|
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: 163.85 E-value: 2.83e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 215 KSPAMRQIVEVIRQV-SRWDTTVLVRGESGTGKELIANAI-------HHHSpragAAFVKFNCAALPDTLLESELFGHEK 286
Cdd:COG4650 189 RNAAFNRLIEQIERVaIRSRAPILLTGPTGAGKSQLARRIyelkkarHQVS----GRFVEVNCATLRGDGAMSALFGHVK 264
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 287 GAFTGAVRQRKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHFR 366
Cdd:COG4650 265 GAFTGAVSDRAGLLRSADGGVLFLDEIGELGLDEQAMLLRAIEEKRFLPVGSDKEVSSDFQLIAGTNRDLRQEVAEGRFR 344
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 367 EDLYYRLNVMPIALPPLRERQEDIA-----ELAHFlvrkiGQHQGRTLRISEGAIRLLMEY------SWPGNVRELENCL 435
Cdd:COG4650 345 EDLLARINLWTFRLPGLAERREDIEpnldyELARF-----AREQGRRVRFNKEARARYLAFatspeaLWSGNFRDLNASV 419
|
250
....*....|....*..
gi 1709668812 436 ERSAVMSESGLIDRDVI 452
Cdd:COG4650 420 TRMATLAEGGRITVALV 436
|
|
| PspF |
COG1221 |
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain ... |
236-433 |
1.00e-33 |
|
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: 136.01 E-value: 1.00e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 236 VLVRGESGTGKELIANAIHHHSPRAG-----AAFVKFNCAalpD-----TLLESELFGHEKGAFTGAVRQRKGRFELADG 305
Cdd:COG1221 133 TLILGPTGVGKSFFAELMYEYAIEIGvlpedAPFVVFNCA---DyannpQLLMSQLFGYVKGAFTGADKDKEGLIEKADG 209
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 306 GTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLR-VNVRIIAATNrhlE--EEVRLGHFRedlyyRLNVMPIALPP 382
Cdd:COG1221 210 GILFLDEVHRLPPEGQEMLFTFMDKGIYRRLGETEKTRkANVRIIFATT---EdpESSLLKTFL-----RRIPMVIKLPS 281
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*.
gi 1709668812 383 LRER--QEDIAELAHFL---VRKIgqhqGRTLRISEGAIRLLMEYSWPGNVRELEN 433
Cdd:COG1221 282 LEERslEERLELIKHFFkeeAKRL----NKPIKVSKEVLKALLLYDCPGNIGQLKS 333
|
|
| AAA |
cd00009 |
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ... |
217-374 |
3.17e-25 |
|
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: 101.45 E-value: 3.17e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 217 PAMRQIVEVIRQVSRWDT--TVLVRGESGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLESELFGHEkgaftgAVR 294
Cdd:cd00009 1 VGQEEAIEALREALELPPpkNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHF------LVR 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 295 QRKGRFELADGGTLFLDEIGESSASFQAKLLRILQEGEMERVGgdetlRVNVRIIAATNRHLEeevrlGHFREDLYYRLN 374
Cdd:cd00009 75 LLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRID-----RENVRVIGATNRPLL-----GDLDRALYDRLD 144
|
|
| GAF |
smart00065 |
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ... |
39-184 |
5.20e-21 |
|
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.
Pssm-ID: 214500 [Multi-domain] Cd Length: 149 Bit Score: 89.36 E-value: 5.20e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 39 TLQEVLSVLHNDAFMQHGMICLYDsEQEILSIEALQQTGQqpLPGSTQIRYRPGEGLVGTVLAQGQSLVLPRVADDQRFL 118
Cdd:smart00065 5 LLQTILEELRQLLGADRVLIYLVD-ENDRGELVLVAADGL--TLPTLGIRFPLDEGLAGRVAETGRPLNIPDVEADPLFA 81
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1709668812 119 -DRLSLYDYDLPFIAVPLMGPNaRPIGVLAAQPMARQEERLPACTRFLETVANLVAQTIRLMILPAS 184
Cdd:smart00065 82 eDLLGRYQGVRSFLAVPLVADG-ELVGVLALHNKKSPRPFTEEDEELLQALANQLAIALANAQLYEE 147
|
|
| Sigma54_activ_2 |
pfam14532 |
Sigma-54 interaction domain; |
213-383 |
2.67e-18 |
|
Sigma-54 interaction domain;
Pssm-ID: 434021 [Multi-domain] Cd Length: 138 Bit Score: 81.23 E-value: 2.67e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 213 VGKSPAMRQIVEVIRQVSRWDTTVLVRGESGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLESelfghekgaftga 292
Cdd:pfam14532 1 LGASAAIQEIKRRLEQAAQSTLPVFLTGEPGSGKEFCARYLHNPSTPWVQPFDIEYLAHAPLELLEQ------------- 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 293 vrqrkgrfelADGGTLFLDEIGESSASFQAKLLRILQEGEmervggdetlRVNVRIIAATNRHLEEEVRLGHFREDLYYR 372
Cdd:pfam14532 68 ----------AKGGTLYLKDIADLSKALQKGLLLLLAKAE----------GYRVRLVCTSSKDLPQLAAAGLFDEQLYFE 127
|
170
....*....|.
gi 1709668812 373 LNVMPIALPPL 383
Cdd:pfam14532 128 LSALRLHVPPL 138
|
|
| AAA |
smart00382 |
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ... |
235-373 |
9.70e-12 |
|
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: 62.78 E-value: 9.70e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 235 TVLVRGESGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLES---ELFGHEKGAFTGAVRQRKgRFELA---DGGTL 308
Cdd:smart00382 4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQlllIIVGGKKASGSGELRLRL-ALALArklKPDVL 82
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1709668812 309 FLDEIGESSASFQAKLLRILQEgemERVGGDETLRVNVRIIAATNR--HLEEEVRLGHFREDLYYRL 373
Cdd:smart00382 83 ILDEITSLLDAEQEALLLLLEE---LRLLLLLKSEKNLTVILTTNDekDLGPALLRRRFDRRIVLLL 146
|
|
| HTH_8 |
pfam02954 |
Bacterial regulatory protein, Fis family; |
481-515 |
2.57e-09 |
|
Bacterial regulatory protein, Fis family;
Pssm-ID: 427077 [Multi-domain] Cd Length: 40 Bit Score: 52.78 E-value: 2.57e-09
10 20 30
....*....|....*....|....*....|....*
gi 1709668812 481 ERQRLIAALEKAGWVQAKAARLLGMTPRQVAYRIQ 515
Cdd:pfam02954 5 EKELIEAALERTGGNKSKAARLLGISRRTLYRKLK 39
|
|
| GAF_2 |
pfam13185 |
GAF domain; The GAF domain is named after some of the proteins it is found in, including ... |
33-177 |
8.06e-09 |
|
GAF domain; The GAF domain is named after some of the proteins it is found in, including cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA. It is also found in guanylyl cyclases and phytochromes. The structure of a GAF domain shows that the domain shares a similar fold with the PAS domain. This domain can bind O2, CO and NO (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Pssm-ID: 433019 [Multi-domain] Cd Length: 137 Bit Score: 54.01 E-value: 8.06e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 33 ATEASKTLQEVLSVLHNDAFMQHGMICLYDSEQEILSIEALQQTGQQPlpgstqIRYRPGEGLVGTVLAQGQSLVLPRVA 112
Cdd:pfam13185 1 AADLEELLDAVLEAAVELGASAVGFILLVDDDGRLAAWGGAADELSAA------LDDPPGEGLVGEALRTGRPVIVNDLA 74
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1709668812 113 DDQRFLDRLSLYDYDLPFIAVPLMGpNARPIGVLAAQPMARQ---EERLpactRFLETVANLVAQTIR 177
Cdd:pfam13185 75 ADPAKKGLPAGHAGLRSFLSVPLVS-GGRVVGVLALGSNRPGafdEEDL----ELLELLAEQAAIAIE 137
|
|
| PtsP |
COG3605 |
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]; |
18-177 |
4.37e-08 |
|
Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms];
Pssm-ID: 442824 [Multi-domain] Cd Length: 188 Bit Score: 53.36 E-value: 4.37e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 18 QQFTAMQRISVVLSRATEASKTLQEVLSVLHNDAFMQHGMICLYDSEQEILSIEA---LQQTGQQplpgstQIRYRPGEG 94
Cdd:COG3605 1 EMLKALRRISEAVASALDLDEALDRIVRRIAEALGVDVCSIYLLDPDGGRLELRAtegLNPEAVG------KVRLPLGEG 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 95 LVGTVLAQGQSLVLPRVADDQRFLDRLSLYDYDLP-FIAVPLMGpNARPIGVLAAQPMAR----QEErlpacTRFLETVA 169
Cdd:COG3605 75 LVGLVAERGEPLNLADAASHPRFKYFPETGEEGFRsFLGVPIIR-RGRVLGVLVVQSREPreftEEE-----VEFLVTLA 148
|
....*...
gi 1709668812 170 NLVAQTIR 177
Cdd:COG3605 149 AQLAEAIA 156
|
|
| GAF |
pfam01590 |
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ... |
39-176 |
1.33e-06 |
|
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Pssm-ID: 460259 [Multi-domain] Cd Length: 133 Bit Score: 47.86 E-value: 1.33e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 39 TLQEVLSVLHNDAFMQHGMICLYDSEQEILSIEALQQTGQQPLpgstqiRYRPGEGlvGTVLAQGQSLVLPRVADDQRFL 118
Cdd:pfam01590 5 ILQTILEELRELLGADRCALYLPDADGLEYLPPGARWLKAAGL------EIPPGTG--VTVLRTGRPLVVPDAAGDPRFL 76
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1709668812 119 DRLSLY-DYDLP-FIAVPLMGpNARPIGVLAA---QPMARQEERlpactRFLETVANLVAQTI 176
Cdd:pfam01590 77 DPLLLLrNFGIRsLLAVPIID-DGELLGVLVLhhpRPPFTEEEL-----ELLEVLADQVAIAL 133
|
|
| AAA_5 |
pfam07728 |
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ... |
236-386 |
2.86e-06 |
|
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: 46.90 E-value: 2.86e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 236 VLVRGESGTGKELIANAIHHHSPRAGAAFVkfncaALPDTLLESELFG----------HEKGAFTGAVRqrkgrfelaDG 305
Cdd:pfam07728 2 VLLVGPPGTGKTELAERLAAALSNRPVFYV-----QLTRDTTEEDLFGrrnidpggasWVDGPLVRAAR---------EG 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 306 GTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRV---NVRIIAATNrhleeevrlghfreDLYYRLNVMpiaLPP 382
Cdd:pfam07728 68 EIAVLDEINRANPDVLNSLLSLLDERRLLLPDGGELVKAapdGFRLIATMN--------------PLDRGLNEL---SPA 130
|
....
gi 1709668812 383 LRER 386
Cdd:pfam07728 131 LRSR 134
|
|
| AAA |
pfam00004 |
ATPase family associated with various cellular activities (AAA); AAA family proteins often ... |
236-354 |
1.16e-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: 42.20 E-value: 1.16e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 236 VLVRGESGTGKELIANAIHHHsprAGAAFVKFNCaalpdtlleSELFGHEKGAFTGAVRQrkgRFELADGGT---LFLDE 312
Cdd:pfam00004 1 LLLYGPPGTGKTTLAKAVAKE---LGAPFIEISG---------SELVSKYVGESEKRLRE---LFEAAKKLApcvIFIDE 65
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 1709668812 313 I-------GESSASFQAKLLRILQEgEMErvgGDETLRVNVRIIAATNR 354
Cdd:pfam00004 66 IdalagsrGSGGDSESRRVVNQLLT-ELD---GFTSSNSKVIVIAATNR 110
|
|
| RPT1 |
COG1222 |
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ... |
185-354 |
6.34e-04 |
|
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones];
Pssm-ID: 440835 [Multi-domain] Cd Length: 326 Bit Score: 41.92 E-value: 6.34e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 185 PALSSRQPPKVERPPACSSSRGVGLDNMVGKSPAMRQIVE-VIRQVSRWD----------TTVLVRGESGTGKELIANAI 253
Cdd:COG1222 53 ANLTQKRLGTPRGTAVPAESPDVTFDDIGGLDEQIEEIREaVELPLKNPElfrkygieppKGVLLYGPPGTGKTLLAKAV 132
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 254 HHhspRAGAAFVKFNCAALPDTLL-ESElfghekgaftgavrqRKGR--FELADGGT---LFLDEI---------GESSA 318
Cdd:COG1222 133 AG---ELGAPFIRVRGSELVSKYIgEGA---------------RNVRevFELAREKApsiIFIDEIdaiaarrtdDGTSG 194
|
170 180 190
....*....|....*....|....*....|....*.
gi 1709668812 319 SFQAKLLRILQEgeMErvgGDETlRVNVRIIAATNR 354
Cdd:COG1222 195 EVQRTVNQLLAE--LD---GFES-RGDVLIIAATNR 224
|
|
| PRK03992 |
PRK03992 |
proteasome-activating nucleotidase; Provisional |
236-354 |
7.43e-04 |
|
proteasome-activating nucleotidase; Provisional
Pssm-ID: 179699 [Multi-domain] Cd Length: 389 Bit Score: 41.74 E-value: 7.43e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 236 VLVRGESGTGKELIANAIHHHsprAGAAFVKfncaalpdtLLESEL---FGHEkgaftGA--VRQRkgrFELA---DGGT 307
Cdd:PRK03992 168 VLLYGPPGTGKTLLAKAVAHE---TNATFIR---------VVGSELvqkFIGE-----GArlVREL---FELArekAPSI 227
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 1709668812 308 LFLDEI----------GES-SASFQAKLLRILqeGEMErvGGDEtlRVNVRIIAATNR 354
Cdd:PRK03992 228 IFIDEIdaiaakrtdsGTSgDREVQRTLMQLL--AEMD--GFDP--RGNVKIIAATNR 279
|
|
| RecA-like_PAN_like |
cd19502 |
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ... |
236-354 |
8.32e-04 |
|
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily contains ATPase subunits of the eukaryotic 26S proteasome, and of the archaeal proteasome which carry out ATP-dependent degradation of substrates of the ubiquitin-proteasome pathway. The eukaryotic 26S proteasome consists of a proteolytic 20S core particle (CP), and a 19S regulatory particle (RP) which provides the ATP-dependence and the specificity for ubiquitinated proteins. In the archaea the RP is a homohexameric complex of proteasome-activating nucleotidase (PAN). This subfamily also includes various eukaryotic 26S subunits including, proteasome 26S subunit, ATPase 2 (PSMC2, also known as S7 and MSS1) which is a member of the 19S RP and has a chaperone like activity; and proteasome 20S subunit alpha 6 (PSMA6, also known as IOTA, p27K, and PROS27) which is a member of the 20S CP. This RecA-like_PAN subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.
Pssm-ID: 410910 [Multi-domain] Cd Length: 171 Bit Score: 40.40 E-value: 8.32e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 236 VLVRGESGTGKELIANAIHHHSpraGAAFVKfncaalpdtLLESELFghEKGAFTGAvRQRKGRFELA---DGGTLFLDE 312
Cdd:cd19502 40 VLLYGPPGTGKTLLAKAVANHT---DATFIR---------VVGSELV--QKYIGEGA-RLVRELFEMArekAPSIIFIDE 104
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 1709668812 313 I-------GESSASFQAKLLRILQEGEMERVGGDEtlRVNVRIIAATNR 354
Cdd:cd19502 105 IdaigakrFDSGTGGDREVQRTMLELLNQLDGFDP--RGNIKVIMATNR 151
|
|
| AAA_16 |
pfam13191 |
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ... |
213-328 |
1.63e-03 |
|
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.
Pssm-ID: 433025 [Multi-domain] Cd Length: 167 Bit Score: 39.41 E-value: 1.63e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 213 VGKSPAMRQIVEVIRQVSRWDTT-VLVRGESGTGKELIANAIHHHSPRAGAAFVKFNC------AALPDTLLESELFGHE 285
Cdd:pfam13191 3 VGREEELEQLLDALDRVRSGRPPsVLLTGEAGTGKTTLLRELLRALERDGGYFLRGKCdenlpySPLLEALTREGLLRQL 82
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 1709668812 286 KGAFTGAVRQRkGRFELADGGTLFLDEIGESSASFQAKLLRIL 328
Cdd:pfam13191 83 LDELESSLLEA-WRAALLEALAPVPELPGDLAERLLDLLLRLL 124
|
|
| RecA-like_ClpB_Hsp104-like |
cd19499 |
Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and ... |
213-378 |
2.00e-03 |
|
Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and eukaryotic Heat shock protein 104 (Hsp104) are ATP-dependent molecular chaperones and essential proteins of the heat-shock response. ClpB/Hsp104 ATPases, in concert with the DnaK/Hsp70 chaperone system, disaggregate and reactivate aggregated proteins. This RecA-like_ClpB_Hsp104_like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.
Pssm-ID: 410907 [Multi-domain] Cd Length: 178 Bit Score: 39.47 E-value: 2.00e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 213 VGKSPAMRQIVEVIRQV-------SRWDTTVLVRGESGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLESELFG-- 283
Cdd:cd19499 14 VGQDEAVKAVSDAIRRAraglsdpNRPIGSFLFLGPTGVGKTELAKALAELLFGDEDNLIRIDMSEYMEKHSVSRLIGap 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 284 ------HEKGAFTGAVRQRkgRFeladgGTLFLDEIGESSASFQAKLLRILQEGEMERVGGDETLRVNVRIIAATNrhle 357
Cdd:cd19499 94 pgyvgyTEGGQLTEAVRRK--PY-----SVVLLDEIEKAHPDVQNLLLQVLDDGRLTDSHGRTVDFKNTIIIMTSN---- 162
|
170 180
....*....|....*....|.
gi 1709668812 358 eevrlgHFREDLYYRLNVMPI 378
Cdd:cd19499 163 ------HFRPEFLNRIDEIVV 177
|
|
| COG1223 |
COG1223 |
Predicted ATPase, AAA+ superfamily [General function prediction only]; |
209-354 |
4.08e-03 |
|
Predicted ATPase, AAA+ superfamily [General function prediction only];
Pssm-ID: 440836 [Multi-domain] Cd Length: 246 Bit Score: 39.10 E-value: 4.08e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 209 LDNMVGKSPAMRQIVEVIRQVSRWD----------TTVLVRGESGTGKELIANAIHHhspRAGAAFVKFNcaalPDTLLe 278
Cdd:COG1223 1 LDDVVGQEEAKKKLKLIIKELRRREnlrkfglwppRKILFYGPPGTGKTMLAEALAG---ELKLPLLTVR----LDSLI- 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 279 SELFGhekgafTGAVRQRKgRFELA--DGGTLFLDEigessasFQA--KLLRILQE-GEMERV-----GGDETLRVNVRI 348
Cdd:COG1223 73 GSYLG------ETARNLRK-LFDFArrAPCVIFFDE-------FDAiaKDRGDQNDvGEVKRVvnallQELDGLPSGSVV 138
|
....*.
gi 1709668812 349 IAATNR 354
Cdd:COG1223 139 IAATNH 144
|
|
| GAF |
COG2203 |
GAF domain [Signal transduction mechanisms]; |
8-492 |
4.10e-03 |
|
GAF domain [Signal transduction mechanisms];
Pssm-ID: 441805 [Multi-domain] Cd Length: 712 Bit Score: 39.79 E-value: 4.10e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 8 DTTVRRFDLSQQFTAMQRISVVLSRATEASKTLQEVLSVLHNDAFMQHGMICLYDSEQEILSIEAlqqtgQQPLPGSTQI 87
Cdd:COG2203 180 LLTQRARLELERLALLNEISQALRSALDLEELLQRILELAGELLGADRGAILLVDEDGGELELVA-----APGLPEEELG 254
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 88 RYRPGEGLVGTVLAQGQSLVLPRVADDQRFLDRLSLYDYDLP---FIAVPLMGPNaRPIGVLAA---QPMARQEERLpac 161
Cdd:COG2203 255 RLPLGEGLAGRALRTGEPVVVNDASTDPRFAPSLRELLLALGirsLLCVPLLVDG-RLIGVLALyskEPRAFTEEDL--- 330
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 162 tRFLETVANLVAQTIRLMILPASPALSSRQppkverppacSSSRGVGLDNMVGKSPAMRQIVEVIRQVSRWDTTVLVRGE 241
Cdd:COG2203 331 -ELLEALADQAAIAIERARLYEALEAALAA----------LLQELALLRLLLDLELTLLRLRQLLLELLLALLLLLSLLG 399
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 242 SGTGKELIANAIHHHSPRAGAAFVKFNCAALPDTLLESELFGHEKGAFTGAVRQRKGRFELADGGTLFLDEIGESSASFQ 321
Cdd:COG2203 400 AELLLLLLDAADLSGLLALEGLLLLDLLLLLLLLRRILLLRVLRRLLLGDEEGLVLLLALAELELLEILELLVLLAVILL 479
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 322 AKLLRILQEGEMERVGGDETLRVNVRIIAATNRHLEEEVRLGHFREDLYYRLNVMPIALPPLRERQEDIAELAHFLVRKI 401
Cdd:COG2203 480 ALALLAALLLLLLLLLALLALSALAVLASLLLALLLLLLLLLLLLLLGLLAALAADLLLLAAALLEDLLILLLVLLLERE 559
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 402 GQHQGRTLRISEGAIRLLMEYSWPGNVRELENCLERSAVMSESGLIDRDVILFTHQDRPAKALPASGPAEDSWLDNSLDE 481
Cdd:COG2203 560 LLTLVGVLLLLGLSVLLIELALALILALALLELLLVAVGDLLLLERDLLLLLVLLVRLLLELLVVTLELTVLVVLAAVED 639
|
490
....*....|.
gi 1709668812 482 RQRLIAALEKA 492
Cdd:COG2203 640 SALLLRLALAL 650
|
|
| MoxR |
COG0714 |
MoxR-like ATPase [General function prediction only]; MoxR-like ATPase is part of the Pathway ... |
236-332 |
4.45e-03 |
|
MoxR-like ATPase [General function prediction only]; MoxR-like ATPase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis
Pssm-ID: 440478 [Multi-domain] Cd Length: 292 Bit Score: 39.00 E-value: 4.45e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 236 VLVRGESGTGKELIANAIHHHSpraGAAFVKFNCAalPDtLLESELFGHEKgaftgaVRQRKGRFELADG----GTLFLD 311
Cdd:COG0714 34 LLLEGVPGVGKTTLAKALARAL---GLPFIRIQFT--PD-LLPSDILGTYI------YDQQTGEFEFRPGplfaNVLLAD 101
|
90 100
....*....|....*....|.
gi 1709668812 312 EIGESSASFQAKLLRILQEGE 332
Cdd:COG0714 102 EINRAPPKTQSALLEAMEERQ 122
|
|
| RecA-like_protease |
cd19481 |
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ... |
220-354 |
7.78e-03 |
|
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.
Pssm-ID: 410889 [Multi-domain] Cd Length: 158 Bit Score: 37.26 E-value: 7.78e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1709668812 220 RQIVEVIRQVSRWDT-------TVLVRGESGTGKELIANAIHHHSpraGAAFVKFNCaalpdtlleSELFGHEKGAFTGA 292
Cdd:cd19481 6 REAVEAPRRGSRLRRyglglpkGILLYGPPGTGKTLLAKALAGEL---GLPLIVVKL---------SSLLSKYVGESEKN 73
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1709668812 293 VRQRkgrFELAD---GGTLFLDEI-----GESSASFQAKLLRILQE--GEMERVGGDEtlrvNVRIIAATNR 354
Cdd:cd19481 74 LRKI---FERARrlaPCILFIDEIdaigrKRDSSGESGELRRVLNQllTELDGVNSRS----KVLVIAATNR 138
|
|
| |
