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Conserved domains on  [gi|16130771|ref|NP_417345|]
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putative sigma(54)-dependent transcriptional regulator YgeV [Escherichia coli str. K-12 substr. MG1655]

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 ...
 158-589 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: 532.04  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 158 ISKIFATMIDNMDQGVLVVDDENRVQFVNQTALKTLGVVQNNIIGKPIR--FRPLTFESNFTHG--HMQHIVSWDDKSEL 233
Cdd:COG3829   9 LEEELEAILDSLDDGIIVVDADGRITYVNRAAERILGLPREEVIGKNVTelIPNSPLLEVLKTGkpVTGVIQKTGGKGKT 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 234 IIGQLHNI--QGRQLFLMAFHQSHTSFS-----------VANAPDEPHIEQLVGECRVMRQLKRLISRIAPSPSSVMVVG 300
Cdd:COG3829  89 VIVTAIPIfeDGEVIGAVETFRDITELKrlerklreeelERGLSAKYTFDDIIGKSPAMKELLELAKRVAKSDSTVLILG 168

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 301 ESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGAFTGASANGKTGLIQAANTGTLFLDEIGDMPLM 380
Cdd:COG3829 169 ESGTGKELFARAIHNASPRRDGPFVAVNCAAIPENLLESELFGYEKGAFTGAKKGGKPGLFELADGGTLFLDEIGEMPLS 248

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 381 LQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFREDLFYRLNVIPITLPPLRERQEDIELLVHYFLH 460
Cdd:COG3829 249 LQAKLLRVLQEKEVRRVGGTKPIPVDVRIIAATNRDLEEMVEEGRFREDLYYRLNVIPIHIPPLRERKEDIPLLAEHFLE 328

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 461 LHTRRLGSVYPGIAPDVVEILRKHRWPGNLRELSNLMEYLVNVVpSGEVIDSTLLPPNLLNNGTTEQsdvtevSEAHLSL 540
Cdd:COG3829 329 KFNKKYGKNIKGISPEALELLLAYDWPGNVRELENVIERAVVLS-EGDVITPEHLPEYLLEEAEAAS------AAEEGSL 401

                       410       420       430       440       450
                ....*....|....*....|....*....|....*....|....*....|
gi 16130771 541 DDaggtALEEMEKQMIREALSRHNS-KKQVADELGIGIATLYRKIKKYEL 589
Cdd:COG3829 402 KE----ALEEVEKELIEEALEKTGGnKSKAAKALGISRSTLYRKLKKYGI 447
GAF_2 super family cl21515
GAF domain; The GAF domain is named after some of the proteins it is found in, including ...
 12-116 3.22e-04

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).


The actual alignment was detected with superfamily member smart00065:

Pssm-ID: 473894 [Multi-domain]  Cd Length: 149  Bit Score: 41.21  E-value: 3.22e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771     12 QIQPTIQRFARMLASVLQLE---VEIVDENLCR----VAGTGAYGKFLGRQLSGNSRLLRHVLETKTEKVVTQSRFDPLC 84
Cdd:smart00065   1 DLEELLQTILEELRQLLGADrvlIYLVDENDRGelvlVAADGLTLPTLGIRFPLDEGLAGRVAETGRPLNIPDVEADPLF 80

                           90       100       110
                   ....*....|....*....|....*....|..
gi 16130771     85 EGCDSKENCREKAFLGTPVILQDRCVGVISLI 116
Cdd:smart00065  81 AEDLLGRYQGVRSFLAVPLVADGELVGVLALH 112
 
Name Accession Description Interval E-value
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 158-589 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: 532.04  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 158 ISKIFATMIDNMDQGVLVVDDENRVQFVNQTALKTLGVVQNNIIGKPIR--FRPLTFESNFTHG--HMQHIVSWDDKSEL 233
Cdd:COG3829   9 LEEELEAILDSLDDGIIVVDADGRITYVNRAAERILGLPREEVIGKNVTelIPNSPLLEVLKTGkpVTGVIQKTGGKGKT 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 234 IIGQLHNI--QGRQLFLMAFHQSHTSFS-----------VANAPDEPHIEQLVGECRVMRQLKRLISRIAPSPSSVMVVG 300
Cdd:COG3829  89 VIVTAIPIfeDGEVIGAVETFRDITELKrlerklreeelERGLSAKYTFDDIIGKSPAMKELLELAKRVAKSDSTVLILG 168

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 301 ESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGAFTGASANGKTGLIQAANTGTLFLDEIGDMPLM 380
Cdd:COG3829 169 ESGTGKELFARAIHNASPRRDGPFVAVNCAAIPENLLESELFGYEKGAFTGAKKGGKPGLFELADGGTLFLDEIGEMPLS 248

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 381 LQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFREDLFYRLNVIPITLPPLRERQEDIELLVHYFLH 460
Cdd:COG3829 249 LQAKLLRVLQEKEVRRVGGTKPIPVDVRIIAATNRDLEEMVEEGRFREDLYYRLNVIPIHIPPLRERKEDIPLLAEHFLE 328

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 461 LHTRRLGSVYPGIAPDVVEILRKHRWPGNLRELSNLMEYLVNVVpSGEVIDSTLLPPNLLNNGTTEQsdvtevSEAHLSL 540
Cdd:COG3829 329 KFNKKYGKNIKGISPEALELLLAYDWPGNVRELENVIERAVVLS-EGDVITPEHLPEYLLEEAEAAS------AAEEGSL 401

                       410       420       430       440       450
                ....*....|....*....|....*....|....*....|....*....|
gi 16130771 541 DDaggtALEEMEKQMIREALSRHNS-KKQVADELGIGIATLYRKIKKYEL 589
Cdd:COG3829 402 KE----ALEEVEKELIEEALEKTGGnKSKAAKALGISRSTLYRKLKKYGI 447
TF_PrdR NF041552
sigma-54 dependent transcriptional regulator PrdR;
102-587 4.76e-120

sigma-54 dependent transcriptional regulator PrdR;


Pssm-ID: 469437 [Multi-domain]  Cd Length: 577  Bit Score: 367.29  E-value: 4.76e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  102 PVILQDRCVGVIsliavtheQQEHISD----NLREFSDYVRHIstifvsklledqgpgdniskifatmIDNMDQGVLVVD 177
Cdd:NF041552 105 PVLENGKVIGVI--------RQEDIRDyfymKLEEMGETLKHI-------------------------LDNIHEAVCVID 151

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  178 DENRVQFVNQTALKTLGVVQNNIIGKPIR-FRPLTF----------ESN------------------FTHGHMQHIVSWD 228
Cdd:NF041552 152 KEGIVILWNKSAEKLYGVKSEEIVGKPLEeFFPNALllkvlktkkpIENvyhspkegsyviisavpiFINGEFIGVVSTD 231

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  229 -DKSELII--GQLHNIQGRQLFL-MAFHQ-SHTSFSvanapdephieQLVGECRVMRQLKRLISRIAPSPSSVMVVGESG 303
Cdd:NF041552 232 rDITEVKNlsKELEKAKEKLEYLeEEVKKiSEDSFG-----------KIIGKSKKIIKKIEIAKQVAKTNSSVLITGESG 300

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  304 TGKEVVARAIHKLSGRRNkPFIAINCAAIPEQLLESELFGYVKGAFTGASANGKTGLIQAANTGTLFLDEIGDMPLMLQA 383
Cdd:NF041552 301 TGKEVFARAIHQASGRKG-PFVPVNCSAIPEELFESEFFGYEEGAFTGALKKGKIGKFELANNGTLFLDEIGDMPLSMQA 379

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  384 KLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFREDLFYRLNVIPITLPPLRERQEDIELLVHYFLHLHT 463
Cdd:NF041552 380 KLLRVLQEKQVRRVGGEKYIKINVRIISATNKDLKKMVKEGKFREDLYYRLNVVEIELPPLRERKEDIPLLINYFLKEIC 459

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  464 RRLGSVYPGIAPDVVEILRKHRWPGNLRELSNLMEYLVnVVPSGEVIDSTLLPPNLLNNGTTEqsdvtEVSEAHLSLDDA 543
Cdd:NF041552 460 KENNKEIPKIDKEVYDILQNYKWKGNIRELKNTIEHLV-VLSKNGTITKDSIPEYILESVKKK-----EDEEGDYPLDLN 533

                        490       500       510       520
                 ....*....|....*....|....*....|....*....|....*
gi 16130771  544 ggTALEEMEKQMIREALSRHN-SKKQVADELGIGIATLYRKIKKY 587
Cdd:NF041552 534 --KAVEKLEIDTIKKALEMSNgNKAKAAKLLNIPRSTLYYKLKQY 576
Sigma54_activat pfam00158
Sigma-54 interaction domain;
272-440 8.86e-107

Sigma-54 interaction domain;


Pssm-ID: 425491 [Multi-domain]  Cd Length: 168  Bit Score: 318.19  E-value: 8.86e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   272 LVGECRVMRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGAFTG 351
Cdd:pfam00158   1 IIGESPAMQEVLEQAKRVAPTDAPVLITGESGTGKELFARAIHQLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   352 ASANGKtGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFREDLF 431
Cdd:pfam00158  81 ADSDRK-GLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTKPIKVDVRIIAATNRDLEEAVAEGRFREDLY 159


                  ....*....
gi 16130771   432 YRLNVIPIT 440
Cdd:pfam00158 160 YRLNVIPIE 168
ntrC TIGR01818
nitrogen regulation protein NR(I); This model represents NtrC, a DNA-binding response ...
 272-585 1.05e-105

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: 326.31  E-value: 1.05e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   272 LVGECRVMRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGAFTG 351
Cdd:TIGR01818 136 LIGEAPAMQEVFRAIGRLSRSDITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPKDLIESELFGHEKGAFTG 215

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   352 AsANGKTGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFREDLF 431
Cdd:TIGR01818 216 A-NTRRQGRFEQADGGTLFLDEIGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQNLEALVRQGKFREDLF 294

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   432 YRLNVIPITLPPLRERQEDIELLVHYFLHLHTRRLGSVYPGIAPDVVEILRKHRWPGNLRELSNLMEYLVnVVPSGEVID 511
Cdd:TIGR01818 295 HRLNVIRIHLPPLRERREDIPRLARHFLALAARELDVEPKLLDPEALERLKQLRWPGNVRQLENLCRWLT-VMASGDEVL 373

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   512 STLLPPNLLNNGT-------TEQSDVTEVSEAHLSLDDAGGT------ALEEMEKQMIREALSRHNSKKQ-VADELGIGI 577
Cdd:TIGR01818 374 VSDLPAELALTGRpasapdsDGQDSWDEALEAWAKQALSRGEqglldrALPEFERPLLEAALQHTRGHKQeAAALLGWGR 453


                  ....*...
gi 16130771   578 ATLYRKIK 585
Cdd:TIGR01818 454 NTLTRKLK 461
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
253-582 7.96e-100

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 312.49  E-value: 7.96e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  253 QSHTSFSVANAPDEPHIEqLVGECRVMRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAI 332
Cdd:PRK05022 171 LPQDVAEFLRQEALKEGE-MIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAAL 249

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  333 PEQLLESELFGYVKGAFTGASANgKTGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISA 412
Cdd:PRK05022 250 PESLAESELFGHVKGAFTGAISN-RSGKFELADGGTLFLDEIGELPLALQAKLLRVLQYGEIQRVGSDRSLRVDVRVIAA 328

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  413 TNQNLAQFIAEGKFREDLFYRLNVIPITLPPLRERQEDIELLVHYFLHLHTRRLG--SVypGIAPDVVEILRKHRWPGNL 490
Cdd:PRK05022 329 TNRDLREEVRAGRFRADLYHRLSVFPLSVPPLRERGDDVLLLAGYFLEQNRARLGlrSL--RLSPAAQAALLAYDWPGNV 406

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  491 RELsnlmEYLVN--VV------PSGEV-IDSTLLPPNLLNNGTTEQSDVTEVSEAHLSLDDaggtALEEMEKQMIREALS 561
Cdd:PRK05022 407 REL----EHVISraALlarargAGRIVtLEAQHLDLPAEVALPPPEAAAAPAAVVSQNLRE----ATEAFQRQLIRQALA 478

                        330       340
                 ....*....|....*....|..
gi 16130771  562 RHNSK-KQVADELGIGIATLYR 582
Cdd:PRK05022 479 QHQGNwAAAARALELDRANLHR 500
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 277-443 3.76e-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: 3.76e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 277 RVMRQLKRLISRiaPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKgaftgasANG 356
Cdd:cd00009   5 EAIEALREALEL--PPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFL-------VRL 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 357 KTGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIgasspIQVDIRIISATNQNLaqfiaEGKFREDLFYRLNV 436
Cdd:cd00009  76 LFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRI-----DRENVRVIGATNRPL-----LGDLDRALYDRLDI 145


                ....*..
gi 16130771 437 IpITLPP 443
Cdd:cd00009 146 R-IVIPL 151
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 292-414 1.15e-11

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 62.78  E-value: 1.15e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771    292 SPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGAFTGAS----ANGKTGLIQAANTG 367
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSgelrLRLALALARKLKPD 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 16130771    368 TLFLDEIGDMPLMLQAKLLRAIEAREILpigASSPIQVDIRIISATN 414
Cdd:smart00382  81 VLILDEITSLLDAEQEALLLLLEELRLL---LLLKSEKNLTVILTTN 124
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 12-116 3.22e-04

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: 41.21  E-value: 3.22e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771     12 QIQPTIQRFARMLASVLQLE---VEIVDENLCR----VAGTGAYGKFLGRQLSGNSRLLRHVLETKTEKVVTQSRFDPLC 84
Cdd:smart00065   1 DLEELLQTILEELRQLLGADrvlIYLVDENDRGelvlVAADGLTLPTLGIRFPLDEGLAGRVAETGRPLNIPDVEADPLF 80

                           90       100       110
                   ....*....|....*....|....*....|..
gi 16130771     85 EGCDSKENCREKAFLGTPVILQDRCVGVISLI 116
Cdd:smart00065  81 AEDLLGRYQGVRSFLAVPLVADGELVGVLALH 112
 
Name Accession Description Interval E-value
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 158-589 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: 532.04  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 158 ISKIFATMIDNMDQGVLVVDDENRVQFVNQTALKTLGVVQNNIIGKPIR--FRPLTFESNFTHG--HMQHIVSWDDKSEL 233
Cdd:COG3829   9 LEEELEAILDSLDDGIIVVDADGRITYVNRAAERILGLPREEVIGKNVTelIPNSPLLEVLKTGkpVTGVIQKTGGKGKT 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 234 IIGQLHNI--QGRQLFLMAFHQSHTSFS-----------VANAPDEPHIEQLVGECRVMRQLKRLISRIAPSPSSVMVVG 300
Cdd:COG3829  89 VIVTAIPIfeDGEVIGAVETFRDITELKrlerklreeelERGLSAKYTFDDIIGKSPAMKELLELAKRVAKSDSTVLILG 168

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 301 ESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGAFTGASANGKTGLIQAANTGTLFLDEIGDMPLM 380
Cdd:COG3829 169 ESGTGKELFARAIHNASPRRDGPFVAVNCAAIPENLLESELFGYEKGAFTGAKKGGKPGLFELADGGTLFLDEIGEMPLS 248

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 381 LQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFREDLFYRLNVIPITLPPLRERQEDIELLVHYFLH 460
Cdd:COG3829 249 LQAKLLRVLQEKEVRRVGGTKPIPVDVRIIAATNRDLEEMVEEGRFREDLYYRLNVIPIHIPPLRERKEDIPLLAEHFLE 328

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 461 LHTRRLGSVYPGIAPDVVEILRKHRWPGNLRELSNLMEYLVNVVpSGEVIDSTLLPPNLLNNGTTEQsdvtevSEAHLSL 540
Cdd:COG3829 329 KFNKKYGKNIKGISPEALELLLAYDWPGNVRELENVIERAVVLS-EGDVITPEHLPEYLLEEAEAAS------AAEEGSL 401

                       410       420       430       440       450
                ....*....|....*....|....*....|....*....|....*....|
gi 16130771 541 DDaggtALEEMEKQMIREALSRHNS-KKQVADELGIGIATLYRKIKKYEL 589
Cdd:COG3829 402 KE----ALEEVEKELIEEALEKTGGnKSKAAKALGISRSTLYRKLKKYGI 447
AcoR COG3284
Transcriptional regulator DhaR of acetoin/glycerol metabolism [Transcription];
166-587 3.33e-147

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


Pssm-ID: 442514 [Multi-domain]  Cd Length: 625  Bit Score: 438.57  E-value: 3.33e-147
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 166 IDNMDQGVLVVDDENRVQFVNQTALKTLGVVQNNIIGKPIrfrpltfeSNFTHGHMQHIVSWDDKSELIIGQLHNIQGRQ 245
Cdd:COG3284 222 LGSLSEGLLAFDEDGRIVAANRAARRLLGLADAALLGRPL--------EELFGLDLEALPDGARRAPASPRPLRLRDGRR 293

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 246 LFLMAF---HQSHTSFSVANAPDEPHIEQLVGECRVMRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHKLSGRRNK 322
Cdd:COG3284 294 LGALLRlrpARRAARAAPAGAPAPAALAALAGGDPAMRRALRRARRLADRDIPVLILGETGTGKELFARAIHAASPRADG 373

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 323 PFIAINCAAIPEQLLESELFGYVKGAFTGASANGKTGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSP 402
Cdd:COG3284 374 PFVAVNCAAIPEELIESELFGYEPGAFTGARRKGRPGKIEQADGGTLFLDEIGDMPLALQARLLRVLQEREVTPLGGTKP 453

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 403 IQVDIRIISATNQNLAQFIAEGKFREDLFYRLNVIPITLPPLRERqEDIELLVHYFLHLHTRRLGSVYpgIAPDVVEILR 482
Cdd:COG3284 454 IPVDVRLIAATHRDLRELVAAGRFREDLYYRLNGLTLTLPPLRER-EDLPALIEHLLRELAAGRGPLR--LSPEALALLA 530

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 483 KHRWPGNLRELSNLMEYLVNVVPsGEVIDSTLLPPnllnngtteqsDVTEVSEAHLSLDDAGGTALEEMEKQMIREALSR 562
Cdd:COG3284 531 AYPWPGNVRELRNVLRTALALAD-GGVITVEDLPD-----------ELRAELAAAAPAAAAPLTSLEEAERDAILRALRA 598

                       410       420
                ....*....|....*....|....*.
gi 16130771 563 HNSKK-QVADELGIGIATLYRKIKKY 587
Cdd:COG3284 599 CGGNVsAAARALGISRSTLYRKLKRY 624
AtoC COG2204
DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, ...
 270-587 1.60e-138

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: 408.97  E-value: 1.60e-138
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 270 EQLVGECRVMRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGAF 349
Cdd:COG2204 131 SGLIGRSPAMQEVRRLIEKVAPSDATVLITGESGTGKELVARAIHRLSPRADGPFVAVNCAAIPEELLESELFGHEKGAF 210

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 350 TGASANgKTGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFRED 429
Cdd:COG2204 211 TGAVAR-RIGKFELADGGTLFLDEIGEMPLALQAKLLRVLQEREFERVGGNKPIPVDVRVIAATNRDLEELVEEGRFRED 289

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 430 LFYRLNVIPITLPPLRERQEDIELLVHYFLHLHTRRLGSVYPgIAPDVVEILRKHRWPGNLRELSNLMEYLVnVVPSGEV 509
Cdd:COG2204 290 LYYRLNVFPIELPPLRERREDIPLLARHFLARFAAELGKPVK-LSPEALEALLAYDWPGNVRELENVIERAV-ILADGEV 367

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16130771 510 IDSTLLPpnllnngtteqsdvtevseahlslddaggTALEEMEKQMIREALSRHN-SKKQVADELGIGIATLYRKIKKY 587
Cdd:COG2204 368 ITAEDLP-----------------------------EALEEVERELIERALEETGgNVSRAAELLGISRRTLYRKLKKY 417
TF_PrdR NF041552
sigma-54 dependent transcriptional regulator PrdR;
102-587 4.76e-120

sigma-54 dependent transcriptional regulator PrdR;


Pssm-ID: 469437 [Multi-domain]  Cd Length: 577  Bit Score: 367.29  E-value: 4.76e-120
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  102 PVILQDRCVGVIsliavtheQQEHISD----NLREFSDYVRHIstifvsklledqgpgdniskifatmIDNMDQGVLVVD 177
Cdd:NF041552 105 PVLENGKVIGVI--------RQEDIRDyfymKLEEMGETLKHI-------------------------LDNIHEAVCVID 151

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  178 DENRVQFVNQTALKTLGVVQNNIIGKPIR-FRPLTF----------ESN------------------FTHGHMQHIVSWD 228
Cdd:NF041552 152 KEGIVILWNKSAEKLYGVKSEEIVGKPLEeFFPNALllkvlktkkpIENvyhspkegsyviisavpiFINGEFIGVVSTD 231

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  229 -DKSELII--GQLHNIQGRQLFL-MAFHQ-SHTSFSvanapdephieQLVGECRVMRQLKRLISRIAPSPSSVMVVGESG 303
Cdd:NF041552 232 rDITEVKNlsKELEKAKEKLEYLeEEVKKiSEDSFG-----------KIIGKSKKIIKKIEIAKQVAKTNSSVLITGESG 300

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  304 TGKEVVARAIHKLSGRRNkPFIAINCAAIPEQLLESELFGYVKGAFTGASANGKTGLIQAANTGTLFLDEIGDMPLMLQA 383
Cdd:NF041552 301 TGKEVFARAIHQASGRKG-PFVPVNCSAIPEELFESEFFGYEEGAFTGALKKGKIGKFELANNGTLFLDEIGDMPLSMQA 379

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  384 KLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFREDLFYRLNVIPITLPPLRERQEDIELLVHYFLHLHT 463
Cdd:NF041552 380 KLLRVLQEKQVRRVGGEKYIKINVRIISATNKDLKKMVKEGKFREDLYYRLNVVEIELPPLRERKEDIPLLINYFLKEIC 459

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  464 RRLGSVYPGIAPDVVEILRKHRWPGNLRELSNLMEYLVnVVPSGEVIDSTLLPPNLLNNGTTEqsdvtEVSEAHLSLDDA 543
Cdd:NF041552 460 KENNKEIPKIDKEVYDILQNYKWKGNIRELKNTIEHLV-VLSKNGTITKDSIPEYILESVKKK-----EDEEGDYPLDLN 533

                        490       500       510       520
                 ....*....|....*....|....*....|....*....|....*
gi 16130771  544 ggTALEEMEKQMIREALSRHN-SKKQVADELGIGIATLYRKIKKY 587
Cdd:NF041552 534 --KAVEKLEIDTIKKALEMSNgNKAKAAKLLNIPRSTLYYKLKQY 576
Sigma54_activat pfam00158
Sigma-54 interaction domain;
272-440 8.86e-107

Sigma-54 interaction domain;


Pssm-ID: 425491 [Multi-domain]  Cd Length: 168  Bit Score: 318.19  E-value: 8.86e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   272 LVGECRVMRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGAFTG 351
Cdd:pfam00158   1 IIGESPAMQEVLEQAKRVAPTDAPVLITGESGTGKELFARAIHQLSPRADGPFVAVNCAAIPEELLESELFGHEKGAFTG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   352 ASANGKtGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFREDLF 431
Cdd:pfam00158  81 ADSDRK-GLFELADGGTLFLDEIGELPLELQAKLLRVLQEGEFERVGGTKPIKVDVRIIAATNRDLEEAVAEGRFREDLY 159


                  ....*....
gi 16130771   432 YRLNVIPIT 440
Cdd:pfam00158 160 YRLNVIPIE 168
ntrC TIGR01818
nitrogen regulation protein NR(I); This model represents NtrC, a DNA-binding response ...
 272-585 1.05e-105

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: 326.31  E-value: 1.05e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   272 LVGECRVMRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGAFTG 351
Cdd:TIGR01818 136 LIGEAPAMQEVFRAIGRLSRSDITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPKDLIESELFGHEKGAFTG 215

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   352 AsANGKTGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFREDLF 431
Cdd:TIGR01818 216 A-NTRRQGRFEQADGGTLFLDEIGDMPLDAQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATHQNLEALVRQGKFREDLF 294

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   432 YRLNVIPITLPPLRERQEDIELLVHYFLHLHTRRLGSVYPGIAPDVVEILRKHRWPGNLRELSNLMEYLVnVVPSGEVID 511
Cdd:TIGR01818 295 HRLNVIRIHLPPLRERREDIPRLARHFLALAARELDVEPKLLDPEALERLKQLRWPGNVRQLENLCRWLT-VMASGDEVL 373

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   512 STLLPPNLLNNGT-------TEQSDVTEVSEAHLSLDDAGGT------ALEEMEKQMIREALSRHNSKKQ-VADELGIGI 577
Cdd:TIGR01818 374 VSDLPAELALTGRpasapdsDGQDSWDEALEAWAKQALSRGEqglldrALPEFERPLLEAALQHTRGHKQeAAALLGWGR 453


                  ....*...
gi 16130771   578 ATLYRKIK 585
Cdd:TIGR01818 454 NTLTRKLK 461
PEP_resp_reg TIGR02915
PEP-CTERM-box response regulator transcription factor; Members of this protein family share ...
 269-589 6.21e-102

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: 315.92  E-value: 6.21e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   269 IEQLVGECRVMRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGA 348
Cdd:TIGR02915 138 LRGLITSSPGMQKICRTIEKIAPSDITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIPENLLESELFGYEKGA 217

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   349 FTGAsANGKTGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFRE 428
Cdd:TIGR02915 218 FTGA-VKQTLGKIEYAHGGTLFLDEIGDLPLNLQAKLLRFLQERVIERLGGREEIPVDVRIVCATNQDLKRMIAEGTFRE 296

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   429 DLFYRLNVIPITLPPLRERQEDIELLVHYFLHLHTRRLGSVYPGIAPDVVEILRKHRWPGNLRELSNLMEYLVNVVPSGE 508
Cdd:TIGR02915 297 DLFYRIAEISITIPPLRSRDGDAVLLANAFLERFARELKRKTKGFTDDALRALEAHAWPGNVRELENKVKRAVIMAEGNQ 376

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   509 VIDSTLlppnllnnGTTEQSDVTEVSEAHLSLddaggtALEEMEKQMIREALSRHN-SKKQVADELGIGIATLYRKIKKY 587
Cdd:TIGR02915 377 ITAEDL--------GLDARERAETPLEVNLRE------VRERAEREAVRKAIARVDgNIARAAELLGITRPTLYDLMKKH 442


                  ..
gi 16130771   588 EL 589
Cdd:TIGR02915 443 GI 444
PRK05022 PRK05022
nitric oxide reductase transcriptional regulator NorR;
253-582 7.96e-100

nitric oxide reductase transcriptional regulator NorR;


Pssm-ID: 235331 [Multi-domain]  Cd Length: 509  Bit Score: 312.49  E-value: 7.96e-100
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  253 QSHTSFSVANAPDEPHIEqLVGECRVMRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAI 332
Cdd:PRK05022 171 LPQDVAEFLRQEALKEGE-MIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAAL 249

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  333 PEQLLESELFGYVKGAFTGASANgKTGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISA 412
Cdd:PRK05022 250 PESLAESELFGHVKGAFTGAISN-RSGKFELADGGTLFLDEIGELPLALQAKLLRVLQYGEIQRVGSDRSLRVDVRVIAA 328

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  413 TNQNLAQFIAEGKFREDLFYRLNVIPITLPPLRERQEDIELLVHYFLHLHTRRLG--SVypGIAPDVVEILRKHRWPGNL 490
Cdd:PRK05022 329 TNRDLREEVRAGRFRADLYHRLSVFPLSVPPLRERGDDVLLLAGYFLEQNRARLGlrSL--RLSPAAQAALLAYDWPGNV 406

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  491 RELsnlmEYLVN--VV------PSGEV-IDSTLLPPNLLNNGTTEQSDVTEVSEAHLSLDDaggtALEEMEKQMIREALS 561
Cdd:PRK05022 407 REL----EHVISraALlarargAGRIVtLEAQHLDLPAEVALPPPEAAAAPAAVVSQNLRE----ATEAFQRQLIRQALA 478

                        330       340
                 ....*....|....*....|..
gi 16130771  562 RHNSK-KQVADELGIGIATLYR 582
Cdd:PRK05022 479 QHQGNwAAAARALELDRANLHR 500
PRK15424 PRK15424
propionate catabolism operon regulatory protein PrpR; Provisional
 250-586 3.07e-99

propionate catabolism operon regulatory protein PrpR; Provisional


Pssm-ID: 237963 [Multi-domain]  Cd Length: 538  Bit Score: 312.04  E-value: 3.07e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  250 AFHQ----------SHTSFSVANAPDEPH-IEQLVGECRVMRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHK--- 315
Cdd:PRK15424 188 AFEDaldmtrmtlrHNTHYATRNALRTRYvLGDLLGQSPQMEQVRQTILLYARSSAAVLIQGETGTGKELAAQAIHReyf 267

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  316 -----LSGRRNKPFIAINCAAIPEQLLESELFGYVKGAFTGASANGKTGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIE 390
Cdd:PRK15424 268 arhdaRQGKKSHPFVAVNCGAIAESLLEAELFGYEEGAFTGSRRGGRAGLFEIAHGGTLFLDEIGEMPLPLQTRLLRVLE 347

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  391 AREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFREDLFYRLNVIPITLPPLRERQEDIELLVHYFLHlhtRRLGSVY 470
Cdd:PRK15424 348 EKEVTRVGGHQPVPVDVRVISATHCDLEEDVRQGRFRRDLFYRLSILRLQLPPLRERVADILPLAESFLK---QSLAALS 424

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  471 PGIAPDVVEILRKH-------RWPGNLRELSNLMEYLVnVVPSGEVIDStlLPPNLLNNGTTEQSdvtevseahlslDDA 543
Cdd:PRK15424 425 APFSAALRQGLQQCetlllhyDWPGNVRELRNLMERLA-LFLSVEPTPD--LTPQFLQLLLPELA------------RES 489

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....
gi 16130771  544 GGTALEEMEKQMIREALSRHNSKKQVADE-LGIGIATLYRKIKK 586
Cdd:PRK15424 490 AKTPAPRLLAATLQQALERFNGDKTAAANyLGISRTTLWRRLKA 533
TyrR COG3283
Transcriptional regulator TyrR of aromatic amino acids metabolism [Transcription, Amino acid ...
 162-587 1.39e-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: 304.42  E-value: 1.39e-96
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 162 FATMIDNMDQGVLVVDDENRVQFVNQTALKTLGVVQNNIIGKPI----------------RFRPLTFESNFtHGH---MQ 222
Cdd:COG3283  82 LDALLEALPDPVFSIDLKGKIELANPAALSLLGLSEEELIGQPLsellkgfnfsrwlesnEPRPQSERVVI-NGQdylAD 160

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 223 ----HIVSWDDKSELIIG--QLHNIQ--GRQLflMAFHQSHTSfsvanapdepHIEQLVGECRVMRQLKRLISRIAPSPS 294
Cdd:COG3283 161 ilpiYLPDEEGKSILAGAvvTLKSAArlGEQL--QALQVNDDS----------GFDHIVASSPKMRQVIRQAKKMAMLDA 228

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 295 SVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGAFtGASANGKTGLIQAANTGTLFLDEI 374
Cdd:COG3283 229 PLLIQGETGTGKELLARACHLASPRGDKPFLALNCAALPDDVAESELFGYAPGAF-GNAREGKKGLFEQANGGTVFLDEI 307

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 375 GDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFREDLFYRLNVIPITLPPLRERQEDIELL 454
Cdd:COG3283 308 GEMSPQLQAKLLRFLQDGTFRRVGEEQEVKVDVRVICATQKDLAELVQEGEFREDLYYRLNVLTLTLPPLRERKSDILPL 387

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 455 VHYFLHLHTRRLGSVYPGIAPDVVEILRKHRWPGNLRELSNLMEYLVnvvpsgevidsTLLPPNLLnngTTEQSDVTEVS 534
Cdd:COG3283 388 AEHFVARFSQQLGRPRPRLSPDLVDFLQSYPWPGNVRQLENALYRAV-----------SLLEGDEL---TPEDLQLPEYA 453

                       410       420       430       440       450       460
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 535 EAHLSLDDAGGTALEEMEKQMIREALSR----HNSKKQVADELGI---GIAtlyRKIKKY 587
Cdd:COG3283 454 ASAGLLDDLLEGSLDEIVKRFERSLLRRlypsYPSTRKLAKRLGVshtAIA---NKLREY 510
PRK11361 PRK11361
acetoacetate metabolism transcriptional regulator AtoC;
279-587 2.26e-95

acetoacetate metabolism transcriptional regulator AtoC;


Pssm-ID: 183099 [Multi-domain]  Cd Length: 457  Bit Score: 299.46  E-value: 2.26e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  279 MRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGAFTGASANgKT 358
Cdd:PRK11361 152 MMDICKDTAKIALSQASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGHEKGAFTGAQTL-RQ 230

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  359 GLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFREDLFYRLNVIP 438
Cdd:PRK11361 231 GLFERANEGTLLLDEIGEMPLVLQAKLLRILQEREFERIGGHQTIKVDIRIIAATNRDLQAMVKEGTFREDLFYRLNVIH 310

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  439 ITLPPLRERQEDIELLVHYFLHLHTRRLGSVYPGIAPDVVEILRKHRWPGNLRELSNLMEYLVnVVPSGEVIDSTLLPPN 518
Cdd:PRK11361 311 LILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAWSWPGNIRELSNVIERAV-VMNSGPIIFSEDLPPQ 389

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16130771  519 LlnngtteQSDVTEVSEAHLSLDdaGGTALEEM----EKQMIREALSRH-NSKKQVADELGIGIATLYRKIKKY 587
Cdd:PRK11361 390 I-------RQPVCNAGEVKTAPV--GERNLKEEikrvEKRIIMEVLEQQeGNRTRTALMLGISRRALMYKLQEY 454
propionate_PrpR TIGR02329
propionate catabolism operon regulatory protein PrpR; At least five distinct pathways exists ...
 269-586 3.94e-95

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: 301.01  E-value: 3.94e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   269 IEQLVGECRVMRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGA 348
Cdd:TIGR02329 211 LDDLLGASAPMEQVRALVRLYARSDATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIAESLLEAELFGYEEGA 290

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   349 FTGASANGKTGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFRE 428
Cdd:TIGR02329 291 FTGARRGGRTGLIEAAHRGTLFLDEIGEMPLPLQTRLLRVLEEREVVRVGGTEPVPVDVRVVAATHCALTTAVQQGRFRR 370

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   429 DLFYRLNVIPITLPPLRERQEDI-----ELLVHYFLHLHTRRLGSVYPGIAPdVVEILRKHRWPGNLRELSNLMEYL--- 500
Cdd:TIGR02329 371 DLFYRLSILRIALPPLRERPGDIlplaaEYLVQAAAALRLPDSEAAAQVLAG-VADPLQRYPWPGNVRELRNLVERLale 449

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   501 VNVVPSGEvidstlLPPNLLNNGTTEQSDvtEVSEAHLSLDDAGGTALEEMEkqMIREALSRHNSKKQ-VADELGIGIAT 579
Cdd:TIGR02329 450 LSAMPAGA------LTPDVLRALAPELAE--ASGKGKTSALSLRERSRVEAL--AVRAALERFGGDRDaAAKALGISRTT 519


                  ....*..
gi 16130771   580 LYRKIKK 586
Cdd:TIGR02329 520 LWRRLKA 526
nifA TIGR01817
Nif-specific regulatory protein; This model represents NifA, a DNA-binding regulatory protein ...
 272-498 3.44e-86

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: 277.75  E-value: 3.44e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   272 LVGECRVMRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGAFTG 351
Cdd:TIGR01817 198 IIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYLSPRAKRPFVKVNCAALSETLLESELFGHEKGAFTG 277

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   352 ASANGKtGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFREDLF 431
Cdd:TIGR01817 278 AIAQRK-GRFELADGGTLFLDEIGEISPAFQAKLLRVLQEGEFERVGGNRTLKVDVRLVAATNRDLEEAVAKGEFRADLY 356

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 16130771   432 YRLNVIPITLPPLRERQEDIELLVHYFL----HLHTRRLgsvypGIAPDVVEILRKHRWPGNLRELSNLME 498
Cdd:TIGR01817 357 YRINVVPIFLPPLRERREDIPLLAEAFLekfnRENGRPL-----TITPSAIRVLMSCKWPGNVRELENCLE 422
glnG PRK10923
nitrogen regulation protein NR(I); Provisional
 262-586 7.77e-86

nitrogen regulation protein NR(I); Provisional


Pssm-ID: 182842 [Multi-domain]  Cd Length: 469  Bit Score: 275.21  E-value: 7.77e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  262 NAPDEPHIEQLVGECRVMRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESEL 341
Cdd:PRK10923 130 NIQVNGPTTDIIGEAPAMQDVFRIIGRLSRSSISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIPKDLIESEL 209

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  342 FGYVKGAFTGASaNGKTGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFI 421
Cdd:PRK10923 210 FGHEKGAFTGAN-TIRQGRFEQADGGTLFLDEIGDMPLDVQTRLLRVLADGQFYRVGGYAPVKVDVRIIAATHQNLEQRV 288

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  422 AEGKFREDLFYRLNVIPITLPPLRERQEDIELLVHYFLHLHTRRLGSVYPGIAPDVVEILRKHRWPGNLRELSNLMEYLV 501
Cdd:PRK10923 289 QEGKFREDLFHRLNVIRVHLPPLRERREDIPRLARHFLQVAARELGVEAKLLHPETEAALTRLAWPGNVRQLENTCRWLT 368

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  502 NVVPSGEVIDSTlLPPNLLnnGTTEQSDVTEVSEAHLSL--------------DDAGGTALEEMEKQMIREALSRHNSKK 567
Cdd:PRK10923 369 VMAAGQEVLIQD-LPGELF--ESTVPESTSQMQPDSWATllaqwadralrsghQNLLSEAQPELERTLLTTALRHTQGHK 445

                        330       340
                 ....*....|....*....|
gi 16130771  568 QVADE-LGIGIATLYRKIKK 586
Cdd:PRK10923 446 QEAARlLGWGRNTLTRKLKE 465
PRK10365 PRK10365
sigma-54-dependent response regulator transcription factor ZraR;
272-586 3.72e-84

sigma-54-dependent response regulator transcription factor ZraR;


Pssm-ID: 182412 [Multi-domain]  Cd Length: 441  Bit Score: 269.59  E-value: 3.72e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  272 LVGECRVMRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGAFTG 351
Cdd:PRK10365 141 MVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHASSARSEKPLVTLNCAALNESLLESELFGHEKGAFTG 220

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  352 ASANgKTGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFREDLF 431
Cdd:PRK10365 221 ADKR-REGRFVEADGGTLFLDEIGDISPMMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATHRDLAAEVNAGRFRQDLY 299

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  432 YRLNVIPITLPPLRERQEDIELLVHYFLHLHTRRLGSVYPGIAPDVVEILRKHRWPGNLRELSNLMEYLVnVVPSGEVID 511
Cdd:PRK10365 300 YRLNVVAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDWPGNIRELENAVERAV-VLLTGEYIS 378

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16130771  512 STLLPpnllnngtteqsdvteVSEAHLSLDDAGGTALE---EMEKQMIREALSRH-NSKKQVADELGIGIATLYRKIKK 586
Cdd:PRK10365 379 ERELP----------------LAIASTPIPLGQSQDIQplvEVEKEVILAALEKTgGNKTEAARQLGITRKTLLAKLSR 441
PRK15115 PRK15115
response regulator GlrR; Provisional
 261-515 1.37e-81

response regulator GlrR; Provisional


Pssm-ID: 185070 [Multi-domain]  Cd Length: 444  Bit Score: 263.24  E-value: 1.37e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  261 ANAPDEPHIEQLVGECRVMRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESE 340
Cdd:PRK15115 125 APATDERWREAIVTRSPLMLRLLEQARMVAQSDVSVLINGQSGTGKEILAQAIHNASPRASKPFIAINCGALPEQLLESE 204

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  341 LFGYVKGAFTGASANgKTGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQF 420
Cdd:PRK15115 205 LFGHARGAFTGAVSN-REGLFQAAEGGTLFLDEIGDMPAPLQVKLLRVLQERKVRPLGSNRDIDIDVRIISATHRDLPKA 283

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  421 IAEGKFREDLFYRLNVIPITLPPLRERQEDIELLVHYFLHLHTRRLGSVYPGIAPDVVEILRKHRWPGNLRELSNLMEYL 500
Cdd:PRK15115 284 MARGEFREDLYYRLNVVSLKIPALAERTEDIPLLANHLLRQAAERHKPFVRAFSTDAMKRLMTASWPGNVRQLVNVIEQC 363

                        250
                 ....*....|....*
gi 16130771  501 VnVVPSGEVIDSTLL 515
Cdd:PRK15115 364 V-ALTSSPVISDALV 377
FhlA COG3604
FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis ...
 284-589 2.09e-78

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: 251.31  E-value: 2.09e-78
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 284 RLISRIApSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESelfgyvkgaftgasangktgliqa 363
Cdd:COG3604 107 RLLETLA-SLAAVAILGETGTGKELVANAIHELSPRADKPFVKVNCAALPESLLES------------------------ 161

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 364 antgtlfldeigdmplmlqakllraIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFREDLFYRLNVIPITLPP 443
Cdd:COG3604 162 -------------------------LQEGEFERVGGDETIKVDVRIIAATNRDLEEEVAEGRFREDLYYRLNVFPIRLPP 216

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 444 LRERQEDIELLVHYFLHLHTRRLGSVYPGIAPDVVEILRKHRWPGNLRELSNLMEYLVnVVPSGEVIDSTLLPPnllnng 523
Cdd:COG3604 217 LRERREDIPLLAEHFLEKFSRRLGKPILRLSPEALEALMAYPWPGNVRELENVIERAV-ILAEGGVLDADDLAP------ 289

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16130771 524 tteqsdvtevseahlslddAGGTALEEMEKQMIREALSRHNSKK-QVADELGIGIATLYRKIKKYEL 589
Cdd:COG3604 290 -------------------GSREALEEVEREHILEALERTGGNIaGAARLLGLTPSTLRSRMKKLGI 337
PRK15429 PRK15429
formate hydrogenlyase transcriptional activator FlhA;
266-586 5.42e-77

formate hydrogenlyase transcriptional activator FlhA;


Pssm-ID: 237965 [Multi-domain]  Cd Length: 686  Bit Score: 257.84  E-value: 5.42e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  266 EPHIEQLVGECRVMRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYV 345
Cdd:PRK15429 372 DSEFGEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPAGLLESDLFGHE 451

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  346 KGAFTGASANgKTGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGK 425
Cdd:PRK15429 452 RGAFTGASAQ-RIGRFELADKSSLFLDEVGDMPLELQPKLLRVLQEQEFERLGSNKIIQTDVRLIAATNRDLKKMVADRE 530

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  426 FREDLFYRLNVIPITLPPLRERQEDIELLVHYFLHLHTRRLGSVYPGIAPDVVEILRKHRWPGNLRELSNLMEYLVnvvp 505
Cdd:PRK15429 531 FRSDLYYRLNVFPIHLPPLRERPEDIPLLVKAFTFKIARRMGRNIDSIPAETLRTLSNMEWPGNVRELENVIERAV---- 606

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  506 sgevidstllppnLLNNGTTEQSDVTEVSEAHLSLDDAGGTALE--EMEKQMIREALSRHN----SKKQVADELGIGIAT 579
Cdd:PRK15429 607 -------------LLTRGNVLQLSLPDITLPEPETPPAATVVAQegEDEYQLIVRVLKETNgvvaGPKGAAQRLGLKRTT 673


                 ....*..
gi 16130771  580 LYRKIKK 586
Cdd:PRK15429 674 LLSRMKR 680
pspF PRK11608
phage shock protein operon transcriptional activator; Provisional
 269-590 1.25e-74

phage shock protein operon transcriptional activator; Provisional


Pssm-ID: 236936 [Multi-domain]  Cd Length: 326  Bit Score: 241.11  E-value: 1.25e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  269 IEQLVGECRVMRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGA 348
Cdd:PRK11608   5 KDNLLGEANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLLDSELFGHEAGA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  349 FTGASaNGKTGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFRE 428
Cdd:PRK11608  85 FTGAQ-KRHPGRFERADGGTLFLDELATAPMLVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPAMVAEGKFRA 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  429 DLFYRLNVIPITLPPLRERQEDIELLVHYFLHLHTRRLG-SVYPGIAPDVVEILRKHRWPGNLRELSNLMEYLV-NVVPS 506
Cdd:PRK11608 164 DLLDRLAFDVVQLPPLRERQSDIMLMAEHFAIQMCRELGlPLFPGFTERARETLLNYRWPGNIRELKNVVERSVyRHGTS 243

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  507 GEVIDSTLLPPNLLNNGTTEQSDVTEVSEAHLSLDdaggtaLEE----MEKQMIREAL--SRHNSKKqVADELGIGIATL 580
Cdd:PRK11608 244 EYPLDNIIIDPFKRRPAEEAIAVSETTSLPTLPLD------LREwqhqQEKELLQRSLqqAKFNQKR-AAELLGLTYHQL 316

                        330
                 ....*....|
gi 16130771  581 YRKIKKYELL 590
Cdd:PRK11608 317 RALLKKHQIL 326
PRK10820 PRK10820
transcriptional regulator TyrR;
164-495 1.65e-68

transcriptional regulator TyrR;


Pssm-ID: 236769 [Multi-domain]  Cd Length: 520  Bit Score: 230.73  E-value: 1.65e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  164 TMIDNMDQGVLVVDDENRVQFVNQTALKTLGVVQNNIIGKPI----------RFrpltFESNFTHGHMQHIVswddksel 233
Cdd:PRK10820  84 ALLEALPEPVLSIDMKGKVELANPASCQLFGQSEEKLRNHTAaqlingfnflRW----LESEPQDSHNEHVV-------- 151

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  234 iigqlhnIQGrQLFLMAFHQSHtsfsvanAPDEPHIEQLVG-------ECRVMRQLKRLISR--------IAPSPSSVMV 298
Cdd:PRK10820 152 -------ING-QDFLMEITPVY-------LQDENDQHVLVGavvmlrsTARMGRQLQNLAVNddsafsqiVAVSPKMRQV 216

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  299 V----------------GESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGAFTGAsANGKTGLIQ 362
Cdd:PRK10820 217 VeqarklamldapllitGDTGTGKDLLAYACHLRSPRGKKPFLALNCASIPDDVVESELFGHAPGAYPNA-LEGKKGFFE 295

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  363 AANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFREDLFYRLNVIPITLP 442
Cdd:PRK10820 296 QANGGSVLLDEIGEMSPRMQAKLLRFLNDGTFRRVGEDHEVHVDVRVICATQKNLVELVQKGEFREDLYYRLNVLTLNLP 375

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|...
gi 16130771  443 PLRERQEDIELLVHYFLHLHTRRLGSVYPGIAPDVVEILRKHRWPGNLRELSN 495
Cdd:PRK10820 376 PLRDRPQDIMPLTELFVARFADEQGVPRPKLAADLNTVLTRYGWPGNVRQLKN 428
PRK11388 PRK11388
DNA-binding transcriptional regulator DhaR; Provisional
 165-589 1.42e-64

DNA-binding transcriptional regulator DhaR; Provisional


Pssm-ID: 183114 [Multi-domain]  Cd Length: 638  Bit Score: 223.02  E-value: 1.42e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  165 MIDNMDQGVLVVDDENRVQFVNQTALKTLGVVQNNIIGKPIrFRPLTFESNF----THGH-MQHI-VSWDDKSELI---- 234
Cdd:PRK11388 208 LLESMDDGVIAWDEQGNLQFLNAQAARLLRLDATASQGRAI-TELLTLPAVLqqaiKQAHpLKHVeVTFESQGQFIdavi 286

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  235 -------------IGQLHNI-QGRQLflMAFHQSHTSFSvanapdephIEQLVGECRVMRQLKRLISRIAPSPSSVMVVG 300
Cdd:PRK11388 287 tlkpiiegqgtsfILLLHPVeQMRQL--MTSQLGKVSHT---------FDHMPQDSPQMRRLIHFGRQAAKSSFPVLLCG 355

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  301 ESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFgyvkGAFTGASANGKTGLIQAANTGTLFLDEIGDMPLM 380
Cdd:PRK11388 356 EEGVGKALLAQAIHNESERAAGPYIAVNCQLYPDEALAEEFL----GSDRTDSENGRLSKFELAHGGTLFLEKVEYLSPE 431

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  381 LQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFREDLFYRLNVIPITLPPLRERQEDIELLVHYFLH 460
Cdd:PRK11388 432 LQSALLQVLKTGVITRLDSRRLIPVDVRVIATTTADLAMLVEQNRFSRQLYYALHAFEITIPPLRMRREDIPALVNNKLR 511

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771  461 LHTRRLGSVYPgIAPDVVEILRKHRWPGNLRELSNLMEYLVNVVPSGeVIDSTLLPPNLLNNGTTEQSDVTEVSEAhlsl 540
Cdd:PRK11388 512 SLEKRFSTRLK-IDDDALARLVSYRWPGNDFELRSVIENLALSSDNG-RIRLSDLPEHLFTEQATDDVSATRLSTS---- 585

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|
gi 16130771  541 ddaggTALEEMEKQ-MIREALSRHNSKKQVADELGIGIATLYRKIKKYEL 589
Cdd:PRK11388 586 -----LSLAELEKEaIINAAQVCGGRIQEMAALLGIGRTTLWRKMKQHGI 630
RtcR COG4650
Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a ...
 284-494 4.39e-48

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


Pssm-ID: 443688 [Multi-domain]  Cd Length: 534  Bit Score: 175.79  E-value: 4.39e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 284 RLISRI----APSPSSVMVVGESGTGKEVVARAIHKLSGRRNK---PFIAINCAAIPEQLLESELFGYVKGAFTGAsANG 356
Cdd:COG4650 195 RLIEQIervaIRSRAPILLTGPTGAGKSQLARRIYELKKARHQvsgRFVEVNCATLRGDGAMSALFGHVKGAFTGA-VSD 273

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 357 KTGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQVDIRIISATNQNLAQFIAEGKFREDLFYRLNV 436
Cdd:COG4650 274 RAGLLRSADGGVLFLDEIGELGLDEQAMLLRAIEEKRFLPVGSDKEVSSDFQLIAGTNRDLRQEVAEGRFREDLLARINL 353

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 437 IPITLPPLRERQEDIELLVHYFLHLHTRRLGS----------VYPGIA--PDVveilrkhRWPGNLRELS 494
Cdd:COG4650 354 WTFRLPGLAERREDIEPNLDYELARFAREQGRrvrfnkearaRYLAFAtsPEA-------LWSGNFRDLN 416
PspF COG1221
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain ...
 296-521 4.12e-30

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: 125.99  E-value: 4.12e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 296 VMVVGESGTGKEVVARAIH---KLSGR--RNKPFIAINCA--AIPEQLLESELFGYVKGAFTGASANgKTGLIQAANTGT 368
Cdd:COG1221 133 TLILGPTGVGKSFFAELMYeyaIEIGVlpEDAPFVVFNCAdyANNPQLLMSQLFGYVKGAFTGADKD-KEGLIEKADGGI 211

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 369 LFLDEIGDMPLMLQAKLLRAIEAREILPIGASSP-IQVDIRIISATNQN-----LAQFIaegkfRedlfyRlnvIP--IT 440
Cdd:COG1221 212 LFLDEVHRLPPEGQEMLFTFMDKGIYRRLGETEKtRKANVRIIFATTEDpesslLKTFL-----R-----R---IPmvIK 278

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 441 LPPLRER--QEDIElLVHYFLHLHTRRLG-SVYpgIAPDVVEILRKHRWPGNLRELSNLME------YLVNVVPSGEV-- 509
Cdd:COG1221 279 LPSLEERslEERLE-LIKHFFKEEAKRLNkPIK--VSKEVLKALLLYDCPGNIGQLKSDIQlacakaFLNYITNKKEEie 355

                       250
                ....*....|..
gi 16130771 510 IDSTLLPPNLLN 521
Cdd:COG1221 356 ITLSDLPENVKK 367
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 277-443 3.76e-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: 3.76e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 277 RVMRQLKRLISRiaPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKgaftgasANG 356
Cdd:cd00009   5 EAIEALREALEL--PPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFL-------VRL 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 357 KTGLIQAANTGTLFLDEIGDMPLMLQAKLLRAIEAREILPIgasspIQVDIRIISATNQNLaqfiaEGKFREDLFYRLNV 436
Cdd:cd00009  76 LFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRI-----DRENVRVIGATNRPL-----LGDLDRALYDRLDI 145


                ....*..
gi 16130771 437 IpITLPP 443
Cdd:cd00009 146 R-IVIPL 151
Sigma54_activ_2 pfam14532
Sigma-54 interaction domain;
273-444 3.90e-20

Sigma-54 interaction domain;


Pssm-ID: 434021 [Multi-domain]  Cd Length: 138  Bit Score: 86.63  E-value: 3.90e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   273 VGECRVMRQLKRLISRIAPSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESelfgyvkgaftga 352
Cdd:pfam14532   1 LGASAAIQEIKRRLEQAAQSTLPVFLTGEPGSGKEFCARYLHNPSTPWVQPFDIEYLAHAPLELLEQ------------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   353 sangktgliqaANTGTLFLDEIGDMPLMLQAKLLRAIEAREilpigasspiQVDIRIISATNQNLAQFIAEGKFREDLFY 432
Cdd:pfam14532  68 -----------AKGGTLYLKDIADLSKALQKGLLLLLAKAE----------GYRVRLVCTSSKDLPQLAAAGLFDEQLYF 126

                         170
                  ....*....|..
gi 16130771   433 RLNVIPITLPPL 444
Cdd:pfam14532 127 ELSALRLHVPPL 138
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 292-414 1.15e-11

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 62.78  E-value: 1.15e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771    292 SPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINCAAIPEQLLESELFGYVKGAFTGAS----ANGKTGLIQAANTG 367
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSgelrLRLALALARKLKPD 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 16130771    368 TLFLDEIGDMPLMLQAKLLRAIEAREILpigASSPIQVDIRIISATN 414
Cdd:smart00382  81 VLILDEITSLLDAEQEALLLLLEELRLL---LLLKSEKNLTVILTTN 124
HTH_8 pfam02954
Bacterial regulatory protein, Fis family;
548-586 5.14e-10

Bacterial regulatory protein, Fis family;


Pssm-ID: 427077 [Multi-domain]  Cd Length: 40  Bit Score: 54.71  E-value: 5.14e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 16130771   548 LEEMEKQMIREALSRHN-SKKQVADELGIGIATLYRKIKK 586
Cdd:pfam02954   1 LEEVEKELIEAALERTGgNKSKAARLLGISRRTLYRKLKK 40
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 295-414 7.89e-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: 45.75  E-value: 7.89e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   295 SVMVVGESGTGK-EVVARAIHKLSGRrnkPFIAINCaaiPEQLLESELFG----------YVKGAFTGAsanGKTGLIqa 363
Cdd:pfam07728   1 GVLLVGPPGTGKtELAERLAAALSNR---PVFYVQL---TRDTTEEDLFGrrnidpggasWVDGPLVRA---AREGEI-- 69

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 16130771   364 antgtLFLDEIGDMPLMLQAKLLRAIEAREILPIGASSPIQV---DIRIISATN 414
Cdd:pfam07728  70 -----AVLDEINRANPDVLNSLLSLLDERRLLLPDGGELVKAapdGFRLIATMN 118
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 162-205 1.34e-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: 43.16  E-value: 1.34e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 16130771    162 FATMIDNMDQGVLVVDDENRVQFVNQTALKTLGVVQNNIIGKPI 205
Cdd:smart00091   3 LRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSL 46
AAA_16 pfam13191
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 271-388 1.82e-05

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: 45.19  E-value: 1.82e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771   271 QLVGECRVMRQLKRLISRI-APSPSSVMVVGESGTGKEVVARAIHKLSGRRNKPFIAINC------AAIPEQLLESELFG 343
Cdd:pfam13191   1 RLVGREEELEQLLDALDRVrSGRPPSVLLTGEAGTGKTTLLRELLRALERDGGYFLRGKCdenlpySPLLEALTREGLLR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 16130771   344 YVKGA--FTGASANGKTGLIQAANTGTLFLDEIGDMPLMLQAKLLRA 388
Cdd:pfam13191  81 QLLDEleSSLLEAWRAALLEALAPVPELPGDLAERLLDLLLRLLDLL 127
NtrB COG3852
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];
162-206 5.21e-05

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


Pssm-ID: 443061 [Multi-domain]  Cd Length: 361  Bit Score: 45.61  E-value: 5.21e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 16130771 162 FATMIDNMDQGVLVVDDENRVQFVNQTALKTLGVVQNNIIGKPIR 206
Cdd:COG3852   9 LRAILDSLPDAVIVLDADGRITYVNPAAERLLGLSAEELLGRPLA 53
PAS_8 pfam13188
PAS domain; PAS domains are involved in many signalling proteins where they are used as a ...
 162-194 8.87e-05

PAS domain; PAS domains are involved in many signalling proteins where they are used as a signal sensor domain. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Heme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. This domain recognizes oxygen and CO (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 463802 [Multi-domain]  Cd Length: 65  Bit Score: 40.61  E-value: 8.87e-05
                          10        20        30
                  ....*....|....*....|....*....|...
gi 16130771   162 FATMIDNMDQGVLVVDDENRVQFVNQTALKTLG 194
Cdd:pfam13188   3 LRALFESSPDGILVLDEGGRIIYVNPAALELLG 35
HTH_50 pfam18024
Helix-turn-helix domain; The TyrR protein of Haemophilus influenzae is a 36-kD transcription ...
 548-589 2.10e-04

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


Pssm-ID: 407862 [Multi-domain]  Cd Length: 50  Bit Score: 39.32  E-value: 2.10e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 16130771   548 LEEMEKQMIREALSRHNSKKQVADELGIGIATLYRKIKKYEL 589
Cdd:pfam18024   8 VSYIERELIGAAYENYKSARKVAKALGLSHTTIANKMKRYGI 49
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
 12-116 3.22e-04

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: 41.21  E-value: 3.22e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771     12 QIQPTIQRFARMLASVLQLE---VEIVDENLCR----VAGTGAYGKFLGRQLSGNSRLLRHVLETKTEKVVTQSRFDPLC 84
Cdd:smart00065   1 DLEELLQTILEELRQLLGADrvlIYLVDENDRGelvlVAADGLTLPTLGIRFPLDEGLAGRVAETGRPLNIPDVEADPLF 80

                           90       100       110
                   ....*....|....*....|....*....|..
gi 16130771     85 EGCDSKENCREKAFLGTPVILQDRCVGVISLI 116
Cdd:smart00065  81 AEDLLGRYQGVRSFLAVPLVADGELVGVLALH 112
NtrY COG5000
Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism ...
 164-205 6.44e-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: 42.26  E-value: 6.44e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 16130771 164 TMIDNMDQGVLVVDDENRVQFVNQTALKTLGVVQNNIIGKPI 205
Cdd:COG5000  94 TILENLPAGVIVLDADGRITLANPAAERLLGIPLEELIGKPL 135
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 169-205 3.50e-03

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: 37.23  E-value: 3.50e-03
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 16130771 169 MDQGVLVVDDENRVQFVNQTALKTLGVVQNNIIGKPI 205
Cdd:cd00130   1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSL 37
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 162-205 4.86e-03

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: 37.01  E-value: 4.86e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 16130771   162 FATMIDNMDQGVLVVDDENRVQFVNQTALKTLGVVQNNIIGKPI 205
Cdd:pfam00989   3 LRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSL 46
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 265-374 6.52e-03

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 39.12  E-value: 6.52e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130771 265 DEPHIEQLVGECRVMRQLKRLISRI-----------APSPSSVMVVGESGTGKEVVARAIHKLSGRrnkPFIAINCAAIP 333
Cdd:COG0464 152 REAILDDLGGLEEVKEELRELVALPlkrpelreeygLPPPRGLLLYGPPGTGKTLLARALAGELGL---PLIEVDLSDLV 228

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 16130771 334 EQLL-ESElfGYVKGAFTGASANGKtgliqaantGTLFLDEI 374
Cdd:COG0464 229 SKYVgETE--KNLREVFDKARGLAP---------CVLFIDEA 259
PRK11360 PRK11360
two-component system sensor histidine kinase AtoS;
164-206 9.07e-03

two-component system sensor histidine kinase AtoS;


Pssm-ID: 236901 [Multi-domain]  Cd Length: 607  Bit Score: 38.80  E-value: 9.07e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 16130771  164 TMIDNMDQGVLVVDDENRVQFVNQTALKTLGVVQNNIIGKPIR 206
Cdd:PRK11360 266 LILESIADGVIAIDRQGKITTMNPAAEVITGLQRHELVGKPYS 308
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 553-582 9.15e-03

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 34.22  E-value: 9.15e-03
                        10        20        30
                ....*....|....*....|....*....|
gi 16130771 553 KQMIREALSRHNSKKQVADELGIGIATLYR 582
Cdd:cd00569  11 IAEARRLLAAGESVAEIARELGVSRSTLYR 40
 
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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