254780855

254780855

NADH dehydrogenase subunit D

GeneID in NCBI database:8209870Locus tag:CLIBASIA_03750
Protein GI in NCBI database:254780855Protein Accession:YP_003065268.1
Gene range:+(824157, 825347)Protein Length:396aa
Gene description:NADH dehydrogenase subunit D
COG prediction:[C] NADH:ubiquinone oxidoreductase 49 kD subunit 7
KEGG prediction:nuoD; NADH dehydrogenase subunit D (EC:1.6.99.5); K00333 NADH dehydrogenase I subunit D [EC:1.6.5.3]
SEED prediction:NADH-ubiquinone oxidoreductase chain D (EC 1.6.5.3)
Pathway involved in KEGG:Oxidative phosphorylation [PATH:las00190]
Subsystem involved in SEED:Respiratory Complex I
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSAT1 TM-Helix
MEMSAT_SVM2 TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390------
MDKKKSRSFTINFGPQHPAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQAVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQAMDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSFPSALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECYSELDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPKRADMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAPGYAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR
cccccccEEEEEcccccccccccEEEEEEEEccEEEEEEEEccccHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHcccccccccEEEccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHcccEEEccHHHHHHHccccccccccccccccccccccccccccccccEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccccccEEEEEEccccEEEEEEEEcccccEEEEEEccccHHHHHHHHHHHccccccHHHHHHHHcccccccccc
ccccccccEEEccccccccccccEEEEEcccccEEEcccccccccccccHHHHHHHHHHHccccccHHHcccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHcccHHHHHHcccccccccccccHHHHHHHHHHHcHHHHHHHHHHcccccHHHHcccccccccHHHHHHccccccEEEcccccccccccccccHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccEEccccccccccHHHHHHHHHHHHHHHHHHHcccccccccEEEEEEcccccEEEEEEEcccccccccEEccccHHHHHHHHHHHcccccHHHHEHHccccEEEccccc
mdkkksrsftinfgpqhpaaHGVLRLILELDgeivervdphigllhrgTEKLIETKtflqavpyfdrldyvapmNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTqamdvgaltpplwgfeEREKLMVFYErasgsrmhaayfrpggvhqdippelvedigcwcdsfpsalndisdlltgnrifkqrnvnigtvkledawgwgfsgvmirgsgaawdlrksqpyecyseldfdipigkhgdcYDRYLVRMMEMRESVKIIRQCVNRLlgknkvgpvsasdpkivppkradmKRSMESLIHHFKlytegyhvpvgevyaaveapkgefgvylisdggnkpyrckirapgyAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR
mdkkksrsftinfgpqhpaahGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQAVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQAMDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSFPSALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECYSeldfdipigkhGDCYDRYLVRMMEMRESVKIIRQCVNRLlgknkvgpvsasdpkivppkraDMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAPGYAHLQAMEFLCKGHQLADVSAILGSLDivfgevdr
MDKKKSRSFTINFGPQHPAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQAVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQAMDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSFPSALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECYSELDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPKRADMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAPGYAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR
****KSR*FTINFGPQHPAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQAVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQAMDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSFPSALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECYSELDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPKRADMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAPGYAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR
********FTINFGPQHPAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQAVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQAMDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSFPSALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECYSELDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPKRADMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAPGYAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR
*****SRSFTINFGPQHPAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQAVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQAMDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSFPSALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECYSELDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPKRADMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAPGYAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooo
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MDKKKSRSFTINFGPQHPAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQAVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQAMDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSFPSALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECYSELDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPKRADMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAPGYAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR
MDKKKSRSFTINFGPQHPAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQAVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQAMDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSFPSALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECYSELDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPKRADMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAPGYAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR
MDKKKSRSFTINFGPQHPAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQAVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQAMDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSFPSALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECYSELDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPKRADMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAPGYAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target396 NADH dehydrogenase subunit D [Candidatus Liberibacter a
315122723396 NADH dehydrogenase subunit D [Candidatus Liberibacter s 1 0.0
222085578396 NADH-ubiquinone oxidoreductase chain D protein [Agrobac 1 0.0
116251469396 NADH dehydrogenase subunit D [Rhizobium leguminosarum b 1 0.0
209548865396 NADH dehydrogenase subunit D [Rhizobium leguminosarum b 1 0.0
86357240396 NADH dehydrogenase subunit D [Rhizobium etli CFN 42] Le 1 0.0
241204089396 NADH dehydrogenase subunit D [Rhizobium leguminosarum b 1 0.0
190891288396 NADH-ubiquinone oxidoreductase, chain D [Rhizobium etli 1 0.0
327188490396 NADH-ubiquinone oxidoreductase protein, chain D [Rhizob 1 0.0
15965020396 NADH dehydrogenase subunit D [Sinorhizobium meliloti 10 1 0.0
150396114396 NADH dehydrogenase subunit D [Sinorhizobium medicae WSM 1 0.0
>gi|315122723|ref|YP_004063212.1| NADH dehydrogenase subunit D [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 396 Back     alignment and organism information
 Score =  765 bits (1975), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 366/396 (92%), Positives = 383/396 (96%)

Query: 1   MDKKKSRSFTINFGPQHPAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQ 60
           M +KK R FT+NFGPQHPAAHGVLRLILELDGE+VERVDPHIGLLHRGTEKLIETKTFLQ
Sbjct: 1   MGEKKIRGFTMNFGPQHPAAHGVLRLILELDGEVVERVDPHIGLLHRGTEKLIETKTFLQ 60

Query: 61  AVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQA 120
           AVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQA
Sbjct: 61  AVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQA 120

Query: 121 MDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSF 180
           MDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPP LVEDIGCWCDSF
Sbjct: 121 MDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPVLVEDIGCWCDSF 180

Query: 181 PSALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECY 240
           P+ L+DIS LLT +RIFKQRNV+IGTVKLEDAWG GFSGVMIRGSGAAWDLRKSQPYECY
Sbjct: 181 PAVLDDISGLLTESRIFKQRNVDIGTVKLEDAWGLGFSGVMIRGSGAAWDLRKSQPYECY 240

Query: 241 SELDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPK 300
           +ELDFDIPIGK GDCYDRYLVRMMEMRES+KIIRQCV+RLLG N+VGPV ASD KI+PP+
Sbjct: 241 AELDFDIPIGKKGDCYDRYLVRMMEMRESIKIIRQCVDRLLGDNRVGPVFASDSKIIPPR 300

Query: 301 RADMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAP 360
           RADMKRSME+LIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYL+SDG NKPYRC+IRAP
Sbjct: 301 RADMKRSMEALIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLVSDGSNKPYRCRIRAP 360

Query: 361 GYAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR 396
           G+AHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR
Sbjct: 361 GFAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR 396


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222085578|ref|YP_002544108.1| NADH-ubiquinone oxidoreductase chain D protein [Agrobacterium radiobacter K84] Length = 396 Back     alignment and organism information
>gi|116251469|ref|YP_767307.1| NADH dehydrogenase subunit D [Rhizobium leguminosarum bv. viciae 3841] Length = 396 Back     alignment and organism information
>gi|209548865|ref|YP_002280782.1| NADH dehydrogenase subunit D [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 396 Back     alignment and organism information
>gi|86357240|ref|YP_469132.1| NADH dehydrogenase subunit D [Rhizobium etli CFN 42] Length = 396 Back     alignment and organism information
>gi|241204089|ref|YP_002975185.1| NADH dehydrogenase subunit D [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 396 Back     alignment and organism information
>gi|190891288|ref|YP_001977830.1| NADH-ubiquinone oxidoreductase, chain D [Rhizobium etli CIAT 652] Length = 396 Back     alignment and organism information
>gi|327188490|gb|EGE55704.1| NADH-ubiquinone oxidoreductase protein, chain D [Rhizobium etli CNPAF512] Length = 396 Back     alignment and organism information
>gi|15965020|ref|NP_385373.1| NADH dehydrogenase subunit D [Sinorhizobium meliloti 1021] Length = 396 Back     alignment and organism information
>gi|150396114|ref|YP_001326581.1| NADH dehydrogenase subunit D [Sinorhizobium medicae WSM419] Length = 396 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target396 NADH dehydrogenase subunit D [Candidatus Liberibacter a
PRK06075392 PRK06075, PRK06075, NADH dehydrogenase subunit D; Valid 0.0
TIGR01962386 TIGR01962, NuoD, NADH dehydrogenase I, D subunit 1e-179
KOG2870452 KOG2870, KOG2870, KOG2870, NADH:ubiquinone oxidoreducta 1e-171
PRK12322366 PRK12322, PRK12322, NADH dehydrogenase subunit D; Provi 1e-115
PRK13292788 PRK13292, PRK13292, trifunctional NADH dehydrogenase I 1e-110
PRK11742575 PRK11742, PRK11742, bifunctional NADH:ubiquinone oxidor 1e-105
PRK07415394 PRK07415, PRK07415, NAD(P)H-quinone oxidoreductase subu 1e-96
CHL00017393 CHL00017, ndhH, NADH dehydrogenase subunit 7 8e-93
COG3261382 COG3261, HycE, Ni,Fe-hydrogenase III large subunit [Ene 1e-59
COG0649398 COG0649, NuoD, NADH:ubiquinone oxidoreductase 49 kD sub 0.0
pfam00346272 pfam00346, Complex1_49kDa, Respiratory-chain NADH dehyd 1e-116
COG3259441 COG3259, FrhA, Coenzyme F420-reducing hydrogenase, alph 2e-04
>gnl|CDD|180385 PRK06075, PRK06075, NADH dehydrogenase subunit D; Validated Back     alignment and domain information
>gnl|CDD|162627 TIGR01962, NuoD, NADH dehydrogenase I, D subunit Back     alignment and domain information
>gnl|CDD|38081 KOG2870, KOG2870, KOG2870, NADH:ubiquinone oxidoreductase, NDUFS2/49 kDa subunit [Energy production and conversion] Back     alignment and domain information
>gnl|CDD|183437 PRK12322, PRK12322, NADH dehydrogenase subunit D; Provisional Back     alignment and domain information
>gnl|CDD|183955 PRK13292, PRK13292, trifunctional NADH dehydrogenase I subunit B/C/D; Provisional Back     alignment and domain information
>gnl|CDD|183294 PRK11742, PRK11742, bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional Back     alignment and domain information
>gnl|CDD|180969 PRK07415, PRK07415, NAD(P)H-quinone oxidoreductase subunit H; Validated Back     alignment and domain information
>gnl|CDD|176960 CHL00017, ndhH, NADH dehydrogenase subunit 7 Back     alignment and domain information
>gnl|CDD|33072 COG3261, HycE, Ni,Fe-hydrogenase III large subunit [Energy production and conversion] Back     alignment and domain information
>gnl|CDD|30994 COG0649, NuoD, NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion] Back     alignment and domain information
>gnl|CDD|144077 pfam00346, Complex1_49kDa, Respiratory-chain NADH dehydrogenase, 49 Kd subunit Back     alignment and domain information
>gnl|CDD|33070 COG3259, FrhA, Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 396 NADH dehydrogenase subunit D [Candidatus Liberibacter a
TIGR03295411 frhA coenzyme F420 hydrogenase, subunit alpha. This mod 100.0
PRK10170597 hydrogenase 1 large subunit; Provisional 100.0
PRK10467567 hydrogenase 2 large subunit; Provisional 100.0
PRK06075392 NADH dehydrogenase subunit D; Validated 100.0
PRK11742575 bifunctional NADH:ubiquinone oxidoreductase subunit C/D 100.0
PRK07415394 NAD(P)H-quinone oxidoreductase subunit H; Validated 100.0
PRK12322366 NADH dehydrogenase subunit D; Provisional 100.0
PRK13292784 trifunctional NADH dehydrogenase I subunit B/C/D; Provi 100.0
CHL00017393 ndhH NADH dehydrogenase subunit 7 100.0
COG3261382 HycE Ni,Fe-hydrogenase III large subunit [Energy produc 100.0
TIGR01962408 NuoD NADH dehydrogenase I, D subunit; InterPro: IPR0102 100.0
COG0374545 HyaB Ni,Fe-hydrogenase I large subunit [Energy producti 100.0
COG0649398 NuoD NADH:ubiquinone oxidoreductase 49 kD subunit 7 [En 100.0
COG3259441 FrhA Coenzyme F420-reducing hydrogenase, alpha subunit 100.0
KOG2870452 consensus 100.0
pfam00374504 NiFeSe_Hases Nickel-dependent hydrogenase. 100.0
pfam00346272 Complex1_49kDa Respiratory-chain NADH dehydrogenase, 49 100.0
>TIGR03295 frhA coenzyme F420 hydrogenase, subunit alpha Back     alignment and domain information
>PRK10170 hydrogenase 1 large subunit; Provisional Back     alignment and domain information
>PRK10467 hydrogenase 2 large subunit; Provisional Back     alignment and domain information
>PRK06075 NADH dehydrogenase subunit D; Validated Back     alignment and domain information
>PRK11742 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional Back     alignment and domain information
>PRK07415 NAD(P)H-quinone oxidoreductase subunit H; Validated Back     alignment and domain information
>PRK12322 NADH dehydrogenase subunit D; Provisional Back     alignment and domain information
>PRK13292 trifunctional NADH dehydrogenase I subunit B/C/D; Provisional Back     alignment and domain information
>CHL00017 ndhH NADH dehydrogenase subunit 7 Back     alignment and domain information
>COG3261 HycE Ni,Fe-hydrogenase III large subunit [Energy production and conversion] Back     alignment and domain information
>TIGR01962 NuoD NADH dehydrogenase I, D subunit; InterPro: IPR010219 This entry recognises specifically the D subunit of NADH dehydrogenase I complex Back     alignment and domain information
>COG0374 HyaB Ni,Fe-hydrogenase I large subunit [Energy production and conversion] Back     alignment and domain information
>COG0649 NuoD NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion] Back     alignment and domain information
>COG3259 FrhA Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion] Back     alignment and domain information
>KOG2870 consensus Back     alignment and domain information
>pfam00374 NiFeSe_Hases Nickel-dependent hydrogenase Back     alignment and domain information
>pfam00346 Complex1_49kDa Respiratory-chain NADH dehydrogenase, 49 Kd subunit Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target396 NADH dehydrogenase subunit D [Candidatus Liberibacter a
2fug_4409 Crystal Structure Of The Hydrophilic Domain Of Resp 1e-117
1cc1_L498 Crystal Structure Of A Reduced, Active Form Of The 2e-51
2wpn_B482 Structure Of The Oxidised, As-Isolated Nifese Hydro 2e-47
1yq9_H536 Structure Of The Unready Oxidized Form Of [nife] Hy 1e-45
1frv_B536 Crystal Structure Of The Oxidized Form Of Ni-Fe Hyd 2e-44
2frv_L536 Crystal Structure Of The Oxidized Form Of Ni-Fe Hyd 2e-26
1yrq_N549 Structure Of The Ready Oxidized Form Of [nife]-Hydr 7e-25
3h3x_Q549 Structure Of The V74m Large Subunit Mutant Of Ni-Fe 1e-24
1frf_L564 Crystal Structure Of The Ni-Fe Hydrogenase From Des 1e-24
3cur_H549 Structure Of A Double Methionine Mutant Of Ni-Fe Hy 1e-24
1yqw_Q549 Structure Of The Oxidized Unready Form Of Ni-Fe Hyd 7e-24
1h2r_L534 Three-Dimensional Structure Of Ni-Fe Hydrogenase Fr 4e-23
1h2a_L567 Single Crystals Of Hydrogenase From Desulfovibrio V 5e-23
3cus_Q549 Structure Of A Double IlePHE MUTANT OF NI-Fe Hydrog 6e-23
1ubh_L534 Three-Dimensional Structure Of The Carbon Monoxide 2e-22
3myr_B561 Crystal Structure Of [nife] Hydrogenase From Alloch 1e-20
1e3d_B542 [nife] Hydrogenase From Desulfovibrio Desulfuricans 5e-22
1wuj_L534 Three-Dimensional Structure Of The Ni-B State Of [n 9e-21
1wuh_L534 Three-Dimensional Structure Of The Ni-A State Of [n 9e-21
2frv_L 536 Crystal Structure Of The Oxidized Form Of Ni-Fe Hyd 1e-23
1yrq_N 549 Structure Of The Ready Oxidized Form Of [nife]-Hydr 3e-21
3h3x_Q 549 Structure Of The V74m Large Subunit Mutant Of Ni-Fe 9e-21
1frf_L 564 Crystal Structure Of The Ni-Fe Hydrogenase From Des 3e-21
3cur_H 549 Structure Of A Double Methionine Mutant Of Ni-Fe Hy 1e-20
1yqw_Q 549 Structure Of The Oxidized Unready Form Of Ni-Fe Hyd 3e-21
1h2r_L 534 Three-Dimensional Structure Of Ni-Fe Hydrogenase Fr 2e-21
1h2a_L 567 Single Crystals Of Hydrogenase From Desulfovibrio V 2e-21
3cus_Q 549 Structure Of A Double IlePHE MUTANT OF NI-Fe Hydrog 2e-21
1ubh_L 534 Three-Dimensional Structure Of The Carbon Monoxide 2e-21
3myr_B 561 Crystal Structure Of [nife] Hydrogenase From Alloch 3e-22
1e3d_B 542 [nife] Hydrogenase From Desulfovibrio Desulfuricans 4e-21
1wuj_L 534 Three-Dimensional Structure Of The Ni-B State Of [n 2e-21
1wuh_L 534 Three-Dimensional Structure Of The Ni-A State Of [n 4e-20
gi|90109657|pdb|2FUG|4 Chain 4, Crystal Structure Of The Hydrophilic Domain Of Respiratory Complex I From Thermus Thermophilus Length = 409 Back     alignment and structure
 Score =  427 bits (1099), Expect = e-117,   Method: Composition-based stats.
 Identities = 180/394 (45%), Positives = 257/394 (65%), Gaps = 4/394 (1%)

Query: 3   KKKSRSFTINFGPQHPAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQAV 62
           + ++   T+N GPQHP+ HGVLRL++ L GE V  V PHIG LH G EK +E +T+LQ +
Sbjct: 20  ELRTEVMTLNVGPQHPSTHGVLRLMVTLSGEEVLEVVPHIGYLHTGFEKTMEHRTYLQNI 79

Query: 63  PYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQAMD 122
            Y  R+DY+     + AYALAVEKLLG  +P R + IRV+ +E+ R+ SHL+ + T  +D
Sbjct: 80  TYTPRMDYLHSFAHDLAYALAVEKLLGAVVPPRAETIRVILNELSRLASHLVFLGTGLLD 139

Query: 123 VGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSFPS 182
           +GALTP  + F ERE ++  +E  +G R H  Y R GGV +D+P E V ++    +  P 
Sbjct: 140 LGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGVKEDLPEEFVPELKKLLEVLPH 199

Query: 183 ALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECYSE 242
            +++   L   + IF +R   +G +  E A   G +G  +R SG  +D+RK+ PY  Y  
Sbjct: 200 RIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGSLRASGVNYDVRKAYPYSGYET 259

Query: 243 LDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPKRA 302
             FD+P+G+ GD +DR LVR+ EMRESVKII+Q + RL    + GPV   +P+I PP R 
Sbjct: 260 YTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALERL----EPGPVRDPNPQITPPPRH 315

Query: 303 DMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAPGY 362
            ++ SME++I+HFK YTEG+H P GEVY   E+ +GE G Y++SDGG+ PYR K+RAP +
Sbjct: 316 LLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGELGYYIVSDGGSMPYRVKVRAPSF 375

Query: 363 AHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR 396
            +LQ++ + CKG Q+ D+ AI+ SLD V G+VDR
Sbjct: 376 VNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR 409


>gi|5542158|pdb|1CC1|L Chain L, Crystal Structure Of A Reduced, Active Form Of The Ni-Fe-Se Hydrogenase From Desulfomicrobium Baculatum Length = 498 Back     alignment and structure
>gi|66361138|pdb|1YQ9|H Chain H, Structure Of The Unready Oxidized Form Of [nife] Hydrogenase Length = 536 Back     alignment and structure
>gi|1943536|pdb|1FRV|B Chain B, Crystal Structure Of The Oxidized Form Of Ni-Fe Hydrogenase Length = 536 Back     alignment and structure
>gi|3318795|pdb|2FRV|L Chain L, Crystal Structure Of The Oxidized Form Of Ni-Fe Hydrogenase Length = 536 Back     alignment and structure
>gi|254574956|pdb|3H3X|Q Chain Q, Structure Of The V74m Large Subunit Mutant Of Ni-Fe Hydrogenase In An Oxidized State Length = 549 Back     alignment and structure
>gi|6730012|pdb|1FRF|L Chain L, Crystal Structure Of The Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans Length = 564 Back     alignment and structure
>gi|195927486|pdb|3CUR|H Chain H, Structure Of A Double Methionine Mutant Of Ni-Fe Hydrogenase Length = 549 Back     alignment and structure
>gi|66361157|pdb|1YQW|Q Chain Q, Structure Of The Oxidized Unready Form Of Ni-Fe Hydrogenase Length = 549 Back     alignment and structure
>gi|6730443|pdb|1H2R|L Chain L, Three-Dimensional Structure Of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F In The Reduced Form At 1.4 A Resolution Length = 534 Back     alignment and structure
>gi|4558287|pdb|1H2A|L Chain L, Single Crystals Of Hydrogenase From Desulfovibrio Vulgaris Length = 567 Back     alignment and structure
>gi|195927492|pdb|3CUS|Q Chain Q, Structure Of A Double IlePHE MUTANT OF NI-Fe Hydrogenase Refined At 2.2 Angstrom Resolution Length = 549 Back     alignment and structure
>gi|30750150|pdb|1UBH|L Chain L, Three-Dimensional Structure Of The Carbon Monoxide Complex Of [nife]hydrogenase From Desulufovibrio Vulgaris Miyazaki F Length = 534 Back     alignment and structure
>gi|302148813|pdb|3MYR|B Chain B, Crystal Structure Of [nife] Hydrogenase From Allochromatium Vinosum In Its Ni-A State Length = 561 Back     alignment and structure
>gi|14719751|pdb|1E3D|B Chain B, [nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 Length = 542 Back     alignment and structure
>gi|85543891|pdb|1WUJ|L Chain L, Three-Dimensional Structure Of The Ni-B State Of [nife]hydrogenase From Desulufovibrio Vulgaris Miyazaki F Length = 534 Back     alignment and structure
>gi|85543887|pdb|1WUH|L Chain L, Three-Dimensional Structure Of The Ni-A State Of [nife]hydrogenase From Desulufovibrio Vulgaris Miyazaki F Length = 534 Back     alignment and structure
>gi|3318795|pdb|2FRV|L Chain L, Crystal Structure Of The Oxidized Form Of Ni-Fe Hydrogenase Length = 536 Back     alignment and structure
>gi|254574956|pdb|3H3X|Q Chain Q, Structure Of The V74m Large Subunit Mutant Of Ni-Fe Hydrogenase In An Oxidized State Length = 549 Back     alignment and structure
>gi|6730012|pdb|1FRF|L Chain L, Crystal Structure Of The Ni-Fe Hydrogenase From Desulfovibrio Fructosovorans Length = 564 Back     alignment and structure
>gi|195927486|pdb|3CUR|H Chain H, Structure Of A Double Methionine Mutant Of Ni-Fe Hydrogenase Length = 549 Back     alignment and structure
>gi|66361157|pdb|1YQW|Q Chain Q, Structure Of The Oxidized Unready Form Of Ni-Fe Hydrogenase Length = 549 Back     alignment and structure
>gi|6730443|pdb|1H2R|L Chain L, Three-Dimensional Structure Of Ni-Fe Hydrogenase From Desulfivibrio Vulgaris Miyazaki F In The Reduced Form At 1.4 A Resolution Length = 534 Back     alignment and structure
>gi|4558287|pdb|1H2A|L Chain L, Single Crystals Of Hydrogenase From Desulfovibrio Vulgaris Length = 567 Back     alignment and structure
>gi|195927492|pdb|3CUS|Q Chain Q, Structure Of A Double IlePHE MUTANT OF NI-Fe Hydrogenase Refined At 2.2 Angstrom Resolution Length = 549 Back     alignment and structure
>gi|30750150|pdb|1UBH|L Chain L, Three-Dimensional Structure Of The Carbon Monoxide Complex Of [nife]hydrogenase From Desulufovibrio Vulgaris Miyazaki F Length = 534 Back     alignment and structure
>gi|302148813|pdb|3MYR|B Chain B, Crystal Structure Of [nife] Hydrogenase From Allochromatium Vinosum In Its Ni-A State Length = 561 Back     alignment and structure
>gi|14719751|pdb|1E3D|B Chain B, [nife] Hydrogenase From Desulfovibrio Desulfuricans Atcc 27774 Length = 542 Back     alignment and structure
>gi|85543891|pdb|1WUJ|L Chain L, Three-Dimensional Structure Of The Ni-B State Of [nife]hydrogenase From Desulufovibrio Vulgaris Miyazaki F Length = 534 Back     alignment and structure
>gi|85543887|pdb|1WUH|L Chain L, Three-Dimensional Structure Of The Ni-A State Of [nife]hydrogenase From Desulufovibrio Vulgaris Miyazaki F Length = 534 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target396 NADH dehydrogenase subunit D [Candidatus Liberibacter a
3i9v_4409 NADH-quinone oxidoreductase subunit 4; electron transpo 1e-109
1cc1_L498 Hydrogenase (large subunit); NI-Fe-Se hydrogenase, oxid 3e-51
2wpn_B495 Periplasmic [nifese] hydrogenase, large subunit, seleno 4e-48
1wui_L 534 Periplasmic [NIFE] hydrogenase large subunit; high reso 1e-27
1yq9_H 536 Periplasmic [NIFE] hydrogenase large subunit; oxidoredu 3e-25
1yqw_Q 549 Periplasmic [NIFE] hydrogenase large subunit; NI-Fe hyd 4e-24
1wui_L534 Periplasmic [NIFE] hydrogenase large subunit; high reso 2e-13
1yqw_Q549 Periplasmic [NIFE] hydrogenase large subunit; NI-Fe hyd 2e-16
1e3d_B542 [NIFE] hydrogenase large subunit; molecular modelling, 6e-15
1yq9_H536 Periplasmic [NIFE] hydrogenase large subunit; oxidoredu 2e-13
1e3d_B 542 [NIFE] hydrogenase large subunit; molecular modelling, 8e-24
3myr_B 561 Nickel-dependent hydrogenase large subunit; [NIFE] hydr 5e-10
>3i9v_4 NADH-quinone oxidoreductase subunit 4; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_4* 3iam_4* 3ias_4* Length = 409 Back     alignment and structure
 Score =  391 bits (1004), Expect = e-109
 Identities = 180/395 (45%), Positives = 257/395 (65%), Gaps = 4/395 (1%)

Query: 2   DKKKSRSFTINFGPQHPAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQA 61
            + ++   T+N GPQHP+ HGVLRL++ L GE V  V PHIG LH G EK +E +T+LQ 
Sbjct: 19  KELRTEVMTLNVGPQHPSTHGVLRLMVTLSGEEVLEVVPHIGYLHTGFEKTMEHRTYLQN 78

Query: 62  VPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQAM 121
           + Y  R+DY+     + AYALAVEKLLG  +P R + IRV+ +E+ R+ SHL+ + T  +
Sbjct: 79  ITYTPRMDYLHSFAHDLAYALAVEKLLGAVVPPRAETIRVILNELSRLASHLVFLGTGLL 138

Query: 122 DVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSFP 181
           D+GALTP  + F ERE ++  +E  +G R H  Y R GGV +D+P E V ++    +  P
Sbjct: 139 DLGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGVKEDLPEEFVPELKKLLEVLP 198

Query: 182 SALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECYS 241
             +++   L   + IF +R   +G +  E A   G +G  +R SG  +D+RK+ PY  Y 
Sbjct: 199 HRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGSLRASGVNYDVRKAYPYSGYE 258

Query: 242 ELDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPKR 301
              FD+P+G+ GD +DR LVR+ EMRESVKII+Q + RL    + GPV   +P+I PP R
Sbjct: 259 TYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALERL----EPGPVRDPNPQITPPPR 314

Query: 302 ADMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAPG 361
             ++ SME++I+HFK YTEG+H P GEVY   E+ +GE G Y++SDGG+ PYR K+RAP 
Sbjct: 315 HLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGELGYYIVSDGGSMPYRVKVRAPS 374

Query: 362 YAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR 396
           + +LQ++ + CKG Q+ D+ AI+ SLD V G+VDR
Sbjct: 375 FVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR 409


>1cc1_L Hydrogenase (large subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfovibrio baculatus} SCOP: e.18.1.1 Length = 498 Back     alignment and structure
>2wpn_B Periplasmic [nifese] hydrogenase, large subunit, selenocysteine-containing; metal-binding, oxidoreductase, oxygen tolerance; HET: FSX SBY PSW; 2.04A {Desulfovibrio vulgaris} Length = 495 Back     alignment and structure
>1wui_L Periplasmic [NIFE] hydrogenase large subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str} SCOP: e.18.1.1 PDB: 1ubj_L 1ubh_L 1ubl_L 1ubm_L 1ubo_L 1ubr_L 1ubt_L 1ubu_L 1wuh_L* 1ubk_L* 1wuj_L 1wuk_L 1wul_L 1h2r_L 1h2a_L Length = 534 Back     alignment and structure
>1yq9_H Periplasmic [NIFE] hydrogenase large subunit; oxidoreductase; 2.35A {Desulfovibrio gigas} SCOP: e.18.1.1 PDB: 2frv_L 1frv_B Length = 536 Back     alignment and structure
>1yqw_Q Periplasmic [NIFE] hydrogenase large subunit; NI-Fe hydrogenase unready state, oxidoreductase; 1.83A {Desulfovibrio fructosovorans} PDB: 1yrq_H 3h3x_Q 3cus_Q 3cur_H 1frf_L Length = 549 Back     alignment and structure
>1wui_L Periplasmic [NIFE] hydrogenase large subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str} SCOP: e.18.1.1 PDB: 1ubj_L 1ubh_L 1ubl_L 1ubm_L 1ubo_L 1ubr_L 1ubt_L 1ubu_L 1wuh_L* 1ubk_L* 1wuj_L 1wuk_L 1wul_L 1h2r_L 1h2a_L Length = 534 Back     alignment and structure
>1yqw_Q Periplasmic [NIFE] hydrogenase large subunit; NI-Fe hydrogenase unready state, oxidoreductase; 1.83A {Desulfovibrio fructosovorans} PDB: 1yrq_H 3h3x_Q 3cus_Q 3cur_H 1frf_L Length = 549 Back     alignment and structure
>1e3d_B [NIFE] hydrogenase large subunit; molecular modelling, electron transfer; HET: FSX; 1.8A {Desulfovibrio desulfuricans} SCOP: e.18.1.1 Length = 542 Back     alignment and structure
>1yq9_H Periplasmic [NIFE] hydrogenase large subunit; oxidoreductase; 2.35A {Desulfovibrio gigas} SCOP: e.18.1.1 PDB: 2frv_L 1frv_B Length = 536 Back     alignment and structure
>1e3d_B [NIFE] hydrogenase large subunit; molecular modelling, electron transfer; HET: FSX; 1.8A {Desulfovibrio desulfuricans} SCOP: e.18.1.1 Length = 542 Back     alignment and structure
>3myr_B Nickel-dependent hydrogenase large subunit; [NIFE] hydrogenase, photosynthetic P sulfur bacterium, iron-sulfur cluster, NI-A state; HET: SF4; 2.10A {Allochromatium vinosum} Length = 561 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target396 NADH dehydrogenase subunit D [Candidatus Liberibacter a
3i9v_4409 NADH-quinone oxidoreductase subunit 4; electron transpo 100.0
1wui_L534 Periplasmic [NIFE] hydrogenase large subunit; high reso 100.0
2wpn_B495 Periplasmic [nifese] hydrogenase, large subunit, seleno 100.0
1cc1_L498 Hydrogenase (large subunit); NI-Fe-Se hydrogenase, oxid 100.0
1yqw_Q549 Periplasmic [NIFE] hydrogenase large subunit; NI-Fe hyd 100.0
1e3d_B542 [NIFE] hydrogenase large subunit; molecular modelling, 100.0
1yq9_H536 Periplasmic [NIFE] hydrogenase large subunit; oxidoredu 100.0
3myr_B561 Nickel-dependent hydrogenase large subunit; [NIFE] hydr 100.0
>3i9v_4 NADH-quinone oxidoreductase subunit 4; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_4* 3iam_4* 3ias_4* 3m9s_4* Back     alignment and structure
Probab=100.00  E-value=0  Score=653.85  Aligned_cols=390  Identities=45%  Similarity=0.831  Sum_probs=357.1

Q ss_pred             CCCCCEEEEEECCCCCCCCCCEEEEEEEECCEEEEEEEEECCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             44561599840686866677559999983998999998804115788987409898785544312123448889999999
Q gi|254780855|r    3 KKKSRSFTINFGPQHPAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQAVPYFDRLDYVAPMNQEHAYAL   82 (396)
Q Consensus         3 ~~~~~~~~~~~gp~~~~~~g~l~~~~~v~~~~V~~a~~~~g~~~RGfE~il~Gr~~~da~~it~RICGIC~~aH~~Aa~~   82 (396)
                      +.+++.|+|++||+||+++||+|++++||||+|+++++++||+|||||+||+||+|+|++.||+|||||||+||++|+++
T Consensus        20 ~~~~~~~~~~~Gp~hp~~~g~~r~~~~vdGe~V~~~~~~~G~~hRGfEkil~gr~~~~a~~i~~RICGiC~~aH~~A~~~   99 (409)
T 3i9v_4           20 ELRTEVMTLNVGPQHPSTHGVLRLMVTLSGEEVLEVVPHIGYLHTGFEKTMEHRTYLQNITYTPRMDYLHSFAHDLAYAL   99 (409)
T ss_dssp             ------CBCCBC-------CCCEECCBCSSSSCCBCCEECCTTCCCHHHHGGGSCTTGGGGTSTTSSSSSCHHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCCCCCCEEEEEEECCCEEEEEEEECCCCCHHHHHHHCCCCHHHHHHHCCCCCCCCHHHHHHHHHH
T ss_conf             45775699832898888888718999970989999788357643789999759996881002162012248689999999


Q ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCC
Q ss_conf             99998388578889999999999999998899987433430564189999999999997899755976476336536200
Q gi|254780855|r   83 AVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQAMDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVH  162 (396)
Q Consensus        83 AiE~a~gi~vp~~a~llR~Ll~~~e~i~sH~~h~~~l~~~~~~~~~~~~~~~~r~~~~~~~~~~gG~~~Hp~~~vpGGv~  162 (396)
                      |+|+|+|++||++++++|+|++++++||||++|+|.++.+++....+..+++.|++++++++.++|.++|+...++||+.
T Consensus       100 AvE~a~gi~vp~ra~~lR~ll~e~~~i~sHll~~~~l~~~~~~~~~~~~~~~~r~~~~~~~~~~~g~~~~~~~~~~ggv~  179 (409)
T 3i9v_4          100 AVEKLLGAVVPPRAETIRVILNELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGVK  179 (409)
T ss_dssp             HHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHSSSSSCCCBCSSBBS
T ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCEEECCCCCCCCEE
T ss_conf             99998299788789999999999999999999871236313561588889999999999999860763110331224430


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHCCEEEECCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCC
Q ss_conf             07898999999999999999999999998448333442122112303333102356651013676010210175443346
Q gi|254780855|r  163 QDIPPELVEDIGCWCDSFPSALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECYSE  242 (396)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~G~~~~~~g~~~~~r~~~~~~~~~~  242 (396)
                      ..++......+...++.......+..+++...+.+..+....|..........+..|+..++++++++.++..||..+..
T Consensus       180 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~g~g~~~~~~a~~~g~~~~~~~~~~v~~d~~~~~p~~~~~~  259 (409)
T 3i9v_4          180 EDLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGSLRASGVNYDVRKAYPYSGYET  259 (409)
T ss_dssp             SCCCTTHHHHHHHHHHHHHHHHHHHHHHHHSCTTHHHHHSSSSCBCHHHHHHHTCCSSSSGGGTCCCCHHHHSCCSSGGG
T ss_pred             ECCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHCCCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             36871677999999999999999999987508366763288600037889854877654566530343322366434566


Q ss_pred             CCCCCEEECCCCCHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             77540010123201221100011687589999999621035786720111123030448999975675430575557776
Q gi|254780855|r  243 LDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPKRADMKRSMESLIHHFKLYTEGY  322 (396)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~l~~~~~~~~~~~  322 (396)
                      .++...+...++.+++...+..+..+|..+..+...+.+....    ..............+....+.+........+..
T Consensus       260 ~~~~~~~~~~Gd~~~~~~v~~~~~~~s~~~~~~~~~~~~~g~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  335 (409)
T 3i9v_4          260 YTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALERLEPGPV----RDPNPQITPPPRHLLETSMEAVIYHFKHYTEGF  335 (409)
T ss_dssp             SCCCCCCCSSBCHHHHHHHHHHHHHHHHHHHHHHHHTCCCCCC----BCCCTTTSCCCGGGGGTCHHHHHHHHHHHHSCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC----CCCCHHHCCHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             6766677558862112122355555556778999975778761----000023130679999986664331354566677


Q ss_pred             CCCCCCEEEEEECCCCEEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHCCCCCCHHHHHHHHCCCCCCCCCC
Q ss_conf             15897489999889511799999879980889998358756868899997088057599989760912055359
Q gi|254780855|r  323 HVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAPGYAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR  396 (396)
Q Consensus       323 ~~~~G~GvG~vEAPRG~L~H~~~~~~~g~i~~~~ii~PT~~N~~~~e~al~G~~i~D~~~iirSfDpC~sC~dr  396 (396)
                      ++|+|+|+|+||||||+|+|||++|++|+|++||||+||+||++++|++|+|++++|++++|||||||+|||||
T Consensus       336 ~~p~Geg~g~vEAPRG~L~H~~~~d~~G~i~~~~ii~PT~~N~~~le~al~G~~i~D~~~iirS~DpC~sc~dr  409 (409)
T 3i9v_4          336 HPPKGEVYVPTESARGELGYYIVSDGGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR  409 (409)
T ss_dssp             CCCSEEEECCEEETTEEEEEEEEECSSSSCSEEEEECHHHHTTTTTTTTTSSSCSGGGTHHHHTTCCCHHHHHC
T ss_pred             CCCCCEEEEEEECCCEEEEEEEEECCCCEEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCC
T ss_conf             58986799999858710899999979984999999898888999999997799178999998525975237789



>1wui_L Periplasmic [NIFE] hydrogenase large subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str} SCOP: e.18.1.1 PDB: 1ubj_L 1ubh_L 1ubl_L 1ubm_L 1ubo_L 1ubr_L 1ubt_L 1ubu_L 1wuh_L* 1ubk_L* 1wuj_L 1wuk_L 1wul_L 1h2r_L 1h2a_L Back     alignment and structure
>2wpn_B Periplasmic [nifese] hydrogenase, large subunit, selenocysteine-containing; metal-binding, oxidoreductase, oxygen tolerance; HET: FSX SBY PSW; 2.04A {Desulfovibrio vulgaris} Back     alignment and structure
>1cc1_L Hydrogenase (large subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfomicrobium baculatum} SCOP: e.18.1.1 Back     alignment and structure
>1yqw_Q Periplasmic [NIFE] hydrogenase large subunit; NI-Fe hydrogenase unready state, oxidoreductase; 1.83A {Desulfovibrio fructosovorans} PDB: 1yrq_H 3h3x_Q 3cus_Q 3cur_H 1frf_L Back     alignment and structure
>1e3d_B [NIFE] hydrogenase large subunit; molecular modelling, electron transfer; HET: FSX; 1.8A {Desulfovibrio desulfuricans} SCOP: e.18.1.1 Back     alignment and structure
>1yq9_H Periplasmic [NIFE] hydrogenase large subunit; oxidoreductase; 2.35A {Desulfovibrio gigas} SCOP: e.18.1.1 PDB: 2frv_L 1frv_B Back     alignment and structure
>3myr_B Nickel-dependent hydrogenase large subunit; [NIFE] hydrogenase, photosynthetic P sulfur bacterium, iron-sulfur cluster, NI-A state; HET: SF4; 2.10A {Allochromatium vinosum} Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 396 NADH dehydrogenase subunit D [Candidatus Liberibacter a
d2fug41375 e.18.1.2 (4:35-409) NADH-quinone oxidoreductase chain 4 1e-111
d1cc1l_487 e.18.1.1 (L:) Nickel-iron hydrogenase, large subunit {D 1e-52
d1wuil1534 e.18.1.1 (L:19-552) Nickel-iron hydrogenase, large subu 3e-23
d1yq9h1530 e.18.1.1 (H:7-536) Nickel-iron hydrogenase, large subun 2e-27
d1frfl_ 543 e.18.1.1 (L:) Nickel-iron hydrogenase, large subunit {D 4e-28
d1frfl_543 e.18.1.1 (L:) Nickel-iron hydrogenase, large subunit {D 1e-20
d1e3db_ 537 e.18.1.1 (B:) Nickel-iron hydrogenase, large subunit {D 8e-28
d1wuil1 534 e.18.1.1 (L:19-552) Nickel-iron hydrogenase, large subu 2e-27
d1yq9h1 530 e.18.1.1 (H:7-536) Nickel-iron hydrogenase, large subun 4e-27
d1e3db_537 e.18.1.1 (B:) Nickel-iron hydrogenase, large subunit {D 2e-18
>d2fug41 e.18.1.2 (4:35-409) NADH-quinone oxidoreductase chain 4, Nqo4 {Thermus thermophilus [TaxId: 274]} Length = 375 Back     information, alignment and structure

class: Multi-domain proteins (alpha and beta)
fold: HydB/Nqo4-like
superfamily: HydB/Nqo4-like
family: Nqo4-like
domain: NADH-quinone oxidoreductase chain 4, Nqo4
species: Thermus thermophilus [TaxId: 274]
 Score =  394 bits (1013), Expect = e-111
 Identities = 174/379 (45%), Positives = 247/379 (65%), Gaps = 4/379 (1%)

Query: 18  PAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQAVPYFDRLDYVAPMNQE 77
           P+ HGVLRL++ L GE V  V PHIG LH G EK +E +T+LQ + Y  R+DY+     +
Sbjct: 1   PSTHGVLRLMVTLSGEEVLEVVPHIGYLHTGFEKTMEHRTYLQNITYTPRMDYLHSFAHD 60

Query: 78  HAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQAMDVGALTPPLWGFEERE 137
            AYALAVEKLLG  +P R + IRV+ +E+ R+ SHL+ + T  +D+GALTP  + F ERE
Sbjct: 61  LAYALAVEKLLGAVVPPRAETIRVILNELSRLASHLVFLGTGLLDLGALTPFFYAFRERE 120

Query: 138 KLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWCDSFPSALNDISDLLTGNRIF 197
            ++  +E  +G R H  Y R GGV +D+P E V ++    +  P  +++   L   + IF
Sbjct: 121 TILDLFEWVTGQRFHHNYIRIGGVKEDLPEEFVPELKKLLEVLPHRIDEYEALFAESPIF 180

Query: 198 KQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECYSELDFDIPIGKHGDCYD 257
            +R   +G +  E A   G +G  +R SG  +D+RK+ PY  Y    FD+P+G+ GD +D
Sbjct: 181 YERARGVGVIPPEVAIDLGLTGGSLRASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFD 240

Query: 258 RYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPKRADMKRSMESLIHHFKL 317
           R LVR+ EMRESVKII+Q + RL    + GPV   +P+I PP R  ++ SME++I+HFK 
Sbjct: 241 RMLVRIREMRESVKIIKQALERL----EPGPVRDPNPQITPPPRHLLETSMEAVIYHFKH 296

Query: 318 YTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAPGYAHLQAMEFLCKGHQL 377
           YTEG+H P GEVY   E+ +GE G Y++SDGG+ PYR K+RAP + +LQ++ + CKG Q+
Sbjct: 297 YTEGFHPPKGEVYVPTESARGELGYYIVSDGGSMPYRVKVRAPSFVNLQSLPYACKGEQV 356

Query: 378 ADVSAILGSLDIVFGEVDR 396
            D+ AI+ SLD V G+VDR
Sbjct: 357 PDMVAIIASLDPVMGDVDR 375


>d1cc1l_ e.18.1.1 (L:) Nickel-iron hydrogenase, large subunit {Desulfomicrobium baculatum [TaxId: 899]} Length = 487 Back     information, alignment and structure
>d1wuil1 e.18.1.1 (L:19-552) Nickel-iron hydrogenase, large subunit {Desulfovibrio vulgaris [TaxId: 881]} Length = 534 Back     information, alignment and structure
>d1yq9h1 e.18.1.1 (H:7-536) Nickel-iron hydrogenase, large subunit {Desulfovibrio gigas [TaxId: 879]} Length = 530 Back     information, alignment and structure
>d1frfl_ e.18.1.1 (L:) Nickel-iron hydrogenase, large subunit {Desulfovibrio fructosovorans [TaxId: 878]} Length = 543 Back     information, alignment and structure
>d1frfl_ e.18.1.1 (L:) Nickel-iron hydrogenase, large subunit {Desulfovibrio fructosovorans [TaxId: 878]} Length = 543 Back     information, alignment and structure
>d1e3db_ e.18.1.1 (B:) Nickel-iron hydrogenase, large subunit {Desulfovibrio desulfuricans [TaxId: 876]} Length = 537 Back     information, alignment and structure
>d1wuil1 e.18.1.1 (L:19-552) Nickel-iron hydrogenase, large subunit {Desulfovibrio vulgaris [TaxId: 881]} Length = 534 Back     information, alignment and structure
>d1yq9h1 e.18.1.1 (H:7-536) Nickel-iron hydrogenase, large subunit {Desulfovibrio gigas [TaxId: 879]} Length = 530 Back     information, alignment and structure
>d1e3db_ e.18.1.1 (B:) Nickel-iron hydrogenase, large subunit {Desulfovibrio desulfuricans [TaxId: 876]} Length = 537 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target396 NADH dehydrogenase subunit D [Candidatus Liberibacter a
d2fug41375 NADH-quinone oxidoreductase chain 4, Nqo4 {Thermus ther 100.0
d1yq9h1530 Nickel-iron hydrogenase, large subunit {Desulfovibrio g 100.0
d1cc1l_487 Nickel-iron hydrogenase, large subunit {Desulfomicrobiu 100.0
d1frfl_543 Nickel-iron hydrogenase, large subunit {Desulfovibrio f 100.0
d1wuil1534 Nickel-iron hydrogenase, large subunit {Desulfovibrio v 100.0
d1e3db_537 Nickel-iron hydrogenase, large subunit {Desulfovibrio d 100.0
>d2fug41 e.18.1.2 (4:35-409) NADH-quinone oxidoreductase chain 4, Nqo4 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
class: Multi-domain proteins (alpha and beta)
fold: HydB/Nqo4-like
superfamily: HydB/Nqo4-like
family: Nqo4-like
domain: NADH-quinone oxidoreductase chain 4, Nqo4
species: Thermus thermophilus [TaxId: 274]
Probab=100.00  E-value=0  Score=643.13  Aligned_cols=375  Identities=45%  Similarity=0.805  Sum_probs=339.1

Q ss_pred             CCCCCCEEEEEEEECCEEEEEEEEECCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             66677559999983998999998804115788987409898785544312123448889999999999983885788899
Q gi|254780855|r   18 PAAHGVLRLILELDGEIVERVDPHIGLLHRGTEKLIETKTFLQAVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQ   97 (396)
Q Consensus        18 ~~~~g~l~~~~~v~~~~V~~a~~~~g~~~RGfE~il~Gr~~~da~~it~RICGIC~~aH~~Aa~~AiE~a~gi~vp~~a~   97 (396)
                      |..|||+|++++||||+|+||++++|++|||||+||+||+|+|++.||+|||||||+||++|+++|+|+|+|++||++++
T Consensus         1 p~~hG~~r~~~~v~ge~V~~a~~~ig~~~RGfEk~l~Gr~~~da~~i~~RICGIC~~aH~~A~~~AlE~a~gv~~p~~a~   80 (375)
T d2fug41           1 PSTHGVLRLMVTLSGEEVLEVVPHIGYLHTGFEKTMEHRTYLQNITYTPRMDYLHSFAHDLAYALAVEKLLGAVVPPRAE   80 (375)
T ss_dssp             CEEECSSSCEEEECCSSSCCEEEECCTTCCCHHHHGGGSCHHHHHHHGGGTTSSSHHHHHHHHHHHHHHHTTCCCCHHHH
T ss_pred             CCCCCEEEEEEEECCCEEEEEEEEECCCCHHHHHHHCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHH
T ss_conf             99885289999976988999898306652689998749996882212063111038799999999999991998899999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCCCCHHHHHHHHHHH
Q ss_conf             99999999999998899987433430564189999999999997899755976476336536200078989999999999
Q gi|254780855|r   98 LIRVLYSEIGRILSHLLNVTTQAMDVGALTPPLWGFEEREKLMVFYERASGSRMHAAYFRPGGVHQDIPPELVEDIGCWC  177 (396)
Q Consensus        98 llR~Ll~~~e~i~sH~~h~~~l~~~~~~~~~~~~~~~~r~~~~~~~~~~gG~~~Hp~~~vpGGv~~~~~~~~~~~~~~~~  177 (396)
                      ++|+|++++|+||||++|||+++.+++....+...+++++.++++++.++|+++|+++++|||+++.++...+..+...+
T Consensus        81 ~lR~l~~~~e~i~sH~l~~~~l~~~~~~~~~~~~~~~~r~~~~~~~~~~~G~~~h~~~~~~gG~~~~~~~~~~~~~~~~~  160 (375)
T d2fug41          81 TIRVILNELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGVKEDLPEEFVPELKKLL  160 (375)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHTSSSSSCCCEETTEESSCCCTTHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEECCEECCCEEECCCHHHHHHHHHHH
T ss_conf             99999999988767999999834520024388899999899999999846865520521202302279867889999998


Q ss_pred             HHHHHHHHHHHHHHHCCHHHHHHHCCEEEECCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCEEECCCCCHH
Q ss_conf             99999999999998448333442122112303333102356651013676010210175443346775400101232012
Q gi|254780855|r  178 DSFPSALNDISDLLTGNRIFKQRNVNIGTVKLEDAWGWGFSGVMIRGSGAAWDLRKSQPYECYSELDFDIPIGKHGDCYD  257 (396)
Q Consensus       178 ~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~G~~~~~~g~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~  257 (396)
                      +...+.+.+..+++...+.+..++...+..........+..|+..+.+|.+.+.++..++..+...++...+...+++++
T Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~  240 (375)
T d2fug41         161 EVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGSLRASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFD  240 (375)
T ss_dssp             TTTTTTTHHHHHHHSSCSCCTTSCSCCCCSSSCSTTTTTTCCSSCCSSCCTTTTTCCSSCCCC-----CCCCCCSSSSHH
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             76088778898740367500002577533451023315765554555642133120067554556565534424776432


Q ss_pred             HHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCC
Q ss_conf             21100011687589999999621035786720111123030448999975675430575557776158974899998895
Q gi|254780855|r  258 RYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKIVPPKRADMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPK  337 (396)
Q Consensus       258 ~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~l~~~~~~~~~~~~~~~G~GvG~vEAPR  337 (396)
                      +...+..+..++..+..+...+..................    ..+....+..........+.+++|+|+|+|+|||||
T Consensus       241 ~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~G~g~g~vEApR  316 (375)
T d2fug41         241 RMLVRIREMRESVKIIKQALERLEPGPVRDPNPQITPPPR----HLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESAR  316 (375)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSCCCSCCBCCCTTTSCCCT----TCTTTCTTHHHHHHHHHHSCCCCCSCCCCCCBCCSS
T ss_pred             CCHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCHHHCCHHH----HHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECCC
T ss_conf             1021344442146899989974889874434411033569----999755454101344456677689957999997488


Q ss_pred             CEEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHCCCCCCHHHHHHHHCCCCCCCCCC
Q ss_conf             11799999879980889998358756868899997088057599989760912055359
Q gi|254780855|r  338 GEFGVYLISDGGNKPYRCKIRAPGYAHLQAMEFLCKGHQLADVSAILGSLDIVFGEVDR  396 (396)
Q Consensus       338 G~L~H~~~~~~~g~i~~~~ii~PT~~N~~~~e~al~G~~i~D~~~iirSfDpC~sC~dr  396 (396)
                      |+|+|||++|++|+|++||||+||+||++++|++|+|++++|+++++||||||+|||||
T Consensus       317 G~L~H~~~~d~~g~i~~~~ii~PT~~N~~~~e~al~G~~i~D~~~iirSfDpC~sC~dr  375 (375)
T d2fug41         317 GELGYYIVSDGGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR  375 (375)
T ss_dssp             SCBCEEEECCSSSSCSEEEECCSHHHHTTTHHHHTTTSCGGGTTHHHHTTCCCHHHHHC
T ss_pred             EEEEEEEEECCCCCEEEEEEECCCHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCC
T ss_conf             67999999989981899999898877999999996799167899998567976447898



>d1yq9h1 e.18.1.1 (H:7-536) Nickel-iron hydrogenase, large subunit {Desulfovibrio gigas [TaxId: 879]} Back     information, alignment and structure
>d1cc1l_ e.18.1.1 (L:) Nickel-iron hydrogenase, large subunit {Desulfomicrobium baculatum [TaxId: 899]} Back     information, alignment and structure
>d1frfl_ e.18.1.1 (L:) Nickel-iron hydrogenase, large subunit {Desulfovibrio fructosovorans [TaxId: 878]} Back     information, alignment and structure
>d1wuil1 e.18.1.1 (L:19-552) Nickel-iron hydrogenase, large subunit {Desulfovibrio vulgaris [TaxId: 881]} Back     information, alignment and structure
>d1e3db_ e.18.1.1 (B:) Nickel-iron hydrogenase, large subunit {Desulfovibrio desulfuricans [TaxId: 876]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 396 NADH dehydrogenase subunit D [Candidatus Liberibac
3i9v_4_109-308_384-409226 (4:109-308,4:384-409) NADH-quinone oxidoreductase 3e-64
1yq9_H_56-492437 (H:56-492) Periplasmic [NIFE] hydrogenase large su 2e-50
1yq9_H_56-492437 (H:56-492) Periplasmic [NIFE] hydrogenase large su 4e-17
3i9v_4_76-108_309-383108 (4:76-108,4:309-383) NADH-quinone oxidoreductase s 1e-30
3i9v_4_76-108_309-383108 (4:76-108,4:309-383) NADH-quinone oxidoreductase s 4e-14
1wui_L_47-490444 (L:47-490) Periplasmic [NIFE] hydrogenase large su 2e-28
1wui_L_47-490444 (L:47-490) Periplasmic [NIFE] hydrogenase large su 5e-28
2wpn_B_84-224_327-388203 (B:84-224,B:327-388) Periplasmic [nifese] hydrogen 9e-23
3i9v_4_1-7575 (4:1-75) NADH-quinone oxidoreductase subunit 4; el 2e-20
1cc1_L_61-92_242-280_406-454120 (L:61-92,L:242-280,L:406-454) Hydrogenase (large s 1e-04
>3i9v_4 (4:109-308,4:384-409) NADH-quinone oxidoreductase subunit 4; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_4* 3iam_4* 3ias_4*Length = 226 Back     alignment and structure
 Score =  239 bits (612), Expect = 3e-64
 Identities = 77/198 (38%), Positives = 116/198 (58%)

Query: 92  IPIRGQLIRVLYSEIGRILSHLLNVTTQAMDVGALTPPLWGFEEREKLMVFYERASGSRM 151
           +P R + IRV+ +E+ R+ SHL+ + T  +D+GALTP  + F ERE ++  +E  +G R 
Sbjct: 1   VPPRAETIRVILNELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRF 60

Query: 152 HAAYFRPGGVHQDIPPELVEDIGCWCDSFPSALNDISDLLTGNRIFKQRNVNIGTVKLED 211
           H  Y R GGV +D+P E V ++    +  P  +++   L   + IF +R   +G +  E 
Sbjct: 61  HHNYIRIGGVKEDLPEEFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEV 120

Query: 212 AWGWGFSGVMIRGSGAAWDLRKSQPYECYSELDFDIPIGKHGDCYDRYLVRMMEMRESVK 271
           A   G +G  +R SG  +D+RK+ PY  Y    FD+P+G+ GD +DR LVR+ EMRESVK
Sbjct: 121 AIDLGLTGGSLRASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVK 180

Query: 272 IIRQCVNRLLGKNKVGPV 289
           II+Q + RL       P 
Sbjct: 181 IIKQALERLEPGPVRDPN 198


>1yq9_H (H:56-492) Periplasmic [NIFE] hydrogenase large subunit; oxidoreductase; 2.35A {Desulfovibrio gigas}Length = 437 Back     alignment and structure
>1yq9_H (H:56-492) Periplasmic [NIFE] hydrogenase large subunit; oxidoreductase; 2.35A {Desulfovibrio gigas}Length = 437 Back     alignment and structure
>3i9v_4 (4:76-108,4:309-383) NADH-quinone oxidoreductase subunit 4; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_4* 3iam_4* 3ias_4*Length = 108 Back     alignment and structure
>3i9v_4 (4:76-108,4:309-383) NADH-quinone oxidoreductase subunit 4; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_4* 3iam_4* 3ias_4*Length = 108 Back     alignment and structure
>1wui_L (L:47-490) Periplasmic [NIFE] hydrogenase large subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str}Length = 444 Back     alignment and structure
>1wui_L (L:47-490) Periplasmic [NIFE] hydrogenase large subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str}Length = 444 Back     alignment and structure
>3i9v_4 (4:1-75) NADH-quinone oxidoreductase subunit 4; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_4* 3iam_4* 3ias_4*Length = 75 Back     alignment and structure
>1cc1_L (L:61-92,L:242-280,L:406-454) Hydrogenase (large subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfovibrio baculatus}Length = 120 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target396 NADH dehydrogenase subunit D [Candidatus Liberibacter a
1wui_L_47-490444 Periplasmic [NIFE] hydrogenase large subunit; high 100.0
1yq9_H_56-492437 Periplasmic [NIFE] hydrogenase large subunit; oxid 100.0
3i9v_4_109-308_384-409226 NADH-quinone oxidoreductase subunit 4; electron tr 99.95
1cc1_L_93-241_281-405274 Hydrogenase (large subunit); NI-Fe-Se hydrogenase, 99.9
1yqw_Q_95-282_382-458265 Periplasmic [NIFE] hydrogenase large subunit; NI-F 99.78
1yqw_Q_63-94_283-381_459-505178 Periplasmic [NIFE] hydrogenase large subunit; NI-F 99.93
1cc1_L_61-92_242-280_406-454120 Hydrogenase (large subunit); NI-Fe-Se hydrogenase, 99.87
1e3d_B_62-93_451-50789 [NIFE] hydrogenase large subunit; molecular modell 99.84
3i9v_4_76-108_309-383108 NADH-quinone oxidoreductase subunit 4; electron tr 98.89
2wpn_B_52-83_389-42872 Periplasmic [nifese] hydrogenase, large subunit, s 98.87
2wpn_B_84-224_327-388203 Periplasmic [nifese] hydrogenase, large subunit, s 99.6
1yq9_H_56-492437 Periplasmic [NIFE] hydrogenase large subunit; oxid 99.54
3i9v_4_1-7575 NADH-quinone oxidoreductase subunit 4; electron tr 99.26
1yq9_H_1-55_493-53699 Periplasmic [NIFE] hydrogenase large subunit; oxid 99.08
1cc1_L_1-60_455-498104 Hydrogenase (large subunit); NI-Fe-Se hydrogenase, 99.07
1yqw_Q_1-62_506-549106 Periplasmic [NIFE] hydrogenase large subunit; NI-F 99.06
1e3d_B_1-6161 [NIFE] hydrogenase large subunit; molecular modell 99.04
1wui_L_1-46_491-53490 Periplasmic [NIFE] hydrogenase large subunit; high 98.82
2wpn_B_1-51_429-482105 Periplasmic [nifese] hydrogenase, large subunit, s 98.78
2wpn_B_1-51_429-482105 Periplasmic [nifese] hydrogenase, large subunit, s 98.97
1cc1_L_1-60_455-498104 Hydrogenase (large subunit); NI-Fe-Se hydrogenase, 98.8
1yq9_H_1-55_493-53699 Periplasmic [NIFE] hydrogenase large subunit; oxid 98.77
1yqw_Q_1-62_506-549106 Periplasmic [NIFE] hydrogenase large subunit; NI-F 98.75
1wui_L_1-46_491-53490 Periplasmic [NIFE] hydrogenase large subunit; high 98.71
2wpn_B_52-83_389-42872 Periplasmic [nifese] hydrogenase, large subunit, s 98.83
1e3d_B_94-128_239-279_375-450152 [NIFE] hydrogenase large subunit; molecular modell 98.52
>1wui_L (L:47-490) Periplasmic [NIFE] hydrogenase large subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str} Back     alignment and structure
Probab=100.00  E-value=0  Score=360.70  Aligned_cols=288  Identities=11%  Similarity=-0.014  Sum_probs=219.7

Q ss_pred             HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH----
Q ss_conf             4098987855443121234488899999999999838857888999999999999999889998743343056418----
Q gi|254780855|r   53 IETKTFLQAVPYFDRLDYVAPMNQEHAYALAVEKLLGIEIPIRGQLIRVLYSEIGRILSHLLNVTTQAMDVGALTP----  128 (396)
Q Consensus        53 l~Gr~~~da~~it~RICGIC~~aH~~Aa~~AiE~a~gi~vp~~a~llR~Ll~~~e~i~sH~~h~~~l~~~~~~~~~----  128 (396)
                      |+||+|+|++.+|+|||||||++|++|+++|+|+|+||+||++|+++|+|++++|+|+||++|+|.++.+++....    
T Consensus         1 l~gr~~~~~~~~~~Ricgic~~~h~~a~~~a~e~~~gi~~p~~a~~~R~i~~~~eri~~hl~~~~~~~~~~~~~~~~~~~   80 (444)
T 1wui_L            1 LKGRDPRDAQHFTQRTCGVXTYTHALASTRCVDNAVGVHIPKNATYIRNLVLGAQYLHDHIVHFYHLHALDFVDVTAALK   80 (444)
T ss_dssp             HTTSCGGGHHHHHHTTCSSSTTHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGTCCTGGGGG
T ss_pred             HCCCCHHHHHHHHHHHHEECHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHCCCCCCCC
T ss_conf             67999789776742000417878999999999998299889889999999999999998998998762223136632443


Q ss_pred             -------------------------------------------------------------------HHHHHHHHHHHHH
Q ss_conf             -------------------------------------------------------------------9999999999997
Q gi|254780855|r  129 -------------------------------------------------------------------PLWGFEEREKLMV  141 (396)
Q Consensus       129 -------------------------------------------------------------------~~~~~~~r~~~~~  141 (396)
                                                                                         +.......+...+
T Consensus        81 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (444)
T 1wui_L           81 ADPAKAAKVASSISPRKTTAADLKAVQDKLKTFVETGQLGPFTNAYFLGGHPAYYLDPETNLIATAHYLEALRLQVKAAR  160 (444)
T ss_dssp             CCHHHHHHHHHHHSSSCCCHHHHHHHHHHHHHHHHTTCCGGGTTCTTTTCCTTCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             57467999864127522346779999899999886400477665434578751347710003567789999999999999


Q ss_pred             HHHHHCCCCCCCCEEEECCCCCCCCHHHHHH--HHHHHHHHHHHHHH--------HHHHHHC------------------
Q ss_conf             8997559764763365362000789899999--99999999999999--------9999844------------------
Q gi|254780855|r  142 FYERASGSRMHAAYFRPGGVHQDIPPELVED--IGCWCDSFPSALND--------ISDLLTG------------------  193 (396)
Q Consensus       142 ~~~~~gG~~~Hp~~~vpGGv~~~~~~~~~~~--~~~~~~~~~~~~~~--------~~~~~~~------------------  193 (396)
                      .++.++|+.+|+...+++|.+......+...  .....+....+..+        ....+.+                  
T Consensus       161 ~i~~l~~~~~~~~~~~~~~~~~~g~~~d~r~~~~~~~~~e~~~~~~~~~~r~~~r~~e~~~s~~~~~~~~~~~~~~~~~~  240 (444)
T 1wui_L          161 AMAVFGAKNPHTQFTVVGGVTCYDALTPQRIAEFEALWKETKAFVDEVYIPDLLVVAAAYKDWTQYGGTDNFITFGEFPK  240 (444)
T ss_dssp             HHHHHHSCSSSCCCEETTEECCGGGGSHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTGGGGGSCCCSCEEEEEEEES
T ss_pred             HHHHHCCCCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHCCCCCCCCCHHHCCC
T ss_conf             99997288745550002654246788889999999999999999999999899999875401665178654220200356


Q ss_pred             --------------------------------------------------------CHHHHHHHCCEEEECCCCCCCCCC
Q ss_conf             --------------------------------------------------------833344212211230333310235
Q gi|254780855|r  194 --------------------------------------------------------NRIFKQRNVNIGTVKLEDAWGWGF  217 (396)
Q Consensus       194 --------------------------------------------------------~~~~~~~~~~~g~~~~~~~~~~~~  217 (396)
                                                                              ......+....+.........++.
T Consensus       241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~g~~~~~~a~~~~~  320 (444)
T 1wui_L          241 DEYDLNSRFFKPGVVFKRDFKNIKPFDKMQIEEHVRHSWYEGAEARHPWKGQTQPKYTDLHGDDRYSWMKAPRYMGEPME  320 (444)
T ss_dssp             STTCGGGEEEEEEEESTTCTTSCBCCCGGGEEEECTTBTBSSSCCBCGGGCCCCBCCCCTTBTTBCBSSCEEEETTBCCB
T ss_pred             CCCCCHHCEECCCEEECCCCCEECCCCHHHHHCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCCCCCCEE
T ss_conf             55530111003654885875410455726643045166515864247666666665222466565300125312896536


Q ss_pred             CCCCCCCCCC-CCHHHHCCCCCCCCCCCCCCEEECCCCCHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHH
Q ss_conf             6651013676-010210175443346775400101232012211000116875899999996210357867201111230
Q gi|254780855|r  218 SGVMIRGSGA-AWDLRKSQPYECYSELDFDIPIGKHGDCYDRYLVRMMEMRESVKIIRQCVNRLLGKNKVGPVSASDPKI  296 (396)
Q Consensus       218 ~G~~~~~~g~-~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~  296 (396)
                      +||.+|.+|. .++.|+..||..|...++...+...++++++..+|..+..+|..+.++++++.+....           
T Consensus       321 ~Gp~AR~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~gd~~~R~~~R~~E~~~s~~~i~~~l~~~~~~~~-----------  389 (444)
T 1wui_L          321 TGPLAQVLIAYSQGHPKVKAVTDAVLAKLGVGPEALFSTLGRTAARGIETAVIAEYVGVMLQEYKDNIA-----------  389 (444)
T ss_dssp             CSHHHHHHHHHHTTCHHHHHHHHHHHHHHTCCGGGGSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------
T ss_pred             ECHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-----------
T ss_conf             223788766543067448999999998649987665888999999999999999999999996352144-----------


Q ss_pred             CCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCEEEEEEEECCCCCEEEEEEECCCCCCHHH
Q ss_conf             30448999975675430575557776158974899998895117999998799808899983587568688
Q gi|254780855|r  297 VPPKRADMKRSMESLIHHFKLYTEGYHVPVGEVYAAVEAPKGEFGVYLISDGGNKPYRCKIRAPGYAHLQA  367 (396)
Q Consensus       297 ~~~~~~~~~~~~e~l~~~~~~~~~~~~~~~G~GvG~vEAPRG~L~H~~~~~~~g~i~~~~ii~PT~~N~~~  367 (396)
                                     ........+...+++|+|+|++|||||+|+||+++| ||||++|||++||+||++|
T Consensus       390 ---------------~~~~~~~~~~~~~~~g~g~g~~EapRG~l~h~~~~~-~gki~~~~i~~Pt~~N~~p  444 (444)
T 1wui_L          390 ---------------KGDNVICAPWEMPKQAEGVGFVNAPRGGLSHWIRIE-DGKIGNFQLVVPSTWTLGP  444 (444)
T ss_dssp             ---------------TTCCCCBCCCCCCSSEEEEEEEEETTEEEEEEEEEE-TTEEEEEEEECHHHHHHCC
T ss_pred             ---------------CCCCCCCCCCCCCCCEEEEEEEECCCEEEEEEEEEE-CCEEEEEEEECCCCCCCCC
T ss_conf             ---------------578642377779986189999988875179999981-9989798898987021564



>1yq9_H (H:56-492) Periplasmic [NIFE] hydrogenase large subunit; oxidoreductase; 2.35A {Desulfovibrio gigas} Back     alignment and structure
>3i9v_4 (4:109-308,4:384-409) NADH-quinone oxidoreductase subunit 4; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_4* 3iam_4* 3ias_4* Back     alignment and structure
>1cc1_L (L:93-241,L:281-405) Hydrogenase (large subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfovibrio baculatus} Back     alignment and structure
>1yqw_Q (Q:95-282,Q:382-458) Periplasmic [NIFE] hydrogenase large subunit; NI-Fe hydrogenase unready state, oxidoreductase; 1.83A {Desulfovibrio fructosovorans} PDB: 1yrq_H 3h3x_Q 3cus_Q 3cur_H 1frf_L Back     alignment and structure
>1yqw_Q (Q:63-94,Q:283-381,Q:459-505) Periplasmic [NIFE] hydrogenase large subunit; NI-Fe hydrogenase unready state, oxidoreductase; 1.83A {Desulfovibrio fructosovorans} PDB: 1yrq_H 3h3x_Q 3cus_Q 3cur_H 1frf_L Back     alignment and structure
>1cc1_L (L:61-92,L:242-280,L:406-454) Hydrogenase (large subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfovibrio baculatus} Back     alignment and structure
>1e3d_B (B:62-93,B:451-507) [NIFE] hydrogenase large subunit; molecular modelling, electron transfer; HET: FSX; 1.8A {Desulfovibrio desulfuricans} Back     alignment and structure
>3i9v_4 (4:76-108,4:309-383) NADH-quinone oxidoreductase subunit 4; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_4* 3iam_4* 3ias_4* Back     alignment and structure
>1yq9_H (H:56-492) Periplasmic [NIFE] hydrogenase large subunit; oxidoreductase; 2.35A {Desulfovibrio gigas} Back     alignment and structure
>3i9v_4 (4:1-75) NADH-quinone oxidoreductase subunit 4; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_4* 3iam_4* 3ias_4* Back     alignment and structure
>1yq9_H (H:1-55,H:493-536) Periplasmic [NIFE] hydrogenase large subunit; oxidoreductase; 2.35A {Desulfovibrio gigas} Back     alignment and structure
>1cc1_L (L:1-60,L:455-498) Hydrogenase (large subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfovibrio baculatus} Back     alignment and structure
>1yqw_Q (Q:1-62,Q:506-549) Periplasmic [NIFE] hydrogenase large subunit; NI-Fe hydrogenase unready state, oxidoreductase; 1.83A {Desulfovibrio fructosovorans} PDB: 1yrq_H 3h3x_Q 3cus_Q 3cur_H 1frf_L Back     alignment and structure
>1e3d_B (B:1-61) [NIFE] hydrogenase large subunit; molecular modelling, electron transfer; HET: FSX; 1.8A {Desulfovibrio desulfuricans} Back     alignment and structure
>1wui_L (L:1-46,L:491-534) Periplasmic [NIFE] hydrogenase large subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str} Back     alignment and structure
>1cc1_L (L:1-60,L:455-498) Hydrogenase (large subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfovibrio baculatus} Back     alignment and structure
>1yq9_H (H:1-55,H:493-536) Periplasmic [NIFE] hydrogenase large subunit; oxidoreductase; 2.35A {Desulfovibrio gigas} Back     alignment and structure
>1yqw_Q (Q:1-62,Q:506-549) Periplasmic [NIFE] hydrogenase large subunit; NI-Fe hydrogenase unready state, oxidoreductase; 1.83A {Desulfovibrio fructosovorans} PDB: 1yrq_H 3h3x_Q 3cus_Q 3cur_H 1frf_L Back     alignment and structure
>1wui_L (L:1-46,L:491-534) Periplasmic [NIFE] hydrogenase large subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str} Back     alignment and structure
>1e3d_B (B:94-128,B:239-279,B:375-450) [NIFE] hydrogenase large subunit; molecular modelling, electron transfer; HET: FSX; 1.8A {Desulfovibrio desulfuricans} Back     alignment and structure