Psyllid ID: psy5227

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------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-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690---

MGRILGPYKPNPQKNSPYECGFKEFGDKLINWTRTSSMWPMTFGLACCAIEMMHAGASRYDLDRFGIMFRPSPRQSDVMIVAGTLCNKMAPALRKVYDQMTEPKWVISMGSCANGGGYYHYSYSVVRGCDRIVPVDVYIPGCPPTAEALLYDYYSTMKILRDHVNFRFEQLIDLCGIDYSIYNKNINSDNSNKNLRFAIVLHLLSLNYNWRLRVRVFAENNELPRLHSITSLWSSANWYEREAFDLFGIFFDGHDDLRRLLTDYGFVGHPFRKDFPVIEIKSYKLNFGPQHPAAHGVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMCNEHAYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIGAMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDLPEIMPQYKSSIIRNNKATKILNENRQGSLLDFIEDFTNRFPKNIDEYETLLTDNRIWKQRLVGIGVVSPERALSMGFTGPMLRGSGVKWDLRKKQPYEIYNLLNFDIPIGKNGDSYDRYLVRIEEMRQSNKIIKQCIKWLRSNKGPVISNNNKITSPARINMKSNMEDLIHHFKLFTEGFYVPLGEIYSCVEHPKGEFGIYLVSDGANKPYRIKIRSPGFAHLQSLSEMISGHMISDVVTIIGTQDIVFGEIDR

ccccccccccccccccccccccccccccHHcccccccccHHHHHHHHHHHHHHHcccccccccccccccccccccccEEEEEccHHHHHHHHHHHHHHHcccccEEEEccccccccccEEEEEEEEEcccccccccccccccccEEEEccccHHHHHHHHHHcccccccEEEEcccccccccccccccccccccccEEEEEEEEEcccccEEEEEEEEcccccccccccccccccccccccccccccccEEcccccccccccccccccccccccccccccccEEEccccccccccHHHEEEEEEccEEEEEEccccccccHHHHHHccccccccccccccHHHHcccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHcHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHcccEEccHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEEcccccccccHHHHHHcHHHHHHHHcccccccccccccEEEEEcccccccEEEEEEccccccEEEEEcccccHHHHHHHHHHccccHHHHHHHHcccccccccccc

cccEccccccccccccccccHHHHcHHHHHHHccccccHHHHHHHHHHHHHHHccccccccHHHccEEEcccccHccEEEEEcHHHHHHHHHHHHHHHHHccccEEEEEcccccccccccccEEEEEcccccccEEEEccccccEEEEcHHHHHHHHHHHHHccccccHEEEEHHHccHHHHHHccccccccccccEEEEEEEEEEcccccEEEEEEcccccccccccccccccccccccHHHHHHccEEEcccccccEEcccccccccccccccccHcccEEEEEcccccccHccEEEEEEEccccEEEEccccHcHHHHHHHHHHHHccHHHHcccccHHHHHHHHHcHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHcccccHHHEcccccccccccccccccccccccHHHHHHHHHHHHccHHHHHHHHHHHcHHHHHHHHHHHHcccHHHHccccEEEEcHHHHHHcccccccHccccccccHcccccccHHccEEEEEEcccccccccHEEEEHHHHHHHHHHHHHHHHHcccccccEEccccccccccHHHHHHHHHHHHHHHHHHccccccccccEEEEEEccccccEEEEEEccccccEEEEEccccHHHHHHHHHHHccccHHHHHHHHHcHHEEEccccc

mgrilgpykpnpqknspyecgfkefgDKLINwtrtssmwpmtfGLACCAIEMMHagasrydldrfgimfrpsprqsdvMIVAGTLCNKMAPALRKVYDqmtepkwvismgscangggyyhysysvvrgcdrivpvdvyipgcpptaeALLYDYYSTMKILRDHVNFRFEQLIDLCGidysiynkninsdnsnkNLRFAIVLHLLSLNYNWRLRVRVFaennelprlhsITSLWssanwyereafdlfgiffdgHDDLRRLLTdygfvghpfrkdfpvieiksyklnfgpqhpaaHGVLRLILELEgevvrkadphiglLHRATEKLAEQRTYlqslpymdrldYVSMMCNEHAYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIGAMGVLLYAFREREDLLDCYEAVSGARMhaayyrpggvyrdlpeimpqYKSSIIRNNKATKILNENRQGSLLDFIEDFTNRFPKNIDEYETLLTDNRIWKQRLVGigvvsperalsmgftgpmlrgsgvkwdlrkkqpyeiynllnfdipigkngdsyDRYLVRIEEMRQSNKIIKQCIKWLRsnkgpvisnnnkitsparinmKSNMEDLIHHFklftegfyvplgeiyscvehpkgefgiylvsdgankpyrikirspgfaHLQSLSEMISGHMISDVVTIIGTQDIVFGEIDR

mgrilgpykpnpqknspyeCGFKEFGDKLINWTRTSSMWPMTFGLACCAIEMMHAGASRYDLDRFGIMFRPSPRQSDVMIVAGTLCNKMAPALRKVYDQMTEPKWVISMGSCANGGGYYHYSYSVVRGCDRIVPVDVYIPGCPPTAEALLYDYYSTMKILRDHVNFRFEQLIDLCGIDYSIYNKNINSDNSNKNLRFAIVLHLLSLNYNWRLRVRVFAennelprlhsitSLWSSANWYEREAFDLFGIFFDGHDDLRRLLTDYGFVGHPFRKDFPVIEIKSYKLNFGPQHPAAHGVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMCNEHAYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIGAMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDLPEIMPQYKSSIIRNNKATKILNENRQGSLLDFIEDFTNRFPKNIDEYETlltdnriwkqRLVGIGVVsperalsmgftgpmlrgsgvkwdlrkKQPYEIYNLlnfdipigkngDSYDRYLVRIEEMRQSNKIIKQCIKWLrsnkgpvisnnnkitspariNMKSNMEDLIHHFKLFTEGFYVPLGEIYSCVEHPKGEFGIYLVSDGANKPYRIKIRSPGFAHLQSLSEMISGHMISDVVTIIGTQDIVFGEIDR

MGRILGPYKPNPQKNSPYECGFKEFGDKLINWTRTSSMWPMTFGLACCAIEMMHAGASRYDLDRFGIMFRPSPRQSDVMIVAGTLCNKMAPALRKVYDQMTEPKWVISMGSCANgggyyhysysvvrgCDRIVPVDVYIPGCPPTAEALLYDYYSTMKILRDHVNFRFEQLIDLCGIDysiynkninsdnsnknLRFAIVLHLLSLNYNWRLRVRVFAENNELPRLHSITSLWSSANWYEREAFDLFGIFFDGHDDLRRLLTDYGFVGHPFRKDFPVIEIKSYKLNFGPQHPAAHGVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMCNEHAYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIGAMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDLPEIMPQYKSSIIRNNKATKILNENRQGSLLDFIEDFTNRFPKNIDEYETLLTDNRIWKQRLVGIGVVSPERALSMGFTGPMLRGSGVKWDLRKKQPYEIYNLLNFDIPIGKNGDSYDRYLVRIEEMRQSNKIIKQCIKWLRSNKGPVISNNNKITSPARINMKSNMEDLIHHFKLFTEGFYVPLGEIYSCVEHPKGEFGIYLVSDGANKPYRIKIRSPGFAHLQSLSEMISGHMISDVVTIIGTQDIVFGEIDR

*****************YECGFKEFGDKLINWTRTSSMWPMTFGLACCAIEMMHAGASRYDLDRFGIMFRPSPRQSDVMIVAGTLCNKMAPALRKVYDQMTEPKWVISMGSCANGGGYYHYSYSVVRGCDRIVPVDVYIPGCPPTAEALLYDYYSTMKILRDHVNFRFEQLIDLCGIDYSIYNKNINSDNSNKNLRFAIVLHLLSLNYNWRLRVRVFAENNELPRLHSITSLWSSANWYEREAFDLFGIFFDGHDDLRRLLTDYGFVGHPFRKDFPVIEIKSYKLNFGPQHPAAHGVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMCNEHAYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIGAMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDLPEIMPQYKSSIIRNNKATKILNENRQGSLLDFIEDFTNRFPKNIDEYETLLTDNRIWKQRLVGIGVVSPERALSMGFTGPMLRGSGVKWDLRKKQPYEIYNLLNFDIPIGKNGDSYDRYLVRIEEMRQSNKIIKQCIKWLRSNKGPVISN*********INMKSNMEDLIHHFKLFTEGFYVPLGEIYSCVEHPKGEFGIYLVSDGANKPYRIKIRSPGFAHLQSLSEMISGHMISDVVTIIGTQDIVFGE***

*****G**********P**CGFKEFGDKLINWTRTSSMWPMTFGLACCAIEMMHAGASRYDLDRFGIMFRPSPRQSDVMIVAGTLCNKMAPALRKVYDQMTEPKWVISMGSCANGGGYYHYSYSVVRGCDRIVPVDVYIPGCPPTAEALLYDYYSTMKILRDHVNFRFEQLIDLCGIDYSIYNKNINSDNSNKNLRFAIVLHLLSLNYNWRLRVRVFAENNELPRLHSITSLWSSANWYEREAFDLFGIFFDGHDDLRRLLTDYGFVGHPFRKDFPVIEIKSYKLNFGPQHPAAHGVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMCNEHAYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIGAMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDLPEIMPQYKSSIIRNNKATKILNENRQGSLLDFIEDFTNRFPKNIDEYETLLTDNRIWKQRLVGIGVVSPERALSMGFTGPMLRGSGVKWDLRKKQPYEIYNLLNFDIPIGKNGDSYDRYLVRIEEMRQSNKIIKQCIKWLRSNKGPVISNNNKITSPARINMKSNMEDLIHHFKLFTEGFYVPLGEIYSCVEHPKGEFGIYLVSDGANKPYRIKIRSPGFAHLQSLSEMISGHMISDVVTIIGTQDIVFGEIDR

**RILGPYKPNPQKNSPYECGFKEFGDKLINWTRTSSMWPMTFGLACCAIEMMHAGASRYDLDRFGIMFRPSPRQSDVMIVAGTLCNKMAPALRKVYDQMTEPKWVISMGSCANGGGYYHYSYSVVRGCDRIVPVDVYIPGCPPTAEALLYDYYSTMKILRDHVNFRFEQLIDLCGIDYSIYNKNINSDNSNKNLRFAIVLHLLSLNYNWRLRVRVFAENNELPRLHSITSLWSSANWYEREAFDLFGIFFDGHDDLRRLLTDYGFVGHPFRKDFPVIEIKSYKLNFGPQHPAAHGVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMCNEHAYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIGAMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDLPEIMPQYKSSIIRNNKATKILNENRQGSLLDFIEDFTNRFPKNIDEYETLLTDNRIWKQRLVGIGVVSPERALSMGFTGPMLRGSGVKWDLRKKQPYEIYNLLNFDIPIGKNGDSYDRYLVRIEEMRQSNKIIKQCIKWLRSNKGPVISNNNKITSPARINMKSNMEDLIHHFKLFTEGFYVPLGEIYSCVEHPKGEFGIYLVSDGANKPYRIKIRSPGFAHLQSLSEMISGHMISDVVTIIGTQDIVFGEI**

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		693	2.2.26 [Sep-21-2011]
A6SY08		417	NADH-quinone oxidoreducta	yes	N/A	0.598	0.995	0.821	0.0
A4G641		417	NADH-quinone oxidoreducta	yes	N/A	0.598	0.995	0.814	0.0
Q2YA24		417	NADH-quinone oxidoreducta	yes	N/A	0.598	0.995	0.787	0.0
B2JDM5		417	NADH-quinone oxidoreducta	yes	N/A	0.598	0.995	0.790	0.0
Q1LPW0		417	NADH-quinone oxidoreducta	yes	N/A	0.598	0.995	0.785	0.0
B3R3X0		417	NADH-quinone oxidoreducta	yes	N/A	0.598	0.995	0.785	0.0
B2T2F0		417	NADH-quinone oxidoreducta	yes	N/A	0.598	0.995	0.785	0.0
B2U7Q8		417	NADH-quinone oxidoreducta	yes	N/A	0.598	0.995	0.780	0.0
Q142H0		417	NADH-quinone oxidoreducta	yes	N/A	0.598	0.995	0.785	0.0
Q0KCS7		417	NADH-quinone oxidoreducta	yes	N/A	0.598	0.995	0.780	0.0

>sp\|A6SY08\|NUOD_JANMA NADH-quinone oxidoreductase subunit D OS=Janthinobacterium sp. (strain Marseille) GN=nuoD PE=3 SV=1	Back alignment and function desciption

 Score =  754 bits (1946), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 341/415 (82%), Positives = 390/415 (93%)

Query: 279 EIKSYKLNFGPQHPAAHGVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPY 338
           EIK+Y LNFGPQHPAAHGVLRL+LEL+GEV+++ADPHIGLLHRATEKLAEQ+TYLQS+PY
Sbjct: 3   EIKNYTLNFGPQHPAAHGVLRLVLELDGEVIQRADPHIGLLHRATEKLAEQKTYLQSVPY 62

Query: 339 MDRLDYVSMMCNEHAYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIG 398
           MDRLDYVSMMCNEHAYVMAIEK+LNI++P+RAQYIRVMFDEITR+LNHLMW+G+H+LD+G
Sbjct: 63  MDRLDYVSMMCNEHAYVMAIEKMLNIEVPLRAQYIRVMFDEITRILNHLMWLGAHALDVG 122

Query: 399 AMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDLPEIMPQYKSSIIRNNKATK 458
           AMGV LYAFREREDL+DCYEAVSGARMHAAYYRPGGVYRDLP+ MPQ+K+SIIRN KA  
Sbjct: 123 AMGVFLYAFREREDLMDCYEAVSGARMHAAYYRPGGVYRDLPDTMPQHKASIIRNAKAIS 182

Query: 459 ILNENRQGSLLDFIEDFTNRFPKNIDEYETLLTDNRIWKQRLVGIGVVSPERALSMGFTG 518
            LNENRQGSLLDFIEDFTNRFP  +DEYETLLTDNRIWKQRLVGIGVVSPERA++MGFTG
Sbjct: 183 QLNENRQGSLLDFIEDFTNRFPTYVDEYETLLTDNRIWKQRLVGIGVVSPERAMAMGFTG 242

Query: 519 PMLRGSGVKWDLRKKQPYEIYNLLNFDIPIGKNGDSYDRYLVRIEEMRQSNKIIKQCIKW 578
            MLRGSGV+WDLRKKQPYE+Y+L++FDIP+G NGD YDRYLVR+EEMRQSN+IIKQC++W
Sbjct: 243 AMLRGSGVEWDLRKKQPYEVYDLMDFDIPVGTNGDCYDRYLVRVEEMRQSNRIIKQCVEW 302

Query: 579 LRSNKGPVISNNNKITSPARINMKSNMEDLIHHFKLFTEGFYVPLGEIYSCVEHPKGEFG 638
           LR+N GPV+++N+K+  P+R+ MKSNMEDLIHHFKLFTEGF+VP GE Y+ VEHPKGEFG
Sbjct: 303 LRNNAGPVMTDNHKVAPPSRVGMKSNMEDLIHHFKLFTEGFHVPTGEAYAAVEHPKGEFG 362

Query: 639 IYLVSDGANKPYRIKIRSPGFAHLQSLSEMISGHMISDVVTIIGTQDIVFGEIDR 693
           +YL+SDGANKPYR+KIR+PGF HLQ L EM  GHMI+D VTIIGTQDIVFGEIDR
Sbjct: 363 VYLISDGANKPYRMKIRAPGFPHLQGLDEMAKGHMIADAVTIIGTQDIVFGEIDR 417

NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient.
Janthinobacterium sp. (strain Marseille) (taxid: 375286)
EC: 1EC: .EC: 6EC: .EC: 9EC: 9EC: .EC: 5

>sp\|A4G641\|NUOD_HERAR NADH-quinone oxidoreductase subunit D OS=Herminiimonas arsenicoxydans GN=nuoD PE=3 SV=1	Back alignment and function description

>sp\|Q2YA24\|NUOD_NITMU NADH-quinone oxidoreductase subunit D OS=Nitrosospira multiformis (strain ATCC 25196 / NCIMB 11849) GN=nuoD PE=3 SV=1	Back alignment and function description

>sp\|B2JDM5\|NUOD_BURP8 NADH-quinone oxidoreductase subunit D OS=Burkholderia phymatum (strain DSM 17167 / STM815) GN=nuoD PE=3 SV=1	Back alignment and function description

>sp\|Q1LPW0\|NUOD_RALME NADH-quinone oxidoreductase subunit D OS=Ralstonia metallidurans (strain CH34 / ATCC 43123 / DSM 2839) GN=nuoD PE=3 SV=1	Back alignment and function description

>sp\|B3R3X0\|NUOD_CUPTR NADH-quinone oxidoreductase subunit D OS=Cupriavidus taiwanensis (strain R1 / LMG 19424) GN=nuoD PE=3 SV=1	Back alignment and function description

>sp\|B2T2F0\|NUOD_BURPP NADH-quinone oxidoreductase subunit D OS=Burkholderia phytofirmans (strain DSM 17436 / PsJN) GN=nuoD PE=3 SV=1	Back alignment and function description

>sp\|B2U7Q8\|NUOD_RALPJ NADH-quinone oxidoreductase subunit D OS=Ralstonia pickettii (strain 12J) GN=nuoD PE=3 SV=1	Back alignment and function description

>sp\|Q142H0\|NUOD_BURXL NADH-quinone oxidoreductase subunit D OS=Burkholderia xenovorans (strain LB400) GN=nuoD PE=3 SV=1	Back alignment and function description

>sp\|Q0KCS7\|NUOD_CUPNH NADH-quinone oxidoreductase subunit D OS=Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) GN=nuoD PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		693
399020459		417	NADH dehydrogenase I, D subunit [Herbasp	0.598	0.995	0.850	0.0
152979920		417	NADH dehydrogenase subunit D [Janthinoba	0.598	0.995	0.821	0.0
134095028		417	NADH dehydrogenase subunit D [Herminiimo	0.598	0.995	0.814	0.0
329914959		417	NADH-ubiquinone oxidoreductase chain D [	0.598	0.995	0.816	0.0
398836856		417	NADH dehydrogenase I, D subunit [Herbasp	0.598	0.995	0.826	0.0
409405592		417	NADH dehydrogenase I subunit D [Herbaspi	0.598	0.995	0.826	0.0
300311098		417	NADH dehydrogenase I subunit D [Herbaspi	0.598	0.995	0.821	0.0
415950781		417	NADH-quinone oxidoreductase subunit D [H	0.598	0.995	0.819	0.0
340786784		417	NADH-ubiquinone oxidoreductase subunit D	0.598	0.995	0.814	0.0
413000577		417	NADH dehydrogenase subunit D [uncultured	0.598	0.995	0.809	0.0

>gi\|399020459\|ref\|ZP_10722589.1\| NADH dehydrogenase I, D subunit [Herbaspirillum sp. CF444] gi\|398094874\|gb\|EJL85228.1\| NADH dehydrogenase I, D subunit [Herbaspirillum sp. CF444]	Back alignment and taxonomy information

 Score =  765 bits (1975), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 353/415 (85%), Positives = 396/415 (95%)

Query: 279 EIKSYKLNFGPQHPAAHGVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPY 338
           EIK+Y LNFGPQHPAAHGVLRL+LEL+GEV+++ADPHIGLLHRATEKLAEQ+TYLQS+PY
Sbjct: 3   EIKNYTLNFGPQHPAAHGVLRLVLELDGEVIQRADPHIGLLHRATEKLAEQKTYLQSVPY 62

Query: 339 MDRLDYVSMMCNEHAYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIG 398
           MDRLDYVSMMCNEHAYVMAIEKLL I++P+RAQYIRVMFDE+TRLLNHLMWIG+H LD+G
Sbjct: 63  MDRLDYVSMMCNEHAYVMAIEKLLGIEVPLRAQYIRVMFDEMTRLLNHLMWIGAHGLDVG 122

Query: 399 AMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDLPEIMPQYKSSIIRNNKATK 458
           AMGVLLYAFREREDL+DCYEAVSGARMHAAYYRPGGVYRDLP+ MPQYK+SI+RN+KA K
Sbjct: 123 AMGVLLYAFREREDLMDCYEAVSGARMHAAYYRPGGVYRDLPDTMPQYKASIMRNDKAIK 182

Query: 459 ILNENRQGSLLDFIEDFTNRFPKNIDEYETLLTDNRIWKQRLVGIGVVSPERALSMGFTG 518
            LNENRQGS+LDFIEDFTNRFPK +DEYETLLTDNRIWKQRLVGIGVVSPERAL+MGFTG
Sbjct: 183 QLNENRQGSMLDFIEDFTNRFPKYVDEYETLLTDNRIWKQRLVGIGVVSPERALAMGFTG 242

Query: 519 PMLRGSGVKWDLRKKQPYEIYNLLNFDIPIGKNGDSYDRYLVRIEEMRQSNKIIKQCIKW 578
           PMLRGSG++WDLRKKQPYE+Y+LL+FDIP+GKNGDSYDRYLVR+EEMRQSN+IIKQC++W
Sbjct: 243 PMLRGSGIEWDLRKKQPYEVYDLLDFDIPVGKNGDSYDRYLVRVEEMRQSNRIIKQCVEW 302

Query: 579 LRSNKGPVISNNNKITSPARINMKSNMEDLIHHFKLFTEGFYVPLGEIYSCVEHPKGEFG 638
           LR+N GPVI +N+KI  P R++MKSNMEDLIHHFKLFTEGF+VP GE Y+ VEHPKGEFG
Sbjct: 303 LRNNPGPVIIDNHKIAPPPRMDMKSNMEDLIHHFKLFTEGFHVPPGETYAAVEHPKGEFG 362

Query: 639 IYLVSDGANKPYRIKIRSPGFAHLQSLSEMISGHMISDVVTIIGTQDIVFGEIDR 693
           IYLVSDGANKPYR+KIR+PGFAHL SL+EM  GHMI+D VTIIGTQDIVFGEIDR
Sbjct: 363 IYLVSDGANKPYRMKIRAPGFAHLSSLNEMAKGHMIADAVTIIGTQDIVFGEIDR 417

Source: Herbaspirillum sp. CF444

Species: Herbaspirillum sp. CF444

Genus: Herbaspirillum

Family: Oxalobacteraceae

Order: Burkholderiales

Class: Betaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

>gi\|152979920\|ref\|YP_001353155.1\| NADH dehydrogenase subunit D [Janthinobacterium sp. Marseille] gi\|229891400\|sp\|A6SY08.1\|NUOD_JANMA RecName: Full=NADH-quinone oxidoreductase subunit D; AltName: Full=NADH dehydrogenase I subunit D; AltName: Full=NDH-1 subunit D gi\|151279997\|gb\|ABR88407.1\| NADH dehydrogenase I chain D [Janthinobacterium sp. Marseille]	Back alignment and taxonomy information

>gi\|134095028\|ref\|YP_001100103.1\| NADH dehydrogenase subunit D [Herminiimonas arsenicoxydans] gi\|229891399\|sp\|A4G641.1\|NUOD_HERAR RecName: Full=NADH-quinone oxidoreductase subunit D; AltName: Full=NADH dehydrogenase I subunit D; AltName: Full=NDH-1 subunit D gi\|133738931\|emb\|CAL61978.1\| NADH-ubiquinone oxidoreductase D subunit (NADH dehydrogenase subunit D) [Herminiimonas arsenicoxydans]	Back alignment and taxonomy information

>gi\|329914959\|ref\|ZP_08276195.1\| NADH-ubiquinone oxidoreductase chain D [Oxalobacteraceae bacterium IMCC9480] gi\|327545009\|gb\|EGF30334.1\| NADH-ubiquinone oxidoreductase chain D [Oxalobacteraceae bacterium IMCC9480]	Back alignment and taxonomy information

>gi\|398836856\|ref\|ZP_10594182.1\| NADH dehydrogenase I, D subunit [Herbaspirillum sp. YR522] gi\|398210643\|gb\|EJM97285.1\| NADH dehydrogenase I, D subunit [Herbaspirillum sp. YR522]	Back alignment and taxonomy information

>gi\|409405592\|ref\|ZP_11254054.1\| NADH dehydrogenase I subunit D [Herbaspirillum sp. GW103] gi\|386434141\|gb\|EIJ46966.1\| NADH dehydrogenase I subunit D [Herbaspirillum sp. GW103]	Back alignment and taxonomy information

>gi\|300311098\|ref\|YP_003775190.1\| NADH dehydrogenase I subunit D [Herbaspirillum seropedicae SmR1] gi\|300073883\|gb\|ADJ63282.1\| NADH dehydrogenase I (Chain D) oxidoreductase protein [Herbaspirillum seropedicae SmR1]	Back alignment and taxonomy information

>gi\|415950781\|ref\|ZP_11557001.1\| NADH-quinone oxidoreductase subunit D [Herbaspirillum frisingense GSF30] gi\|407757587\|gb\|EKF67542.1\| NADH-quinone oxidoreductase subunit D [Herbaspirillum frisingense GSF30]	Back alignment and taxonomy information

>gi\|340786784\|ref\|YP_004752249.1\| NADH-ubiquinone oxidoreductase subunit D [Collimonas fungivorans Ter331] gi\|340552051\|gb\|AEK61426.1\| NADH-ubiquinone oxidoreductase chain D [Collimonas fungivorans Ter331]	Back alignment and taxonomy information

>gi\|413000577\|emb\|CCO25577.1\| NADH dehydrogenase subunit D [uncultured bacterium]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		693
TIGR_CMR\|CBU_1445		417	CBU_1445 "NADH dehydrogenase I	0.598	0.995	0.713	4.2e-166
TIGR_CMR\|GSU_3444		792	GSU_3444 "NADH dehydrogenase I	0.317	0.277	0.436	1.8e-141
ZFIN\|ZDB-GENE-051120-30		462	zgc:123301 "zgc:123301" [Danio	0.323	0.484	0.592	1.4e-135
UNIPROTKB\|Q0MQG3		463	NDUFS2 "NADH dehydrogenase [ub	0.323	0.483	0.579	2.8e-135
RGD\|1307109		463	Ndufs2 "NADH dehydrogenase (ub	0.323	0.483	0.592	3.6e-135
UNIPROTKB\|Q641Y2		463	Ndufs2 "NADH dehydrogenase [ub	0.323	0.483	0.592	3.6e-135
UNIPROTKB\|F1PVM9		463	NDUFS2 "Uncharacterized protei	0.323	0.483	0.584	5.9e-135
MGI\|MGI:2385112		463	Ndufs2 "NADH dehydrogenase (ub	0.323	0.483	0.592	5.9e-135
UNIPROTKB\|O75306		463	NDUFS2 "NADH dehydrogenase [ub	0.323	0.483	0.575	7.5e-135
UNIPROTKB\|Q0MQG4		463	NDUFS2 "NADH dehydrogenase [ub	0.323	0.483	0.575	7.5e-135

TIGR_CMR\|CBU_1445 CBU_1445 "NADH dehydrogenase I, D subunit" [Coxiella burnetii RSA 493 (taxid:227377)]	Back alignment and assigned GO terms

 Score = 1616 (573.9 bits), Expect = 4.2e-166, P = 4.2e-166
 Identities = 296/415 (71%), Positives = 351/415 (84%)

Query:   279 EIKSYKLNFGPQHPAAHGVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPY 338
             E+++Y  NFGPQHPAAHGVLRLI+E++GEV+++ DPHIGLLHRATEKLAE + Y Q++ Y
Sbjct:     3 EVRNYTFNFGPQHPAAHGVLRLIVEVDGEVIQRIDPHIGLLHRATEKLAESKPYNQTIGY 62

Query:   339 MDRLDYVSMMCNEHAYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIG 398
             MDRLDYVSMM NEH YV+AIEKLL I+ PIRA+YIR MFDEITR+LNHL+W+G+H+LD+G
Sbjct:    63 MDRLDYVSMMANEHGYVLAIEKLLGIEPPIRAKYIRTMFDEITRILNHLLWLGAHALDVG 122

Query:   399 AMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDLPEIMPQYKSSIIRNNKATK 458
             AM V LY FREREDL+DCYEAVSGARMHA YYRPGGVYRDLP+ MP+YK S   N KA K
Sbjct:   123 AMTVFLYCFREREDLMDCYEAVSGARMHATYYRPGGVYRDLPDSMPKYKPSRWHNEKAVK 182

Query:   459 ILNENRQGSLLDFIEDFTNRFPKNIDEYETLLTDNRIWKQRLVGIGVVSPERALSMGFTG 518
              +NE R+GSLLDFI DFT RFP  IDEYE+LLTDNRIWKQR VGIGVVS ERAL +GFTG
Sbjct:   183 KMNEAREGSLLDFIWDFTARFPNLIDEYESLLTDNRIWKQRTVGIGVVSAERALQLGFTG 242

Query:   519 PMLRGSGVKWDLRKKQPYEIYNLLNFDIPIGKNGDSYDRYLVRIEEMRQSNKIIKQCIKW 578
             PMLR SGV+WDLRKKQPY  Y+ ++FDIPIG+ GD YDRYLVRIEEMRQSN+II+QC++W
Sbjct:   243 PMLRASGVEWDLRKKQPYAAYDRVDFDIPIGREGDCYDRYLVRIEEMRQSNRIIRQCVEW 302

Query:   579 LRSNKGPVISNNNKITSPARINMKSNMEDLIHHFKLFTEGFYVPLGEIYSCVEHPKGEFG 638
             LR N G V+ ++ KI  P R  MK +ME LIHHFKLFTEG+ VP GE Y+ VE PKGEFG
Sbjct:   303 LRKNPGSVMIDDYKIVPPQREVMKRDMEALIHHFKLFTEGYIVPEGEAYAAVEQPKGEFG 362

Query:   639 IYLVSDGANKPYRIKIRSPGFAHLQSLSEMISGHMISDVVTIIGTQDIVFGEIDR 693
             +Y+VSDGANKPYR+K+R+  + HL +++EM  GHMI+D+V II + DIVFGEIDR
Sbjct:   363 VYIVSDGANKPYRVKVRAASYPHLAAMNEMCRGHMIADLVAIISSIDIVFGEIDR 417

GO:0006120 "mitochondrial electron transport, NADH to ubiquinone" evidence=ISS

GO:0008137 "NADH dehydrogenase (ubiquinone) activity" evidence=ISS

TIGR_CMR\|GSU_3444 GSU_3444 "NADH dehydrogenase I, B/C/D subunits" [Geobacter sulfurreducens PCA (taxid:243231)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-051120-30 zgc:123301 "zgc:123301" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|Q0MQG3 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" [Pongo pygmaeus (taxid:9600)]	Back alignment and assigned GO terms

RGD\|1307109 Ndufs2 "NADH dehydrogenase (ubiquinone) Fe-S protein 2" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q641Y2 Ndufs2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|F1PVM9 NDUFS2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

MGI\|MGI:2385112 Ndufs2 "NADH dehydrogenase (ubiquinone) Fe-S protein 2" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|O75306 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|Q0MQG4 NDUFS2 "NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial" [Gorilla gorilla gorilla (taxid:9595)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
A1WLP1	NUOD_VEREI	1, ., 6, ., 9, 9, ., 5	0.7493	0.5988	0.9952	yes	N/A
Q1LPW0	NUOD_RALME	1, ., 6, ., 9, 9, ., 5	0.7855	0.5988	0.9952	yes	N/A
A6SY08	NUOD_JANMA	1, ., 6, ., 9, 9, ., 5	0.8216	0.5988	0.9952	yes	N/A
A1VM63	NUOD_POLNA	1, ., 6, ., 9, 9, ., 5	0.7662	0.5988	0.9952	yes	N/A
A9AFZ0	NUOD_BURM1	1, ., 6, ., 9, 9, ., 5	0.7879	0.5988	0.9952	yes	N/A
A2S456	NUOD_BURM9	1, ., 6, ., 9, 9, ., 5	0.7831	0.5988	0.9952	yes	N/A
Q1BV16	NUOD_BURCA	1, ., 6, ., 9, 9, ., 5	0.7855	0.5988	0.9952	yes	N/A
Q39EE8	NUOD_BURS3	1, ., 6, ., 9, 9, ., 5	0.7855	0.5988	0.9952	yes	N/A
B3R3X0	NUOD_CUPTR	1, ., 6, ., 9, 9, ., 5	0.7855	0.5988	0.9952	yes	N/A
B2T2F0	NUOD_BURPP	1, ., 6, ., 9, 9, ., 5	0.7855	0.5988	0.9952	yes	N/A
Q0AHJ7	NUOD_NITEC	1, ., 6, ., 9, 9, ., 5	0.7662	0.5988	0.9952	yes	N/A
Q62IN8	NUOD_BURMA	1, ., 6, ., 9, 9, ., 5	0.7831	0.5988	0.9952	yes	N/A
A3MIA4	NUOD_BURM7	1, ., 6, ., 9, 9, ., 5	0.7831	0.5988	0.9952	yes	N/A
Q0KCS7	NUOD_CUPNH	1, ., 6, ., 9, 9, ., 5	0.7807	0.5988	0.9952	yes	N/A
A3N7M0	NUOD_BURP6	1, ., 6, ., 9, 9, ., 5	0.7831	0.5988	0.9952	yes	N/A
Q47HH3	NUOD_DECAR	1, ., 6, ., 9, 9, ., 5	0.7542	0.5988	0.9952	yes	N/A
B1XUK1	NUOD_POLNS	1, ., 6, ., 9, 9, ., 5	0.7542	0.5988	0.9952	yes	N/A
Q2KV09	NUOD_BORA1	1, ., 6, ., 9, 9, ., 5	0.7716	0.5988	0.9928	yes	N/A
B1Y830	NUOD_LEPCP	1, ., 6, ., 9, 9, ., 5	0.7518	0.5988	0.9952	yes	N/A
Q0BDD3	NUOD_BURCM	1, ., 6, ., 9, 9, ., 5	0.7831	0.5988	0.9952	yes	N/A
Q127X5	NUOD_POLSJ	1, ., 6, ., 9, 9, ., 5	0.7542	0.5988	0.9952	yes	N/A
A1W4M5	NUOD_ACISJ	1, ., 6, ., 9, 9, ., 5	0.7566	0.5988	0.9952	yes	N/A
A9II07	NUOD_BORPD	1, ., 6, ., 9, 9, ., 5	0.7908	0.5988	0.9928	yes	N/A
B2U7Q8	NUOD_RALPJ	1, ., 6, ., 9, 9, ., 5	0.7807	0.5988	0.9952	yes	N/A
B1YTQ4	NUOD_BURA4	1, ., 6, ., 9, 9, ., 5	0.7831	0.5988	0.9952	yes	N/A
Q82TU6	NUOD_NITEU	1, ., 6, ., 9, 9, ., 5	0.7807	0.5988	0.9952	yes	N/A
B4E5L9	NUOD_BURCJ	1, ., 6, ., 9, 9, ., 5	0.7855	0.5988	0.9952	yes	N/A
Q473U0	NUOD_CUPPJ	1, ., 6, ., 9, 9, ., 5	0.7807	0.5988	0.9952	yes	N/A
A1TLL9	NUOD_ACIAC	1, ., 6, ., 9, 9, ., 5	0.7662	0.5988	0.9952	yes	N/A
A4SXQ0	NUOD_POLSQ	1, ., 6, ., 9, 9, ., 5	0.7529	0.6017	1.0	yes	N/A
A2SFM9	NUOD_METPP	1, ., 6, ., 9, 9, ., 5	0.7710	0.5988	0.9952	yes	N/A
Q63VN0	NUOD_BURPS	1, ., 6, ., 9, 9, ., 5	0.7831	0.5988	0.9952	yes	N/A
Q3JUA6	NUOD_BURP1	1, ., 6, ., 9, 9, ., 5	0.7831	0.5988	0.9952	yes	N/A
B1JVN8	NUOD_BURCC	1, ., 6, ., 9, 9, ., 5	0.7855	0.5988	0.9952	yes	N/A
Q142H0	NUOD_BURXL	1, ., 6, ., 9, 9, ., 5	0.7855	0.5988	0.9952	yes	N/A
Q0A778	NUOD_ALHEH	1, ., 6, ., 9, 9, ., 5	0.7373	0.5988	0.9952	yes	N/A
Q7WCU2	NUOD_BORBR	1, ., 6, ., 9, 9, ., 5	0.7812	0.5988	0.9928	yes	N/A
Q1GZL2	NUOD_METFK	1, ., 6, ., 9, 9, ., 5	0.7927	0.5988	0.9952	yes	N/A
Q2SZN2	NUOD_BURTA	1, ., 6, ., 9, 9, ., 5	0.7807	0.5988	0.9952	yes	N/A
A4JGC7	NUOD_BURVG	1, ., 6, ., 9, 9, ., 5	0.7831	0.5988	0.9952	yes	N/A
Q3SJQ4	NUOD_THIDA	1, ., 6, ., 9, 9, ., 5	0.7783	0.5988	0.9952	yes	N/A
A0K920	NUOD_BURCH	1, ., 6, ., 9, 9, ., 5	0.7855	0.5988	0.9952	yes	N/A
B2JDM5	NUOD_BURP8	1, ., 6, ., 9, 9, ., 5	0.7903	0.5988	0.9952	yes	N/A
Q2YA24	NUOD_NITMU	1, ., 6, ., 9, 9, ., 5	0.7879	0.5988	0.9952	yes	N/A
A1V2L9	NUOD_BURMS	1, ., 6, ., 9, 9, ., 5	0.7831	0.5988	0.9952	yes	N/A
Q7VZQ2	NUOD_BORPE	1, ., 6, ., 9, 9, ., 5	0.7812	0.5988	0.9928	yes	N/A
A4G641	NUOD_HERAR	1, ., 6, ., 9, 9, ., 5	0.8144	0.5988	0.9952	yes	N/A
Q7W5B0	NUOD_BORPA	1, ., 6, ., 9, 9, ., 5	0.7812	0.5988	0.9928	yes	N/A
Q7NZH8	NUOD_CHRVO	1, ., 6, ., 9, 9, ., 5	0.7614	0.5988	0.9952	yes	N/A
A3NTA9	NUOD_BURP0	1, ., 6, ., 9, 9, ., 5	0.7831	0.5988	0.9952	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
4th Layer	1.6.99.5	0.914
3rd Layer	1.6.99	0.921

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Alignment Graph	Length	Definition	E-value
Query		693
PRK06075		392	PRK06075, PRK06075, NADH dehydrogenase subunit D;	0.0
COG0649		398	COG0649, NuoD, NADH:ubiquinone oxidoreductase 49 k	0.0
TIGR01962		386	TIGR01962, NuoD, NADH dehydrogenase I, D subunit	0.0
PRK13292		788	PRK13292, PRK13292, trifunctional NADH dehydrogena	1e-164
PRK11742		575	PRK11742, PRK11742, bifunctional NADH:ubiquinone o	1e-158
PRK12322		366	PRK12322, PRK12322, NADH dehydrogenase subunit D;	1e-142
pfam00346		272	pfam00346, Complex1_49kDa, Respiratory-chain NADH	1e-125
PRK07415		394	PRK07415, PRK07415, NAD(P)H-quinone oxidoreductase	1e-119
CHL00017		393	CHL00017, ndhH, NADH dehydrogenase subunit 7	1e-113
PRK06411		183	PRK06411, PRK06411, NADH dehydrogenase subunit B;	1e-97
COG0377		194	COG0377, NuoB, NADH:ubiquinone oxidoreductase 20 k	1e-89
TIGR01957		145	TIGR01957, nuoB_fam, NADH-quinone oxidoreductase,	7e-88
COG3261		382	COG3261, HycE, Ni,Fe-hydrogenase III large subunit	3e-68
PRK14815		183	PRK14815, PRK14815, NADH dehydrogenase subunit B;	2e-61
PRK14819		264	PRK14819, PRK14819, NADH dehydrogenase subunit B;	1e-60
PRK14813		189	PRK14813, PRK14813, NADH dehydrogenase subunit B;	2e-59
PRK14818		173	PRK14818, PRK14818, NADH dehydrogenase subunit B;	4e-59
PRK06074		189	PRK06074, PRK06074, NADH dehydrogenase subunit C;	5e-54
PRK13292		788	PRK13292, PRK13292, trifunctional NADH dehydrogena	6e-54
PRK14816		182	PRK14816, PRK14816, NADH dehydrogenase subunit B;	1e-53
PRK14820		180	PRK14820, PRK14820, NADH dehydrogenase subunit B;	1e-47
CHL00023		225	CHL00023, ndhK, NADH dehydrogenase subunit K	6e-47
PRK14814		186	PRK14814, PRK14814, NADH dehydrogenase subunit B;	3e-46
PRK14817		181	PRK14817, PRK14817, NADH dehydrogenase subunit B;	2e-44
TIGR01961		121	TIGR01961, NuoC_fam, NADH (or F420H2) dehydrogenas	3e-42
COG0852		176	COG0852, NuoC, NADH:ubiquinone oxidoreductase 27 k	3e-41
COG3260		148	COG3260, COG3260, Ni,Fe-hydrogenase III small subu	3e-39
pfam01058		122	pfam01058, Oxidored_q6, NADH ubiquinone oxidoreduc	5e-34
pfam00329		103	pfam00329, Complex1_30kDa, Respiratory-chain NADH	7e-33
PRK07785		235	PRK07785, PRK07785, NADH dehydrogenase subunit C;	2e-22
PRK08491		263	PRK08491, PRK08491, NADH dehydrogenase subunit C;	5e-22
PRK07735		430	PRK07735, PRK07735, NADH dehydrogenase subunit C;	9e-22
PRK12494		172	PRK12494, PRK12494, NADH dehydrogenase subunit J;	4e-14
CHL00012		158	CHL00012, ndhJ, NADH dehydrogenase subunit J	5e-11
COG3262		165	COG3262, HycE, Ni,Fe-hydrogenase III component G [	6e-09
COG1941		247	COG1941, FrhG, Coenzyme F420-reducing hydrogenase,	4e-06
TIGR03294		228	TIGR03294, FrhG, coenzyme F420 hydrogenase, subuni	6e-06
PRK06602		121	PRK06602, PRK06602, NADH:ubiquinone oxidoreductase	1e-05
COG0838		123	COG0838, NuoA, NADH:ubiquinone oxidoreductase subu	8e-05

>gnl\|CDD\|180385 PRK06075, PRK06075, NADH dehydrogenase subunit D; Validated	Back alignment and domain information

 Score =  756 bits (1956), Expect = 0.0
 Identities = 277/415 (66%), Positives = 332/415 (80%), Gaps = 25/415 (6%)

Query: 279 EIKSYKLNFGPQHPAAHGVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPY 338
           EI++Y LNFGPQHPAAHGVLRLILEL+GEVV +ADPHIG LHR TEKLAE RTYLQ++PY
Sbjct: 3   EIRNYTLNFGPQHPAAHGVLRLILELDGEVVVRADPHIGYLHRGTEKLAEYRTYLQAIPY 62

Query: 339 MDRLDYVSMMCNEHAYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIG 398
            DRLDYVS M NEHAY +A+EKLL I++P RAQYIRV+F E+ R+L+HL+W+G+H+LD+G
Sbjct: 63  FDRLDYVSPMNNEHAYCLAVEKLLGIEVPERAQYIRVLFLELNRILSHLLWLGTHALDLG 122

Query: 399 AMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDLPEIMPQYKSSIIRNNKATK 458
           AM V L+ FRERE LLD YEAV+GARMH AY RPGGV RDLP+ + +             
Sbjct: 123 AMTVFLWGFREREKLLDLYEAVTGARMHHAYIRPGGVRRDLPDGLLED------------ 170

Query: 459 ILNENRQGSLLDFIEDFTNRFPKNIDEYETLLTDNRIWKQRLVGIGVVSPERALSMGFTG 518
                        I DF + FPK +D+YETLLTDNRIWKQRLVG+GVVS ERAL++GFTG
Sbjct: 171 -------------IRDFLDYFPKRLDDYETLLTDNRIWKQRLVGVGVVSKERALALGFTG 217

Query: 519 PMLRGSGVKWDLRKKQPYEIYNLLNFDIPIGKNGDSYDRYLVRIEEMRQSNKIIKQCIKW 578
           PMLR SGV WDLRK QPYE+Y+ L+FD+P+GKNGD YDRYLVR+EEMRQS +II+QC+  
Sbjct: 218 PMLRASGVAWDLRKSQPYEVYDELDFDVPVGKNGDCYDRYLVRVEEMRQSLRIIEQCLDR 277

Query: 579 LRSNKGPVISNNNKITSPARINMKSNMEDLIHHFKLFTEGFYVPLGEIYSCVEHPKGEFG 638
           LR   GPV+ ++ KI  PAR+ MK++ME LIHHFKL TEGF VP GE+Y+ VE PKGEFG
Sbjct: 278 LRPPPGPVMVDDPKIAPPARLEMKTSMEALIHHFKLVTEGFRVPAGEVYAAVESPKGEFG 337

Query: 639 IYLVSDGANKPYRIKIRSPGFAHLQSLSEMISGHMISDVVTIIGTQDIVFGEIDR 693
           +YLVSDG NKPYR+KIR+P FAHLQ+L EM  GHM++DVV IIG+ DIVFGE+DR
Sbjct: 338 VYLVSDGGNKPYRVKIRAPSFAHLQALDEMCRGHMLADVVAIIGSLDIVFGEVDR 392

Length = 392

>gnl\|CDD\|223722 COG0649, NuoD, NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]	Back alignment and domain information

>gnl\|CDD\|233658 TIGR01962, NuoD, NADH dehydrogenase I, D subunit	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\|236965 PRK11742, PRK11742, bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional	Back alignment and domain information

>gnl\|CDD\|183437 PRK12322, PRK12322, NADH dehydrogenase subunit D; Provisional	Back alignment and domain information

>gnl\|CDD\|215871 pfam00346, Complex1_49kDa, Respiratory-chain NADH dehydrogenase, 49 Kd subunit	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\|235797 PRK06411, PRK06411, NADH dehydrogenase subunit B; Validated	Back alignment and domain information

>gnl\|CDD\|223454 COG0377, NuoB, NADH:ubiquinone oxidoreductase 20 kD subunit and related Fe-S oxidoreductases [Energy production and conversion]	Back alignment and domain information

>gnl\|CDD\|233656 TIGR01957, nuoB_fam, NADH-quinone oxidoreductase, B subunit	Back alignment and domain information

>gnl\|CDD\|225800 COG3261, HycE, Ni,Fe-hydrogenase III large subunit [Energy production and conversion]	Back alignment and domain information

>gnl\|CDD\|237821 PRK14815, PRK14815, NADH dehydrogenase subunit B; Provisional	Back alignment and domain information

>gnl\|CDD\|237822 PRK14819, PRK14819, NADH dehydrogenase subunit B; Provisional	Back alignment and domain information

>gnl\|CDD\|173274 PRK14813, PRK14813, NADH dehydrogenase subunit B; Provisional	Back alignment and domain information

>gnl\|CDD\|173279 PRK14818, PRK14818, NADH dehydrogenase subunit B; Provisional	Back alignment and domain information

>gnl\|CDD\|235691 PRK06074, PRK06074, NADH dehydrogenase subunit C; 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\|173277 PRK14816, PRK14816, NADH dehydrogenase subunit B; Provisional	Back alignment and domain information

>gnl\|CDD\|184833 PRK14820, PRK14820, NADH dehydrogenase subunit B; Provisional	Back alignment and domain information

>gnl\|CDD\|214337 CHL00023, ndhK, NADH dehydrogenase subunit K	Back alignment and domain information

>gnl\|CDD\|173275 PRK14814, PRK14814, NADH dehydrogenase subunit B; Provisional	Back alignment and domain information

>gnl\|CDD\|173278 PRK14817, PRK14817, NADH dehydrogenase subunit B; Provisional	Back alignment and domain information

>gnl\|CDD\|233657 TIGR01961, NuoC_fam, NADH (or F420H2) dehydrogenase, subunit C	Back alignment and domain information

>gnl\|CDD\|223921 COG0852, NuoC, NADH:ubiquinone oxidoreductase 27 kD subunit [Energy production and conversion]	Back alignment and domain information

>gnl\|CDD\|225799 COG3260, COG3260, Ni,Fe-hydrogenase III small subunit [Energy production and conversion]	Back alignment and domain information

>gnl\|CDD\|216271 pfam01058, Oxidored_q6, NADH ubiquinone oxidoreductase, 20 Kd subunit	Back alignment and domain information

>gnl\|CDD\|201159 pfam00329, Complex1_30kDa, Respiratory-chain NADH dehydrogenase, 30 Kd subunit	Back alignment and domain information

>gnl\|CDD\|181115 PRK07785, PRK07785, NADH dehydrogenase subunit C; Provisional	Back alignment and domain information

>gnl\|CDD\|181449 PRK08491, PRK08491, NADH dehydrogenase subunit C; Provisional	Back alignment and domain information

>gnl\|CDD\|236081 PRK07735, PRK07735, NADH dehydrogenase subunit C; Validated	Back alignment and domain information

>gnl\|CDD\|183557 PRK12494, PRK12494, NADH dehydrogenase subunit J; Provisional	Back alignment and domain information

>gnl\|CDD\|176955 CHL00012, ndhJ, NADH dehydrogenase subunit J	Back alignment and domain information

>gnl\|CDD\|225801 COG3262, HycE, Ni,Fe-hydrogenase III component G [Energy production and conversion]	Back alignment and domain information

>gnl\|CDD\|224852 COG1941, FrhG, Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]	Back alignment and domain information

>gnl\|CDD\|132337 TIGR03294, FrhG, coenzyme F420 hydrogenase, subunit gamma	Back alignment and domain information

>gnl\|CDD\|180638 PRK06602, PRK06602, NADH:ubiquinone oxidoreductase subunit A; Validated	Back alignment and domain information

>gnl\|CDD\|223908 COG0838, NuoA, NADH:ubiquinone oxidoreductase subunit 3 (chain A) [Energy production and conversion]	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		693
PRK13292		788	trifunctional NADH dehydrogenase I subunit B/C/D;	100.0
PRK11742		575	bifunctional NADH:ubiquinone oxidoreductase subuni	100.0
COG0649		398	NuoD NADH:ubiquinone oxidoreductase 49 kD subunit	100.0
PRK06075		392	NADH dehydrogenase subunit D; Validated	100.0
CHL00017		393	ndhH NADH dehydrogenase subunit 7	100.0
TIGR01962		386	NuoD NADH dehydrogenase I, D subunit. This model r	100.0
PRK12322		366	NADH dehydrogenase subunit D; Provisional	100.0
PRK07415		394	NAD(P)H-quinone oxidoreductase subunit H; Validate	100.0
COG3261		382	HycE Ni,Fe-hydrogenase III large subunit [Energy p	100.0
KOG2870\|consensus		452		100.0
TIGR03295		411	frhA coenzyme F420 hydrogenase, subunit alpha. Thi	100.0
PF00346		272	Complex1_49kDa: Respiratory-chain NADH dehydrogena	100.0
PRK10467		567	hydrogenase 2 large subunit; Provisional	100.0
COG3259		441	FrhA Coenzyme F420-reducing hydrogenase, alpha sub	100.0
PRK10170		597	hydrogenase 1 large subunit; Provisional	100.0
COG0374		545	HyaB Ni,Fe-hydrogenase I large subunit [Energy pro	100.0
PF00374		507	NiFeSe_Hases: Nickel-dependent hydrogenase; InterP	100.0
PRK14818		173	NADH dehydrogenase subunit B; Provisional	100.0
COG0377		194	NuoB NADH:ubiquinone oxidoreductase 20 kD subunit	100.0
PRK14813		189	NADH dehydrogenase subunit B; Provisional	100.0
COG3260		148	Ni,Fe-hydrogenase III small subunit [Energy produc	100.0
CHL00023		225	ndhK NADH dehydrogenase subunit K	100.0
TIGR01957		145	nuoB_fam NADH-quinone oxidoreductase, B subunit. T	100.0
KOG1687\|consensus		168		100.0
PRK14816		182	NADH dehydrogenase subunit B; Provisional	100.0
PRK06411		183	NADH dehydrogenase subunit B; Validated	100.0
PRK14817		181	NADH dehydrogenase subunit B; Provisional	100.0
PRK14815		183	NADH dehydrogenase subunit B; Provisional	100.0
PRK14820		180	NADH dehydrogenase subunit B; Provisional	100.0
PRK14814		186	NADH dehydrogenase subunit B; Provisional	100.0
PRK14819		264	NADH dehydrogenase subunit B; Provisional	100.0
COG0852		176	NuoC NADH:ubiquinone oxidoreductase 27 kD subunit	99.97
CHL00012		158	ndhJ NADH dehydrogenase subunit J	99.97
PRK07735		430	NADH dehydrogenase subunit C; Validated	99.97
PRK07785		235	NADH dehydrogenase subunit C; Provisional	99.97
TIGR01961		121	NuoC_fam NADH (or F420H2) dehydrogenase, subunit C	99.95
PRK06074		189	NADH dehydrogenase subunit C; Provisional	99.94
PRK08491		263	NADH dehydrogenase subunit C; Provisional	99.94
PF00329		103	Complex1_30kDa: Respiratory-chain NADH dehydrogena	99.94
PRK12494		172	NADH dehydrogenase subunit J; Provisional	99.94
PF01058		131	Oxidored_q6: NADH ubiquinone oxidoreductase, 20 Kd	99.93
TIGR03294		228	FrhG coenzyme F420 hydrogenase, subunit gamma. Thi	99.93
KOG1713\|consensus		191		99.92
PRK10468		371	hydrogenase 2 small subunit; Provisional	99.89
TIGR00391		365	hydA hydrogenase (NiFe) small subunit (hydA). Call	99.88
COG1941		247	FrhG Coenzyme F420-reducing hydrogenase, gamma sub	99.86
COG1740		355	HyaA Ni,Fe-hydrogenase I small subunit [Energy pro	99.82
COG3262		165	HycE Ni,Fe-hydrogenase III component G [Energy pro	99.76
KOG4662\|consensus		122		98.55
MTH00092		111	ND3 NADH dehydrogenase subunit 3; Provisional	98.38
CHL00022		120	ndhC NADH dehydrogenase subunit 3	98.29
MTH00136		116	ND3 NADH dehydrogenase subunit 3; Provisional	98.25
PRK06602		121	NADH:ubiquinone oxidoreductase subunit A; Validate	98.23
MTH00042		116	ND3 NADH dehydrogenase subunit 3; Validated	98.22
MTH00106		115	ND3 NADH dehydrogenase subunit 3; Provisional	98.22
MTH00069		114	ND3 NADH dehydrogenase subunit 3; Provisional	98.21
MTH00018		113	ND3 NADH dehydrogenase subunit 3; Validated	98.2
COG0838		123	NuoA NADH:ubiquinone oxidoreductase subunit 3 (cha	98.2
PRK07928		119	NADH dehydrogenase subunit A; Validated	98.19
MTH00113		114	ND3 NADH dehydrogenase subunit 3; Provisional	98.18
MTH00202		117	ND3 NADH dehydrogenase subunit 3; Provisional	98.18
PRK06073		124	NADH dehydrogenase subunit A; Validated	98.18
PRK07756		122	NADH dehydrogenase subunit A; Validated	98.15
MTH00148		117	ND3 NADH dehydrogenase subunit 3; Provisional	98.15
MTH00055		118	ND3 NADH dehydrogenase subunit 3; Provisional	98.15
MTH00203		112	ND3 NADH dehydrogenase subunit 3; Provisional	98.12
MTH00161		113	ND3 NADH dehydrogenase subunit 3; Provisional	98.07
MTH00012		117	ND3 NADH dehydrogenase subunit 3; Validated	98.06
MTH00030		123	ND3 NADH dehydrogenase subunit 3; Provisional	98.04
PRK08489		129	NADH dehydrogenase subunit A; Validated	97.82
PF00507		102	Oxidored_q4: NADH-ubiquinone/plastoquinone oxidore	97.67
PRK06432		144	NADH dehydrogenase subunit A; Validated	97.6
MTH00060		116	ND3 NADH dehydrogenase subunit 3; Provisional	97.59

>PRK13292 trifunctional NADH dehydrogenase I subunit B/C/D; Provisional	Back alignment and domain information

Probab=100.00  E-value=6.2e-153  Score=1315.74  Aligned_cols=633  Identities=46%  Similarity=0.863  Sum_probs=592.8

Q ss_pred             ccccccccccccccccCCCCCchHHHHHhhcCCccccccccc-eeccCCCCccEEEEccccCCCcHHHHHHHHHHcCCCc
Q psy5227          26 GDKLINWTRTSSMWPMTFGLACCAIEMMHAGASRYDLDRFGI-MFRPSPRQSDVMIVAGTLCNKMAPALRKVYDQMTEPK  104 (693)
Q Consensus        26 ~~~rir~~r~~~lw~~~~~c~gc~~e~l~~~~~~~d~~~~~~-~~~~~p~~~Dil~veG~v~~~~~~~~~~~~~~~~~~~  104 (693)
                      -++.++|+|++|+|+++|+|+||++|++++.+|.||++|||+ .+++||||||+++|||+||.+|.+.++++|++||+||
T Consensus        12 ~~~~~~~~r~~s~w~~~~~~~cc~~E~~~~~~~~~D~~r~G~~~~~~sPr~aD~llv~G~vt~~~~~~l~~~~~~~p~pk   91 (788)
T PRK13292         12 LDDLINWGRANSLWPMFFGLSCCFVEMMTSFTSRYDISRFGAEVLRGTPREADLMVIAGTVFKKMAPSILRLYEQMAEPK   91 (788)
T ss_pred             HHHHHHHHhhCCCcceecCCccHHHHHHHhcCCcCCHHHcCCCccCCCcccceEEEEecCCcHhhHHHHHHHHHhCCCCC
Confidence            356789999999999999999999999999999999999999 5899999999999999999999999999999999999


Q ss_pred             eEEeecccCCCCCcCCcCCccccCcceeeecceeccCCCCChhhhHHHHHHHHHHHhh----------------------
Q psy5227         105 WVISMGSCANGGGYYHYSYSVVRGCDRIVPVDVYIPGCPPTAEALLYDYYSTMKILRD----------------------  162 (693)
Q Consensus       105 ~vva~G~CA~~GGi~~~~~~~~~~~~~~v~vd~~ipGCPp~p~~i~~~l~~ll~~Lr~----------------------  162 (693)
                      +|||+|+||++||+| ++|+.+.|+++++|||++||||||+|++|++++..+.+.++.                      
T Consensus        92 ~via~G~Ca~~GG~~-~~y~~~~g~~~~ipVDv~iPGCPP~Pe~i~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (788)
T PRK13292         92 WVISMGSCANSGGMY-DVYSVVQGVNQILPVDVYIPGCPPRPEAFLQGLMLLQEKIRREERPARPVLHLQGGSQGTTRPI  170 (788)
T ss_pred             EEEEecccccCCCCc-CccccccCcCCcccccEEccCCCCCHHHHHHHHHHHHHHhhcCcccchhhhhhccCCcccCccc
Confidence            999999999999999 799999999999999999999999999999988876443321                      


Q ss_pred             --------------------------------------------------------------------------------
Q psy5227         163 --------------------------------------------------------------------------------  162 (693)
Q Consensus       163 --------------------------------------------------------------------------------  162 (693)
                                                                                                      
T Consensus       171 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~f~~~v~~~~~~~~~~~~~v  250 (788)
T PRK13292        171 LVDGATKSRDTRGPGMEGIAIRGTAVQHPRFAGSRSDEMWRPPAPKHPYPDFGLAGELEGAFGDDVRLDEGATDMLTYRC  250 (788)
T ss_pred             eeccccccccccCCCcccccccccccCCCcccccchhhhcCCCcccCCCCHHHHHHHHHHHcccceEeeeecCCcEEEEE
Confidence                                                                                            


Q ss_pred             --------------hcccccccccccccccccccccccCCCCCCCCCcEEEEEEeeccccCeEEEEEEeecCCCCCCcCc
Q psy5227         163 --------------HVNFRFEQLIDLCGIDYSIYNKNINSDNSNKNLRFAIVLHLLSLNYNWRLRVRVFAENNELPRLHS  228 (693)
Q Consensus       163 --------------~~~~~fd~L~~~~~vd~~~~~~~~~~~~~~~~~~~~~vyh~~~~~~~~~l~v~v~~~~~~~~~~~s  228 (693)
                                    +.+.+|++|.++|||||..+..      ...+++|+++|||.|+..+.+++|+|.+++ ++|++||
T Consensus       251 ~~e~l~~v~~~Lk~~~~~~f~~L~ditaVD~~~~~~------~~~~~~f~vvY~l~s~~~~~~i~vkv~~~~-~~p~~pS  323 (788)
T PRK13292        251 PPELVPEVLRHLKKRASSPFRRLEDLAAVDESCRRD------REKFPDFTVNYHLLSFDTPGHVRIKTELRG-RTPELPS  323 (788)
T ss_pred             cHHHHHHHHHHHHhCcCCCCceeeeEEEEeCCcccc------cCcCCcEEEEEEEEeCCCCcEEEEEEEeCC-CCCCCCc
Confidence                          1123588889999999863211      113568999999999998889999999887 7899999


Q ss_pred             ccccccccchhhhhhccccCceecCCCCCccccccCCCCCCCCCCCCcch---------------------------hhc
Q psy5227         229 ITSLWSSANWYEREAFDLFGIFFDGHDDLRRLLTDYGFVGHPFRKDFPVI---------------------------EIK  281 (693)
Q Consensus       229 ~~~~~~~a~~~Ere~~d~~Gi~~~g~pd~r~~~~~~~~~~~plrk~~~~~---------------------------~~~  281 (693)
                      |+++||+|+|+|||+||||||.|+||||+|||++|++|++|||||||+..                           +++
T Consensus       324 l~~i~p~A~~~ERE~~D~~Gi~f~ghPdlrr~l~~~~w~~~PLRkD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  403 (788)
T PRK13292        324 ATGVFPAANWYEREAFDMFGIRFAGHPNLRRILMPPDWEGHPLRKEHPFRATEMPPYTRDDARRLQPLPAGDFFDRVDEE  403 (788)
T ss_pred             hHhhhccCChhHHHHHHhcCceeCCCCCCccccCCccCCCCCCCCCCCCCccccCcccccccccccccccccccccCCCc
Confidence            99999999999999999999999999999999999999999999998742                           224


Q ss_pred             cccccCcccCCCCccceEEEEEEcCCeEEEEEeeeccchhhHHHHhhCCCcCccccccccccccchhhHHHHHHHHHHHH
Q psy5227         282 SYKLNFGPQHPAAHGVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMCNEHAYVMAIEKL  361 (693)
Q Consensus       282 ~~~~~~GP~hp~~~G~~r~~l~v~Ge~I~~~~~~~g~~hRG~Ekllegr~~~~a~~l~~RIcGic~~ah~~A~~~AvE~a  361 (693)
                      .+++++||+||+++|++||++.++||+|+++++++||.|||+||++|+|++.|++++++||||+|+++|++|||+|||++
T Consensus       404 ~~~l~vGP~Hpg~~gp~rf~l~ldGE~I~~~e~~iGY~HRGiEKl~E~r~~~q~i~l~eRi~g~~s~~~~~ay~~AVE~l  483 (788)
T PRK13292        404 TLILNLGPQHPGTHGIIRFVLKLDGEEIVDMDSDIGYHHRGAEKIGERQHWNQFIPYTDRIDYLAGVQNNLAYVNSVETL  483 (788)
T ss_pred             eEEEecCCCCCCCCCCeEEEEEEcCCEEEEEEeecCchhHHHHHHHcCCCHHHhchhhcccccchhhHHHHHHHHHHHHH
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHccCCccCCceeeCccccCCCC
Q psy5227         362 LNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIGAMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDLPE  441 (693)
Q Consensus       362 ~gievp~ra~~lR~ll~elerI~sHl~~lg~~~~~~g~~~~~~~~~~~Re~~~~i~~~~~G~r~~~~~~~pGGv~~~~~~  441 (693)
                      +|++||+|||++|+|++|+|||+|||+|+|.++.++|+.+.+++++++||+++++++.+||+|+|+++++||||+.|+++
T Consensus       484 ~gievP~RA~~iRvil~ELeRI~sHL~~lg~~~~diG~~t~~~~~~~~RE~i~~l~e~ltG~R~~~~~~rpGGV~~Dl~~  563 (788)
T PRK13292        484 CGIEVPDRAIYIRVMLSELFRIANHLVWLGTFAADVGAMTPVFYTFTDREKIFDIVEMITGGRMHPAWFRIGGVAEDLPE  563 (788)
T ss_pred             hCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHhccccccCCceeCcccccCCH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCccchhhhhhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhccChhhhhccccccccChhhhhhcCCccccc
Q psy5227         442 IMPQYKSSIIRNNKATKILNENRQGSLLDFIEDFTNRFPKNIDEYETLLTDNRIWKQRLVGIGVVSPERALSMGFTGPML  521 (693)
Q Consensus       442 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~R~~~~G~l~~~~a~~~g~~Gp~a  521 (693)
                      +                         ++++++++++.+++.++++.+++.+|+++.+|++|+|+++.++|.++|++||++
T Consensus       564 ~-------------------------~~~~i~~~l~~~~~~l~e~~~l~~~n~i~~~R~~gvGvls~e~A~~~G~tGP~a  618 (788)
T PRK13292        564 G-------------------------WKEAVEAFLRWFPGRLKEYEDLLTGNPIFKARLKGVGVITRDEAVEWGISGPNL  618 (788)
T ss_pred             H-------------------------HHHHHHHHHHHHHHHHHHHHHHHhcCchHHhhcCCEEecCHHHHHHhCCcccee
Confidence            7                         899999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCccCCCCCcCCcccccccccccccCCCCChHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCcccCCCcccchhhhhh
Q psy5227         522 RGSGVKWDLRKKQPYEIYNLLNFDIPIGKNGDSYDRYLVRIEEMRQSNKIIKQCIKWLRSNKGPVISNNNKITSPARINM  601 (693)
Q Consensus       522 RasG~~~D~R~~~py~~Y~~~~~~~~~~~~gd~~aR~~vR~~Ei~~s~~ii~q~l~~l~~~~g~~~~~~~~~~~p~~~~~  601 (693)
                      ||||+++|+|++.||..|++++|++++.++||+|||++||+.||.||++||+|+++++|  +|++......+.+|.+.+.
T Consensus       619 RASGv~~D~Rk~~PY~~Y~~ldf~v~v~~~GD~~aR~~VR~~Ei~eSl~II~Q~l~~lp--~G~~~~~~~~~~~p~~~~~  696 (788)
T PRK13292        619 RACGLAWDLRKKMPYGGYDRFDFEVPTAEGGDCYARYLVRMEEMRQSLRIVRQAAAGMP--GGRWISDDYRYVLPQKRDT  696 (788)
T ss_pred             ecccCccccccCCCccccccCCcCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhCC--CCCccccccccCCcccccc
Confidence            99999999999999999999999999999999999999999999999999999999999  8887665544445544445


Q ss_pred             chhhhhhhhhhcccccccccCcceEEEEeeCCcceeEEEEEECCCCceeEEEEeCCcccCHHHHHHHHcCCChhhHHHHh
Q psy5227         602 KSNMEDLIHHFKLFTEGFYVPLGEIYSCVEHPKGEFGIYLVSDGANKPYRIKIRSPGFAHLQSLSEMISGHMISDVVTII  681 (693)
Q Consensus       602 ~~~~~~~i~~~~~~~~~~~~~~Geg~g~vEapRG~L~h~v~~d~~g~i~r~~i~~PS~~N~~~le~~l~G~~i~d~~~ii  681 (693)
                      ..++|++|+||.....+..+|.|++++.+|||||+++||+++|++++++|++||+||+.||++|+.+++|+.++|+++|+
T Consensus       697 ~~~~e~~i~~f~~~~~~~~~p~Ge~~~~vEapRGE~~~yv~sdg~~~pyR~kIR~PSf~Nl~al~~~~~G~~iaD~~~i~  776 (788)
T PRK13292        697 LKDIESLIHHFVNVTRGPAPPKGECYAAIEAPKGENGYFVVSDGLNIAYRMRIRTPSFPHIQALPLLSRGWLVADFLAII  776 (788)
T ss_pred             ccchHHhhhhccccccCCCCCCceEEEEEEcCCceEEEEEEECCCCcEEEEEEeCCCHhHHHHHHHHHCCCeechHHHHh
Confidence            57899999999988777778899999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccccccCCC
Q psy5227         682 GTQDIVFGEIDR  693 (693)
Q Consensus       682 ~S~DpC~sc~dr  693 (693)
                      +|||||++|+||
T Consensus       777 ~S~D~v~ge~DR  788 (788)
T PRK13292        777 GSIDFVLADLDR  788 (788)
T ss_pred             hCcCCCcCCCCC
Confidence            999999999998

>PRK11742 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional	Back alignment and domain information

>COG0649 NuoD NADH:ubiquinone oxidoreductase 49 kD subunit 7 [Energy production and conversion]	Back alignment and domain information

>PRK06075 NADH dehydrogenase subunit D; Validated	Back alignment and domain information

>CHL00017 ndhH NADH dehydrogenase subunit 7	Back alignment and domain information

>TIGR01962 NuoD NADH dehydrogenase I, D subunit	Back alignment and domain information

>PRK12322 NADH dehydrogenase subunit D; Provisional	Back alignment and domain information

>PRK07415 NAD(P)H-quinone oxidoreductase subunit H; Validated	Back alignment and domain information

>COG3261 HycE Ni,Fe-hydrogenase III large subunit [Energy production and conversion]	Back alignment and domain information

>KOG2870\|consensus	Back alignment and domain information

>TIGR03295 frhA coenzyme F420 hydrogenase, subunit alpha	Back alignment and domain information

>PF00346 Complex1_49kDa: Respiratory-chain NADH dehydrogenase, 49 Kd subunit; InterPro: IPR001135 This entry represents subunit D (NuoD) of NADH-quinone oxidoreductase (1	Back alignment and domain information

>PRK10467 hydrogenase 2 large subunit; Provisional	Back alignment and domain information

>COG3259 FrhA Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]	Back alignment and domain information

>PRK10170 hydrogenase 1 large subunit; Provisional	Back alignment and domain information

>COG0374 HyaB Ni,Fe-hydrogenase I large subunit [Energy production and conversion]	Back alignment and domain information

>PF00374 NiFeSe_Hases: Nickel-dependent hydrogenase; InterPro: IPR001501 Hydrogenases are enzymes that catalyze the reversible activation of hydrogen and which occur widely in prokaryotes as well as in some eukaryotes	Back alignment and domain information

>PRK14818 NADH dehydrogenase subunit B; Provisional	Back alignment and domain information

>COG0377 NuoB NADH:ubiquinone oxidoreductase 20 kD subunit and related Fe-S oxidoreductases [Energy production and conversion]	Back alignment and domain information

>PRK14813 NADH dehydrogenase subunit B; Provisional	Back alignment and domain information

>COG3260 Ni,Fe-hydrogenase III small subunit [Energy production and conversion]	Back alignment and domain information

>CHL00023 ndhK NADH dehydrogenase subunit K	Back alignment and domain information

>TIGR01957 nuoB_fam NADH-quinone oxidoreductase, B subunit	Back alignment and domain information

>KOG1687\|consensus	Back alignment and domain information

>PRK14816 NADH dehydrogenase subunit B; Provisional	Back alignment and domain information

>PRK06411 NADH dehydrogenase subunit B; Validated	Back alignment and domain information

>PRK14817 NADH dehydrogenase subunit B; Provisional	Back alignment and domain information

>PRK14815 NADH dehydrogenase subunit B; Provisional	Back alignment and domain information

>PRK14820 NADH dehydrogenase subunit B; Provisional	Back alignment and domain information

>PRK14814 NADH dehydrogenase subunit B; Provisional	Back alignment and domain information

>PRK14819 NADH dehydrogenase subunit B; Provisional	Back alignment and domain information

>COG0852 NuoC NADH:ubiquinone oxidoreductase 27 kD subunit [Energy production and conversion]	Back alignment and domain information

>CHL00012 ndhJ NADH dehydrogenase subunit J	Back alignment and domain information

>PRK07735 NADH dehydrogenase subunit C; Validated	Back alignment and domain information

>PRK07785 NADH dehydrogenase subunit C; Provisional	Back alignment and domain information

>TIGR01961 NuoC_fam NADH (or F420H2) dehydrogenase, subunit C	Back alignment and domain information

>PRK06074 NADH dehydrogenase subunit C; Provisional	Back alignment and domain information

>PRK08491 NADH dehydrogenase subunit C; Provisional	Back alignment and domain information

>PF00329 Complex1_30kDa: Respiratory-chain NADH dehydrogenase, 30 Kd subunit; InterPro: IPR001268 NADH:ubiquinone oxidoreductase (complex I) (1	Back alignment and domain information

>PRK12494 NADH dehydrogenase subunit J; Provisional	Back alignment and domain information

>PF01058 Oxidored_q6: NADH ubiquinone oxidoreductase, 20 Kd subunit; InterPro: IPR006137 NADH:ubiquinone oxidoreductase (complex I) (1	Back alignment and domain information

>TIGR03294 FrhG coenzyme F420 hydrogenase, subunit gamma	Back alignment and domain information

>KOG1713\|consensus	Back alignment and domain information

>PRK10468 hydrogenase 2 small subunit; Provisional	Back alignment and domain information

>TIGR00391 hydA hydrogenase (NiFe) small subunit (hydA)	Back alignment and domain information

>COG1941 FrhG Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]	Back alignment and domain information

>COG1740 HyaA Ni,Fe-hydrogenase I small subunit [Energy production and conversion]	Back alignment and domain information

>COG3262 HycE Ni,Fe-hydrogenase III component G [Energy production and conversion]	Back alignment and domain information

>KOG4662\|consensus	Back alignment and domain information

>MTH00092 ND3 NADH dehydrogenase subunit 3; Provisional	Back alignment and domain information

>CHL00022 ndhC NADH dehydrogenase subunit 3	Back alignment and domain information

>MTH00136 ND3 NADH dehydrogenase subunit 3; Provisional	Back alignment and domain information

>PRK06602 NADH:ubiquinone oxidoreductase subunit A; Validated	Back alignment and domain information

>MTH00042 ND3 NADH dehydrogenase subunit 3; Validated	Back alignment and domain information

>MTH00106 ND3 NADH dehydrogenase subunit 3; Provisional	Back alignment and domain information

>MTH00069 ND3 NADH dehydrogenase subunit 3; Provisional	Back alignment and domain information

>MTH00018 ND3 NADH dehydrogenase subunit 3; Validated	Back alignment and domain information

>COG0838 NuoA NADH:ubiquinone oxidoreductase subunit 3 (chain A) [Energy production and conversion]	Back alignment and domain information

>PRK07928 NADH dehydrogenase subunit A; Validated	Back alignment and domain information

>MTH00113 ND3 NADH dehydrogenase subunit 3; Provisional	Back alignment and domain information

>MTH00202 ND3 NADH dehydrogenase subunit 3; Provisional	Back alignment and domain information

>PRK06073 NADH dehydrogenase subunit A; Validated	Back alignment and domain information

>PRK07756 NADH dehydrogenase subunit A; Validated	Back alignment and domain information

>MTH00148 ND3 NADH dehydrogenase subunit 3; Provisional	Back alignment and domain information

>MTH00055 ND3 NADH dehydrogenase subunit 3; Provisional	Back alignment and domain information

>MTH00203 ND3 NADH dehydrogenase subunit 3; Provisional	Back alignment and domain information

>MTH00161 ND3 NADH dehydrogenase subunit 3; Provisional	Back alignment and domain information

>MTH00012 ND3 NADH dehydrogenase subunit 3; Validated	Back alignment and domain information

>MTH00030 ND3 NADH dehydrogenase subunit 3; Provisional	Back alignment and domain information

>PRK08489 NADH dehydrogenase subunit A; Validated	Back alignment and domain information

>PF00507 Oxidored_q4: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3; InterPro: IPR000440 NADH:ubiquinone oxidoreductase (complex I) (1	Back alignment and domain information

>PRK06432 NADH dehydrogenase subunit A; Validated	Back alignment and domain information

>MTH00060 ND3 NADH dehydrogenase subunit 3; Provisional	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		693
2fug_4		409	Crystal Structure Of The Hydrophilic Domain Of Resp		1e-101
2fug_6		181	Crystal Structure Of The Hydrophilic Domain Of Resp		7e-40
2fug_5		207	Crystal Structure Of The Hydrophilic Domain Of Resp		5e-17
3mcr_A		213	Crystal Structure Of Nadh Dehydrogenase Subunit C (		7e-08

>pdb|2FUG|4 Chain 4, Crystal Structure Of The Hydrophilic Domain Of Respiratory Complex I From Thermus Thermophilus Length = 409

Back alignment and structure

Iteration: 1

Score = 367 bits (941), Expect = e-101, Method: Compositional matrix adjust. Identities = 188/410 (45%), Positives = 259/410 (63%), Gaps = 29/410 (7%) Query: 285 LNFGPQHPAAHGVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDY 344 LN GPQHP+ HGVLRL++ L GE V + PHIG LH EK E RTYLQ++ Y R+DY Sbjct: 28 LNVGPQHPSTHGVLRLMVTLSGEEVLEVVPHIGYLHTGFEKTMEHRTYLQNITYTPRMDY 87 Query: 345 VSMMCNEHAYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIGAMGVLL 404 + ++ AY +A+EKLL +P RA+ IRV+ +E++RL +HL+++G+ LD+GA+ Sbjct: 88 LHSFAHDLAYALAVEKLLGAVVPPRAETIRVILNELSRLASHLVFLGTGLLDLGALTPFF 147 Query: 405 YAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDLP-EIMPQYKSSIIRNNKATKILNEN 463 YAFRERE +LD +E V+G R H Y R GGV DLP E +P+ K Sbjct: 148 YAFRERETILDLFEWVTGQRFHHNYIRIGGVKEDLPEEFVPELK---------------- 191 Query: 464 RQGSLLDFIEDFTNRFPKNIDEYETLLTDNRIWKQRLVGIGVVSPERALSMGFTGPMLRG 523 LL+ + P IDEYE L ++ I+ +R G+GV+ PE A+ +G TG LR Sbjct: 192 ---KLLEVL-------PHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGSLRA 241 Query: 524 SGVKWDLRKKQPYEIYNLLNFDIPIGKNGDSYDRYLVRIEEMRQSNKIIKQCIKWLRSNK 583 SGV +D+RK PY Y FD+P+G+ GD +DR LVRI EMR+S KIIKQ ++ R Sbjct: 242 SGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALE--RLEP 299 Query: 584 GPVISNNNKITSPARINMKSNMEDLIHHFKLFTEGFYVPLGEIYSCVEHPKGEFGIYLVS 643 GPV N +IT P R ++++ME +I+HFK +TEGF+ P GE+Y E +GE G Y+VS Sbjct: 300 GPVRDPNPQITPPPRHLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGELGYYIVS 359 Query: 644 DGANKPYRIKIRSPGFAHLQSLSEMISGHMISDVVTIIGTQDIVFGEIDR 693 DG + PYR+K+R+P F +LQSL G + D+V II + D V G++DR Sbjct: 360 DGGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR 409

PyMOL of 2fug

>pdb|2FUG|6 Chain 6, Crystal Structure Of The Hydrophilic Domain Of Respiratory Complex I From Thermus Thermophilus Length = 181

Back alignment and structure

>pdb|2FUG|5 Chain 5, Crystal Structure Of The Hydrophilic Domain Of Respiratory Complex I From Thermus Thermophilus Length = 207

Back alignment and structure

>pdb|3MCR|A Chain A, Crystal Structure Of Nadh Dehydrogenase Subunit C (Tfu_2693) From Thermobifida Fusca Yx-Er1 At 2.65 A Resolution Length = 213

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		693
3i9v_4		409	NADH-quinone oxidoreductase subunit 4; electron tr	0.0
3i9v_6		181	NADH-quinone oxidoreductase subunit 6; electron tr	3e-91
3i9v_5		207	NADH-quinone oxidoreductase subunit 5; electron tr	4e-51
3mcr_A		213	NADH dehydrogenase, subunit C; structural genomics	4e-42
1cc1_S		283	Hydrogenase (small subunit); NI-Fe-Se hydrogenase,	3e-10
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-10
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-09
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04
2wpn_A		317	Periplasmic [nifese] hydrogenase, small subunit; m	4e-09
1h2a_S		317	Hydrogenase; SO ligand, hydrogen metabolism, Mg ce	7e-09
3ayx_B		283	Membrane-bound hydrogenase small subunit; oxidored	1e-07
1yqw_A		264	Periplasmic [NIFE] hydrogenase small subunit; NI-F	2e-07
1wui_S		267	Periplasmic [NIFE] hydrogenase small subunit; high	2e-07
2wpn_B		495	Periplasmic [nifese] hydrogenase, large subunit, s	8e-07
3rgw_S		339	Membrane-bound hydrogenase (NIFE) small subunit H;	8e-07
3uqy_S		335	Hydrogenase-1 small chain; membrane-bound hydrogen	2e-06
1yq9_A		264	Periplasmic [NIFE] hydrogenase small subunit; oxid	4e-06
3rko_A		147	NADH-quinone oxidoreductase subunit A; complex I,	6e-06
1cc1_L		498	Hydrogenase (large subunit); NI-Fe-Se hydrogenase,	7e-05
1wui_L		534	Periplasmic [NIFE] hydrogenase large subunit; high	1e-04
3ayx_A		596	Membrane-bound hydrogenase large subunit; oxidored	2e-04
1e3d_B		542	[NIFE] hydrogenase large subunit; molecular modell	3e-04
1yqw_Q		549	Periplasmic [NIFE] hydrogenase large subunit; NI-F	5e-04
3myr_A		269	Hydrogenase (NIFE) small subunit HYDA; [NIFE] hydr	5e-04

>3i9v_4 NADH-quinone oxidoreductase subunit 4; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_4* 2fug_4* 3iam_4* 3ias_4* 3m9s_4* Length = 409	Back alignment and structure

 Score =  739 bits (1910), Expect = 0.0
 Identities = 184/416 (44%), Positives = 256/416 (61%), Gaps = 27/416 (6%)

Query: 278 IEIKSYKLNFGPQHPAAHGVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLP 337
           +  +   LN GPQHP+ HGVLRL++ L GE V +  PHIG LH   EK  E RTYLQ++ 
Sbjct: 21  LRTEVMTLNVGPQHPSTHGVLRLMVTLSGEEVLEVVPHIGYLHTGFEKTMEHRTYLQNIT 80

Query: 338 YMDRLDYVSMMCNEHAYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDI 397
           Y  R+DY+    ++ AY +A+EKLL   +P RA+ IRV+ +E++RL +HL+++G+  LD+
Sbjct: 81  YTPRMDYLHSFAHDLAYALAVEKLLGAVVPPRAETIRVILNELSRLASHLVFLGTGLLDL 140

Query: 398 GAMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDLPEIMPQYKSSIIRNNKAT 457
           GA+    YAFRERE +LD +E V+G R H  Y R GGV  DLPE                
Sbjct: 141 GALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGVKEDLPE---------------- 184

Query: 458 KILNENRQGSLLDFIEDFTNRFPKNIDEYETLLTDNRIWKQRLVGIGVVSPERALSMGFT 517
                      +  ++      P  IDEYE L  ++ I+ +R  G+GV+ PE A+ +G T
Sbjct: 185 ---------EFVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLT 235

Query: 518 GPMLRGSGVKWDLRKKQPYEIYNLLNFDIPIGKNGDSYDRYLVRIEEMRQSNKIIKQCIK 577
           G  LR SGV +D+RK  PY  Y    FD+P+G+ GD +DR LVRI EMR+S KIIKQ ++
Sbjct: 236 GGSLRASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALE 295

Query: 578 WLRSNKGPVISNNNKITSPARINMKSNMEDLIHHFKLFTEGFYVPLGEIYSCVEHPKGEF 637
            L    GPV   N +IT P R  ++++ME +I+HFK +TEGF+ P GE+Y   E  +GE 
Sbjct: 296 RLEP--GPVRDPNPQITPPPRHLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGEL 353

Query: 638 GIYLVSDGANKPYRIKIRSPGFAHLQSLSEMISGHMISDVVTIIGTQDIVFGEIDR 693
           G Y+VSDG + PYR+K+R+P F +LQSL     G  + D+V II + D V G++DR
Sbjct: 354 GYYIVSDGGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR 409

PyMOL of 3i9v

>3i9v_6 NADH-quinone oxidoreductase subunit 6; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_6* 2fug_6* 3iam_6* 3ias_6* 3m9s_6* Length = 181	Back alignment and structure

>3i9v_5 NADH-quinone oxidoreductase subunit 5; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_5* 2fug_5* 3iam_5* 3ias_5* 3m9s_5* Length = 207	Back alignment and structure

>3mcr_A NADH dehydrogenase, subunit C; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; 2.65A {Thermobifida fusca} Length = 213	Back alignment and structure

>1cc1_S Hydrogenase (small subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfomicrobium baculatum} SCOP: e.19.1.1 Length = 283	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>2wpn_A Periplasmic [nifese] hydrogenase, small subunit; metal-binding, oxidoreductase, oxygen tolerance; HET: FSX SBY PSW; 2.04A {Desulfovibrio vulgaris} Length = 317	Back alignment and structure

>1h2a_S Hydrogenase; SO ligand, hydrogen metabolism, Mg center, MIR, MAD, oxidoreductase; 1.80A {Desulfovibrio vulgaris str} SCOP: e.19.1.1 Length = 317	Back alignment and structure

>3ayx_B Membrane-bound hydrogenase small subunit; oxidoreductase, membrane-bound NI-Fe hydrogenase; 1.18A {Hydrogenovibrio marinus} PDB: 3ayy_B 3ayz_B Length = 283	Back alignment and structure

>1yqw_A Periplasmic [NIFE] hydrogenase small subunit; NI-Fe hydrogenase unready state, oxidoreductase; 1.83A {Desulfovibrio fructosovorans} PDB: 3cur_A 3cus_A 3h3x_A 1yrq_A 1frf_S Length = 264	Back alignment and structure

>1wui_S Periplasmic [NIFE] hydrogenase small subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str} SCOP: e.19.1.1 PDB: 1h2r_S 1ubj_S 1ubh_S 1ubl_S 1ubm_S 1ubo_S 1ubr_S 1ubt_S 1ubu_S 1wuh_S* 1ubk_S* 1wuj_S 1wuk_S 1wul_S 1e3d_A* Length = 267	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

>3rgw_S Membrane-bound hydrogenase (NIFE) small subunit H; [NIFE] hydrogenase, high-resolution knallgasbacteria, proteobacteria; 1.50A {Ralstonia eutropha} Length = 339	Back alignment and structure

>3uqy_S Hydrogenase-1 small chain; membrane-bound hydrogenase, oxidoreductase; HET: LMT; 1.47A {Escherichia coli} PDB: 3usc_S* 3use_S* Length = 335	Back alignment and structure

>1yq9_A Periplasmic [NIFE] hydrogenase small subunit; oxidoreductase; 2.35A {Desulfovibrio gigas} SCOP: e.19.1.1 PDB: 2frv_S 1frv_A Length = 264	Back alignment and structure

>3rko_A NADH-quinone oxidoreductase subunit A; complex I, proton pump, membrane protein, Na ubiquinone, cytoplasmic membrane; HET: LFA CA7; 3.00A {Escherichia coli} Length = 147	Back alignment and structure

>1cc1_L Hydrogenase (large subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfomicrobium baculatum} SCOP: e.18.1.1 Length = 498	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

>3ayx_A Membrane-bound hydrogenase large subunit; oxidoreductase, membrane-bound NI-Fe hydrogenase; 1.18A {Hydrogenovibrio marinus} PDB: 3ayy_A 3ayz_A 3rgw_L Length = 596	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

>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

>3myr_A Hydrogenase (NIFE) small subunit HYDA; [NIFE] hydrogenase, photosynthetic P sulfur bacterium, iron-sulfur cluster, NI-A state; HET: SF4; 2.10A {Allochromatium vinosum} Length = 269	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		693
3i9v_4		409	NADH-quinone oxidoreductase subunit 4; electron tr	100.0
2wpn_B		495	Periplasmic [nifese] hydrogenase, large subunit, s	100.0
1wui_L		534	Periplasmic [NIFE] hydrogenase large subunit; high	100.0
1yqw_Q		549	Periplasmic [NIFE] hydrogenase large subunit; NI-F	100.0
1cc1_L		498	Hydrogenase (large subunit); NI-Fe-Se hydrogenase,	100.0
1e3d_B		542	[NIFE] hydrogenase large subunit; molecular modell	100.0
1yq9_H		536	Periplasmic [NIFE] hydrogenase large subunit; oxid	100.0
3ayx_A		596	Membrane-bound hydrogenase large subunit; oxidored	100.0
3myr_B		561	Nickel-dependent hydrogenase large subunit; [NIFE]	100.0
3uqy_L		582	Hydrogenase-1 large chain; membrane-bound hydrogen	100.0
3i9v_6		181	NADH-quinone oxidoreductase subunit 6; electron tr	100.0
3i9v_5		207	NADH-quinone oxidoreductase subunit 5; electron tr	100.0
1yq9_A		264	Periplasmic [NIFE] hydrogenase small subunit; oxid	99.95
1wui_S		267	Periplasmic [NIFE] hydrogenase small subunit; high	99.95
1h2a_S		317	Hydrogenase; SO ligand, hydrogen metabolism, Mg ce	99.95
1cc1_S		283	Hydrogenase (small subunit); NI-Fe-Se hydrogenase,	99.95
2wpn_A		317	Periplasmic [nifese] hydrogenase, small subunit; m	99.95
3ayx_B		283	Membrane-bound hydrogenase small subunit; oxidored	99.94
1yqw_A		264	Periplasmic [NIFE] hydrogenase small subunit; NI-F	99.93
3rgw_S		339	Membrane-bound hydrogenase (NIFE) small subunit H;	99.93
3myr_A		269	Hydrogenase (NIFE) small subunit HYDA; [NIFE] hydr	99.93
3uqy_S		335	Hydrogenase-1 small chain; membrane-bound hydrogen	99.93
3mcr_A		213	NADH dehydrogenase, subunit C; structural genomics	99.9
3rko_A		147	NADH-quinone oxidoreductase subunit A; complex I,	98.26

>3i9v_4 NADH-quinone oxidoreductase subunit 4; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_4* 2fug_4* 3iam_4* 3ias_4* 3m9s_4*	Back alignment and structure

Probab=100.00  E-value=5.2e-100  Score=828.50  Aligned_cols=387  Identities=48%  Similarity=0.847  Sum_probs=371.8

Q ss_pred             hccccccCcccCCCCccceEEEEEEcCCeEEEEEeeeccchhhHHHHhhCCCcCccccccccccccchhhHHHHHHHHHH
Q psy5227         280 IKSYKLNFGPQHPAAHGVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMCNEHAYVMAIE  359 (693)
Q Consensus       280 ~~~~~~~~GP~hp~~~G~~r~~l~v~Ge~I~~~~~~~g~~hRG~Ekllegr~~~~a~~l~~RIcGic~~ah~~A~~~AvE  359 (693)
                      .+.+++|+||+||++|||+||.+.++||+|+++++++||.||||||+++||++.|++++++||||+|+++|++||++|+|
T Consensus        23 ~~~~~l~~GP~Hp~~~G~lrl~l~ldge~V~~a~~~~g~~hRG~Ekl~egr~~~~~~~~~~Ricgic~~~h~~A~~~AvE  102 (409)
T 3i9v_4           23 TEVMTLNVGPQHPSTHGVLRLMVTLSGEEVLEVVPHIGYLHTGFEKTMEHRTYLQNITYTPRMDYLHSFAHDLAYALAVE  102 (409)
T ss_dssp             ---CBCCBC-------CCCEECCBCSSSSCCBCCEECCTTCCCHHHHGGGSCTTGGGGTSTTSSSSSCHHHHHHHHHHHH
T ss_pred             CCeEEEEeCCCCCCCCCceEEEEEEeCCEEEEEEEEecCCchhHHHHHcCCCHHHHHHHhhhhhhccHHHHHHHHHHHHH
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHccCCccCCceeeCccccCC
Q psy5227         360 KLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIGAMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDL  439 (693)
Q Consensus       360 ~a~gievp~ra~~lR~ll~elerI~sHl~~lg~~~~~~g~~~~~~~~~~~Re~~~~i~~~~~G~r~~~~~~~pGGv~~~~  439 (693)
                      +++|+++|++|+++|+|++|+|||+|||+|++.++.|+|+.+.+++++++||.++++++.+||+|+|+++++||||++|+
T Consensus       103 ~~~gievP~ra~~iR~l~~eleRI~sHll~lg~~a~d~G~~t~~~~~~~~RE~~~~i~e~~~G~R~h~~~~~pGGv~~dl  182 (409)
T 3i9v_4          103 KLLGAVVPPRAETIRVILNELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGVKEDL  182 (409)
T ss_dssp             HHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHSSSSSCCCBCSSBBSSCC
T ss_pred             HHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHHHHHHHHcCCccccCceeeCCeecCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCccchhhhhhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhccChhhhhccccccccChhhhhhcCCccc
Q psy5227         440 PEIMPQYKSSIIRNNKATKILNENRQGSLLDFIEDFTNRFPKNIDEYETLLTDNRIWKQRLVGIGVVSPERALSMGFTGP  519 (693)
Q Consensus       440 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~R~~~~G~l~~~~a~~~g~~Gp  519 (693)
                      +++                         +++++.+.++++++.++++.+++.+|++|.+|++|+|+++.++|.+||+|||
T Consensus       183 ~~~-------------------------~~~~i~~~l~~~~~~~~e~~~l~~~n~i~~~R~~gvGvl~~e~A~~~g~tGp  237 (409)
T 3i9v_4          183 PEE-------------------------FVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGG  237 (409)
T ss_dssp             CTT-------------------------HHHHHHHHHHHHHHHHHHHHHHHHSCTTHHHHHSSSSCBCHHHHHHHTCCSS
T ss_pred             CHH-------------------------HHHHHHHHHHHHHHHHHHHHHHHhhChHHHhhcCCccccCHHHHHHhCCcCc
Confidence            998                         8889999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCccCCCCCcCCcccccccccccccCCCCChHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCcccCCCcccchhhh
Q psy5227         520 MLRGSGVKWDLRKKQPYEIYNLLNFDIPIGKNGDSYDRYLVRIEEMRQSNKIIKQCIKWLRSNKGPVISNNNKITSPARI  599 (693)
Q Consensus       520 ~aRasG~~~D~R~~~py~~Y~~~~~~~~~~~~gd~~aR~~vR~~Ei~~s~~ii~q~l~~l~~~~g~~~~~~~~~~~p~~~  599 (693)
                      ++||||+++|+|+++||..|++++|++|++++||+|||++||+.|+.||++||+|++++||  +|++..+.+...+|.+.
T Consensus       238 ~~RaSGv~~D~R~~~PY~~Y~~~~f~v~~~~~GD~~aR~~VR~~E~~qSl~ii~q~l~~lp--~G~~~~~~~~~~~p~~~  315 (409)
T 3i9v_4          238 SLRASGVNYDVRKAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALERLE--PGPVRDPNPQITPPPRH  315 (409)
T ss_dssp             SSGGGTCCCCHHHHSCCSSGGGSCCCCCCCSSBCHHHHHHHHHHHHHHHHHHHHHHHHTCC--CCCCBCCCTTTSCCCGG
T ss_pred             ccccCCCccchhhcCcchhhccCCCCCccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhCC--CCCcccccccccCCchh
Confidence            9999999999999999999999999999999999999999999999999999999999999  89999888877788899


Q ss_pred             hhchhhhhhhhhhcccccccccCcceEEEEeeCCcceeEEEEEECCCCceeEEEEeCCcccCHHHHHHHHcCCChhhHHH
Q psy5227         600 NMKSNMEDLIHHFKLFTEGFYVPLGEIYSCVEHPKGEFGIYLVSDGANKPYRIKIRSPGFAHLQSLSEMISGHMISDVVT  679 (693)
Q Consensus       600 ~~~~~~~~~i~~~~~~~~~~~~~~Geg~g~vEapRG~L~h~v~~d~~g~i~r~~i~~PS~~N~~~le~~l~G~~i~d~~~  679 (693)
                      +++..+|++|+||++++.++++|+|++|+++|||||+++||+++|++++|+|++||+|||+||++|+.+++|+.++|+++
T Consensus       316 ~~~~~~e~li~hf~~~~~~~~~p~Ge~~~~vEapRGe~~~~~~sdg~~~p~R~kir~Psf~nl~~l~~~~~G~~iaD~~~  395 (409)
T 3i9v_4          316 LLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGELGYYIVSDGGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVA  395 (409)
T ss_dssp             GGGTCHHHHHHHHHHHHSCCCCCSEEEECCEEETTEEEEEEEEECSSSSCSEEEEECHHHHTTTTTTTTTSSSCSGGGTH
T ss_pred             hhhcchHHhhhhhhcccccccCCCceEEEEEEcCCcEEEEEEEECCCCcEEEEEEECCChHHHHHHHHHHCCCcchHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcccccccccCCC
Q psy5227         680 IIGTQDIVFGEIDR  693 (693)
Q Consensus       680 ii~S~DpC~sc~dr  693 (693)
                      |++|||||++|+||
T Consensus       396 i~~S~D~~~~e~DR  409 (409)
T 3i9v_4          396 IIASLDPVMGDVDR  409 (409)
T ss_dssp             HHHTTCCCHHHHHC
T ss_pred             HHhCcCCCcccccC
Confidence            99999999999998

PyMOL of 3i9v

>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

>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

>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

>1cc1_L Hydrogenase (large subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfomicrobium baculatum} SCOP: e.18.1.1	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

>3ayx_A Membrane-bound hydrogenase large subunit; oxidoreductase, membrane-bound NI-Fe hydrogenase; 1.18A {Hydrogenovibrio marinus} PDB: 3ayy_A 3ayz_A 3rgw_L	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} SCOP: e.18.1.0	Back alignment and structure

>3uqy_L Hydrogenase-1 large chain; membrane-bound hydrogenase, oxidoreductase; HET: LMT; 1.47A {Escherichia coli} PDB: 3usc_L* 3use_L*	Back alignment and structure

>3i9v_6 NADH-quinone oxidoreductase subunit 6; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_6* 2fug_6* 3iam_6* 3ias_6* 3m9s_6*	Back alignment and structure

>3i9v_5 NADH-quinone oxidoreductase subunit 5; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_5* 2fug_5* 3iam_5* 3ias_5* 3m9s_5*	Back alignment and structure

>1yq9_A Periplasmic [NIFE] hydrogenase small subunit; oxidoreductase; 2.35A {Desulfovibrio gigas} SCOP: e.19.1.1 PDB: 2frv_S 1frv_A	Back alignment and structure

>1wui_S Periplasmic [NIFE] hydrogenase small subunit; high resolution [NIFE]hydrogenase, oxidoreductase, NI-A state, unready state; HET: NFC; 1.04A {Desulfovibrio vulgaris str} SCOP: e.19.1.1 PDB: 1h2r_S 1ubj_S 1ubh_S 1ubl_S 1ubm_S 1ubo_S 1ubr_S 1ubt_S 1ubu_S 1wuh_S* 1ubk_S* 1wuj_S 1wuk_S 1wul_S 1e3d_A*	Back alignment and structure

>1h2a_S Hydrogenase; SO ligand, hydrogen metabolism, Mg center, MIR, MAD, oxidoreductase; 1.80A {Desulfovibrio vulgaris str} SCOP: e.19.1.1	Back alignment and structure

>1cc1_S Hydrogenase (small subunit); NI-Fe-Se hydrogenase, oxidoreductase; 2.15A {Desulfomicrobium baculatum} SCOP: e.19.1.1	Back alignment and structure

>2wpn_A Periplasmic [nifese] hydrogenase, small subunit; metal-binding, oxidoreductase, oxygen tolerance; HET: FSX SBY PSW; 2.04A {Desulfovibrio vulgaris}	Back alignment and structure

>3ayx_B Membrane-bound hydrogenase small subunit; oxidoreductase, membrane-bound NI-Fe hydrogenase; 1.18A {Hydrogenovibrio marinus} PDB: 3ayy_B 3ayz_B	Back alignment and structure

>1yqw_A Periplasmic [NIFE] hydrogenase small subunit; NI-Fe hydrogenase unready state, oxidoreductase; 1.83A {Desulfovibrio fructosovorans} PDB: 3cur_A 3cus_A 3h3x_A 1yrq_A 1frf_S	Back alignment and structure

>3rgw_S Membrane-bound hydrogenase (NIFE) small subunit H; [NIFE] hydrogenase, high-resolution knallgasbacteria, proteobacteria; 1.50A {Ralstonia eutropha}	Back alignment and structure

>3myr_A Hydrogenase (NIFE) small subunit HYDA; [NIFE] hydrogenase, photosynthetic P sulfur bacterium, iron-sulfur cluster, NI-A state; HET: SF4; 2.10A {Allochromatium vinosum} SCOP: e.19.1.0	Back alignment and structure

>3uqy_S Hydrogenase-1 small chain; membrane-bound hydrogenase, oxidoreductase; HET: LMT; 1.47A {Escherichia coli} PDB: 3usc_S* 3use_S*	Back alignment and structure

>3mcr_A NADH dehydrogenase, subunit C; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; 2.65A {Thermobifida fusca}	Back alignment and structure

>3rko_A NADH-quinone oxidoreductase subunit A; complex I, proton pump, membrane protein, Na ubiquinone, cytoplasmic membrane; HET: LFA CA7; 3.00A {Escherichia coli}	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		693
d2fug41		375	e.18.1.2 (4:35-409) NADH-quinone oxidoreductase ch	1e-123
d2fug61		161	e.19.1.2 (6:15-175) NAD-quinone oxidoreductase cha	1e-59
d1cc1l_		487	e.18.1.1 (L:) Nickel-iron hydrogenase, large subun	2e-49
d1frfl_		543	e.18.1.1 (L:) Nickel-iron hydrogenase, large subun	7e-33
d1yq9h1		530	e.18.1.1 (H:7-536) Nickel-iron hydrogenase, large	5e-32
d2fug51		196	d.307.1.1 (5:1-196) NADH-quinone oxidoreductase ch	2e-29
d1wuil1		534	e.18.1.1 (L:19-552) Nickel-iron hydrogenase, large	5e-29
d1wuil1		534	e.18.1.1 (L:19-552) Nickel-iron hydrogenase, large	1e-25
d1e3db_		537	e.18.1.1 (B:) Nickel-iron hydrogenase, large subun	1e-28
d1wuis1		267	e.19.1.1 (S:1-267) Nickel-iron hydrogenase, small	8e-16
d1yq9a1		261	e.19.1.1 (A:4-264) Nickel-iron hydrogenase, small	6e-14
d1cc1s_		278	e.19.1.1 (S:) Nickel-iron hydrogenase, small subun	4e-13
d1frfs_		261	e.19.1.1 (S:) Nickel-iron hydrogenase, small subun	1e-12

>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 =  370 bits (951), Expect = e-123
 Identities = 178/402 (44%), Positives = 245/402 (60%), Gaps = 27/402 (6%)

Query: 292 PAAHGVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMCNE 351
           P+ HGVLRL++ L GE V +  PHIG LH   EK  E RTYLQ++ Y  R+DY+    ++
Sbjct: 1   PSTHGVLRLMVTLSGEEVLEVVPHIGYLHTGFEKTMEHRTYLQNITYTPRMDYLHSFAHD 60

Query: 352 HAYVMAIEKLLNIKIPIRAQYIRVMFDEITRLLNHLMWIGSHSLDIGAMGVLLYAFRERE 411
            AY +A+EKLL   +P RA+ IRV+ +E++RL +HL+++G+  LD+GA+    YAFRERE
Sbjct: 61  LAYALAVEKLLGAVVPPRAETIRVILNELSRLASHLVFLGTGLLDLGALTPFFYAFRERE 120

Query: 412 DLLDCYEAVSGARMHAAYYRPGGVYRDLPEIMPQYKSSIIRNNKATKILNENRQGSLLDF 471
            +LD +E V+G R H  Y R GGV  DLPE                              
Sbjct: 121 TILDLFEWVTGQRFHHNYIRIGGVKEDLPEEFV-------------------------PE 155

Query: 472 IEDFTNRFPKNIDEYETLLTDNRIWKQRLVGIGVVSPERALSMGFTGPMLRGSGVKWDLR 531
           ++      P  IDEYE L  ++ I+ +R  G+GV+ PE A+ +G TG  LR SGV +D+R
Sbjct: 156 LKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGSLRASGVNYDVR 215

Query: 532 KKQPYEIYNLLNFDIPIGKNGDSYDRYLVRIEEMRQSNKIIKQCIKWLRSNKGPVISNNN 591
           K  PY  Y    FD+P+G+ GD +DR LVRI EMR+S KIIKQ     R   GPV   N 
Sbjct: 216 KAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQA--LERLEPGPVRDPNP 273

Query: 592 KITSPARINMKSNMEDLIHHFKLFTEGFYVPLGEIYSCVEHPKGEFGIYLVSDGANKPYR 651
           +IT P R  ++++ME +I+HFK +TEGF+ P GE+Y   E  +GE G Y+VSDG + PYR
Sbjct: 274 QITPPPRHLLETSMEAVIYHFKHYTEGFHPPKGEVYVPTESARGELGYYIVSDGGSMPYR 333

Query: 652 IKIRSPGFAHLQSLSEMISGHMISDVVTIIGTQDIVFGEIDR 693
           +K+R+P F +LQSL     G  + D+V II + D V G++DR
Sbjct: 334 VKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDVDR 375

PyMOL of d2fug41

>d2fug61 e.19.1.2 (6:15-175) NAD-quinone oxidoreductase chain 6, Nqo6 {Thermus thermophilus [TaxId: 274]} Length = 161	Back information, alignment and structure

>d1cc1l_ e.18.1.1 (L:) Nickel-iron hydrogenase, large subunit {Desulfomicrobium baculatum [TaxId: 899]} Length = 487	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

>d1yq9h1 e.18.1.1 (H:7-536) Nickel-iron hydrogenase, large subunit {Desulfovibrio gigas [TaxId: 879]} Length = 530	Back information, alignment and structure

>d2fug51 d.307.1.1 (5:1-196) NADH-quinone oxidoreductase chain 5, Nqo5 {Thermus thermophilus [TaxId: 274]} Length = 196	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

>d1wuil1 e.18.1.1 (L:19-552) Nickel-iron hydrogenase, large subunit {Desulfovibrio vulgaris [TaxId: 881]} Length = 534	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

>d1wuis1 e.19.1.1 (S:1-267) Nickel-iron hydrogenase, small subunit {Desulfovibrio vulgaris [TaxId: 881]} Length = 267	Back information, alignment and structure

>d1yq9a1 e.19.1.1 (A:4-264) Nickel-iron hydrogenase, small subunit {Desulfovibrio gigas [TaxId: 879]} Length = 261	Back information, alignment and structure

>d1cc1s_ e.19.1.1 (S:) Nickel-iron hydrogenase, small subunit {Desulfomicrobium baculatum [TaxId: 899]} Length = 278	Back information, alignment and structure

>d1frfs_ e.19.1.1 (S:) Nickel-iron hydrogenase, small subunit {Desulfovibrio fructosovorans [TaxId: 878]} Length = 261	Back information, alignment and structure

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		693
d2fug41		375	NADH-quinone oxidoreductase chain 4, Nqo4 {Thermus	100.0
d1wuil1		534	Nickel-iron hydrogenase, large subunit {Desulfovib	100.0
d1cc1l_		487	Nickel-iron hydrogenase, large subunit {Desulfomic	100.0
d1yq9h1		530	Nickel-iron hydrogenase, large subunit {Desulfovib	100.0
d1e3db_		537	Nickel-iron hydrogenase, large subunit {Desulfovib	100.0
d1frfl_		543	Nickel-iron hydrogenase, large subunit {Desulfovib	100.0
d2fug61		161	NAD-quinone oxidoreductase chain 6, Nqo6 {Thermus	100.0
d2fug51		196	NADH-quinone oxidoreductase chain 5, Nqo5 {Thermus	99.97
d1wuis1		267	Nickel-iron hydrogenase, small subunit {Desulfovib	99.91
d1frfs_		261	Nickel-iron hydrogenase, small subunit {Desulfovib	99.9
d1cc1s_		278	Nickel-iron hydrogenase, small subunit {Desulfomic	99.9
d1yq9a1		261	Nickel-iron hydrogenase, small subunit {Desulfovib	99.89

>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=6.9e-77  Score=646.92  Aligned_cols=375  Identities=47%  Similarity=0.847  Sum_probs=337.5

Q ss_pred             CCCccceEEEEEEcCCeEEEEEeeeccchhhHHHHhhCCCcCccccccccccccchhhHHHHHHHHHHHHcCCCCChhhH
Q psy5227         292 PAAHGVLRLILELEGEVVRKADPHIGLLHRATEKLAEQRTYLQSLPYMDRLDYVSMMCNEHAYVMAIEKLLNIKIPIRAQ  371 (693)
Q Consensus       292 p~~~G~~r~~l~v~Ge~I~~~~~~~g~~hRG~Ekllegr~~~~a~~l~~RIcGic~~ah~~A~~~AvE~a~gievp~ra~  371 (693)
                      |++|||+||.+.++||+|+++++++||+||||||+++||++.|++.+|+||||||+++|++|+++|+|+++|+++|++++
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
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHccCCccCCceeeCccccCCCCCCccchhhhh
Q psy5227         372 YIRVMFDEITRLLNHLMWIGSHSLDIGAMGVLLYAFREREDLLDCYEAVSGARMHAAYYRPGGVYRDLPEIMPQYKSSII  451 (693)
Q Consensus       372 ~lR~ll~elerI~sHl~~lg~~~~~~g~~~~~~~~~~~Re~~~~i~~~~~G~r~~~~~~~pGGv~~~~~~~~~~~~~~~~  451 (693)
                      ++|+|++|+||||||++|++.++.+.++.+.+++.+++|+.++++++.++|+|+|+.+++|||++++++..         
T Consensus        81 ~lR~l~~~~e~i~sH~l~~~~l~~~~~~~~~~~~~~~~r~~~~~~~~~~~G~~~h~~~~~~gG~~~~~~~~---------  151 (375)
T d2fug41          81 TIRVILNELSRLASHLVFLGTGLLDLGALTPFFYAFRERETILDLFEWVTGQRFHHNYIRIGGVKEDLPEE---------  151 (375)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHTSSSSSCCCEETTEESSCCCTT---------
T ss_pred             HHHHHHHHHHHHhHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHhcCceeeecceeccceeeCCChH---------
Confidence            99999999999999999999999999999999999999999999999999999999999999999999888         


Q ss_pred             hhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhccChhhhhccccccccChhhhhhcCCcccccCCCCccCCCC
Q psy5227         452 RNNKATKILNENRQGSLLDFIEDFTNRFPKNIDEYETLLTDNRIWKQRLVGIGVVSPERALSMGFTGPMLRGSGVKWDLR  531 (693)
Q Consensus       452 ~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~R~~~~G~l~~~~a~~~g~~Gp~aRasG~~~D~R  531 (693)
                                      .++.+...++.+.+.+.+..+++..++.+..|+.+++.++...+..+|.+||.+|++|++.|.+
T Consensus       152 ----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~  215 (375)
T d2fug41         152 ----------------FVPELKKLLEVLPHRIDEYEALFAESPIFYERARGVGVIPPEVAIDLGLTGGSLRASGVNYDVR  215 (375)
T ss_dssp             ----------------HHHHHHHHTTTTTTTTHHHHHHHSSCSCCTTSCSCCCCSSSCSTTTTTTCCSSCCSSCCTTTTT
T ss_pred             ----------------HHHHHHHHHHhhHHHHHHHHHhhccCcccccccCCcccccchhhhhcCcccccccccccccccc
Confidence                            6667777788888888999999999999999999999999999999999999999999999999


Q ss_pred             CcCCcccccccccccccCCCCChHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCcccCCCcccchhhhhhchhhhhhhhh
Q psy5227         532 KKQPYEIYNLLNFDIPIGKNGDSYDRYLVRIEEMRQSNKIIKQCIKWLRSNKGPVISNNNKITSPARINMKSNMEDLIHH  611 (693)
Q Consensus       532 ~~~py~~Y~~~~~~~~~~~~gd~~aR~~vR~~Ei~~s~~ii~q~l~~l~~~~g~~~~~~~~~~~p~~~~~~~~~~~~i~~  611 (693)
                      ...||..|+..+++.++...||+++|..+|+.|..+|.+++++++...+  .+................+....+....+
T Consensus       216 ~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~s~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  293 (375)
T d2fug41         216 KAYPYSGYETYTFDVPLGERGDVFDRMLVRIREMRESVKIIKQALERLE--PGPVRDPNPQITPPPRHLLETSMEAVIYH  293 (375)
T ss_dssp             CCSSCCCC-----CCCCCCSSSSHHHHHHHHHHHHHHHHHHHHHHHSCC--CSCCBCCCTTTSCCCTTCTTTCTTHHHHH
T ss_pred             cccCcccccccccccccccCCcccccchhhhhhhhcchHHHHHHHHhCC--CCCccccchhhcchhHHHHHhhhhhhhcc
Confidence            9999999999999999999999999999999999999999999999887  66554333222211111222222333333


Q ss_pred             hcccccccccCcceEEEEeeCCcceeEEEEEECCCCceeEEEEeCCcccCHHHHHHHHcCCChhhHHHHhcccccccccC
Q psy5227         612 FKLFTEGFYVPLGEIYSCVEHPKGEFGIYLVSDGANKPYRIKIRSPGFAHLQSLSEMISGHMISDVVTIIGTQDIVFGEI  691 (693)
Q Consensus       612 ~~~~~~~~~~~~Geg~g~vEapRG~L~h~v~~d~~g~i~r~~i~~PS~~N~~~le~~l~G~~i~d~~~ii~S~DpC~sc~  691 (693)
                      ......+++++.|+|+|+||||||+|+||+++|++|+|++|+|++||+||+++|+++++|+.++|+++++||||||+||+
T Consensus       294 ~~~~~~~~~~~~G~g~g~vEApRG~L~H~~~~d~~g~i~~~~ii~PT~~N~~~~e~al~G~~i~D~~~iirSfDpC~sC~  373 (375)
T d2fug41         294 FKHYTEGFHPPKGEVYVPTESARGELGYYIVSDGGSMPYRVKVRAPSFVNLQSLPYACKGEQVPDMVAIIASLDPVMGDV  373 (375)
T ss_dssp             HHHHHSCCCCCSCCCCCCBCCSSSCBCEEEECCSSSSCSEEEECCSHHHHTTTHHHHTTTSCGGGTTHHHHTTCCCHHHH
T ss_pred             ccccccCCcCCCcEEEEEEEcCCeEEEEEEEECCCCcEEEEEEECCCHHHHHHHHHHhCCCchHHHHHHHhcCCCcccCC
Confidence            44445566778999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CC
Q psy5227         692 DR  693 (693)
Q Consensus       692 dr  693 (693)
                      ||
T Consensus       374 dr  375 (375)
T d2fug41         374 DR  375 (375)
T ss_dssp             HC
T ss_pred             CC
Confidence            99

PyMOL of d2fug41

>d1wuil1 e.18.1.1 (L:19-552) Nickel-iron hydrogenase, large subunit {Desulfovibrio vulgaris [TaxId: 881]}	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

>d1yq9h1 e.18.1.1 (H:7-536) Nickel-iron hydrogenase, large subunit {Desulfovibrio gigas [TaxId: 879]}	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

>d1frfl_ e.18.1.1 (L:) Nickel-iron hydrogenase, large subunit {Desulfovibrio fructosovorans [TaxId: 878]}	Back information, alignment and structure

>d2fug61 e.19.1.2 (6:15-175) NAD-quinone oxidoreductase chain 6, Nqo6 {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d2fug51 d.307.1.1 (5:1-196) NADH-quinone oxidoreductase chain 5, Nqo5 {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1wuis1 e.19.1.1 (S:1-267) Nickel-iron hydrogenase, small subunit {Desulfovibrio vulgaris [TaxId: 881]}	Back information, alignment and structure

>d1frfs_ e.19.1.1 (S:) Nickel-iron hydrogenase, small subunit {Desulfovibrio fructosovorans [TaxId: 878]}	Back information, alignment and structure

>d1cc1s_ e.19.1.1 (S:) Nickel-iron hydrogenase, small subunit {Desulfomicrobium baculatum [TaxId: 899]}	Back information, alignment and structure

>d1yq9a1 e.19.1.1 (A:4-264) Nickel-iron hydrogenase, small subunit {Desulfovibrio gigas [TaxId: 879]}	Back information, alignment and structure