254780856

254780856

NADH-quinone oxidoreductase, E subunit

GeneID in NCBI database:8209871Locus tag:CLIBASIA_03755
Protein GI in NCBI database:254780856Protein Accession:YP_003065269.1
Gene range:+(825420, 826076)Protein Length:218aa
Gene description:NADH-quinone oxidoreductase, E subunit
COG prediction:[C] NADH:ubiquinone oxidoreductase 24 kD subunit
KEGG prediction:nuoE; NADH-quinone oxidoreductase, E subunit; K00334 NADH dehydrogenase I subunit E [EC:1.6.5.3]
SEED prediction:NADH-ubiquinone oxidoreductase chain E (EC 1.6.5.3)
Pathway involved in KEGG:Oxidative phosphorylation [PATH:las00190]
Subsystem involved in SEED:Respiratory Complex I
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------22
MSVRRLAEEEFQPSSFSFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFSTGQGDTIRPGPQIDRISSAPAGGLTSLLDNNSKKRGKKKKDDKIS
cccccccccccccccccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHccccHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccEEEEEEcccHHHHHccHHHHHHHHHHHHcccccccccccEEEEEEEEEccccccccEEEEccEEEEcccHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHccccccccHHcccccc
cccccccccccccccccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHcccccEEEEHHHHHHHHcccccccEEEEEEccccccccccHHHHHHHHHHHcccccccccccccEEEEEEEEccccccccEEEEcccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccc
msvrrlaeeefqpssfsfseeSAIWVNEVisryppsrcqsavIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFytqfqlspvgtrahvqvcgttpcmlrgCEKLIEVCRNKihqkplhrnsdgtlswEEVECqgacvnapmvmigkdtyedltPERLEEIIDAFstgqgdtirpgpqidrissapaggltslldnnskkrgkkkkddkis
msvrrlaeeefqpssfsfseesAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIhqkplhrnsdgtlSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFstgqgdtirpgpQIDRissapaggltslldnnskkrgkkkkddkis
MSVRRLAeeefqpssfsfseesAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFSTGQGDTIRPGPQIDRISSAPAGGLTSLLDNNSkkrgkkkkddkIS
**********FQPSSFSFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAF**********************************************
*****************FSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFSTGQGDTIRPGPQIDRISSAPAGGLTSLLDNN**************
****RLAEEEFQPSSFSFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFSTG*******************************************
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MSVRRLAEEEFQPSSFSFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFSTGQGDTIRPGPQIDRISSAPAGGLTSLLDNNSKKRGKKKKDDKIS
MSVRRLAEEEFQPSSFSFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFSTGQGDTIRPGPQIDRISSAPAGGLTSLLDNNSKKRGKKKKDDKIS
MSVRRLAEEEFQPSSFSFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFSTGQGDTIRPGPQIDRISSAPAGGLTSLLDNNSKKRGKKKKDDKIS

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

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

IdentityAlignment graphLength Definition Round E-value
Target218 NADH-quinone oxidoreductase, E subunit [Candidatus Libe
315122722203 NADH-quinone oxidoreductase, E subunit [Candidatus Libe 1 1e-102
218681069 322 NADH dehydrogenase subunit E [Rhizobium etli CIAT 894] 1 7e-92
86357242 385 NADH dehydrogenase subunit E [Rhizobium etli CFN 42] Le 1 9e-92
327188492 385 NADH dehydrogenase subunit E [Rhizobium etli CNPAF512] 1 1e-91
241204091 388 NADH dehydrogenase subunit E [Rhizobium leguminosarum b 1 2e-91
116251470 388 NADH dehydrogenase subunit E [Rhizobium leguminosarum b 1 1e-90
209548867 388 NADH dehydrogenase subunit E [Rhizobium leguminosarum b 1 1e-90
222085580 381 NADH-ubiquinone oxidoreductase chain E protein [Agrobac 1 7e-89
110633380 345 NADH-quinone oxidoreductase, E subunit [Mesorhizobium s 1 8e-89
15888603 369 NADH dehydrogenase subunit E [Agrobacterium tumefaciens 1 6e-88
>gi|315122722|ref|YP_004063211.1| NADH-quinone oxidoreductase, E subunit [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 203 Back     alignment and organism information
 Score =  374 bits (959), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 175/202 (86%), Positives = 188/202 (93%)

Query: 1   MSVRRLAEEEFQPSSFSFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAA 60
           MS+RRLA EEFQPSSFSFSEE+ +W NEV+S+YP SR QSAVIPLLMR QEQEGWVSRAA
Sbjct: 1   MSIRRLAAEEFQPSSFSFSEENIVWANEVMSKYPSSRYQSAVIPLLMRVQEQEGWVSRAA 60

Query: 61  IEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKI 120
           IE VA +LDMAYIRVLEI TFYTQFQL+PVGT AHVQVCGTTPCMLRGCE LIEVCRNKI
Sbjct: 61  IEFVAGMLDMAYIRVLEIVTFYTQFQLAPVGTHAHVQVCGTTPCMLRGCEDLIEVCRNKI 120

Query: 121 HQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFSTGQGDTI 180
           HQKPLHRN +G LSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEII+AFS G+GD+I
Sbjct: 121 HQKPLHRNPEGKLSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIEAFSAGRGDSI 180

Query: 181 RPGPQIDRISSAPAGGLTSLLD 202
           RPGPQIDRISSAPAGGLTSL++
Sbjct: 181 RPGPQIDRISSAPAGGLTSLVE 202


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|218681069|ref|ZP_03528966.1| NADH dehydrogenase subunit E [Rhizobium etli CIAT 894] Length = 322 Back     alignment and organism information
>gi|86357242|ref|YP_469134.1| NADH dehydrogenase subunit E [Rhizobium etli CFN 42] Length = 385 Back     alignment and organism information
>gi|327188492|gb|EGE55706.1| NADH dehydrogenase subunit E [Rhizobium etli CNPAF512] Length = 385 Back     alignment and organism information
>gi|241204091|ref|YP_002975187.1| NADH dehydrogenase subunit E [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 388 Back     alignment and organism information
>gi|116251470|ref|YP_767308.1| NADH dehydrogenase subunit E [Rhizobium leguminosarum bv. viciae 3841] Length = 388 Back     alignment and organism information
>gi|209548867|ref|YP_002280784.1| NADH dehydrogenase subunit E [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 388 Back     alignment and organism information
>gi|222085580|ref|YP_002544110.1| NADH-ubiquinone oxidoreductase chain E protein [Agrobacterium radiobacter K84] Length = 381 Back     alignment and organism information
>gi|110633380|ref|YP_673588.1| NADH-quinone oxidoreductase, E subunit [Mesorhizobium sp. BNC1] Length = 345 Back     alignment and organism information
>gi|15888603|ref|NP_354284.1| NADH dehydrogenase subunit E [Agrobacterium tumefaciens str. C58] Length = 369 Back     alignment and organism information

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

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target218 NADH-quinone oxidoreductase, E subunit [Candidatus Libe
PRK12373 400 PRK12373, PRK12373, NADH dehydrogenase subunit E; Provi 1e-104
KOG3196233 KOG3196, KOG3196, KOG3196, NADH:ubiquinone oxidoreducta 3e-44
PRK07539154 PRK07539, PRK07539, NADH dehydrogenase subunit E; Valid 1e-63
TIGR01958148 TIGR01958, nuoE_fam, NADH-quinone oxidoreductase, E sub 5e-55
COG1905160 COG1905, NuoE, NADH:ubiquinone oxidoreductase 24 kD sub 1e-53
PRK07571169 PRK07571, PRK07571, bidirectional hydrogenase complex p 5e-17
PRK05988156 PRK05988, PRK05988, formate dehydrogenase subunit gamma 4e-12
pfam01257145 pfam01257, Complex1_24kDa, Respiratory-chain NADH dehyd 1e-58
cd0306480 cd03064, TRX_Fd_NuoE, TRX-like [2Fe-2S] Ferredoxin (Fd) 8e-23
cd0298077 cd02980, TRX_Fd_family, Thioredoxin (TRX)-like [2Fe-2S] 2e-14
cd0308180 cd03081, TRX_Fd_NuoE_FDH_gamma, TRX-like [2Fe-2S] Ferre 1e-07
>gnl|CDD|183479 PRK12373, PRK12373, NADH dehydrogenase subunit E; Provisional Back     alignment and domain information
>gnl|CDD|38406 KOG3196, KOG3196, KOG3196, NADH:ubiquinone oxidoreductase, NDUFV2/24 kD subunit [Energy production and conversion] Back     alignment and domain information
>gnl|CDD|181024 PRK07539, PRK07539, NADH dehydrogenase subunit E; Validated Back     alignment and domain information
>gnl|CDD|131013 TIGR01958, nuoE_fam, NADH-quinone oxidoreductase, E subunit Back     alignment and domain information
>gnl|CDD|32089 COG1905, NuoE, NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion] Back     alignment and domain information
>gnl|CDD|136420 PRK07571, PRK07571, bidirectional hydrogenase complex protein HoxE; Reviewed Back     alignment and domain information
>gnl|CDD|180339 PRK05988, PRK05988, formate dehydrogenase subunit gamma; Validated Back     alignment and domain information
>gnl|CDD|144740 pfam01257, Complex1_24kDa, Respiratory-chain NADH dehydrogenase 24 Kd subunit Back     alignment and domain information
>gnl|CDD|48613 cd03064, TRX_Fd_NuoE, TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes Back     alignment and domain information
>gnl|CDD|48529 cd02980, TRX_Fd_family, Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE) Back     alignment and domain information
>gnl|CDD|48630 cd03081, TRX_Fd_NuoE_FDH_gamma, TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD+ to NADH Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 218 NADH-quinone oxidoreductase, E subunit [Candidatus Libe
PRK12373 403 NADH dehydrogenase subunit E; Provisional 100.0
KOG3196233 consensus 100.0
PRK07571169 bidirectional hydrogenase complex protein HoxE; Reviewe 100.0
TIGR01958153 nuoE_fam NADH-quinone oxidoreductase, E subunit; InterP 100.0
PRK07539154 NADH dehydrogenase subunit E; Validated 100.0
PRK05988156 formate dehydrogenase subunit gamma; Validated 100.0
COG1905160 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Ener 100.0
pfam01257145 Complex1_24kDa Respiratory-chain NADH dehydrogenase 24 100.0
cd0308380 TRX_Fd_NuoE_hoxF TRX-like [2Fe-2S] Ferredoxin (Fd) fami 99.94
cd0308180 TRX_Fd_NuoE_FDH_gamma TRX-like [2Fe-2S] Ferredoxin (Fd) 99.94
cd0306480 TRX_Fd_NuoE TRX-like [2Fe-2S] Ferredoxin (Fd) family, N 99.91
cd0298077 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxi 99.58
cd0308272 TRX_Fd_NuoE_W_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd 99.54
cd0306297 TRX_Fd_Sucrase TRX-like [2Fe-2S] Ferredoxin (Fd) family 96.54
cd0306392 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) famil 95.75
COG5469143 Predicted metal-binding protein [Function unknown] 95.22
pfam0729378 DUF1450 Protein of unknown function (DUF1450). This fam 94.22
pfam07845116 DUF1636 Protein of unknown function (DUF1636). The sequ 94.19
pfam06999218 Suc_Fer-like Sucrase/ferredoxin-like. This family conta 93.72
PRK1366978 hypothetical protein; Provisional 93.49
COG341164 Ferredoxin [Energy production and conversion] 97.05
>PRK12373 NADH dehydrogenase subunit E; Provisional Back     alignment and domain information
>KOG3196 consensus Back     alignment and domain information
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed Back     alignment and domain information
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit; InterPro: IPR002023 Respiratory-chain NADH dehydrogenase (ubiquinone) (1 Back     alignment and domain information
>PRK07539 NADH dehydrogenase subunit E; Validated Back     alignment and domain information
>PRK05988 formate dehydrogenase subunit gamma; Validated Back     alignment and domain information
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion] Back     alignment and domain information
>pfam01257 Complex1_24kDa Respiratory-chain NADH dehydrogenase 24 Kd subunit Back     alignment and domain information
>cd03083 TRX_Fd_NuoE_hoxF TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, hoxF; composed of proteins similar to the NAD-reducing hydrogenase (hoxS) alpha subunit of Alcaligenes eutrophus H16 Back     alignment and domain information
>cd03081 TRX_Fd_NuoE_FDH_gamma TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD+ to NADH Back     alignment and domain information
>cd03064 TRX_Fd_NuoE TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes Back     alignment and domain information
>cd02980 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE) Back     alignment and domain information
>cd03082 TRX_Fd_NuoE_W_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E family, Tungsten-containing formate dehydrogenase (W-FDH) beta subunit; composed of proteins similar to the W-FDH beta subunit of Methylobacterium extorquens Back     alignment and domain information
>cd03062 TRX_Fd_Sucrase TRX-like [2Fe-2S] Ferredoxin (Fd) family, Sucrase subfamily; composed of proteins with similarity to a novel plant enzyme, isolated from potato, which contains a Fd-like domain and exhibits sucrolytic activity Back     alignment and domain information
>cd03063 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH Back     alignment and domain information
>COG5469 Predicted metal-binding protein [Function unknown] Back     alignment and domain information
>pfam07293 DUF1450 Protein of unknown function (DUF1450) Back     alignment and domain information
>pfam07845 DUF1636 Protein of unknown function (DUF1636) Back     alignment and domain information
>pfam06999 Suc_Fer-like Sucrase/ferredoxin-like Back     alignment and domain information
>PRK13669 hypothetical protein; Provisional Back     alignment and domain information
>COG3411 Ferredoxin [Energy production and conversion] Back     alignment and domain information

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

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target218 NADH-quinone oxidoreductase, E subunit [Candidatus Libe
2fug_2181 Crystal Structure Of The Hydrophilic Domain Of Resp 1e-31
2auv_A85 Solution Structure Of Hndac : A Thioredoxin-Like [2 9e-13
1f37_A110 Structure Of A Thioredoxin-Like [2fe-2s] Ferredoxin 0.001
gi|90109655|pdb|2FUG|2 Chain 2, Crystal Structure Of The Hydrophilic Domain Of Respiratory Complex I From Thermus Thermophilus Length = 181 Back     alignment and structure
 Score =  140 bits (354), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 51/160 (31%), Positives = 88/160 (55%), Gaps = 2/160 (1%)

Query: 18  FSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLE 77
           F ++   ++ E  ++YPP   ++A++PLL R Q++EGW+    IE +A ++      V+ 
Sbjct: 3   FFDDKQDFLEETFAKYPPEGRRAAIMPLLRRVQQEEGWIRPERIEEIARLVGTTPTEVMG 62

Query: 78  IATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEE 137
           +A+FY+ +Q  P G + H+QVC T  C L G E+L +     +   P     DG  S ++
Sbjct: 63  VASFYSYYQFVPTG-KYHLQVCATLSCKLAGAEELWDYLTETLGIGPGEVTPDGLFSVQK 121

Query: 138 VECQGACVNAPMVMIGKD-TYEDLTPERLEEIIDAFSTGQ 176
           VEC G+C  AP++ +  +   E +T  RLE ++     G+
Sbjct: 122 VECLGSCHTAPVIQVNDEPYVECVTRARLEALLAGLRAGK 161


>gi|157881313|pdb|2AUV|A Chain A, Solution Structure Of Hndac : A Thioredoxin-Like [2fe-2s] Ferredoxin Involved In The Nadp-Reducing Hydrogenase Complex Length = 85 Back     alignment and structure
>gi|9955119|pdb|1F37|A Chain A, Structure Of A Thioredoxin-Like [2fe-2s] Ferredoxin From Aquifex Aeolicus Length = 110 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target218 NADH-quinone oxidoreductase, E subunit [Candidatus Libe
3i9v_2181 NADH-quinone oxidoreductase subunit 2; electron transpo 3e-39
2auv_A85 Potential NAD-reducing hydrogenase subunit; thioredoxin 4e-23
1m2d_A110 [2Fe-2S] ferredoxin; thioredoxin-like fold, [2Fe-2S] cl 2e-11
>3i9v_2 NADH-quinone oxidoreductase subunit 2; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_2* 3iam_2* 3ias_2* Length = 181 Back     alignment and structure
 Score =  156 bits (396), Expect = 3e-39
 Identities = 51/179 (28%), Positives = 90/179 (50%), Gaps = 4/179 (2%)

Query: 17  SFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVL 76
            F ++   ++ E  ++YPP   ++A++PLL R Q++EGW+    IE +A ++      V+
Sbjct: 2   GFFDDKQDFLEETFAKYPPEGRRAAIMPLLRRVQQEEGWIRPERIEEIARLVGTTPTEVM 61

Query: 77  EIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWE 136
            +A+FY+ +Q  P   + H+QVC T  C L G E+L +     +   P     DG  S +
Sbjct: 62  GVASFYSYYQFVPT-GKYHLQVCATLSCKLAGAEELWDYLTETLGIGPGEVTPDGLFSVQ 120

Query: 137 EVECQGACVNAPMVMIGKDTY-EDLTPERLEEIIDAFSTGQGDTIRPGPQIDRISSAPA 194
           +VEC G+C  AP++ +  + Y E +T  RLE ++     G+   +       +      
Sbjct: 121 KVECLGSCHTAPVIQVNDEPYVECVTRARLEALLAGLRAGK--RLEEIELPGKCGHHVH 177


>2auv_A Potential NAD-reducing hydrogenase subunit; thioredoxin, thiordoxin-like, oxidoreductase; NMR {Desulfovibrio fructosovorans} Length = 85 Back     alignment and structure
>1m2d_A [2Fe-2S] ferredoxin; thioredoxin-like fold, [2Fe-2S] cluster, Cys59Ser variant, electron transport; 1.05A {Aquifex aeolicus} SCOP: c.47.1.11 PDB: 1m2a_A 1f37_A 1m2b_A Length = 110 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target218 NADH-quinone oxidoreductase, E subunit [Candidatus Libe
3i9v_2181 NADH-quinone oxidoreductase subunit 2; electron transpo 100.0
2auv_A85 Potential NAD-reducing hydrogenase subunit; thioredoxin 99.92
1m2d_A110 [2Fe-2S] ferredoxin; thioredoxin-like fold, [2Fe-2S] cl 99.4
>3i9v_2 NADH-quinone oxidoreductase subunit 2; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_2* 3iam_2* 3ias_2* 3m9s_2* Back     alignment and structure
Probab=100.00  E-value=0  Score=375.22  Aligned_cols=162  Identities=32%  Similarity=0.677  Sum_probs=156.9

Q ss_pred             CCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCEE
Q ss_conf             56589999999999986784321336999999999982668999999999850887999999997644320222787069
Q gi|254780856|r   16 FSFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAH   95 (218)
Q Consensus        16 f~fs~e~~~~i~~ii~~yP~~~~~salip~L~~vQ~~~G~Ip~eai~~iA~~L~i~~~~V~~VaTFY~~f~~~P~G~k~~   95 (218)
                      +.|+++..+.|++||++||.+++|++|||+||.+|+++||||++++++||+.|++|+++||+|||||+||+++|+| ||+
T Consensus         1 m~~~~~~~~~i~~ii~~Yp~~~~r~all~~L~~iQ~~~GyIp~~al~~iA~~l~v~~a~V~~vatFY~~f~~~p~g-k~~   79 (181)
T 3i9v_2            1 MGFFDDKQDFLEETFAKYPPEGRRAAIMPLLRRVQQEEGWIRPERIEEIARLVGTTPTEVMGVASFYSYYQFVPTG-KYH   79 (181)
T ss_dssp             --CTTTCHHHHHHHHTTSCTTCCGGGHHHHHHHHHHHHSSCCHHHHHHHHHHHTSCHHHHHHHHTTCSSCCSSCCC-SEE
T ss_pred             CCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCC-CEE
T ss_conf             9988889999999998788864776999999999998299099999999999892999999999762502358898-868


Q ss_pred             EEECCCHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCCCCCEEEECCHHH-CCCCHHHHHHHHHHHHC
Q ss_conf             99618835877089248999998827564751778818999532456677886799858341-45889899999999982
Q gi|254780856|r   96 VQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDTY-EDLTPERLEEIIDAFST  174 (218)
Q Consensus        96 I~VC~~~~C~l~G~~~l~~~l~~~Lgi~~gett~DG~ftLe~v~CLG~C~~AP~~~Vn~~~y-~~lt~e~~~~il~~Lr~  174 (218)
                      |+||++++|+++|+++|+++++++|||+.|+||+||+|||++++|||+|++||+|+||++.| ++||++++++||+.||+
T Consensus        80 i~VC~~~~C~~~Ga~~l~~~l~~~Lgi~~gett~Dg~ftle~~~ClG~C~~AP~v~Vn~~~y~~~lt~e~~~~il~~lr~  159 (181)
T 3i9v_2           80 LQVCATLSCKLAGAEELWDYLTETLGIGPGEVTPDGLFSVQKVECLGSCHTAPVIQVNDEPYVECVTRARLEALLAGLRA  159 (181)
T ss_dssp             EEEECSHHHHTTTHHHHHHHHHHHHTCCTTCCCTTSCEEEEEESCCSCGGGCSCEECSSSCCBCCCCHHHHHHHHHHHHT
T ss_pred             EEECCCHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCEEEEECCCCCEECCCCEEEECCEEECCCCCHHHHHHHHHHHHC
T ss_conf             99559768775788689999999819999967899868764221768607898499989873587999999999999986


Q ss_pred             CCCC
Q ss_conf             8899
Q gi|254780856|r  175 GQGD  178 (218)
Q Consensus       175 gk~~  178 (218)
                      |+..
T Consensus       160 g~~~  163 (181)
T 3i9v_2          160 GKRL  163 (181)
T ss_dssp             TCCG
T ss_pred             CCCC
T ss_conf             9999



>2auv_A Potential NAD-reducing hydrogenase subunit; thioredoxin, thiordoxin-like, oxidoreductase; NMR {Desulfovibrio fructosovorans} Back     alignment and structure
>1m2d_A [2Fe-2S] ferredoxin; thioredoxin-like fold, [2Fe-2S] cluster, Cys59Ser variant, electron transport; 1.05A {Aquifex aeolicus} SCOP: c.47.1.11 PDB: 1m2a_A 1f37_A 1m2b_A Back     alignment and structure

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

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

IdentityAlignment graphLength Definition E-value
Target 218 NADH-quinone oxidoreductase, E subunit [Candidatus Libe
d2fug21178 c.47.1.21 (2:3-180) NADH-quinone oxidoreductase chain 2 6e-38
d1m2da_101 c.47.1.11 (A:) Thioredoxin-like 2Fe-2S ferredoxin {Aqui 3e-11
>d2fug21 c.47.1.21 (2:3-180) NADH-quinone oxidoreductase chain 2, NQO2 {Thermus thermophilus [TaxId: 274]} Length = 178 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: NQO2-like
domain: NADH-quinone oxidoreductase chain 2, NQO2
species: Thermus thermophilus [TaxId: 274]
 Score =  151 bits (381), Expect = 6e-38
 Identities = 51/178 (28%), Positives = 89/178 (50%), Gaps = 4/178 (2%)

Query: 18  FSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLE 77
           F ++   ++ E  ++YPP   ++A++PLL R Q++EGW+    IE +A ++      V+ 
Sbjct: 1   FFDDKQDFLEETFAKYPPEGRRAAIMPLLRRVQQEEGWIRPERIEEIARLVGTTPTEVMG 60

Query: 78  IATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEE 137
           +A+FY+ +Q  P   + H+QVC T  C L G E+L +     +   P     DG  S ++
Sbjct: 61  VASFYSYYQFVPT-GKYHLQVCATLSCKLAGAEELWDYLTETLGIGPGEVTPDGLFSVQK 119

Query: 138 VECQGACVNAPMVMIGKDTY-EDLTPERLEEIIDAFSTGQGDTIRPGPQIDRISSAPA 194
           VEC G+C  AP++ +  + Y E +T  RLE ++       G  +       +      
Sbjct: 120 VECLGSCHTAPVIQVNDEPYVECVTRARLEALLAGLR--AGKRLEEIELPGKCGHHVH 175


>d1m2da_ c.47.1.11 (A:) Thioredoxin-like 2Fe-2S ferredoxin {Aquifex aeolicus [TaxId: 63363]} Length = 101 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target218 NADH-quinone oxidoreductase, E subunit [Candidatus Libe
d2fug21178 NADH-quinone oxidoreductase chain 2, NQO2 {Thermus ther 100.0
d1m2da_101 Thioredoxin-like 2Fe-2S ferredoxin {Aquifex aeolicus [T 99.3
>d2fug21 c.47.1.21 (2:3-180) NADH-quinone oxidoreductase chain 2, NQO2 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Thioredoxin fold
superfamily: Thioredoxin-like
family: NQO2-like
domain: NADH-quinone oxidoreductase chain 2, NQO2
species: Thermus thermophilus [TaxId: 274]
Probab=100.00  E-value=0  Score=377.68  Aligned_cols=174  Identities=31%  Similarity=0.635  Sum_probs=161.6

Q ss_pred             CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCEEEE
Q ss_conf             58999999999998678432133699999999998266899999999985088799999999764432022278706999
Q gi|254780856|r   18 FSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHVQ   97 (218)
Q Consensus        18 fs~e~~~~i~~ii~~yP~~~~~salip~L~~vQ~~~G~Ip~eai~~iA~~L~i~~~~V~~VaTFY~~f~~~P~G~k~~I~   97 (218)
                      |+++..+.|++||++||.+++|++|||+||.+|+++||||++++++||+.|+||+++||+|+|||+||+++|+| ||+|+
T Consensus         1 f~~~~~~~i~~ii~~Yp~~~~~~ali~~L~~iQ~~~Gyip~~al~~iA~~l~v~~a~V~~vatFY~~f~~~p~g-k~~i~   79 (178)
T d2fug21           1 FFDDKQDFLEETFAKYPPEGRRAAIMPLLRRVQQEEGWIRPERIEEIARLVGTTPTEVMGVASFYSYYQFVPTG-KYHLQ   79 (178)
T ss_dssp             CTTTTHHHHHHHHHTSCSSCGGGGHHHHHHHHHHHHSSCCHHHHHHHHHHHTSCHHHHHHHHHHSSSSCSSCCC-SEEEE
T ss_pred             CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHHCCHHCCCCCC-CCEEE
T ss_conf             98789999999998788854643899999999998698788999999999797989999999855311035665-40247


Q ss_pred             ECCCHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCCCCCEEEECCHHH-CCCCHHHHHHHHHHHHCCC
Q ss_conf             618835877089248999998827564751778818999532456677886799858341-4588989999999998288
Q gi|254780856|r   98 VCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDTY-EDLTPERLEEIIDAFSTGQ  176 (218)
Q Consensus        98 VC~~~~C~l~G~~~l~~~l~~~Lgi~~gett~DG~ftLe~v~CLG~C~~AP~~~Vn~~~y-~~lt~e~~~~il~~Lr~gk  176 (218)
                      ||++++|+++|+.+|+++++++|||+.|+||+||+|||++++|||+|+.||+|+||++.| ++||++++++||+.||+|+
T Consensus        80 VC~~~~C~~~G~~~l~~~l~~~Lgi~~gett~Dg~ftle~v~ClG~C~~APa~~In~~~y~~~lt~e~~~~il~~lr~~~  159 (178)
T d2fug21          80 VCATLSCKLAGAEELWDYLTETLGIGPGEVTPDGLFSVQKVECLGSCHTAPVIQVNDEPYVECVTRARLEALLAGLRAGK  159 (178)
T ss_dssp             EECSHHHHTTTHHHHHHHHHHHHCCCTTCCCTTSCEEEEEESCCSCTTSSSCEECSSSSBCCSCCHHHHHHHHHHHHTTC
T ss_pred             ECCCHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCCCCEEEECCEEECCCCCHHHHHHHHHHHHCCC
T ss_conf             54715644402033689987631223011169987888975225716889969994977467799999999999998699


Q ss_pred             CC--CCCCCCCCCCCCCCC
Q ss_conf             99--987488478643367
Q gi|254780856|r  177 GD--TIRPGPQIDRISSAP  193 (218)
Q Consensus       177 ~~--~~k~g~~~~r~~~~~  193 (218)
                      ..  .+.|| +.+|..+++
T Consensus       160 ~~~~~~~~~-~~~~~~~~~  177 (178)
T d2fug21         160 RLEEIELPG-KCGHHVHEV  177 (178)
T ss_dssp             CGGGCCCSS-CCCSSBCCC
T ss_pred             CCCCCCCCC-CCCCCCCCC
T ss_conf             998788889-889763147



>d1m2da_ c.47.1.11 (A:) Thioredoxin-like 2Fe-2S ferredoxin {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 218 NADH-quinone oxidoreductase, E subunit [Candidatus
3i9v_2_72-181110 (2:72-181) NADH-quinone oxidoreductase subunit 2; 2e-23
2auv_A_85 (A:) Potential NAD-reducing hydrogenase subunit; t 8e-23
1m2d_A_110 (A:) [2Fe-2S] ferredoxin; thioredoxin-like fold, [ 9e-18
3i9v_2_22-7150 (2:22-71) NADH-quinone oxidoreductase subunit 2; e 2e-14
>3i9v_2 (2:72-181) NADH-quinone oxidoreductase subunit 2; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_2* 3iam_2* 3ias_2*Length = 110 Back     alignment and structure
 Score =  103 bits (259), Expect = 2e-23
 Identities = 29/111 (26%), Positives = 46/111 (41%), Gaps = 4/111 (3%)

Query: 87  LSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVN 146
             P G + H+QVC T  C L G E+L +     +   P     DG  S ++VEC G+C  
Sbjct: 1   FVPTG-KYHLQVCATLSCKLAGAEELWDYLTETLGIGPGEVTPDGLFSVQKVECLGSCHT 59

Query: 147 APMVMI-GKDTYEDLTPERLEEIIDAFSTGQGDTIRPGPQIDRISSAPAGG 196
           AP++ +  +   E +T  RLE ++       G  +       +        
Sbjct: 60  APVIQVNDEPYVECVTRARLEALLAGLR--AGKRLEEIELPGKCGHHVHEV 108


>2auv_A (A:) Potential NAD-reducing hydrogenase subunit; thioredoxin, thiordoxin-like, oxidoreductase; NMR {Desulfovibrio fructosovorans}Length = 85 Back     alignment and structure
>1m2d_A (A:) [2Fe-2S] ferredoxin; thioredoxin-like fold, [2Fe-2S] cluster, Cys59Ser variant, electron transport; 1.05A {Aquifex aeolicus}Length = 110 Back     alignment and structure
>3i9v_2 (2:22-71) NADH-quinone oxidoreductase subunit 2; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_2* 3iam_2* 3ias_2*Length = 50 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target218 NADH-quinone oxidoreductase, E subunit [Candidatus Libe
3i9v_2_72-181110 NADH-quinone oxidoreductase subunit 2; electron tr 99.84
2auv_A_85 Potential NAD-reducing hydrogenase subunit; thiore 99.81
1m2d_A_110 [2Fe-2S] ferredoxin; thioredoxin-like fold, [2Fe-2 99.58
3i9v_2_22-7150 NADH-quinone oxidoreductase subunit 2; electron tr 99.57
>3i9v_2 (2:72-181) NADH-quinone oxidoreductase subunit 2; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_2* 3iam_2* 3ias_2* Back     alignment and structure
Probab=99.84  E-value=1.8e-20  Score=158.69  Aligned_cols=107  Identities=27%  Similarity=0.473  Sum_probs=94.8

Q ss_pred             CCCCCCCEEEEECCCHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCCCCCEEEECCH-HHCCCCHHHH
Q ss_conf             222787069996188358770892489999988275647517788189995324566778867998583-4145889899
Q gi|254780856|r   87 LSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKD-TYEDLTPERL  165 (218)
Q Consensus        87 ~~P~G~k~~I~VC~~~~C~l~G~~~l~~~l~~~Lgi~~gett~DG~ftLe~v~CLG~C~~AP~~~Vn~~-~y~~lt~e~~  165 (218)
                      ++|+| ||+|+||++++|+++|+++++++|+++|+...++++.||.|+++.+.|+|.|+.||+|+|+++ +|+++|++++
T Consensus         1 ~~P~~-k~~I~VC~g~~C~~~G~~~v~~~l~~~l~~~~~~~~~dg~v~~~~t~ClG~C~~gP~v~i~~~~~y~~vt~e~v   79 (110)
T 3i9v_2            1 FVPTG-KYHLQVCATLSCKLAGAEELWDYLTETLGIGPGEVTPDGLFSVQKVECLGSCHTAPVIQVNDEPYVECVTRARL   79 (110)
T ss_dssp             SSCCC-SEEEEEECSHHHHTTTHHHHHHHHHHHHTCCTTCCCTTSCEEEEEESCCSCGGGCSCEECSSSCCBCCCCHHHH
T ss_pred             CCCCC-CEEEEECCCHHHEECCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCCCCCCCEEEECCEEECCCCCHHHH
T ss_conf             35675-43578804502100586125788754222120121699818988764267268899699949774677999999


Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9999999828899987488478643367788
Q gi|254780856|r  166 EEIIDAFSTGQGDTIRPGPQIDRISSAPAGG  196 (218)
Q Consensus       166 ~~il~~Lr~gk~~~~k~g~~~~r~~~~~~~G  196 (218)
                      ++|++.|+.|++.  ....+..+....+..+
T Consensus        80 ~~iv~~l~~g~~v--~~~~~~~~~~~~~~~~  108 (110)
T 3i9v_2           80 EALLAGLRAGKRL--EEIELPGKCGHHVHEV  108 (110)
T ss_dssp             HHHHHHHHTTCCG--GGCCCSSCCCSSBCCC
T ss_pred             HHHHHHHHCCCCC--CCCCCCCCCCCCCCCC
T ss_conf             9999999869999--9788889888862214



>2auv_A (A:) Potential NAD-reducing hydrogenase subunit; thioredoxin, thiordoxin-like, oxidoreductase; NMR {Desulfovibrio fructosovorans} Back     alignment and structure
>1m2d_A (A:) [2Fe-2S] ferredoxin; thioredoxin-like fold, [2Fe-2S] cluster, Cys59Ser variant, electron transport; 1.05A {Aquifex aeolicus} Back     alignment and structure
>3i9v_2 (2:22-71) NADH-quinone oxidoreductase subunit 2; electron transport, respiratory chain, 4Fe- 4S, cell membrane, flavoprotein, FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8} PDB: 2fug_2* 3iam_2* 3ias_2* Back     alignment and structure