Citrus Sinensis ID: 011877

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-----

MSEKFSPTLRIGDLSDFIAPSQNCVVSLKKATFKNPDKPQVSTSSKQQAEPVKISLKDCLACSGCITSAETVMLEKQSLDEFLSNINKGKAVIISLSPQSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARYKQSQESDDERSNSSLPMLSSACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTVMPCYDKKLEAAREDFVFQLDSQEETYRDEGLEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGVAGSSGGYAETVFRHAAKTLFGKVIEGHLEFKTIRNSDFREVALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMACPSGCLNGGGQIKPKPGQSPKELIKTLETIYLENVMLADPFKNPLVRSLYDEWLEQPGSEKAKKHVHTEYHPVVKSITAQLHNW

ccccccccccccccccccccccccccccccccccccccccccccccccccccEEccccccccccHHHHHHHHHHHcccHHHHHHHHcccccEEEEEcHHHHHHHHHHHcccHHHHHHHHHHHHHHccccEEEccHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHccccccEEEEEEEccccHHHHHccccccccccccHHccccccccccccEEEccHHHHHHHHHHccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccccEEEEEcccccEEEEEEEEccEEEEEEEEEEcHHHHHHHHHHHHcccccccEEEEcccccccccccccccccccccHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHccccccccccccccEEcccccccccccccc

ccccccHHHEcccccccccccHHHHHHHHHccccccccEEEccccEEEccccEEccHHcccccccEEEccEEEEEcccHHHHHHHHccccEEEEEEcHHHHHHHHHHHcccccHHHHHHHHHHHHccccEEEcccHHHHHHHHHHHHHHHHHHHHccccccccccccccEEcccccHHHHHHHHHccccHHHHEccEccHHHHHHHHHccHHHHcccccHHHEEEEEEEcccHHHHHHccHHHHHccccccccHcccccccccccEEEEHHHHHHHHHHccccHHccccccccccccccccccEEEcccccccHHHHHHHHHHHHHHccccccccEccHHHcccccEEEEEEEEccEEEEEEEEEcHHHHHHHHHHHHHccccccEEEEEcccccHHHccccccccccccHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHcccccHHHHHHHcccEcccccccccccccc

msekfsptlrigdlsdfiapsqnCVVSLkkatfknpdkpqvstsskqqaepvkISLKdclacsgcitsAETVMLEKQSLDEFLSNINKGKAVIISLSPQSRASlaehfgisplQVFKKLTTFLKSLgvksifdtscsRDLTLIEACNEFIARYKqsqesddersnsslpmlssacpgwICYAEKqlgsyilpyissvkspqqtigATIKHHIcqklgfrpdeiyhvtvmpcydKKLEAAREDFVFQLDSqeetyrdegleipevdsvlttGEVLDLIQLKAVnfealeespldkmltnvddeghlygvagssggyaETVFRHAAKTLFGKVIEGhlefktirnsdfREVALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEvmacpsgclngggqikpkpgqspkELIKTLETIYLEnvmladpfknplvRSLYDEwleqpgsekakkhvhteyhPVVKSITAQLHNW

msekfsptlrigdlsdfiaPSQNCVVSLKKAtfknpdkpqvstsskqqaepvKISLKDCLACSGCITSAETVMLEKQSLDEFLSNINKGKAVIISLSPQSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARYKqsqesddersnsSLPMLSSACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTVMPCYDKKLEAAREDFVFQLDSQeetyrdegleipevdsvLTTGEVLDLIQLKAVNfealeespldKMLTNVDDEGHLYGVAGSSGGYAETVFRHAAKTLFGKVIEGHLEFKTIRNSDFREVALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMACPSGCLngggqikpkpgqsPKELIKTLETIYLENVMLADPFKNPLVRSLYDEWLEQPGSekakkhvhteyhPVVKSITAQLHNW

**********IGDLSDFIAPSQNCVVSL************************KISLKDCLACSGCITSAETVMLEKQSLDEFLSNINKGKAVIISLSPQSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARY*******************SACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTVMPCYDKKLEAAREDFVFQLDSQEETYRDEGLEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGVAGSSGGYAETVFRHAAKTLFGKVIEGHLEFKTIRNSDFREVALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMACPSGCLNGGG************LIKTLETIYLENVMLADPFKNPLVRSLYDEWLE*****************V***********

*****SP**RIGDLSDFIAPSQNCVVSLKKAT********************KISLKDCLACSGCITSAETVMLEKQSLDEFLSNINKGKAVIISLSPQSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIAR****************PMLSSACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTVMPCYDKKLEAAREDFVFQLDSQEETYRDEGLEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDKMLTN***********GSSGGYAETVFRHAAKTLFGKVIEGHLEFKTIRNSDFREVALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMACPSGCLNGGG***********ELIKTLETIYLENVMLADPFKNPLVRSLYDEWLEQPGSEKAKKHVHTEYHPVV*S******NW

********LRIGDLSDFIAPSQNCVVSLKKAT********************KISLKDCLACSGCITSAETVMLEKQSLDEFLSNINKGKAVIISLSPQSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARY****************MLSSACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTVMPCYDKKLEAAREDFVFQLDSQEETYRDEGLEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGVAGSSGGYAETVFRHAAKTLFGKVIEGHLEFKTIRNSDFREVALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMACPSGCLNGGGQIKPKPGQSPKELIKTLETIYLENVMLADPFKNPLVRSLYDEWLEQPGSEKAKKHVHTEYHPVVKSITAQLHNW

****FSPTLRIGDLSDFIAPSQNCVVSLKKATFKNPDKPQVSTSSKQQAEPVKISLKDCLACSGCITSAETVMLEKQSLDEFLSNINKGKAVIISLSPQSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARYKQSQESD*****SSLPMLSSACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTVMPCYDKKLEAAREDFVFQ******T*****LEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGVAGSSGGYAETVFRHAAKTLFGKVIEGHLEFKTIRNSDFREVALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMACPSGCLNGGGQIKPKPGQSPKELIKTLETIYLENVMLADPFKNPLVRSLYDEWLEQPGSEKAKKHVHTEYHPV***********

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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		475	2.2.26 [Sep-21-2011]
Q5BK18		476	Cytosolic Fe-S cluster as	yes	no	0.928	0.926	0.453	1e-114
Q7TMW6		476	Cytosolic Fe-S cluster as	yes	no	0.955	0.953	0.454	1e-114
Q9H6Q4		476	Cytosolic Fe-S cluster as	yes	no	0.96	0.957	0.442	1e-114
Q5RF36		476	Cytosolic Fe-S cluster as	yes	no	0.96	0.957	0.442	1e-113
A4FV58		476	Cytosolic Fe-S cluster as	yes	no	0.955	0.953	0.442	1e-112
A8WH18		476	Cytosolic Fe-S cluster as	yes	no	0.96	0.957	0.446	1e-109
Q54F30		522	Probable cytosolic Fe-S c	yes	no	0.970	0.883	0.421	1e-108
A2RRV9		411	Cytosolic Fe-S cluster as	no	no	0.833	0.963	0.490	1e-106
Q16ML2		478	Probable cytosolic Fe-S c	N/A	no	0.947	0.941	0.397	1e-103
B0WU52		478	Probable cytosolic Fe-S c	N/A	no	0.947	0.941	0.403	1e-102

>sp\|Q5BK18\|NARFL_RAT Cytosolic Fe-S cluster assembly factor NARFL OS=Rattus norvegicus GN=Narfl PE=2 SV=1	Back alignment and function desciption

 Score =  412 bits (1060), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 223/492 (45%), Positives = 307/492 (62%), Gaps = 51/492 (10%)

Query: 1   MSEKFSPTLRIGDLSDFIAPSQNCV--VSLKK---------------ATFK-NPDKPQVS 42
           M+  FS  L++ DL DFI PSQ+C+  V++ K               + F+ NPD     
Sbjct: 1   MASPFSGALQLTDLDDFIGPSQSCIKPVTVAKKPGSGIAKIHIEDDGSYFQVNPD----- 55

Query: 43  TSSKQQAEPVKISLKDCLACSGCITSAETVMLEKQSLDEFLSNINKGKA--------VII 94
               Q+ E  K+SL DCLACSGC+TSAET+++ +QS +E    ++  K         V++
Sbjct: 56  -GRSQKLEKAKVSLNDCLACSGCVTSAETILITQQSHEELRKVLDANKVAAPGQQRLVVV 114

Query: 95  SLSPQSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARYK 154
           S+SPQSRASLA  F +      +KLT+F K +GV  +FDT+ +R+ +L+E+  EF+ R++
Sbjct: 115 SVSPQSRASLAARFQLDSTDTARKLTSFFKKIGVHFVFDTAFARNFSLLESQKEFVQRFR 174

Query: 155 QSQESDDERSNSSLPMLSSACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQ 214
           +   S +     +LPML+SACPGWICYAEK  G++ILPYIS+ +SPQQ +G+ IK    Q
Sbjct: 175 EQANSRE-----ALPMLASACPGWICYAEKTHGNFILPYISTARSPQQVMGSLIKDFFAQ 229

Query: 215 KLGFRPDEIYHVTVMPCYDKKLEAAREDFVFQLDSQEETYRDEGLEIPEVDSVLTTGEVL 274
           +    PD+IYHVTVMPCYDKKLEA+R DF     +QE   RD       VD VLTTGEV 
Sbjct: 230 QQLLTPDKIYHVTVMPCYDKKLEASRPDFF----NQEYQTRD-------VDCVLTTGEVF 278

Query: 275 DLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGVAGSSGGYAETVFRHAAKTLFGKVIEG 334
            L++ + V+   LE  PLD +  +V  E       G SGGY E VFRHAA+ LFG  +  
Sbjct: 279 RLLEEEGVSLSELEPVPLDGLTRSVSAEEPTSHRGGGSGGYLEHVFRHAAQELFGIHV-A 337

Query: 335 HLEFKTIRNSDFREVALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMACPS 394
            + ++ +RN DF+EV LE EG+ LL+FA+ YGF+N+QN+V+K+K  +C Y +VEVMACPS
Sbjct: 338 DVTYQPMRNKDFQEVTLEREGQVLLRFAVAYGFRNIQNLVQKLKRGRCPYHYVEVMACPS 397

Query: 395 GCLNGGGQIKPKPGQSPKELIKTLETIYLENVMLADPFKNPLVRSLYDEWLEQPGSEKAK 454
           GCLNGGGQ+K  P    +EL++ +E +Y   V    P   P V+ LY  WL+   SE+A 
Sbjct: 398 GCLNGGGQLK-APDTEGRELLQQVERLY-SMVRTEAPEDAPGVQELYQHWLQGEDSERAS 455

Query: 455 KHVHTEYHPVVK 466
             +HT+YH V K
Sbjct: 456 HLLHTQYHAVEK 467

Component of the cytosolic iron-sulfur (Fe/S) protein assembly machinery. Required for maturation of extramitochondrial Fe/S proteins. Seems to negatively regulate the level of HIF1A expression, although this effect could be indirect.
Rattus norvegicus (taxid: 10116)

>sp\|Q7TMW6\|NARFL_MOUSE Cytosolic Fe-S cluster assembly factor NARFL OS=Mus musculus GN=Narfl PE=2 SV=2	Back alignment and function description

>sp\|Q9H6Q4\|NARFL_HUMAN Cytosolic Fe-S cluster assembly factor NARFL OS=Homo sapiens GN=NARFL PE=1 SV=1	Back alignment and function description

>sp\|Q5RF36\|NARFL_PONAB Cytosolic Fe-S cluster assembly factor NARFL OS=Pongo abelii GN=NARFL PE=2 SV=1	Back alignment and function description

>sp\|A4FV58\|NARFL_BOVIN Cytosolic Fe-S cluster assembly factor NARFL OS=Bos taurus GN=NARFL PE=2 SV=2	Back alignment and function description

>sp\|A8WH18\|NARFL_XENTR Cytosolic Fe-S cluster assembly factor narfl OS=Xenopus tropicalis GN=narfl PE=2 SV=1	Back alignment and function description

>sp\|Q54F30\|NARF_DICDI Probable cytosolic Fe-S cluster assembly factor narfl OS=Dictyostelium discoideum GN=narfl PE=3 SV=1	Back alignment and function description

>sp\|A2RRV9\|NARFL_DANRE Cytosolic Fe-S cluster assembly factor narfl OS=Danio rerio GN=narfl PE=2 SV=1	Back alignment and function description

>sp\|Q16ML2\|NARF_AEDAE Probable cytosolic Fe-S cluster assembly factor AAEL012261 OS=Aedes aegypti GN=AAEL012261 PE=3 SV=1	Back alignment and function description

>sp\|B0WU52\|NARF_CULQU Probable cytosolic Fe-S cluster assembly factor CPIJ010948 OS=Culex quinquefasciatus GN=CPIJ010948 PE=3 SV=2	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		475
449443528		478	PREDICTED: cytosolic Fe-S cluster assemb	1.0	0.993	0.788	0.0
224086530		478	predicted protein [Populus trichocarpa]	0.995	0.989	0.781	0.0
224139480		471	predicted protein [Populus trichocarpa]	0.991	1.0	0.787	0.0
255563810		475	electron transporter, putative [Ricinus	0.974	0.974	0.810	0.0
359496948		478	PREDICTED: cytosolic Fe-S cluster assemb	1.0	0.993	0.767	0.0
297800500		474	predicted protein [Arabidopsis lyrata su	0.989	0.991	0.747	0.0
356522067		474	PREDICTED: cytosolic Fe-S cluster assemb	0.995	0.997	0.739	0.0
356562481		474	PREDICTED: cytosolic Fe-S cluster assemb	0.995	0.997	0.741	0.0
255647952		474	unknown [Glycine max]	0.995	0.997	0.741	0.0
240255938		474	ferredoxin hydrogenase [Arabidopsis thal	0.991	0.993	0.736	0.0

>gi\|449443528\|ref\|XP_004139529.1\| PREDICTED: cytosolic Fe-S cluster assembly factor NARFL-like [Cucumis sativus] gi\|449505551\|ref\|XP_004162505.1\| PREDICTED: cytosolic Fe-S cluster assembly factor NARFL-like [Cucumis sativus]	Back alignment and taxonomy information

 Score =  799 bits (2064), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/478 (78%), Positives = 428/478 (89%), Gaps = 3/478 (0%)

Query: 1   MSEKFSPTLRIGDLSDFIAPSQNCVVSLK--KATFKNPDKPQVSTSSKQ-QAEPVKISLK 57
           MSEKFS TLRIGDL+DFIAPSQ C+VSLK  KAT   PDK +VS S  Q +AEPVKISLK
Sbjct: 1   MSEKFSATLRIGDLNDFIAPSQACIVSLKGLKATATKPDKVEVSASRMQLKAEPVKISLK 60

Query: 58  DCLACSGCITSAETVMLEKQSLDEFLSNINKGKAVIISLSPQSRASLAEHFGISPLQVFK 117
           DCLACSGC+TSAETVMLEKQSLDEFLSN+NKGK VI+SLSPQSRASLA HFGISPL+VFK
Sbjct: 61  DCLACSGCVTSAETVMLEKQSLDEFLSNLNKGKVVIVSLSPQSRASLAVHFGISPLKVFK 120

Query: 118 KLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARYKQSQESDDERSNSSLPMLSSACPG 177
           KLTTF KS+GVK+IFDTSCSRDLTLIEACNEFIARY+ SQ+ ++E+  SS+PM+SSACPG
Sbjct: 121 KLTTFFKSMGVKAIFDTSCSRDLTLIEACNEFIARYRNSQQDNEEKCKSSVPMISSACPG 180

Query: 178 WICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTVMPCYDKKLE 237
           WICYAEKQ GSYILPYISSVKSPQQ IG+ +KHH+CQKLG R D++YHVTVMPCYDKKLE
Sbjct: 181 WICYAEKQHGSYILPYISSVKSPQQMIGSIVKHHMCQKLGIRSDDVYHVTVMPCYDKKLE 240

Query: 238 AAREDFVFQLDSQEETYRDEGLEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDKMLT 297
           AAREDFVFQLDS  +T   E   I EVDSVLT+GEVL+LIQ+K V+F++LEESPLD+MLT
Sbjct: 241 AAREDFVFQLDSANKTLEAEAHRITEVDSVLTSGEVLELIQMKEVDFKSLEESPLDRMLT 300

Query: 298 NVDDEGHLYGVAGSSGGYAETVFRHAAKTLFGKVIEGHLEFKTIRNSDFREVALEVEGKT 357
           NV++EGHL+GV+GSSGGYAET+FRHAAK LFGK IEG LEFK IRNSDF+E+ LEVEGKT
Sbjct: 301 NVNEEGHLFGVSGSSGGYAETIFRHAAKILFGKDIEGPLEFKLIRNSDFQELTLEVEGKT 360

Query: 358 LLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMACPSGCLNGGGQIKPKPGQSPKELIKT 417
           LLKFALCYGF+NLQN+VRK+K  KCDY F+E+MACPSGCLNGGGQIKPKPGQSPK+LI+ 
Sbjct: 361 LLKFALCYGFRNLQNVVRKIKTGKCDYHFLEIMACPSGCLNGGGQIKPKPGQSPKDLIEL 420

Query: 418 LETIYLENVMLADPFKNPLVRSLYDEWLEQPGSEKAKKHVHTEYHPVVKSITAQLHNW 475
           LE  Y ENV++ DPF NP+V+ +Y EWLE+PGSEKAKKH+HTEYHPVVKSITAQLHNW
Sbjct: 421 LEAAYQENVLMRDPFDNPVVKEIYKEWLEEPGSEKAKKHLHTEYHPVVKSITAQLHNW 478

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224086530\|ref\|XP_002307904.1\| predicted protein [Populus trichocarpa] gi\|222853880\|gb\|EEE91427.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|224139480\|ref\|XP_002323132.1\| predicted protein [Populus trichocarpa] gi\|222867762\|gb\|EEF04893.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|255563810\|ref\|XP_002522906.1\| electron transporter, putative [Ricinus communis] gi\|223537891\|gb\|EEF39506.1\| electron transporter, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|359496948\|ref\|XP_003635380.1\| PREDICTED: cytosolic Fe-S cluster assembly factor NARFL-like [Vitis vinifera] gi\|297744923\|emb\|CBI38438.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297800500\|ref\|XP_002868134.1\| predicted protein [Arabidopsis lyrata subsp. lyrata] gi\|297313970\|gb\|EFH44393.1\| predicted protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|356522067\|ref\|XP_003529671.1\| PREDICTED: cytosolic Fe-S cluster assembly factor NARFL-like [Glycine max]	Back alignment and taxonomy information

>gi\|356562481\|ref\|XP_003549499.1\| PREDICTED: cytosolic Fe-S cluster assembly factor NARFL-like [Glycine max]	Back alignment and taxonomy information

>gi\|255647952\|gb\|ACU24433.1\| unknown [Glycine max]	Back alignment and taxonomy information

>gi\|240255938\|ref\|NP_567496.4\| ferredoxin hydrogenase [Arabidopsis thaliana] gi\|15020824\|emb\|CAC44620.1\| Narf-like protein [Arabidopsis thaliana] gi\|332658348\|gb\|AEE83748.1\| ferredoxin hydrogenase [Arabidopsis thaliana]	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		475
TAIR\|locus:2130634		474	NAR1 "homolog of yeast NAR1" [	0.989	0.991	0.739	1.7e-194
UNIPROTKB\|E1C8S8		476	NARFL "Uncharacterized protein	0.941	0.939	0.477	1.9e-108
UNIPROTKB\|A8WH18		476	narfl "Cytosolic Fe-S cluster	0.96	0.957	0.452	2.5e-106
MGI\|MGI:1914813		476	Narfl "nuclear prelamin A reco	0.96	0.957	0.460	1.1e-105
RGD\|1305982		476	Narfl "nuclear prelamin A reco	0.941	0.939	0.462	1.8e-103
UNIPROTKB\|Q5BK18		476	Narfl "Cytosolic Fe-S cluster	0.941	0.939	0.462	1.8e-103
UNIPROTKB\|Q9H6Q4		476	NARFL "Cytosolic Fe-S cluster	0.96	0.957	0.450	2.9e-103
UNIPROTKB\|A4FV58		476	NARFL "Cytosolic Fe-S cluster	0.96	0.957	0.450	1.6e-102
UNIPROTKB\|Q5RF36		476	NARFL "Cytosolic Fe-S cluster	0.96	0.957	0.448	1.6e-102
UNIPROTKB\|F1RG50		476	NARFL "Uncharacterized protein	0.96	0.957	0.452	3e-101

TAIR\|locus:2130634 NAR1 "homolog of yeast NAR1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1884 (668.3 bits), Expect = 1.7e-194, P = 1.7e-194
 Identities = 354/479 (73%), Positives = 415/479 (86%)

Query:     1 MSEKFSPTLRIGDLSDFIAPSQNCVVSLK--KATFKNPDKPQVSTSSKQQAEPVKISLKD 58
             MSEKFSPTLR+GDL+DFIAPSQ CV+SLK  K   K  D+PQV  + KQQ EPVKISLKD
Sbjct:     1 MSEKFSPTLRLGDLNDFIAPSQACVISLKDSKPIVKKSDRPQVVIAPKQQLEPVKISLKD 60

Query:    59 CLACSGCITSAETVMLEKQSLDEFLSNINKGKAVIISLSPQSRASLAEHFGISPLQVFKK 118
             CLACSGCITSAETVMLEKQSLDEFLS ++KGK V++S+SPQSRASLA H+ ISPLQVFKK
Sbjct:    61 CLACSGCITSAETVMLEKQSLDEFLSALSKGKDVVVSVSPQSRASLAVHYDISPLQVFKK 120

Query:   119 LTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARYKQSQESDDERSNSSLPMLSSACPGW 178
             LTTFLKSLGVK++FDTSCSRDL LIE+CNEF++RYKQ+   D E S S LP+LSSACPGW
Sbjct:   121 LTTFLKSLGVKAVFDTSCSRDLVLIESCNEFVSRYKQANSDDGENSQSPLPVLSSACPGW 180

Query:   179 ICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTVMPCYDKKLEA 238
             ICYAEKQLGSY+LPY+SSVKSPQQ IGA IKHH+CQ LG R  E+YHVTVMPCYDKKLEA
Sbjct:   181 ICYAEKQLGSYVLPYVSSVKSPQQAIGAAIKHHLCQALGLRLHEVYHVTVMPCYDKKLEA 240

Query:   239 AREDFVFQLDSQEETYRDEG-LEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDKMLT 297
             AR+DFVF   +Q     D G L++ EVDSVLTTGE++DLI+LK V+F+ LEESPLD++LT
Sbjct:   241 ARDDFVFDDGTQ-----DNGDLKLTEVDSVLTTGEIMDLIKLKGVDFKDLEESPLDRVLT 295

Query:   298 NVDDEGHLYGVAGSSGGYAETVFRHAAKTLFGKVIEGHLEFKTIRNSDFREVALEVEGKT 357
             NV +EG LYGVAGSSGGYAET+FRHAAK LFG+ IEG LEFKT+RNSDFREV L++EGKT
Sbjct:   296 NVTEEGDLYGVAGSSGGYAETIFRHAAKALFGQTIEGPLEFKTLRNSDFREVTLQLEGKT 355

Query:   358 LLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMACPSGCLNGGGQIKPKPGQSPKELIKT 417
             +LKFALCYGFQNLQNIVR+VK RKCDYQ+VE+MACP+GCLNGGGQIKPK GQS KELI +
Sbjct:   356 VLKFALCYGFQNLQNIVRRVKTRKCDYQYVEIMACPAGCLNGGGQIKPKTGQSQKELIHS 415

Query:   418 LETIYLENVML-ADPFKNPLVRSLYDEWLEQPGSEKAKKHVHTEYHPVVKSITAQLHNW 475
             LE  Y+ +  L  DP++NP  + L++EWL++PGS +AKK++HT+YHPVVKS+T+QL+NW
Sbjct:   416 LEATYMNDTTLNTDPYQNPTAKRLFEEWLKEPGSNEAKKYLHTQYHPVVKSVTSQLNNW 474

GO:0005634 "nucleus" evidence=ISM

GO:0008901 "ferredoxin hydrogenase activity" evidence=ISS

GO:0005829 "cytosol" evidence=IDA

GO:0000278 "mitotic cell cycle" evidence=RCA

GO:0006396 "RNA processing" evidence=RCA

GO:0007059 "chromosome segregation" evidence=RCA

GO:0007129 "synapsis" evidence=RCA

GO:0007131 "reciprocal meiotic recombination" evidence=RCA

GO:0009410 "response to xenobiotic stimulus" evidence=RCA

GO:0042138 "meiotic DNA double-strand break formation" evidence=RCA

GO:0048522 "positive regulation of cellular process" evidence=RCA

UNIPROTKB\|E1C8S8 NARFL "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|A8WH18 narfl "Cytosolic Fe-S cluster assembly factor narfl" [Xenopus (Silurana) tropicalis (taxid:8364)]	Back alignment and assigned GO terms

MGI\|MGI:1914813 Narfl "nuclear prelamin A recognition factor-like" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1305982 Narfl "nuclear prelamin A recognition factor-like" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5BK18 Narfl "Cytosolic Fe-S cluster assembly factor NARFL" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9H6Q4 NARFL "Cytosolic Fe-S cluster assembly factor NARFL" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|A4FV58 NARFL "Cytosolic Fe-S cluster assembly factor NARFL" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5RF36 NARFL "Cytosolic Fe-S cluster assembly factor NARFL" [Pongo abelii (taxid:9601)]	Back alignment and assigned GO terms

UNIPROTKB\|F1RG50 NARFL "Uncharacterized protein" [Sus scrofa (taxid:9823)]	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)
Q5RF36	NARFL_PONAB	No assigned EC number	0.4424	0.96	0.9579	yes	no
Q9H6Q4	NARFL_HUMAN	No assigned EC number	0.4424	0.96	0.9579	yes	no
Q7PWB8	NARF_ANOGA	No assigned EC number	0.3955	0.9473	0.9414	yes	no
A8WH18	NARFL_XENTR	No assigned EC number	0.4464	0.96	0.9579	yes	no
Q9N392	NARF_CAEEL	No assigned EC number	0.3531	0.9178	0.9540	yes	no
A4FV58	NARFL_BOVIN	No assigned EC number	0.4426	0.9557	0.9537	yes	no
Q9Y7N7	NAR1_SCHPO	No assigned EC number	0.3197	0.9178	0.8104	yes	no
B5DK31	NARF_DROPS	No assigned EC number	0.4004	0.9473	0.9433	yes	no
Q8SYS7	NARF_DROME	No assigned EC number	0.4064	0.9473	0.9433	yes	no
Q7TMW6	NARFL_MOUSE	No assigned EC number	0.4547	0.9557	0.9537	yes	no
Q54F30	NARF_DICDI	No assigned EC number	0.4215	0.9705	0.8831	yes	no
Q5BK18	NARFL_RAT	No assigned EC number	0.4532	0.9284	0.9264	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	eugene3.00060160	hypothetical protein (478 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.8947.1.1	Predicted protein (324 aa)	•	•	0.572
	estExt_fgenesh4_pg.C_LG_X0463	hypothetical protein (485 aa)	•	•	0.553
	estExt_fgenesh4_pm.C_LG_V0527	hypothetical protein (254 aa)	•	•	0.514
	estExt_Genewise1_v1.C_LG_II0234	hypothetical protein (254 aa)	•	•	0.509

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		475
pfam02906		272	pfam02906, Fe_hyd_lg_C, Iron only hydrogenase larg	1e-103
COG4624		411	COG4624, COG4624, Iron only hydrogenase large subu	3e-82
TIGR02512		374	TIGR02512, FeFe_hydrog_A, [FeFe] hydrogenase, grou	3e-72
TIGR04105		462	TIGR04105, FeFe_hydrog_B1, [FeFe] hydrogenase, gro	3e-24
smart00902		52	smart00902, Fe_hyd_SSU, Iron hydrogenase small sub	1e-08
pfam02256		60	pfam02256, Fe_hyd_SSU, Iron hydrogenase small subu	1e-08

>gnl\|CDD\|217280 pfam02906, Fe_hyd_lg_C, Iron only hydrogenase large subunit, C-terminal domain	Back alignment and domain information

 Score =  308 bits (791), Expect = e-103
 Identities = 110/315 (34%), Positives = 164/315 (52%), Gaps = 44/315 (13%)

Query: 90  KAVIISLSPQSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEF 149
           K V+  ++P  R +  E FG+ P  V  KL   L+ LG   +FDT+   DLT++E  +EF
Sbjct: 1   KKVVAQIAPAVRVAFGEEFGLPPGTVTGKLVAALRKLGFDYVFDTAFGADLTIMEEASEF 60

Query: 150 IARYKQSQESDDERSNSSLPMLSSACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIK 209
           + R K             LPM +S CP W+ Y EK     +LP +S+ KSP Q  GA IK
Sbjct: 61  LERLK---------KGEKLPMFTSCCPAWVKYVEKYYPE-LLPNLSTCKSPMQMFGALIK 110

Query: 210 HHICQKLGFRPDEIYHVTVMPCYDKKLEAAREDFVFQLDSQEETYRDEGLEIPEVDSVLT 269
                     P +I+ V++MPC  KK EAAR +F                   +VD+VLT
Sbjct: 111 TD--------PPDIFVVSIMPCTAKKFEAARPEFKG-----------------DVDAVLT 145

Query: 270 TGEVLDLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGVAGSSGGYAETVFRHAAKTLFG 329
           T E+  +I+   ++F +LE+   D  L      G ++GV   +GG  E   R A + L G
Sbjct: 146 TRELAAMIKEAGIDFASLEDEEFDSPLGESSGAGRIFGV---TGGVMEAALRTAYELLTG 202

Query: 330 KVIEGHLEFKTIRNSD-FREVALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVE 388
           K +  ++EFK +R  +  +E  +++E    +K A+  G +N + ++ K+K  + DY F+E
Sbjct: 203 KELP-NIEFKQVRGLEGIKEATVDIE----VKVAVVSGLKNARKLLEKIKAGEIDYHFIE 257

Query: 389 VMACPSGCLNGGGQI 403
           VMACP GC+ GGGQ 
Sbjct: 258 VMACPGGCIGGGGQP 272

Length = 272

>gnl\|CDD\|226972 COG4624, COG4624, Iron only hydrogenase large subunit, C-terminal domain [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|233903 TIGR02512, FeFe_hydrog_A, [FeFe] hydrogenase, group A	Back alignment and domain information

>gnl\|CDD\|234472 TIGR04105, FeFe_hydrog_B1, [FeFe] hydrogenase, group B1/B3	Back alignment and domain information

>gnl\|CDD\|214899 smart00902, Fe_hyd_SSU, Iron hydrogenase small subunit	Back alignment and domain information

>gnl\|CDD\|190260 pfam02256, Fe_hyd_SSU, Iron hydrogenase small subunit	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		475
KOG2439		459	consensus Nuclear architecture related protein [Nu	100.0
COG4624		411	Iron only hydrogenase large subunit, C-terminal do	100.0
TIGR02512		374	Fe_only_hydrog hydrogenases, Fe-only. This model d	100.0
PF02906		285	Fe_hyd_lg_C: Iron only hydrogenase large subunit,	100.0
PF02256		60	Fe_hyd_SSU: Iron hydrogenase small subunit; InterP	99.35
PF12837		24	Fer4_6: 4Fe-4S binding domain; InterPro: IPR001450	97.31
PRK12809		639	putative oxidoreductase Fe-S binding subunit; Revi	97.28
PF00037		24	Fer4: 4Fe-4S binding domain; InterPro: IPR001450 T	97.07
PF12797		22	Fer4_2: 4Fe-4S binding domain; InterPro: IPR001450	96.11
COG1034		693	NuoG NADH dehydrogenase/NADH:ubiquinone oxidoreduc	95.96
COG1142		165	HycB Fe-S-cluster-containing hydrogenase component	95.69
PF14697		59	Fer4_21: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE	95.64
PF14697		59	Fer4_21: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE	95.02
PF12800		17	Fer4_4: 4Fe-4S binding domain; InterPro: IPR001450	94.96
COG2768		354	Uncharacterized Fe-S center protein [General funct	94.76
PF13247		98	Fer4_11: 4Fe-4S dicluster domain; PDB: 2VPY_F 2VPX	94.68
TIGR02494		295	PFLE_PFLC glycyl-radical enzyme activating protein	94.66
PF13187		55	Fer4_9: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_	94.39
PF12798		15	Fer4_3: 4Fe-4S binding domain; InterPro: IPR001450	94.3
PRK15449		95	ferredoxin-like protein FixX; Provisional	93.81
PF13237		52	Fer4_10: 4Fe-4S dicluster domain; PDB: 2FGO_A.	93.71
COG0437		203	HybA Fe-S-cluster-containing hydrogenase component	93.32
PF13746		69	Fer4_18: 4Fe-4S dicluster domain	93.17
PF12838		52	Fer4_7: 4Fe-4S dicluster domain; InterPro: IPR0014	93.07
COG3383		978	Uncharacterized anaerobic dehydrogenase [General f	93.02
PRK09626		103	oorD 2-oxoglutarate-acceptor oxidoreductase subuni	92.94
COG1143		172	NuoI Formate hydrogenlyase subunit 6/NADH:ubiquino	92.79
PRK13409		590	putative ATPase RIL; Provisional	92.7
PF13237		52	Fer4_10: 4Fe-4S dicluster domain; PDB: 2FGO_A.	92.53
PRK09625		133	porD pyruvate flavodoxin oxidoreductase subunit de	92.49
PRK09624		105	porD pyuvate ferredoxin oxidoreductase subunit del	92.11
COG1245		591	Predicted ATPase, RNase L inhibitor (RLI) homolog	91.64
COG1145		99	NapF Ferredoxin [Energy production and conversion]	91.25
COG1143		172	NuoI Formate hydrogenlyase subunit 6/NADH:ubiquino	91.19
PRK08348		120	NADH-plastoquinone oxidoreductase subunit; Provisi	90.86
TIGR02936		91	fdxN_nitrog ferredoxin III, nif-specific. Members	90.81
PRK08764		135	ferredoxin; Provisional	90.81
PRK05113		191	electron transport complex protein RnfB; Provision	90.67
PRK08222		181	hydrogenase 4 subunit H; Validated	90.42
TIGR02936		91	fdxN_nitrog ferredoxin III, nif-specific. Members	90.31
PRK06991		270	ferredoxin; Provisional	90.24
PF13459		65	Fer4_15: 4Fe-4S single cluster domain	90.19
TIGR03478		321	DMSO_red_II_bet DMSO reductase family type II enzy	90.19
TIGR01660		492	narH nitrate reductase, beta subunit. The Nitrate	90.03
COG1141		68	Fer Ferredoxin [Energy production and conversion]	89.96
TIGR02179		78	PorD_KorD 2-oxoacid:acceptor oxidoreductase, delta	89.77
TIGR01944		165	rnfB electron transport complex, RnfABCDGE type, B	89.73
CHL00065		81	psaC photosystem I subunit VII	88.99
TIGR00403		183	ndhI NADH-plastoquinone oxidoreductase subunit I p	88.93
PF13187		55	Fer4_9: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_	88.87
PRK09623		105	vorD 2-ketoisovalerate ferredoxin oxidoreductase s	88.87
TIGR02060		132	aprB adenosine phosphosulphate reductase, beta sub	88.67
TIGR00403		183	ndhI NADH-plastoquinone oxidoreductase subunit I p	88.46
COG1146		68	Ferredoxin [Energy production and conversion]	88.39
PRK07569		234	bidirectional hydrogenase complex protein HoxU; Va	88.29
PRK08348		120	NADH-plastoquinone oxidoreductase subunit; Provisi	88.24
TIGR00402		101	napF ferredoxin-type protein NapF. The gene codes	88.0
COG2221		317	DsrA Dissimilatory sulfite reductase (desulfovirid	87.95
PLN00071		81	photosystem I subunit VII; Provisional	87.93
TIGR02066		341	dsrB sulfite reductase, dissimilatory-type beta su	87.91
PRK14993		244	tetrathionate reductase subunit B; Provisional	87.57
PF13370		58	Fer4_13: 4Fe-4S single cluster domain; PDB: 1FXR_A	87.25
TIGR02912		314	sulfite_red_C sulfite reductase, subunit C. Member	87.21
PRK08222		181	hydrogenase 4 subunit H; Validated	87.05
CHL00014		167	ndhI NADH dehydrogenase subunit I	86.63
TIGR01582		283	FDH-beta formate dehydrogenase, beta subunit, Fe-S	86.44
PF12838		52	Fer4_7: 4Fe-4S dicluster domain; InterPro: IPR0014	86.34
TIGR02179		78	PorD_KorD 2-oxoacid:acceptor oxidoreductase, delta	86.03
PRK12387		180	formate hydrogenlyase complex iron-sulfur subunit;	85.9
TIGR02064		402	dsrA sulfite reductase, dissimilatory-type alpha s	85.72
TIGR03149		225	cyt_nit_nrfC cytochrome c nitrite reductase, Fe-S	85.67
CHL00065		81	psaC photosystem I subunit VII	85.45
TIGR02163		255	napH_ ferredoxin-type protein, NapH/MauN family. M	85.43
KOG3256		212	consensus NADH:ubiquinone oxidoreductase, NDUFS8/2	85.38
CHL00014		167	ndhI NADH dehydrogenase subunit I	85.36
TIGR03048		80	PS_I_psaC photosystem I iron-sulfur protein PsaC.	85.26
PRK05888		164	NADH dehydrogenase subunit I; Provisional	84.88
PRK06273		165	ferredoxin; Provisional	84.8
PRK02651		81	photosystem I subunit VII; Provisional	84.75
COG1144		91	Pyruvate:ferredoxin oxidoreductase and related 2-o	84.68
PRK09477		271	napH quinol dehydrogenase membrane component; Prov	84.59
PRK09625		133	porD pyruvate flavodoxin oxidoreductase subunit de	84.42
TIGR02494		295	PFLE_PFLC glycyl-radical enzyme activating protein	84.41
PRK05888		164	NADH dehydrogenase subunit I; Provisional	84.3
PRK06273		165	ferredoxin; Provisional	84.14
TIGR01971		122	NuoI NADH-quinone oxidoreductase, chain I. This mo	84.1
TIGR01971		122	NuoI NADH-quinone oxidoreductase, chain I. This mo	84.04
COG1145		99	NapF Ferredoxin [Energy production and conversion]	83.99
PRK10882		328	hydrogenase 2 protein HybA; Provisional	83.28
TIGR02951		161	DMSO_dmsB DMSO reductase, iron-sulfur subunit. Thi	83.04
PRK12387		180	formate hydrogenlyase complex iron-sulfur subunit;	82.52
PLN00071		81	photosystem I subunit VII; Provisional	82.46
PRK08493		819	NADH dehydrogenase subunit G; Validated	82.44
TIGR03048		80	PS_I_psaC photosystem I iron-sulfur protein PsaC.	82.43
TIGR02512		374	Fe_only_hydrog hydrogenases, Fe-only. This model d	82.4
PRK06259		486	succinate dehydrogenase/fumarate reductase iron-su	81.98
TIGR02910		334	sulfite_red_A sulfite reductase, subunit A. Member	81.25
PRK10194		163	ferredoxin-type protein; Provisional	81.14
PRK02651		81	photosystem I subunit VII; Provisional	81.08
PRK06991		270	ferredoxin; Provisional	80.91
PRK12771		564	putative glutamate synthase (NADPH) small subunit;	80.79
COG1150		195	HdrC Heterodisulfide reductase, subunit C [Energy	80.72
PF13484		67	Fer4_16: 4Fe-4S double cluster binding domain	80.44
PRK09626		103	oorD 2-oxoglutarate-acceptor oxidoreductase subuni	80.08

>KOG2439 consensus Nuclear architecture related protein [Nuclear structure]	Back alignment and domain information

Probab=100.00  E-value=1.3e-119  Score=902.07  Aligned_cols=446  Identities=48%  Similarity=0.823  Sum_probs=401.4

Q ss_pred             CccccCCCCCcccCCCcccccccccCCC----CCCCCCCc---ccccc---CCCCceeeccccccccccchhhcccchhh
Q 011877            6 SPTLRIGDLSDFIAPSQNCVVSLKKATF----KNPDKPQV---STSSK---QQAEPVKISLKDCLACSGCITSAETVMLE   75 (475)
Q Consensus         6 s~~~~~~~lnD~i~p~~~Ci~p~~~~~~----~~~~~~~~---~~~~~---~~~~~a~I~~~dCi~Cg~Cit~c~~~li~   75 (475)
                      |++|+|+||||||+|+++||+|+.....    ++..+.+.   ...++   .++++|+|+++|||||+||||++|+++++
T Consensus         1 s~~l~l~dlnDFi~p~~~CikP~~~~k~~~~~~~~v~~d~~~~v~~e~g~t~~l~~~kISLsDCLACSGCITSaEtVlls   80 (459)
T KOG2439|consen    1 SALLRLSDLNDFIAPSLACIKPLQVSKTKKKKNIRVDADGPYEVIKEKGETHQLEKVKISLSDCLACSGCITSAETVLLS   80 (459)
T ss_pred             CCcccccchhhhhchHHHhccchhhcccccCCcccccCCCcceeecCCCccccccceeeeHHhhhhccCccchhhhhhhh
Confidence            7999999999999999999999976332    22222222   22223   57889999999999999999999999999


Q ss_pred             hccHHHHHHhhcCCC---eEEEEeCcchhhhhhhhcCCChHhHHHHHHHHHHHcCCcEEEechhhhhhhHHHHHHHHHHH
Q 011877           76 KQSLDEFLSNINKGK---AVIISLSPQSRASLAEHFGISPLQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIAR  152 (475)
Q Consensus        76 ~~~~~~~~~~l~~~k---~vV~~iaP~~r~sl~~~fg~~~~~~~~kl~~~Lk~lGf~~V~Dts~gadi~~~e~~~E~~~r  152 (475)
                      +|++.+|++.|++.|   .+||++|||+|+|||++||++..++..+|..|+|+|||+||+||++++++++.|.++||++|
T Consensus        81 ~Qs~~~~~k~l~~~k~~~~lvvsvSPQ~~~slAa~~gls~~e~~~~L~~F~kklgvhyv~DT~~sR~~sl~es~~Efv~~  160 (459)
T KOG2439|consen   81 EQSHKEFLKVLQKSKQQKVLVVSVSPQSRASLAAKYGLSLREAALRLTSFFKKLGVHYVVDTSFSRDFSLSESYEEFVAR  160 (459)
T ss_pred             hhhHHHHHHhhhhccccceEEEecChhHHHHHHHHhCCCHHHHHHHHHHHHHhcCeeEEeehHHHHHHHHHHHHHHHHHH
Confidence            999999999998765   77999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhcccCcccccCCCCCceecCChHHHHHHHHhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHhhCCCCCCeEEEEEEecc
Q 011877          153 YKQSQESDDERSNSSLPMLSSACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTVMPCY  232 (475)
Q Consensus       153 ~~~~~~~~~~~~~~~~P~itS~CPgwV~yiEk~~~P~Lip~LS~vkSPq~i~g~liK~~~~~~~~i~p~~i~~V~I~PC~  232 (475)
                      ++++..      ....||++|+|||||||+||+| |.||||||++||||||+|++||.+++++.++.|++||||++|||+
T Consensus       161 ~r~~~~------~~~~PlLsSaCPG~v~YaEkt~-~~Lip~ls~vkSPQQi~Gslikd~~~~q~~l~p~~v~hvsvMPCf  233 (459)
T KOG2439|consen  161 YRQHSE------EERTPLLSSACPGWVCYAEKTH-GRLIPHLSRVKSPQQIMGSLIKDFFASQQSLSPEKVFHVSVMPCF  233 (459)
T ss_pred             hhcccc------cccccchhhcCCceeEEeeccc-cccchhhhccCCHHHhhhHHHHHHHHHhcCCCccceeeEeecccc
Confidence            886433      3456999999999999999999 889999999999999999999999999999999999999999999


Q ss_pred             hhhHhhhchhhhhhccccccccccCCCCCCCceEEECHHHHHHHHHhcCCCCCCCCCCcccccCCCCCCCCccccccCCc
Q 011877          233 DKKLEAAREDFVFQLDSQEETYRDEGLEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGVAGSS  312 (475)
Q Consensus       233 aKK~Ea~r~~~~~~~~~~~~~~~~~~~~~~~VD~VLT~~El~~ll~~~~i~~~~l~~~~~d~~~~~~s~~g~~~~~~~~S  312 (475)
                      |||+||+|++|...             +.++||||||++|+.+++++.++|+.....+ .|..++..+........||+|
T Consensus       234 DKKLEAsR~~f~~~-------------~~r~~DcVlT~~Ei~k~l~e~~~~l~~~~~~-~d~l~~~~~~~~~~~~~GgsS  299 (459)
T KOG2439|consen  234 DKKLEASREEFKEH-------------GVRDVDCVLTTGEIFKLLEELDFDLPVRDAE-VDTLPSGLSRETVTSNDGGSS  299 (459)
T ss_pred             cHhhhccchhhhcc-------------CCcccceEeehHHHHHHHHhcCcccccccch-hhcccccccccceeeccCCCC
Confidence            99999999999622             4789999999999999999999999876544 555555555444455668999


Q ss_pred             ccHHHHHHHHHHHHHhccccccccceeeecCCCcEEEEEEeCCeeEEEEEEEechHHHHHHHHHHHcCCCCCcEEEecCC
Q 011877          313 GGYAETVFRHAAKTLFGKVIEGHLEFKTIRNSDFREVALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMAC  392 (475)
Q Consensus       313 GG~~e~v~r~~~~~l~~~~~~~~~~~~~~rn~d~~e~~l~~~g~~~~~~a~~~G~~ni~~ll~~lk~g~~~~dfIEvMAC  392 (475)
                      |||+++|+|++++++||..+. ++.++..||.||+|+|++-+|+.++++|.+||||||||+++++|+|+.+|||||||||
T Consensus       300 GGYa~~i~r~aak~lfg~~v~-~~t~k~~rN~Df~e~tl~~~geill~~a~~yGFRNiQNlvrklkk~k~pyhyvEVmAC  378 (459)
T KOG2439|consen  300 GGYAEHIFRHAAKELFGEIVE-PVTYKELRNSDFREVTLEKNGEILLRFAAAYGFRNIQNLVRKLKKGKFPYHYVEVMAC  378 (459)
T ss_pred             cchHHHHHHHHHHHhcCCccc-chhhhhhccccceeeeeecCchHHHHHHHhhhhhHHHHHHHHHhccCCCcceeEEecc
Confidence            999999999999999999875 8889999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccCCCCCcCCCCCCChHHHHHHHHHHHhhcccCCCCCCChHHHHHHHHHhcCCCChhhhcceeeeeecccccccccc
Q 011877          393 PSGCLNGGGQIKPKPGQSPKELIKTLETIYLENVMLADPFKNPLVRSLYDEWLEQPGSEKAKKHVHTEYHPVVKSITAQL  472 (475)
Q Consensus       393 pgGCinGgGq~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~n~~v~~ly~~~l~~p~~~~~~~llhT~y~~~~~~~~~~~  472 (475)
                      ||||+|||||++.++...++++++++|++|.+.+. +.+...|.+.+||++|+.+ ++..++++|||+||+|++.++++.
T Consensus       379 pgGC~NGgGQl~~~~~~~~~~llq~ve~ly~e~~~-~~~e~~~~~~~L~E~w~k~-~~~~~r~~Lht~y~avek~~~sl~  456 (459)
T KOG2439|consen  379 PGGCINGGGQLQTPDGHARKELLQQVEALYGEIPR-RRDESSPTVPKLEEEWLKG-DSKKARKVLHTDYQAVEKDVTSLG  456 (459)
T ss_pred             CccccCCCccccCCccchHHHHHHHHHHhhccCcc-ccCccccchhHHHHHHHhc-Cchhhhhhhcccchhhhcchhhhc
Confidence            99999999999998878889999999999998776 4555668999999999987 778899999999999999999999


Q ss_pred             CCC
Q 011877          473 HNW  475 (475)
Q Consensus       473 ~~w  475 (475)
                      +||
T Consensus       457 ~kW  459 (459)
T KOG2439|consen  457 NKW  459 (459)
T ss_pred             cCC
Confidence            999

>COG4624 Iron only hydrogenase large subunit, C-terminal domain [General function prediction only]	Back alignment and domain information

>TIGR02512 Fe_only_hydrog hydrogenases, Fe-only	Back alignment and domain information

>PF02906 Fe_hyd_lg_C: Iron only hydrogenase large subunit, C-terminal domain; InterPro: IPR004108 Proteins containing this domain may be involved in the mechanism of biological hydrogen activation and contain 4FE-4S clusters	Back alignment and domain information

>PF02256 Fe_hyd_SSU: Iron hydrogenase small subunit; InterPro: IPR003149 Many microorganisms, such as methanogenic, acetogenic, nitrogen-fixing, photosynthetic, or sulphate-reducing bacteria, metabolise hydrogen	Back alignment and domain information

>PF12837 Fer4_6: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters	Back alignment and domain information

>PRK12809 putative oxidoreductase Fe-S binding subunit; Reviewed	Back alignment and domain information

>PF00037 Fer4: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters	Back alignment and domain information

>PF12797 Fer4_2: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters	Back alignment and domain information

>COG1034 NuoG NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G) [Energy production and conversion]	Back alignment and domain information

>COG1142 HycB Fe-S-cluster-containing hydrogenase components 2 [Energy production and conversion]	Back alignment and domain information

>PF14697 Fer4_21: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_C 2O01_C 2WSC_C 3LW5_C 1H7X_C 1H7W_A 1GT8_A 1GTE_B 1GTH_B	Back alignment and domain information

>PF14697 Fer4_21: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_C 2O01_C 2WSC_C 3LW5_C 1H7X_C 1H7W_A 1GT8_A 1GTE_B 1GTH_B	Back alignment and domain information

>PF12800 Fer4_4: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters	Back alignment and domain information

>COG2768 Uncharacterized Fe-S center protein [General function prediction only]	Back alignment and domain information

>PF13247 Fer4_11: 4Fe-4S dicluster domain; PDB: 2VPY_F 2VPX_B 2VPZ_B 2VPW_F 3IR7_B 1Y5N_B 1R27_D 3EGW_B 1Y5I_B 1Q16_B	Back alignment and domain information

>TIGR02494 PFLE_PFLC glycyl-radical enzyme activating protein family	Back alignment and domain information

>PF13187 Fer4_9: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_C 2O01_C 2WSC_C 3LW5_C 2VKR_C 1KQG_B 1KQF_B 3GYX_J	Back alignment and domain information

>PF12798 Fer4_3: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters	Back alignment and domain information

>PRK15449 ferredoxin-like protein FixX; Provisional	Back alignment and domain information

>PF13237 Fer4_10: 4Fe-4S dicluster domain; PDB: 2FGO_A	Back alignment and domain information

>COG0437 HybA Fe-S-cluster-containing hydrogenase components 1 [Energy production and conversion]	Back alignment and domain information

>PF13746 Fer4_18: 4Fe-4S dicluster domain	Back alignment and domain information

>PF12838 Fer4_7: 4Fe-4S dicluster domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters	Back alignment and domain information

>COG3383 Uncharacterized anaerobic dehydrogenase [General function prediction only]	Back alignment and domain information

>PRK09626 oorD 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed	Back alignment and domain information

>COG1143 NuoI Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion]	Back alignment and domain information

>PRK13409 putative ATPase RIL; Provisional	Back alignment and domain information

>PF13237 Fer4_10: 4Fe-4S dicluster domain; PDB: 2FGO_A	Back alignment and domain information

>PRK09625 porD pyruvate flavodoxin oxidoreductase subunit delta; Reviewed	Back alignment and domain information

>PRK09624 porD pyuvate ferredoxin oxidoreductase subunit delta; Reviewed	Back alignment and domain information

>COG1245 Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]	Back alignment and domain information

>COG1145 NapF Ferredoxin [Energy production and conversion]	Back alignment and domain information

>COG1143 NuoI Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion]	Back alignment and domain information

>PRK08348 NADH-plastoquinone oxidoreductase subunit; Provisional	Back alignment and domain information

>TIGR02936 fdxN_nitrog ferredoxin III, nif-specific	Back alignment and domain information

>PRK08764 ferredoxin; Provisional	Back alignment and domain information

>PRK05113 electron transport complex protein RnfB; Provisional	Back alignment and domain information

>PRK08222 hydrogenase 4 subunit H; Validated	Back alignment and domain information

>TIGR02936 fdxN_nitrog ferredoxin III, nif-specific	Back alignment and domain information

>PRK06991 ferredoxin; Provisional	Back alignment and domain information

>PF13459 Fer4_15: 4Fe-4S single cluster domain	Back alignment and domain information

>TIGR03478 DMSO_red_II_bet DMSO reductase family type II enzyme, iron-sulfur subunit	Back alignment and domain information

>TIGR01660 narH nitrate reductase, beta subunit	Back alignment and domain information

>COG1141 Fer Ferredoxin [Energy production and conversion]	Back alignment and domain information

>TIGR02179 PorD_KorD 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family	Back alignment and domain information

>TIGR01944 rnfB electron transport complex, RnfABCDGE type, B subunit	Back alignment and domain information

>CHL00065 psaC photosystem I subunit VII	Back alignment and domain information

>TIGR00403 ndhI NADH-plastoquinone oxidoreductase subunit I protein	Back alignment and domain information

>PF13187 Fer4_9: 4Fe-4S dicluster domain; PDB: 2WSF_C 2WSE_C 2O01_C 2WSC_C 3LW5_C 2VKR_C 1KQG_B 1KQF_B 3GYX_J	Back alignment and domain information

>PRK09623 vorD 2-ketoisovalerate ferredoxin oxidoreductase subunit delta; Reviewed	Back alignment and domain information

>TIGR02060 aprB adenosine phosphosulphate reductase, beta subunit	Back alignment and domain information

>TIGR00403 ndhI NADH-plastoquinone oxidoreductase subunit I protein	Back alignment and domain information

>COG1146 Ferredoxin [Energy production and conversion]	Back alignment and domain information

>PRK07569 bidirectional hydrogenase complex protein HoxU; Validated	Back alignment and domain information

>PRK08348 NADH-plastoquinone oxidoreductase subunit; Provisional	Back alignment and domain information

>TIGR00402 napF ferredoxin-type protein NapF	Back alignment and domain information

>COG2221 DsrA Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Energy production and conversion]	Back alignment and domain information

>PLN00071 photosystem I subunit VII; Provisional	Back alignment and domain information

>TIGR02066 dsrB sulfite reductase, dissimilatory-type beta subunit	Back alignment and domain information

>PRK14993 tetrathionate reductase subunit B; Provisional	Back alignment and domain information

>PF13370 Fer4_13: 4Fe-4S single cluster domain; PDB: 1FXR_A 1DAX_A 1DFD_A 1WTF_A 1IR0_A 1IQZ_A 1SIZ_A 1SJ1_A 3PNI_B 2Z8Q_A	Back alignment and domain information

>TIGR02912 sulfite_red_C sulfite reductase, subunit C	Back alignment and domain information

>PRK08222 hydrogenase 4 subunit H; Validated	Back alignment and domain information

>CHL00014 ndhI NADH dehydrogenase subunit I	Back alignment and domain information

>TIGR01582 FDH-beta formate dehydrogenase, beta subunit, Fe-S containing	Back alignment and domain information

>PF12838 Fer4_7: 4Fe-4S dicluster domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters	Back alignment and domain information

>TIGR02179 PorD_KorD 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family	Back alignment and domain information

>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional	Back alignment and domain information

>TIGR02064 dsrA sulfite reductase, dissimilatory-type alpha subunit	Back alignment and domain information

>TIGR03149 cyt_nit_nrfC cytochrome c nitrite reductase, Fe-S protein	Back alignment and domain information

>CHL00065 psaC photosystem I subunit VII	Back alignment and domain information

>TIGR02163 napH_ ferredoxin-type protein, NapH/MauN family	Back alignment and domain information

>KOG3256 consensus NADH:ubiquinone oxidoreductase, NDUFS8/23 kDa subunit [Energy production and conversion]	Back alignment and domain information

>CHL00014 ndhI NADH dehydrogenase subunit I	Back alignment and domain information

>TIGR03048 PS_I_psaC photosystem I iron-sulfur protein PsaC	Back alignment and domain information

>PRK05888 NADH dehydrogenase subunit I; Provisional	Back alignment and domain information

>PRK06273 ferredoxin; Provisional	Back alignment and domain information

>PRK02651 photosystem I subunit VII; Provisional	Back alignment and domain information

>COG1144 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, delta subunit [Energy production and conversion]	Back alignment and domain information

>PRK09477 napH quinol dehydrogenase membrane component; Provisional	Back alignment and domain information

>PRK09625 porD pyruvate flavodoxin oxidoreductase subunit delta; Reviewed	Back alignment and domain information

>TIGR02494 PFLE_PFLC glycyl-radical enzyme activating protein family	Back alignment and domain information

>PRK05888 NADH dehydrogenase subunit I; Provisional	Back alignment and domain information

>PRK06273 ferredoxin; Provisional	Back alignment and domain information

>TIGR01971 NuoI NADH-quinone oxidoreductase, chain I	Back alignment and domain information

>TIGR01971 NuoI NADH-quinone oxidoreductase, chain I	Back alignment and domain information

>COG1145 NapF Ferredoxin [Energy production and conversion]	Back alignment and domain information

>PRK10882 hydrogenase 2 protein HybA; Provisional	Back alignment and domain information

>TIGR02951 DMSO_dmsB DMSO reductase, iron-sulfur subunit	Back alignment and domain information

>PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional	Back alignment and domain information

>PLN00071 photosystem I subunit VII; Provisional	Back alignment and domain information

>PRK08493 NADH dehydrogenase subunit G; Validated	Back alignment and domain information

>TIGR03048 PS_I_psaC photosystem I iron-sulfur protein PsaC	Back alignment and domain information

>TIGR02512 Fe_only_hydrog hydrogenases, Fe-only	Back alignment and domain information

>PRK06259 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Provisional	Back alignment and domain information

>TIGR02910 sulfite_red_A sulfite reductase, subunit A	Back alignment and domain information

>PRK10194 ferredoxin-type protein; Provisional	Back alignment and domain information

>PRK02651 photosystem I subunit VII; Provisional	Back alignment and domain information

>PRK06991 ferredoxin; Provisional	Back alignment and domain information

>PRK12771 putative glutamate synthase (NADPH) small subunit; Provisional	Back alignment and domain information

>COG1150 HdrC Heterodisulfide reductase, subunit C [Energy production and conversion]	Back alignment and domain information

>PF13484 Fer4_16: 4Fe-4S double cluster binding domain	Back alignment and domain information

>PRK09626 oorD 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed	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		475
3lx4_A		457	Stepwise [fefe]-Hydrogenase H-Cluster Assembly Reve		9e-44
1feh_A		574	Fe-Only Hydrogenase From Clostridium Pasteurianum L		1e-43
1hfe_L		421	1.6 A Resolution Structure Of The Fe-Only Hydrogena		4e-33
1e08_A		371	Structural Model Of The [fe]-HydrogenaseCYTOCHROME		5e-33

>pdb|3LX4|A Chain A, Stepwise [fefe]-Hydrogenase H-Cluster Assembly Revealed In The Structure Of Hyda(Deltaefg) Length = 457

Back alignment and structure

Iteration: 1

Score = 174 bits (441), Expect = 9e-44, Method: Compositional matrix adjust. Identities = 122/423 (28%), Positives = 194/423 (45%), Gaps = 73/423 (17%) Query: 90 KAVIISLSPQSRASLAEHFGISP-LQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNE 148 K V + ++P R ++AE G++P K+L L+ LG +FDT DLT++E +E Sbjct: 45 KHVCVQVAPAVRVAIAETLGLAPGATTPKQLAEGLRRLGFDEVFDTLFGADLTIMEEGSE 104 Query: 149 FIARYKQSQESDDERSNSSLPMLSSACPGWICYAEKQLGSY--ILPYISSVKSPQQTIGA 206 + R + E+ S+ LPM +S CPGWI EK SY ++PY+SS KSPQ + A Sbjct: 105 LLHRLTEHLEAH-PHSDEPLPMFTSCCPGWIAMLEK---SYPDLIPYVSSCKSPQMMLAA 160 Query: 207 TIKHHICQKLGFRPDEIYHVTVMPCYDKKLEAAREDFVFQLDSQEETYRDEGLEIPEVDS 266 +K ++ +K G P ++ V++MPC K+ EA R+ F D T R ++D Sbjct: 161 MVKSYLAEKKGIAPKDMVMVSIMPCTRKQSEADRDWFCVDADP---TLR-------QLDH 210 Query: 267 VLTTGEVLDLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGVAGSSGGYAETVFRHAAKT 326 V+TT E+ ++ + + +N L E D + G L+ G++GG E R A + Sbjct: 211 VITTVELGNIFKERGINLAELPEGEWDNPMGVGSGAGVLF---GTTGGVMEAALRTAYEL 267 Query: 327 LFGKVIEGHLEFKTIRNSD----------------FREV--------------------- 349 G + L +R D F E+ Sbjct: 268 FTGTPLP-RLSLSEVRGMDGIKETNITMVPAPGSKFEELLKHRAAARAEAAAHGTPGPLA 326 Query: 350 --------ALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMACPSGCLNGGG 401 + + G L+ A+ G N + ++ K++ + Y FVE+MACP+GC+ GGG Sbjct: 327 WDGGAGFTSEDGRGGITLRVAVANGLGNAKKLITKMQAGEAKYDFVEIMACPAGCVGGGG 386 Query: 402 QIKPKPGQSPKELIKTLETIYL---ENVMLADPFKNPLVRSLYDEWLEQPGSEKAKKHVH 458 Q P + K + + + E L +NP +R LYD +L +P KA + +H Sbjct: 387 Q----PRSTDKAITQKRQAALYNLDEKSTLRRSHENPSIRELYDTYLGEPLGHKAHELLH 442 Query: 459 TEY 461 T Y Sbjct: 443 THY 445

PyMOL of 3lx4

>pdb|1FEH|A Chain A, Fe-Only Hydrogenase From Clostridium Pasteurianum Length = 574

Back alignment and structure

>pdb|1HFE|L Chain L, 1.6 A Resolution Structure Of The Fe-Only Hydrogenase From Desulfovibrio Desulfuricans Length = 421

Back alignment and structure

>pdb|1E08|A Chain A, Structural Model Of The [fe]-HydrogenaseCYTOCHROME C553 Complex Combining Nmr And Soft-Docking Length = 371

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		475
3c8y_A		574	Iron hydrogenase 1; dithiomethylether, H-cluster,	1e-142
1hfe_L		421	Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larg	1e-134
3lx4_A		457	Fe-hydrogenase; HYDA, H-cluster, [4Fe-4S] cluster,	1e-131
1hfe_S		123	Protein (Fe-only hydrogenase (E.C.1.18.99.1) (smal	6e-31
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-15
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05

>3c8y_A Iron hydrogenase 1; dithiomethylether, H-cluster, iron-sulfur binding, oxidoreductase; HET: HCN; 1.39A {Clostridium pasteurianum} SCOP: c.96.1.1 d.15.4.2 d.58.1.5 PDB: 1c4c_A* 1c4a_A* 1feh_A* Length = 574	Back alignment and structure

 Score =  417 bits (1075), Expect = e-142
 Identities = 122/427 (28%), Positives = 194/427 (45%), Gaps = 36/427 (8%)

Query: 44  SSKQQAEPVKISLKDCLACSGCITSAETVML-EKQSLDEFLSNINKG-KAVIISLSPQSR 101
           +     +       +CL C  CI +     L EK  +D   + +N   K VI++++P  R
Sbjct: 175 TIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEKSHMDRVKNALNAPEKHVIVAMAPSVR 234

Query: 102 ASLAEHFGISP-LQVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARYKQSQESD 160
           AS+ E F +   + V  K+ T L+ LG   IFD +   D+T++E   E + R +      
Sbjct: 235 ASIGELFNMGFGVDVTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIE------ 288

Query: 161 DERSNSSLPMLSSACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRP 220
              +N   PM +S CPGW+  AE      +L  +SS KSPQQ  G   K +     G  P
Sbjct: 289 ---NNGPFPMFTSCCPGWVRQAENYYPE-LLNNLSSAKSPQQIFGTASKTYYPSISGLDP 344

Query: 221 DEIYHVTVMPCYDKKLEAAREDFVFQLDSQEETYRDEGLEIPEVDSVLTTGEVLDLIQLK 280
             ++ VTVMPC  KK EA R                +G  + ++D+V+TT E+  +I+  
Sbjct: 345 KNVFTVTVMPCTSKKFEADRPQM-----------EKDG--LRDIDAVITTRELAKMIKDA 391

Query: 281 AVNFEALEESPLDKMLTNVDDEGHLYGVAGSSGGYAETVFRHAAKTLFGKVIEGHLEFKT 340
            + F  LE+S  D  +      G ++G    +GG  E   R A        +E  +E+K 
Sbjct: 392 KIPFAKLEDSEADPAMGEYSGAGAIFGA---TGGVMEAALRSAKDFAENAELE-DIEYKQ 447

Query: 341 IRNSD-FREVALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMACPSGCLNG 399
           +R  +  +E  +E+        A+  G  NL   ++   + +  Y F+EVMAC  GC+NG
Sbjct: 448 VRGLNGIKEAEVEINNNKY-NVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGGCVNG 506

Query: 400 GGQIKPKPGQSPKELIKTLETIYL----ENVMLADPFKNPLVRSLYDEWLEQPGSEKAKK 455
           GGQ    P    K  IK +    L    E++      +N  +  +Y  +  +PG  +A +
Sbjct: 507 GGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHE 566

Query: 456 HVHTEYH 462
            +H +Y 
Sbjct: 567 ILHFKYK 573

PyMOL of 3c8y

>1hfe_L Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larger subunit)); hydrogene metabolism, periplasm; 1.60A {Desulfovibrio vulgaris subsp} SCOP: c.96.1.1 d.58.1.5 PDB: 1e08_A* 1gx7_A* Length = 421	Back alignment and structure

>3lx4_A Fe-hydrogenase; HYDA, H-cluster, [4Fe-4S] cluster, IR cluster, insertion, biosynthesis, maturation, intermediate, evolution; 1.97A {Chlamydomonas reinhardtii} Length = 457	Back alignment and structure

>1hfe_S Protein (Fe-only hydrogenase (E.C.1.18.99.1) (smaller subunit)); hydrogene metabolism, periplasm; 1.60A {Desulfovibrio vulgaris subsp} SCOP: a.137.4.1 PDB: 1e08_D* 1gx7_D* Length = 123	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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		475
3lx4_A		457	Fe-hydrogenase; HYDA, H-cluster, [4Fe-4S] cluster,	100.0
3c8y_A		574	Iron hydrogenase 1; dithiomethylether, H-cluster,	100.0
1hfe_L		421	Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larg	100.0
1q16_B		512	Respiratory nitrate reductase 1 beta chain; membra	99.94
1hfe_S		123	Protein (Fe-only hydrogenase (E.C.1.18.99.1) (smal	99.79
1ti6_B		274	Pyrogallol hydroxytransferase small subunit; molyb	97.7
1kqf_B		294	FDH-N beta S, formate dehydrogenase, nitrate-induc	96.77
2ivf_B		352	Ethylbenzene dehydrogenase beta-subunit; anaerobic	95.69
1bc6_A		77	7-Fe ferredoxin; electron transport, iron-sulfur;	95.35
7fd1_A		106	FD1, protein (7-Fe ferredoxin I); electron transpo	94.15
1h98_A		78	Ferredoxin; electron transport, thermophilic, iron	94.08
2fdn_A		55	Ferredoxin; electron transport, iron-sulfur, 4Fe-4	93.46
1f2g_A		58	Ferredoxin II; electron transport, FDII desulfovib	92.88
2v2k_A		105	Ferredoxin; iron, transport, iron-sulfur, mycobact	92.86
1dax_A		64	Ferredoxin I; electron transport, electron-transfe	92.84
1xer_A		103	Ferredoxin; electron transport, iron-sulfur, dupli	92.67
1rof_A		60	Ferredoxin; electron transport, iron-sulfur; NMR {	92.6
3eun_A		82	Ferredoxin; electron transport, [4Fe-4S] cluster,	92.49
3mm5_B		366	Sulfite reductase, dissimilatory-type subunit BET;	92.47
3or1_B		386	Sulfite reductase beta; dissimilatory sulfite redu	92.36
2zvs_A		85	Uncharacterized ferredoxin-like protein YFHL; elec	92.3
2fdn_A		55	Ferredoxin; electron transport, iron-sulfur, 4Fe-4	92.23
3j16_B		608	RLI1P; ribosome recycling, translation, eukarya, r	92.23
1rgv_A		80	Ferredoxin; electron transport; 2.90A {Thauera aro	92.22
3eun_A		82	Ferredoxin; electron transport, [4Fe-4S] cluster,	92.19
1rgv_A		80	Ferredoxin; electron transport; 2.90A {Thauera aro	92.18
1jb0_C		80	Photosystem I iron-sulfur center; membrane protein	92.09
2vpz_B		195	NRFC protein; oxidoreductase, molybdopterin guanin	92.03
2fgo_A		82	Ferredoxin; allochromatium vinosum, [4Fe-4S] clust	91.92
3mm5_A		418	Sulfite reductase, dissimilatory-type subunit ALP;	91.75
1iqz_A		81	Ferredoxin; iron-sulfer protein, ultlahigh resolut	91.75
2fgo_A		82	Ferredoxin; allochromatium vinosum, [4Fe-4S] clust	91.68
1dwl_A		59	Ferredoxin I; electron transfer, model, heteronucl	91.62
1kqf_B		294	FDH-N beta S, formate dehydrogenase, nitrate-induc	90.92
1jnr_B		150	Adenylylsulfate reductase; oxidoreductase; HET: FA	90.87
1sj1_A		66	Ferredoxin; thermostability, iron-sulfur cluster,	90.53
1dwl_A		59	Ferredoxin I; electron transfer, model, heteronucl	90.53
3gyx_B		166	Adenylylsulfate reductase; oxidoreductase; HET: FA	90.42
3i9v_9		182	NADH-quinone oxidoreductase subunit 9; electron tr	90.37
1xer_A		103	Ferredoxin; electron transport, iron-sulfur, dupli	90.35
3or1_A		437	Sulfite reductase alpha; dissimilatory sulfite red	90.04
1rof_A		60	Ferredoxin; electron transport, iron-sulfur; NMR {	89.94
2ivf_B		352	Ethylbenzene dehydrogenase beta-subunit; anaerobic	89.81
2zvs_A		85	Uncharacterized ferredoxin-like protein YFHL; elec	89.67
1dax_A		64	Ferredoxin I; electron transport, electron-transfe	89.43
1jb0_C		80	Photosystem I iron-sulfur center; membrane protein	89.23
1f2g_A		58	Ferredoxin II; electron transport, FDII desulfovib	89.23
1bc6_A		77	7-Fe ferredoxin; electron transport, iron-sulfur;	88.39
3i9v_9		182	NADH-quinone oxidoreductase subunit 9; electron tr	86.67
7fd1_A		106	FD1, protein (7-Fe ferredoxin I); electron transpo	86.57
1h98_A		78	Ferredoxin; electron transport, thermophilic, iron	85.84
3gyx_B		166	Adenylylsulfate reductase; oxidoreductase; HET: FA	85.59
2gmh_A		584	Electron transfer flavoprotein-ubiquinone oxidored	85.13
1hfe_L		421	Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larg	84.72
3bk7_A		607	ABC transporter ATP-binding protein; ABC ATPase, i	84.21
2v2k_A		105	Ferredoxin; iron, transport, iron-sulfur, mycobact	83.81
1jnr_B		150	Adenylylsulfate reductase; oxidoreductase; HET: FA	83.23
2wdq_B		238	Succinate dehydrogenase iron-sulfur subunit; succi	81.94
1h0h_B		214	Formate dehydrogenase (small subunit); tungsten se	81.49
2c42_A		1231	Pyruvate-ferredoxin oxidoreductase; 4Fe-4S, iron,	81.33
1iqz_A		81	Ferredoxin; iron-sulfer protein, ultlahigh resolut	81.26
1kf6_B		243	Fumarate reductase iron-sulfur protein; respiratio	80.01

>3lx4_A Fe-hydrogenase; HYDA, H-cluster, [4Fe-4S] cluster, IR cluster, insertion, biosynthesis, maturation, intermediate, evolution; 1.97A {Chlamydomonas reinhardtii}	Back alignment and structure

Probab=100.00  E-value=3.8e-104  Score=823.37  Aligned_cols=381  Identities=31%  Similarity=0.563  Sum_probs=334.1

Q ss_pred             hcccchhhhccHHHHHHhhcCC------CeEEEEeCcchhhhhhhhcCCChHhH-HHHHHHHHHHcCCcEEEechhhhhh
Q 011877           68 SAETVMLEKQSLDEFLSNINKG------KAVIISLSPQSRASLAEHFGISPLQV-FKKLTTFLKSLGVKSIFDTSCSRDL  140 (475)
Q Consensus        68 ~c~~~li~~~~~~~~~~~l~~~------k~vV~~iaP~~r~sl~~~fg~~~~~~-~~kl~~~Lk~lGf~~V~Dts~gadi  140 (475)
                      .+++.+.+.+++++|+++|++.      |++||+||||+|++|+++||++++.. .++|+++||+|||++||||+||||+
T Consensus        17 ~~~~a~~~~~~~~~v~~aL~~~~~~~~~k~vVasvAPavrasl~~~FGl~~~~~t~gkl~~aLk~LGFd~VfDta~gADl   96 (457)
T 3lx4_A           17 AAPAAEAPLSHVQQALAELAKPKDDPTRKHVCVQVAPAVRVAIAETLGLAPGATTPKQLAEGLRRLGFDEVFDTLFGADL   96 (457)
T ss_dssp             --------CCHHHHHHHHHHSCTTCTTCCEEEEEECHHHHHHGGGGGTCCTTCSCHHHHHHHHHHTTCSEEEETHHHHHH
T ss_pred             cccccccccchHHHHHHHHhCcCcccCCceEEEEECcHHHHHHHHHhCCCcccccHHHHHHHHHHcCCCEEEEcHHHHHH
Confidence            3456666778899999999875      68999999999999999999988765 6999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHhhcccCcccccCCCCCceecCChHHHHHHHHhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHhhCCCC
Q 011877          141 TLIEACNEFIARYKQSQESDDERSNSSLPMLSSACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRP  220 (475)
Q Consensus       141 ~~~e~~~E~~~r~~~~~~~~~~~~~~~~P~itS~CPgwV~yiEk~~~P~Lip~LS~vkSPq~i~g~liK~~~~~~~~i~p  220 (475)
                      +++|+++||++|+++..... ...+.++|||||||||||+||||+| |+|+||||+++|||||+|+++|+||+++.|++|
T Consensus        97 ti~EEa~Ef~~r~~~~l~~~-~~~~~~lPmiTScCPgWV~yiEk~y-PeLlp~LSt~kSPqqm~G~liK~y~a~~~gi~p  174 (457)
T 3lx4_A           97 TIMEEGSELLHRLTEHLEAH-PHSDEPLPMFTSCCPGWIAMLEKSY-PDLIPYVSSCKSPQMMLAAMVKSYLAEKKGIAP  174 (457)
T ss_dssp             HHHHHHHHHHHHHHHHHCC------CCSSEECCCCHHHHHHHHHHC-GGGGGGBCCBCCHHHHHHHHHHHHHHHHHTCCG
T ss_pred             HHHHHHHHHHHHHHhhhccc-cccCCCCceEecCCHHHHHHHHHhC-cccccccCCCCCHHHHHHHHHHHHHHHhcCCCc
Confidence            99999999999985321100 0014578999999999999999999 999999999999999999999999999999999


Q ss_pred             CCeEEEEEEecchhhHhhhchhhhhhccccccccccCCCCCCCceEEECHHHHHHHHHhcCCCCCCCCCCcccccCCCCC
Q 011877          221 DEIYHVTVMPCYDKKLEAAREDFVFQLDSQEETYRDEGLEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDKMLTNVD  300 (475)
Q Consensus       221 ~~i~~V~I~PC~aKK~Ea~r~~~~~~~~~~~~~~~~~~~~~~~VD~VLT~~El~~ll~~~~i~~~~l~~~~~d~~~~~~s  300 (475)
                      ++|+|||||||+|||+||.|++|..+          ...+.++||+||||+||.+||++.+||+.++++.++|.+++..|
T Consensus       175 ~~i~vV~ImPC~AKK~EA~R~e~~~~----------~~~g~~dVD~VLTtrEL~~mik~~gId~~~l~~~~~D~p~g~~s  244 (457)
T 3lx4_A          175 KDMVMVSIMPCTRKQSEADRDWFCVD----------ADPTLRQLDHVITTVELGNIFKERGINLAELPEGEWDNPMGVGS  244 (457)
T ss_dssp             GGEEEEEEESCSSHHHHHTCTTCBCC-------------CCBSSCEEEEHHHHHHHHHHTTCCGGGSCCCCCCCTTSSSS
T ss_pred             ccEEEEEEEcccchHHHhcCcccccc----------cccCCccccEEeeHHHHHHHHHHcCCChhhCCcccccccccccC
Confidence            99999999999999999999988531          00135799999999999999999999999999999999999999


Q ss_pred             CCCccccccCCcccHHHHHHHHHHHHHhccccccccceeeecCCC-cEEEEEEeC-------------------------
Q 011877          301 DEGHLYGVAGSSGGYAETVFRHAAKTLFGKVIEGHLEFKTIRNSD-FREVALEVE-------------------------  354 (475)
Q Consensus       301 ~~g~~~~~~~~SGG~~e~v~r~~~~~l~~~~~~~~~~~~~~rn~d-~~e~~l~~~-------------------------  354 (475)
                      +.|++||.   ||||+||++|++++.++|.++. .++|+.+||.| ++|+++.+.                         
T Consensus       245 gaG~iFg~---sGGV~EAv~r~a~~~~~g~~~~-~~~~~~vrg~~g~kea~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~  320 (457)
T 3lx4_A          245 GAGVLFGT---TGGVMEAALRTAYELFTGTPLP-RLSLSEVRGMDGIKETNITMVPAPGSKFEELLKHRAAARAEAAAHG  320 (457)
T ss_dssp             SCSCCSSB---CCCHHHHHHHHHHHHHHSSCCC-CCCCEECTTCTTEEEEEEEECCCTTSHHHHHHHHCCC---------
T ss_pred             CCceecCC---cccHHHHHHHHHHHHhhCCCCc-cccceeecCCCCceEEEEEeccccccchhhhhhhhhhhhhcccccc
Confidence            99999988   9999999999999999999884 78999999985 999998881                         


Q ss_pred             -------------------CeeEEEEEEEechHHHHHHHHHHHcCCCCCcEEEecCCcccccCCCCCcCCCCCCChHHHH
Q 011877          355 -------------------GKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMACPSGCLNGGGQIKPKPGQSPKELI  415 (475)
Q Consensus       355 -------------------g~~~~~~a~~~G~~ni~~ll~~lk~g~~~~dfIEvMACpgGCinGgGq~~~~~~~~~~~~~  415 (475)
                                         |...+|+|+||||+|++++|+++|+|+.+|||||||||||||||||||+++..   ...+.
T Consensus       321 ~~~~~~~~~~~~~~~~~~~~g~~l~vav~~G~~n~~~ll~~~k~G~~~y~fVEvMACPgGCi~GgGQp~~~~---~~~~~  397 (457)
T 3lx4_A          321 TPGPLAWDGGAGFTSEDGRGGITLRVAVANGLGNAKKLITKMQAGEAKYDFVEIMACPAGCVGGGGQPRSTD---KAITQ  397 (457)
T ss_dssp             --CCSCCCSCEEECCTTCCCEEEEEEEEEESHHHHHHHHHHHHHTSSCCSEEEEESSTTCGGGCTTSCCCSC---TTHHH
T ss_pred             cccccccccccccccccCCCCeEEEEEEEcCHHHHHHHHHHHHcCCCCccEEEECCCCccccCCcccccccc---HHHHH
Confidence                               33458999999999999999999999999999999999999999999999753   23455


Q ss_pred             HHHHHHHhhc--ccCCCCCCChHHHHHHHHHhcCCCChhhhcceeeeeeccccc
Q 011877          416 KTLETIYLEN--VMLADPFKNPLVRSLYDEWLEQPGSEKAKKHVHTEYHPVVKS  467 (475)
Q Consensus       416 ~~~~~~y~~~--~~~~~~~~n~~v~~ly~~~l~~p~~~~~~~llhT~y~~~~~~  467 (475)
                      +|++.+|..+  ..+|.|++||.+++||++||++|+++++|+||||+|+++.+.
T Consensus       398 ~r~~~ly~~d~~~~~r~s~eNp~v~~lY~~~l~~p~s~~ah~lLHT~y~~~~~~  451 (457)
T 3lx4_A          398 KRQAALYNLDEKSTLRRSHENPSIRELYDTYLGEPLGHKAHELLHTHYVAGGVE  451 (457)
T ss_dssp             HHHHTSSCHHHHTSBCCGGGCHHHHHHHHHTTCSTTSHHHHHHHBCCCCTTCC-
T ss_pred             HHHHHHHHHhhcCCccCCCcCHHHHHHHHHHhCCCCcHHHHHhcCccccccCcc
Confidence            6888999854  367899999999999999999999999999999999998664

PyMOL of 3lx4

>3c8y_A Iron hydrogenase 1; dithiomethylether, H-cluster, iron-sulfur binding, oxidoreductase; HET: HCN; 1.39A {Clostridium pasteurianum} SCOP: c.96.1.1 d.15.4.2 d.58.1.5 PDB: 1c4c_A* 1c4a_A* 1feh_A*	Back alignment and structure

>1hfe_L Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larger subunit)); hydrogene metabolism, periplasm; 1.60A {Desulfovibrio vulgaris subsp} SCOP: c.96.1.1 d.58.1.5 PDB: 1e08_A* 1gx7_A*	Back alignment and structure

>1q16_B Respiratory nitrate reductase 1 beta chain; membrane protein, electron-transfer, oxidoreductase; HET: FME MD1 HEM AGA 3PH; 1.90A {Escherichia coli} SCOP: d.58.1.5 PDB: 1r27_B* 1siw_B* 1y5i_B* 1y5l_B* 1y5n_B* 3ir5_B* 3ir6_B* 3ir7_B* 1y4z_B* 3egw_B*	Back alignment and structure

>1hfe_S Protein (Fe-only hydrogenase (E.C.1.18.99.1) (smaller subunit)); hydrogene metabolism, periplasm; 1.60A {Desulfovibrio vulgaris subsp} SCOP: a.137.4.1 PDB: 1e08_D* 1gx7_D*	Back alignment and structure

>1ti6_B Pyrogallol hydroxytransferase small subunit; molybdenum binding enzyme, MGD-cofactors, DMSO-reductase family, 4Fe-4S-cluster; HET: MGD BTT; 2.00A {Pelobacter acidigallici} SCOP: b.3.5.1 d.58.1.5 PDB: 1ti2_B* 1ti4_B* 1vld_N* 1vle_N* 1vlf_N*	Back alignment and structure

>1kqf_B FDH-N beta S, formate dehydrogenase, nitrate-inducible, iron-SU subunit; oxidoreductase, selenium, selenocysteine, seCys, molybdenum; HET: MGD HEM CDL; 1.60A {Escherichia coli} SCOP: d.58.1.5 f.23.22.1 PDB: 1kqg_B*	Back alignment and structure

>2ivf_B Ethylbenzene dehydrogenase beta-subunit; anaerobic hydrocarbon degradation, MOCO, Fe/S cluster, MO- B enzyme, DMSO reductase family; HET: MES MGD MD1 HEM; 1.88A {Aromatoleum aromaticum}	Back alignment and structure

>1bc6_A 7-Fe ferredoxin; electron transport, iron-sulfur; NMR {Bacillus schlegelii} SCOP: d.58.1.2 PDB: 1bd6_A 1bqx_A 1bwe_A	Back alignment and structure

>7fd1_A FD1, protein (7-Fe ferredoxin I); electron transport, iron-sulfur; 1.30A {Azotobacter vinelandii} SCOP: d.58.1.2 PDB: 1fda_A 1fdb_A 1fer_A 1axq_A 5fd1_A 6fdr_A 6fd1_A 7fdr_A 1frh_A 1fri_A 1fdd_A 1frl_A 1d3w_A 1frm_A 1frx_A 1g6b_A 1pc4_A 1frj_A 2fd2_A 1fd2_A ...	Back alignment and structure

>1h98_A Ferredoxin; electron transport, thermophilic, iron-sulfur, azotobacter, hydrogen bonds, stability, high resolution; 1.64A {Thermus aquaticus} SCOP: d.58.1.2	Back alignment and structure

>2fdn_A Ferredoxin; electron transport, iron-sulfur, 4Fe-4S; 0.94A {Clostridium acidurici} SCOP: d.58.1.1 PDB: 1fdn_A 1fca_A 1clf_A 1dur_A	Back alignment and structure

>1f2g_A Ferredoxin II; electron transport, FDII desulfovibrio gigas; NMR {Desulfovibrio gigas} SCOP: d.58.1.4 PDB: 1fxd_A	Back alignment and structure

>2v2k_A Ferredoxin; iron, transport, iron-sulfur, mycobacterium tuberculosis, Fe cluster, metal-binding, electron transfer, transport; 1.6A {Mycobacterium smegmatis}	Back alignment and structure

>1dax_A Ferredoxin I; electron transport, electron-transfer protein, 4Fe-4S cluster; NMR {Desulfovibrio africanus} SCOP: d.58.1.4 PDB: 1dfd_A 1fxr_A	Back alignment and structure

>1xer_A Ferredoxin; electron transport, iron-sulfur, duplication; 2.00A {Sulfolobus tokodaii str} SCOP: d.58.1.3 PDB: 2vkr_A	Back alignment and structure

>1rof_A Ferredoxin; electron transport, iron-sulfur; NMR {Thermotoga maritima} SCOP: d.58.1.4 PDB: 1vjw_A	Back alignment and structure

>3eun_A Ferredoxin; electron transport, [4Fe-4S] cluster, 4Fe-4S, iron, iron-sulfur, metal-binding, transport; 1.05A {Allochromatium vinosum} SCOP: d.58.1.1 PDB: 1blu_A 3exy_A	Back alignment and structure

>3mm5_B Sulfite reductase, dissimilatory-type subunit BET; alpha-beta-protein, oxidoreductase; HET: SRM; 1.80A {Archaeoglobus fulgidus} PDB: 3c7b_B* 3mm6_B* 3mm7_B* 3mm8_B* 3mm9_B* 3mma_B* 3mmb_B* 3mmc_B*	Back alignment and structure

>3or1_B Sulfite reductase beta; dissimilatory sulfite reductase, sulfate reduction, oxidored sulfite reduction; HET: SRM; 1.76A {Desulfovibrio gigas} PDB: 3or2_B* 2v4j_B* 2xsj_B*	Back alignment and structure

>2zvs_A Uncharacterized ferredoxin-like protein YFHL; electron transport, [4Fe-4S] clusters, iron-SULF clusters, reduction potential; 1.65A {Escherichia coli}	Back alignment and structure

>2fdn_A Ferredoxin; electron transport, iron-sulfur, 4Fe-4S; 0.94A {Clostridium acidurici} SCOP: d.58.1.1 PDB: 1fdn_A 1fca_A 1clf_A 1dur_A	Back alignment and structure

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}	Back alignment and structure

>1rgv_A Ferredoxin; electron transport; 2.90A {Thauera aromatica} SCOP: d.58.1.1	Back alignment and structure

>3eun_A Ferredoxin; electron transport, [4Fe-4S] cluster, 4Fe-4S, iron, iron-sulfur, metal-binding, transport; 1.05A {Allochromatium vinosum} SCOP: d.58.1.1 PDB: 1blu_A 3exy_A	Back alignment and structure

>1rgv_A Ferredoxin; electron transport; 2.90A {Thauera aromatica} SCOP: d.58.1.1	Back alignment and structure

>1jb0_C Photosystem I iron-sulfur center; membrane protein, multiprotein-pigment complex, photosynthes; HET: CL1 PQN BCR LHG LMG; 2.50A {Synechococcus elongatus} SCOP: d.58.1.2 PDB: 3pcq_C* 1k0t_A 2wsc_C* 2wse_C* 2wsf_C* 3lw5_C* 2o01_C*	Back alignment and structure

>2vpz_B NRFC protein; oxidoreductase, molybdopterin guanine dinucleotide, iron-sulfur, metal-binding, molybdopterin; HET: MGD; 2.40A {Thermus thermophilus} PDB: 2vpx_B* 2vpw_B* 2vpy_B*	Back alignment and structure

>2fgo_A Ferredoxin; allochromatium vinosum, [4Fe-4S] cluster, reduction potential, iron binding protein electron transport; 1.32A {Pseudomonas aeruginosa}	Back alignment and structure

>3mm5_A Sulfite reductase, dissimilatory-type subunit ALP; alpha-beta-protein, oxidoreductase; HET: SRM; 1.80A {Archaeoglobus fulgidus} PDB: 3mm6_A* 3mm7_A* 3mm8_A* 3mm9_A* 3mma_A* 3mmb_A* 3mmc_A* 3c7b_A*	Back alignment and structure

>1iqz_A Ferredoxin; iron-sulfer protein, ultlahigh resolution analysis, geometry of [4Fe-4S] cluster, electron transport; 0.92A {Bacillus thermoproteolyticus} SCOP: d.58.1.4 PDB: 1ir0_A 1wtf_A*	Back alignment and structure

>2fgo_A Ferredoxin; allochromatium vinosum, [4Fe-4S] cluster, reduction potential, iron binding protein electron transport; 1.32A {Pseudomonas aeruginosa}	Back alignment and structure

>1dwl_A Ferredoxin I; electron transfer, model, heteronuclear docking; HET: HEC; NMR {Desulfomicrobium norvegicum} SCOP: i.4.1.1	Back alignment and structure

>1kqf_B FDH-N beta S, formate dehydrogenase, nitrate-inducible, iron-SU subunit; oxidoreductase, selenium, selenocysteine, seCys, molybdenum; HET: MGD HEM CDL; 1.60A {Escherichia coli} SCOP: d.58.1.5 f.23.22.1 PDB: 1kqg_B*	Back alignment and structure

>1jnr_B Adenylylsulfate reductase; oxidoreductase; HET: FAD; 1.60A {Archaeoglobus fulgidus dsm 4304} SCOP: d.58.1.5 PDB: 1jnz_B* 2fja_B* 2fjb_B* 2fjd_B* 2fje_B*	Back alignment and structure

>1sj1_A Ferredoxin; thermostability, iron-sulfur cluster, hexammine cobalt(III), electron transport; HET: NCO; 1.50A {Pyrococcus furiosus} SCOP: d.58.1.4 PDB: 1siz_A* 2z8q_A 3pni_A	Back alignment and structure

>1dwl_A Ferredoxin I; electron transfer, model, heteronuclear docking; HET: HEC; NMR {Desulfomicrobium norvegicum} SCOP: i.4.1.1	Back alignment and structure

>3gyx_B Adenylylsulfate reductase; oxidoreductase; HET: FAD; 3.20A {Desulfovibrio gigas}	Back alignment and structure

>3i9v_9 NADH-quinone oxidoreductase subunit 9; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_8* 2fug_9* 3iam_9* 3ias_9* 3m9s_9*	Back alignment and structure

>1xer_A Ferredoxin; electron transport, iron-sulfur, duplication; 2.00A {Sulfolobus tokodaii str} SCOP: d.58.1.3 PDB: 2vkr_A	Back alignment and structure

>3or1_A Sulfite reductase alpha; dissimilatory sulfite reductase, sulfate reduction, oxidored sulfite reduction; HET: SRM; 1.76A {Desulfovibrio gigas} PDB: 3or2_A* 2v4j_A* 2xsj_A*	Back alignment and structure

>1rof_A Ferredoxin; electron transport, iron-sulfur; NMR {Thermotoga maritima} SCOP: d.58.1.4 PDB: 1vjw_A	Back alignment and structure

>2ivf_B Ethylbenzene dehydrogenase beta-subunit; anaerobic hydrocarbon degradation, MOCO, Fe/S cluster, MO- B enzyme, DMSO reductase family; HET: MES MGD MD1 HEM; 1.88A {Aromatoleum aromaticum}	Back alignment and structure

>2zvs_A Uncharacterized ferredoxin-like protein YFHL; electron transport, [4Fe-4S] clusters, iron-SULF clusters, reduction potential; 1.65A {Escherichia coli}	Back alignment and structure

>1dax_A Ferredoxin I; electron transport, electron-transfer protein, 4Fe-4S cluster; NMR {Desulfovibrio africanus} SCOP: d.58.1.4 PDB: 1dfd_A 1fxr_A	Back alignment and structure

>1jb0_C Photosystem I iron-sulfur center; membrane protein, multiprotein-pigment complex, photosynthes; HET: CL1 PQN BCR LHG LMG; 2.50A {Synechococcus elongatus} SCOP: d.58.1.2 PDB: 3pcq_C* 1k0t_A 2wsc_C* 2wse_C* 2wsf_C* 3lw5_C* 2o01_C*	Back alignment and structure

>1f2g_A Ferredoxin II; electron transport, FDII desulfovibrio gigas; NMR {Desulfovibrio gigas} SCOP: d.58.1.4 PDB: 1fxd_A	Back alignment and structure

>1bc6_A 7-Fe ferredoxin; electron transport, iron-sulfur; NMR {Bacillus schlegelii} SCOP: d.58.1.2 PDB: 1bd6_A 1bqx_A 1bwe_A	Back alignment and structure

>3i9v_9 NADH-quinone oxidoreductase subunit 9; electron transport, respiratory chain, cell flavoprotein, FMN, iron, iron-sulfur, membrane; HET: FMN; 3.10A {Thermus thermophilus} PDB: 2ybb_8* 2fug_9* 3iam_9* 3ias_9* 3m9s_9*	Back alignment and structure

>7fd1_A FD1, protein (7-Fe ferredoxin I); electron transport, iron-sulfur; 1.30A {Azotobacter vinelandii} SCOP: d.58.1.2 PDB: 1fda_A 1fdb_A 1fer_A 1axq_A 5fd1_A 6fdr_A 6fd1_A 7fdr_A 1frh_A 1fri_A 1fdd_A 1frl_A 1d3w_A 1frm_A 1frx_A 1g6b_A 1pc4_A 1frj_A 2fd2_A 1fd2_A ...	Back alignment and structure

>1h98_A Ferredoxin; electron transport, thermophilic, iron-sulfur, azotobacter, hydrogen bonds, stability, high resolution; 1.64A {Thermus aquaticus} SCOP: d.58.1.2	Back alignment and structure

>3gyx_B Adenylylsulfate reductase; oxidoreductase; HET: FAD; 3.20A {Desulfovibrio gigas}	Back alignment and structure

>2gmh_A Electron transfer flavoprotein-ubiquinone oxidoreductase; HET: BHG FAD UQ5; 2.50A {Sus scrofa} SCOP: c.3.1.2 d.16.1.8 d.58.1.6 PDB: 2gmj_A*	Back alignment and structure

>1hfe_L Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larger subunit)); hydrogene metabolism, periplasm; 1.60A {Desulfovibrio vulgaris subsp} SCOP: c.96.1.1 d.58.1.5 PDB: 1e08_A* 1gx7_A*	Back alignment and structure

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*	Back alignment and structure

>2v2k_A Ferredoxin; iron, transport, iron-sulfur, mycobacterium tuberculosis, Fe cluster, metal-binding, electron transfer, transport; 1.6A {Mycobacterium smegmatis}	Back alignment and structure

>1jnr_B Adenylylsulfate reductase; oxidoreductase; HET: FAD; 1.60A {Archaeoglobus fulgidus dsm 4304} SCOP: d.58.1.5 PDB: 1jnz_B* 2fja_B* 2fjb_B* 2fjd_B* 2fje_B*	Back alignment and structure

>2wdq_B Succinate dehydrogenase iron-sulfur subunit; succinate dehydrogenase activity, cell inner membrane, trica acid cycle; HET: FAD HEM CBE; 2.40A {Escherichia coli} PDB: 1nen_B* 2acz_B* 1nek_B* 2wdr_B* 2wdv_B* 2ws3_B* 2wu2_B* 2wu5_B* 2wp9_B*	Back alignment and structure

>1h0h_B Formate dehydrogenase (small subunit); tungsten selenium formate dehydrogenase, selenocysteine, molybdopterin, MGD, iron-sulphur cluster; HET: 2MD MGD EPE; 1.8A {Desulfovibrio gigas} SCOP: d.58.1.5	Back alignment and structure

>2c42_A Pyruvate-ferredoxin oxidoreductase; 4Fe-4S, iron, iron-sulfur, iron-sulfur cluster, pyruvate catabolism, TPP-dependent enzyme; HET: TPP; 1.78A {Desulfovibrio africanus} SCOP: c.36.1.8 c.36.1.12 c.48.1.3 c.64.1.1 d.58.1.5 PDB: 1b0p_A* 1kek_A* 2c3o_A* 2c3p_A* 2c3u_A* 2c3y_A* 2c3m_A* 2pda_A* 2uza_A*	Back alignment and structure

>1iqz_A Ferredoxin; iron-sulfer protein, ultlahigh resolution analysis, geometry of [4Fe-4S] cluster, electron transport; 0.92A {Bacillus thermoproteolyticus} SCOP: d.58.1.4 PDB: 1ir0_A 1wtf_A*	Back alignment and structure

>1kf6_B Fumarate reductase iron-sulfur protein; respiration, fumarate reductace, succinate dehydrogenase, CO quinol, quinone, oxidoreductase; HET: FAD HQO CE1 1PE; 2.70A {Escherichia coli} SCOP: a.1.2.1 d.15.4.2 PDB: 1kfy_B* 1l0v_B* 2b76_B* 3cir_B* 3p4p_B* 3p4q_B* 3p4r_B* 3p4s_B*	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		475
d3c8ya1		365	c.96.1.1 (A:210-574) Fe-only hydrogenase, catalyti	1e-113
d1hfel1		312	c.96.1.1 (L:87-398) Fe-only hydrogenase larger sub	1e-103
d1hfes_		88	a.137.4.1 (S:) Fe-only hydrogenase smaller subunit	2e-11
d1y5ib1		509	d.58.1.5 (B:1-509) Respiratory nitrate reductase 1	4e-08

>d3c8ya1 c.96.1.1 (A:210-574) Fe-only hydrogenase, catalytic domain {Clostridium pasteurianum [TaxId: 1501]} Length = 365	Back information, alignment and structure


class: Alpha and beta proteins (a/b)
fold: Fe-only hydrogenase
superfamily: Fe-only hydrogenase
family: Fe-only hydrogenase
domain: Fe-only hydrogenase, catalytic domain
species: Clostridium pasteurianum [TaxId: 1501]

 Score =  335 bits (860), Expect = e-113
 Identities = 113/390 (28%), Positives = 180/390 (46%), Gaps = 35/390 (8%)

Query: 79  LDEFLSNINKG-KAVIISLSPQSRASLAEHFGISPLQ-VFKKLTTFLKSLGVKSIFDTSC 136
           +D   + +N   K VI++++P  RAS+ E F +     V  K+ T L+ LG   IFD + 
Sbjct: 2   MDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTGKIYTALRQLGFDKIFDINF 61

Query: 137 SRDLTLIEACNEFIARYKQSQESDDERSNSSLPMLSSACPGWICYAEKQLGSYILPYISS 196
             D+T++E   E + R +         +N   PM +S CPGW+  AE      +   +SS
Sbjct: 62  GADMTIMEEATELVQRIE---------NNGPFPMFTSCCPGWVRQAENYYPELL-NNLSS 111

Query: 197 VKSPQQTIGATIKHHICQKLGFRPDEIYHVTVMPCYDKKLEAAREDFVFQLDSQEETYRD 256
            KSPQQ  G   K +     G  P  ++ VTVMPC  KK EA R                
Sbjct: 112 AKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSKKFEADRPQM------------- 158

Query: 257 EGLEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGVAGSSGGYA 316
           E   + ++D+V+TT E+  +I+   + F  LE+S  D  +      G ++G   ++GG  
Sbjct: 159 EKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDSEADPAMGEYSGAGAIFG---ATGGVM 215

Query: 317 ETVFRHAAKTLFGKVIEGHLEFKTIRNSD-FREVALEVEGKTLLKFALCYGFQNLQNIVR 375
           E   R A        +E  +E+K +R  +  +E  +E+        A+  G  NL   ++
Sbjct: 216 EAALRSAKDFAENAELE-DIEYKQVRGLNGIKEAEVEINNNKY-NVAVINGASNLFKFMK 273

Query: 376 KVKMRKCDYQFVEVMACPSGCLNGGGQIKPKPGQSPKELIKTLETIYL----ENVMLADP 431
              + +  Y F+EVMAC  GC+NGGGQ    P    K  IK +    L    E++     
Sbjct: 274 SGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKS 333

Query: 432 FKNPLVRSLYDEWLEQPGSEKAKKHVHTEY 461
            +N  +  +Y  +  +PG  +A + +H +Y
Sbjct: 334 HENTALVKMYQNYFGKPGEGRAHEILHFKY 363

PyMOL of d3c8ya1

>d1hfel1 c.96.1.1 (L:87-398) Fe-only hydrogenase larger subunit, C-domain {Desulfovibrio desulfuricans [TaxId: 876]} Length = 312	Back information, alignment and structure

>d1hfes_ a.137.4.1 (S:) Fe-only hydrogenase smaller subunit {Desulfovibrio desulfuricans [TaxId: 876]} Length = 88	Back information, alignment and structure

>d1y5ib1 d.58.1.5 (B:1-509) Respiratory nitrate reductase 1 beta chain {Escherichia coli [TaxId: 562]} Length = 509	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		475
d3c8ya1		365	Fe-only hydrogenase, catalytic domain {Clostridium	100.0
d1hfel1		312	Fe-only hydrogenase larger subunit, C-domain {Desu	100.0
d1y5ib1		509	Respiratory nitrate reductase 1 beta chain {Escher	99.97
d1hfes_		88	Fe-only hydrogenase smaller subunit {Desulfovibrio	99.3
d1bc6a_		77	Ferredoxin {Bacillus schlegelii [TaxId: 1484]}	96.77
d3c7bb1		65	DsrB insert domain {Archaeoglobus fulgidus [TaxId:	96.75
d1h98a_		77	Ferredoxin {Thermus thermophilus [TaxId: 274]}	96.5
d1dura_		55	Ferredoxin II {Peptostreptococcus asaccharolyticus	96.38
d7fd1a_		106	Ferredoxin {Azotobacter vinelandii [TaxId: 354]}	96.09
d1hfel2		85	Fe-only hydrogenase larger subunit, N-domain {Desu	95.94
d2fdna_		55	Ferredoxin II {Clostridium acidurici [TaxId: 1556]	95.84
d1hfel2		85	Fe-only hydrogenase larger subunit, N-domain {Desu	95.77
d3c8ya3		83	Fe-only hydrogenase, second domain {Clostridium pa	95.53
d1blua_		80	Ferredoxin II {Chromatium vinosum [TaxId: 1049]}	95.03
d1vjwa_		59	Ferredoxin A {Thermotoga maritima [TaxId: 2336]}	95.0
d2fdna_		55	Ferredoxin II {Clostridium acidurici [TaxId: 1556]	94.79
d1blua_		80	Ferredoxin II {Chromatium vinosum [TaxId: 1049]}	94.75
d1sj1a_		66	Fe3S4-ferredoxin PF1909 {Pyrococcus furiosus [TaxI	94.71
d1fxra_		64	Ferredoxin I {Sulfate-reducing bacteria (Desulfovi	94.63
d1vlfn2		195	Transhydroxylase beta subunit, BthL, N-terminal do	94.39
d1rgva_		80	Ferredoxin II {Thauera aromatica [TaxId: 59405]}	94.34
d2fug91		154	NADH-quinone oxidoreductase chain 9, Nqo9 {Thermus	94.27
d1rgva_		80	Ferredoxin II {Thauera aromatica [TaxId: 59405]}	94.18
d1jnrb_		149	Adenylylsulfate reductase B subunit {Archaeon Arch	94.14
d1xera_		103	Ferredoxin {Archaeon Sulfolobus sp. [TaxId: 2288]}	93.96
d1xera_		103	Ferredoxin {Archaeon Sulfolobus sp. [TaxId: 2288]}	93.87
d1dura_		55	Ferredoxin II {Peptostreptococcus asaccharolyticus	93.86
d1jb0c_		80	Photosystem I iron-sulfur protein PsaC {Synechococ	93.6
d1jb0c_		80	Photosystem I iron-sulfur protein PsaC {Synechococ	93.54
d3c8ya3		83	Fe-only hydrogenase, second domain {Clostridium pa	93.51
d1fxda_		58	Ferredoxin I {Desulfovibrio gigas [TaxId: 879]}	93.29
d1gtea5		173	Dihydropyrimidine dehydrogenase, C-terminal domain	93.15
d2c42a5		117	Pyruvate-ferredoxin oxidoreductase, PFOR, domain V	92.98
d1iqza_		81	Ferredoxin {Bacillus thermoproteolyticus [TaxId: 1	92.37
d2fug34		151	NADH-quinone oxidoreductase chain 3, Nqo3, domain	92.37
d1kqfb1		244	Formate dehydrogenase N, iron-sulfur (beta) subuni	91.9
d1bc6a_		77	Ferredoxin {Bacillus schlegelii [TaxId: 1484]}	90.97
d2c42a5		117	Pyruvate-ferredoxin oxidoreductase, PFOR, domain V	89.74
d2v4jb1		69	DsrB insert domain {Desulfovibrio vulgaris [TaxId:	89.04
d2fug91		154	NADH-quinone oxidoreductase chain 9, Nqo9 {Thermus	88.82
d1gtea5		173	Dihydropyrimidine dehydrogenase, C-terminal domain	88.39
d1h98a_		77	Ferredoxin {Thermus thermophilus [TaxId: 274]}	86.48
d7fd1a_		106	Ferredoxin {Azotobacter vinelandii [TaxId: 354]}	85.41
d1jnrb_		149	Adenylylsulfate reductase B subunit {Archaeon Arch	84.92
d1vjwa_		59	Ferredoxin A {Thermotoga maritima [TaxId: 2336]}	83.46
d2fug34		151	NADH-quinone oxidoreductase chain 3, Nqo3, domain	83.21
d2bs2b1		133	Fumarate reductase {Wolinella succinogenes [TaxId:	83.01

>d3c8ya1 c.96.1.1 (A:210-574) Fe-only hydrogenase, catalytic domain {Clostridium pasteurianum [TaxId: 1501]}	Back information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Fe-only hydrogenase
superfamily: Fe-only hydrogenase
family: Fe-only hydrogenase
domain: Fe-only hydrogenase, catalytic domain
species: Clostridium pasteurianum [TaxId: 1501]

Probab=100.00  E-value=2.7e-96  Score=754.73  Aligned_cols=357  Identities=31%  Similarity=0.559  Sum_probs=324.5

Q ss_pred             HHHHHHhhcCC-CeEEEEeCcchhhhhhhhcCCChH-hHHHHHHHHHHHcCCcEEEechhhhhhhHHHHHHHHHHHHhhc
Q 011877           79 LDEFLSNINKG-KAVIISLSPQSRASLAEHFGISPL-QVFKKLTTFLKSLGVKSIFDTSCSRDLTLIEACNEFIARYKQS  156 (475)
Q Consensus        79 ~~~~~~~l~~~-k~vV~~iaP~~r~sl~~~fg~~~~-~~~~kl~~~Lk~lGf~~V~Dts~gadi~~~e~~~E~~~r~~~~  156 (475)
                      +++|+++|+++ |.+||+||||+|+||++.||++++ .+.++|.++||+|||++||||++|||++++|+++||++|+++ 
T Consensus         2 i~~v~~~l~~~~k~vV~siaP~~r~sla~~f~l~~~~~~~~kl~~~lk~LGF~~V~dt~~gad~~~~e~~~E~~~r~~~-   80 (365)
T d3c8ya1           2 MDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIEN-   80 (365)
T ss_dssp             HHHHHHHHHCTTCEEEEEECGGGGGTGGGGGTCCSSCCCHHHHHHHHHHHTCSEEEEHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHhCCCcEEEEEECcHHHHHHHHHhCCCcccccHHHHHHHHHHcCCCEEEEcHHHHHHHHHHHHHHHHHHHhc-
Confidence            57899999875 679999999999999999999874 456999999999999999999999999999999999999875 


Q ss_pred             ccCcccccCCCCCceecCChHHHHHHHHhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHhhCCCCCCeEEEEEEecchhhH
Q 011877          157 QESDDERSNSSLPMLSSACPGWICYAEKQLGSYILPYISSVKSPQQTIGATIKHHICQKLGFRPDEIYHVTVMPCYDKKL  236 (475)
Q Consensus       157 ~~~~~~~~~~~~P~itS~CPgwV~yiEk~~~P~Lip~LS~vkSPq~i~g~liK~~~~~~~~i~p~~i~~V~I~PC~aKK~  236 (475)
                              +.++||||||||||||||||+| |+|+||||+|+|||||+|+++|+++++..|++|++|||||||||+|||+
T Consensus        81 --------~~~~P~isS~CPg~V~yiEk~~-PeLip~ls~v~SP~~~~g~liK~~~~~~~~~~~~~i~~V~I~PC~aKK~  151 (365)
T d3c8ya1          81 --------NGPFPMFTSCCPGWVRQAENYY-PELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSKKF  151 (365)
T ss_dssp             --------TCSCCEECCCCHHHHHHHHHHC-GGGGGGBCCBCCHHHHHHHHHTTHHHHTTCCCGGGEEEEEEESCSHHHH
T ss_pred             --------CCCCCeEEeCCHHHHHHHHHhC-hhhhccccCCCCHHHHHHHHHHHHHHHhcCCCcccEEEEEEecccchhh
Confidence                    5679999999999999999999 9999999999999999999999999999999999999999999999999


Q ss_pred             hhhchhhhhhccccccccccCCCCCCCceEEECHHHHHHHHHhcCCCCCCCCCCcccccCCCCCCCCccccccCCcccHH
Q 011877          237 EAAREDFVFQLDSQEETYRDEGLEIPEVDSVLTTGEVLDLIQLKAVNFEALEESPLDKMLTNVDDEGHLYGVAGSSGGYA  316 (475)
Q Consensus       237 Ea~r~~~~~~~~~~~~~~~~~~~~~~~VD~VLT~~El~~ll~~~~i~~~~l~~~~~d~~~~~~s~~g~~~~~~~~SGG~~  316 (475)
                      ||+|++|..+             +.++||+||||+||.+||++.+|++..++++++|.+++..|+.|.+|+.   |||++
T Consensus       152 Ea~r~e~~~~-------------~~~dVD~VLT~~El~~~l~~~~i~~~~l~~~~~~~~~~~~s~~g~~~~~---sGG~~  215 (365)
T d3c8ya1         152 EADRPQMEKD-------------GLRDIDAVITTRELAKMIKDAKIPFAKLEDSEADPAMGEYSGAGAIFGA---TGGVM  215 (365)
T ss_dssp             HHTCTTSEET-------------TEESCSEEEEHHHHHHHHHHTTCCGGGCCCCCCCGGGTCCCHHHHTTTS---TTHHH
T ss_pred             hhcCcccccC-------------CCCCcCEEeeHHHHHHHHHHcCCChhhCCCcccCCccCCCCcccceeec---cccHH
Confidence            9999998543             2479999999999999999999999999999999998888988998887   99999


Q ss_pred             HHHHHHHHHHHhccccccccceeeecCC-CcEEEEEEeCCeeEEEEEEEechHHHHHHHHHHHcCCCCCcEEEecCCccc
Q 011877          317 ETVFRHAAKTLFGKVIEGHLEFKTIRNS-DFREVALEVEGKTLLKFALCYGFQNLQNIVRKVKMRKCDYQFVEVMACPSG  395 (475)
Q Consensus       317 e~v~r~~~~~l~~~~~~~~~~~~~~rn~-d~~e~~l~~~g~~~~~~a~~~G~~ni~~ll~~lk~g~~~~dfIEvMACpgG  395 (475)
                      ++++|++.+.++|.++. .+.|+.+||. ++++++++++|.+ +++++++||+|++++|++++.|+.+||||||||||||
T Consensus       216 ~~~~~~~~~~~~~~~~~-~~~~~~~rg~~~i~~~~~~~~~~~-~~~~~v~G~~n~~~~l~~~k~~~~~~~fvEvmACpgG  293 (365)
T d3c8ya1         216 EAALRSAKDFAENAELE-DIEYKQVRGLNGIKEAEVEINNNK-YNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGG  293 (365)
T ss_dssp             HHHHHHHHHHHHTCCCS-CCCCGGGCSSCSEEEEEEEETTEE-EEEEEEESHHHHHHHHHTSGGGSSCCCEEEEESSTTS
T ss_pred             HHHHHHHHHhccCCccc-cceeeeccCCCceEEEEEEeCCcE-EEEEEehhHHHHHHHHHHHhcCCCCCeEEEEecCCCC
Confidence            99999999999998874 6788899986 5999999999986 6999999999999999999999999999999999999


Q ss_pred             ccCCCCCcCCCCCCCh--HHHHHHHHHHHhhc--ccCCCCCCChHHHHHHHHHhcCCCChhhhcceeeeeec
Q 011877          396 CLNGGGQIKPKPGQSP--KELIKTLETIYLEN--VMLADPFKNPLVRSLYDEWLEQPGSEKAKKHVHTEYHP  463 (475)
Q Consensus       396 CinGgGq~~~~~~~~~--~~~~~~~~~~y~~~--~~~~~~~~n~~v~~ly~~~l~~p~~~~~~~llhT~y~~  463 (475)
                      |+|||||++.+.....  ..+..|.+.+|..+  ...|.|++||.+.+||++||++|+++++|+||||+|+.
T Consensus       294 CinGgGq~~~~~~~~~~~~~~~~r~~~l~~~d~~~~~r~~~en~~~~~ly~~~l~~p~~~~~~~lLHT~y~~  365 (365)
T d3c8ya1         294 CVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHEILHFKYKK  365 (365)
T ss_dssp             GGGCTTSCCCCHHHHHHSCHHHHHHHHHHHHHHHCSCCSGGGCHHHHHHHHHTTCSTTSHHHHHHSBCCCCC
T ss_pred             CcCCCCcCCCCcchhhhHHHHHHHHHHHHhhhhcCCCCCCccCHHHHHHHHHHhCCCCcHHHHHHhcCCccC
Confidence            9999999987532111  12345677788744  35688999999999999999999999999999999974

PyMOL of d3c8ya1

>d1hfel1 c.96.1.1 (L:87-398) Fe-only hydrogenase larger subunit, C-domain {Desulfovibrio desulfuricans [TaxId: 876]}	Back information, alignment and structure

>d1y5ib1 d.58.1.5 (B:1-509) Respiratory nitrate reductase 1 beta chain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1hfes_ a.137.4.1 (S:) Fe-only hydrogenase smaller subunit {Desulfovibrio desulfuricans [TaxId: 876]}	Back information, alignment and structure

>d1bc6a_ d.58.1.2 (A:) Ferredoxin {Bacillus schlegelii [TaxId: 1484]}	Back information, alignment and structure

>d3c7bb1 d.58.1.5 (B:197-261) DsrB insert domain {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1h98a_ d.58.1.2 (A:) Ferredoxin {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1dura_ d.58.1.1 (A:) Ferredoxin II {Peptostreptococcus asaccharolyticus [TaxId: 1258]}	Back information, alignment and structure

>d7fd1a_ d.58.1.2 (A:) Ferredoxin {Azotobacter vinelandii [TaxId: 354]}	Back information, alignment and structure

>d1hfel2 d.58.1.5 (L:2-86) Fe-only hydrogenase larger subunit, N-domain {Desulfovibrio desulfuricans [TaxId: 876]}	Back information, alignment and structure

>d2fdna_ d.58.1.1 (A:) Ferredoxin II {Clostridium acidurici [TaxId: 1556]}	Back information, alignment and structure

>d1hfel2 d.58.1.5 (L:2-86) Fe-only hydrogenase larger subunit, N-domain {Desulfovibrio desulfuricans [TaxId: 876]}	Back information, alignment and structure

>d3c8ya3 d.58.1.5 (A:127-209) Fe-only hydrogenase, second domain {Clostridium pasteurianum [TaxId: 1501]}	Back information, alignment and structure

>d1blua_ d.58.1.1 (A:) Ferredoxin II {Chromatium vinosum [TaxId: 1049]}	Back information, alignment and structure

>d1vjwa_ d.58.1.4 (A:) Ferredoxin A {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d2fdna_ d.58.1.1 (A:) Ferredoxin II {Clostridium acidurici [TaxId: 1556]}	Back information, alignment and structure

>d1blua_ d.58.1.1 (A:) Ferredoxin II {Chromatium vinosum [TaxId: 1049]}	Back information, alignment and structure

>d1sj1a_ d.58.1.4 (A:) Fe3S4-ferredoxin PF1909 {Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1fxra_ d.58.1.4 (A:) Ferredoxin I {Sulfate-reducing bacteria (Desulfovibrio africanus) [TaxId: 873]}	Back information, alignment and structure

>d1vlfn2 d.58.1.5 (N:1-195) Transhydroxylase beta subunit, BthL, N-terminal domain {Pelobacter acidigallici [TaxId: 35816]}	Back information, alignment and structure

>d1rgva_ d.58.1.1 (A:) Ferredoxin II {Thauera aromatica [TaxId: 59405]}	Back information, alignment and structure

>d2fug91 d.58.1.5 (9:26-179) NADH-quinone oxidoreductase chain 9, Nqo9 {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1rgva_ d.58.1.1 (A:) Ferredoxin II {Thauera aromatica [TaxId: 59405]}	Back information, alignment and structure

>d1jnrb_ d.58.1.5 (B:) Adenylylsulfate reductase B subunit {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1xera_ d.58.1.3 (A:) Ferredoxin {Archaeon Sulfolobus sp. [TaxId: 2288]}	Back information, alignment and structure

>d1xera_ d.58.1.3 (A:) Ferredoxin {Archaeon Sulfolobus sp. [TaxId: 2288]}	Back information, alignment and structure

>d1dura_ d.58.1.1 (A:) Ferredoxin II {Peptostreptococcus asaccharolyticus [TaxId: 1258]}	Back information, alignment and structure

>d1jb0c_ d.58.1.2 (C:) Photosystem I iron-sulfur protein PsaC {Synechococcus elongatus [TaxId: 32046]}	Back information, alignment and structure

>d1jb0c_ d.58.1.2 (C:) Photosystem I iron-sulfur protein PsaC {Synechococcus elongatus [TaxId: 32046]}	Back information, alignment and structure

>d3c8ya3 d.58.1.5 (A:127-209) Fe-only hydrogenase, second domain {Clostridium pasteurianum [TaxId: 1501]}	Back information, alignment and structure

>d1fxda_ d.58.1.4 (A:) Ferredoxin I {Desulfovibrio gigas [TaxId: 879]}	Back information, alignment and structure

>d1gtea5 d.58.1.5 (A:845-1017) Dihydropyrimidine dehydrogenase, C-terminal domain {Pig (Sus scrofa) [TaxId: 9823]}	Back information, alignment and structure

>d2c42a5 d.58.1.5 (A:669-785) Pyruvate-ferredoxin oxidoreductase, PFOR, domain V {Desulfovibrio africanus [TaxId: 873]}	Back information, alignment and structure

>d1iqza_ d.58.1.4 (A:) Ferredoxin {Bacillus thermoproteolyticus [TaxId: 1427]}	Back information, alignment and structure

>d2fug34 d.58.1.5 (3:96-246) NADH-quinone oxidoreductase chain 3, Nqo3, domain 2 {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1kqfb1 d.58.1.5 (B:2-245) Formate dehydrogenase N, iron-sulfur (beta) subunit {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1bc6a_ d.58.1.2 (A:) Ferredoxin {Bacillus schlegelii [TaxId: 1484]}	Back information, alignment and structure

>d2c42a5 d.58.1.5 (A:669-785) Pyruvate-ferredoxin oxidoreductase, PFOR, domain V {Desulfovibrio africanus [TaxId: 873]}	Back information, alignment and structure

>d2v4jb1 d.58.1.5 (B:209-277) DsrB insert domain {Desulfovibrio vulgaris [TaxId: 881]}	Back information, alignment and structure

>d2fug91 d.58.1.5 (9:26-179) NADH-quinone oxidoreductase chain 9, Nqo9 {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1gtea5 d.58.1.5 (A:845-1017) Dihydropyrimidine dehydrogenase, C-terminal domain {Pig (Sus scrofa) [TaxId: 9823]}	Back information, alignment and structure

>d1h98a_ d.58.1.2 (A:) Ferredoxin {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d7fd1a_ d.58.1.2 (A:) Ferredoxin {Azotobacter vinelandii [TaxId: 354]}	Back information, alignment and structure

>d1jnrb_ d.58.1.5 (B:) Adenylylsulfate reductase B subunit {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1vjwa_ d.58.1.4 (A:) Ferredoxin A {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d2fug34 d.58.1.5 (3:96-246) NADH-quinone oxidoreductase chain 3, Nqo3, domain 2 {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d2bs2b1 a.1.2.1 (B:107-239) Fumarate reductase {Wolinella succinogenes [TaxId: 844]}	Back information, alignment and structure