Citrus Sinensis ID: 024285

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-------27

MGLAGNLNSDNLNFFNSQGYVVLESFASDEEIEAMRKQMDHLLDGFDCSTSSVFSTTNQQKVTDDYFYESAEKISFFFEEKAFGDDGNLKQPKELSINKVGHALHELDPVFKKFSRSEKTSNLLHSLGYKRPVDIQSMYIFKQPGIGGEVVPHQDNSFLITEPSTCTGLWLALEDATIINGCLWAIPGSHKNGLVRRFIRGEEGVYFDRPPPSYDQNDFVPIEVKAGSLVLIHGDLIHQSFENQSSKSRHAYSLHVVETDGCRWSQENW

ccccccccHHHHHHHHHccEEEEcccccHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHccccccEEEccccccccccccccccccEEEccccccccHHHHHHHccccHHHHHHHHcccccEEEEEEccccccccccccccccccccccccccccEEEEEEEccccccccEEEEEccccccccEEEEEEccccEEccccccccccccEEEEEEccccEEEEccccEEcccccccccccEEEEEEEEEccccccccccc

ccccccccHHHHHHHHcccEEEEcccccHHHHHHHHHHHHHHHHHcccccccEEEEccHHHcccccEEccccEEEEEEEcccccccccccccHHHHHHHHHHHHHcccHHHHHccccHHHHHHHHHccccccEEEEEEEEEccccccccccccccccEcccccccEEEEEEEHHHccccccEEEEEccccccccEEEEEEccccEEEccccccccccccEEEEEccccEEEEEccEEEcccccccccccEEEEEEEEEccccccccccc

mglagnlnsdnlnffnSQGYvvlesfasDEEIEAMRKQMDHLldgfdcstssvfsttnqqkvtddYFYESAEKISFFFeekafgddgnlkqpkelsinkVGHALHELDPVFKKFSRSEKTSNLLhslgykrpvdiqsmyifkqpgiggevvphqdnsflitepstcTGLWLALEDATIINgclwaipgshknglVRRFIrgeegvyfdrpppsydqndfvpievkAGSLVLIhgdlihqsfenqssksrhaYSLHVVEtdgcrwsqenw

mglagnlnsdnlnFFNSQGYVVLESFASDEEIEAMRKQMDHLLDGFDCSTssvfsttnqqkvtDDYFYESAEKISFFFEEKAFGDDGNLKQPKELSINKVGHALHELDPVFKKFSRSEKTSNLLHSLGYKRPVDIQSMYIFKQPGIGGEVVPHQDNSFLITEPSTCTGLWLALEDATIINGCLWAIPGSHKNGLVRRFIRGEEGVYFDRPPPSYDQNDFVPIEVKAGSLVLIHGDLIHQSFENQSSKSRHAYSLHVVetdgcrwsqenw

MGLAGnlnsdnlnffnsQGYVVLESFASDEEIEAMRKQMDHLLDGFDCSTSSVFSTTNQQKVTDDYFYESAEKISFFFEEKAFGDDGNLKQPKELSINKVGHALHELDPVFKKFSRSEKTSNLLHSLGYKRPVDIQSMYIFKQPGIGGEVVPHQDNSFLITEPSTCTGLWLALEDATIINGCLWAIPGSHKNGLVRRFIRGEEGVYFDRPPPSYDQNDFVPIEVKAGSLVLIHGDLIHQSFENQSSKSRHAYSLHVVETDGCRWSQENW

***********LNFFNSQGYVVLESFASDEEIEAMRKQMDHLLDGFDCSTSSVFSTTNQQKVTDDYFYESAEKISFFFEEKAFGDD********LSINKVGHALHELDPVFKKF******SNLLHSLGYKRPVDIQSMYIFKQPGIGGEVVPHQDNSFLITEPSTCTGLWLALEDATIINGCLWAIPGSHKNGLVRRFIRGEEGVYFDRPPPSYDQNDFVPIEVKAGSLVLIHGDLIHQSF**********YSLHVVETDGC*******

***AGNLNSDNLNFFNSQGYVVLESFASDEEIEAMRKQMDHLLDGFDCSTSSVFSTTNQQKVTDDYFYESAEKISFFFEEKAFGDDGNLKQPKELSINKVGHALHELDPVFKKFSRSEKTSNLLHSLGYKRPVDIQSMYIFKQPGIGGEVVPHQDNSFLITEPSTCTGLWLALEDATIINGCLWAIPGSHKNGLVRRFIRGEEGVYFDRPPPSYDQNDFVPIEVKAGSLVLIHGDLIHQSFENQSSKSRHAYSLHVVETDGCRW***NW

*****NLNSDNLNFFNSQGYVVLESFASDEEIEAMRKQMDHLLDGFDCSTSSVFSTTNQQKVTDDYFYESAEKISFFFEEKAFGDDGNLKQPKELSINKVGHALHELDPVFKKFSRSEKTSNLLHSLGYKRPVDIQSMYIFKQPGIGGEVVPHQDNSFLITEPSTCTGLWLALEDATIINGCLWAIPGSHKNGLVRRFIRGEEGVYFDRPPPSYDQNDFVPIEVKAGSLVLIHGDLIHQSFENQSSKSRHAYSLHVVETDGCRWS****

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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		269	2.2.26 [Sep-21-2011]
Q5SRE7		291	Phytanoyl-CoA dioxygenase	yes	no	0.970	0.896	0.474	3e-66
Q0IIB1		291	Phytanoyl-CoA dioxygenase	yes	no	0.970	0.896	0.474	4e-66
Q5U3U0		291	Phytanoyl-CoA dioxygenase	yes	no	0.970	0.896	0.456	1e-65
Q9DB26		291	Phytanoyl-CoA dioxygenase	yes	no	0.970	0.896	0.456	2e-63
Q5BJP9		291	Phytanoyl-CoA dioxygenase	yes	no	0.970	0.896	0.456	8e-63
Q9NAM7		288	Phytanoyl-CoA dioxygenase	yes	no	0.947	0.885	0.439	1e-59
P0C660		288	Phytanoyl-CoA dioxygenase	N/A	no	0.970	0.906	0.430	7e-58
Q54XH6		281	Phytanoyl-CoA dioxygenase	yes	no	0.973	0.932	0.429	1e-57
O62515		312	Probable phytanoyl-CoA di	no	no	0.557	0.480	0.264	2e-07
O18778		337	Phytanoyl-CoA dioxygenase	no	no	0.858	0.685	0.241	6e-05

>sp\|Q5SRE7\|PHYD1_HUMAN Phytanoyl-CoA dioxygenase domain-containing protein 1 OS=Homo sapiens GN=PHYHD1 PE=1 SV=2	Back alignment and function desciption

 Score =  251 bits (642), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 131/276 (47%), Positives = 172/276 (62%), Gaps = 15/276 (5%)

Query: 7   LNSDNLNFFNSQGYVVLESFASDEEIEAMRKQMDHLLDGFD----CSTSSVFSTTNQQKV 62
           L+   L  F   G++VLE F S EE  AM++++  ++   D    C T   FST  ++++
Sbjct: 4   LSPSQLQKFQQDGFLVLEGFLSAEECVAMQQRIGEIVAEMDVPLHCRTE--FSTQEEEQL 61

Query: 63  ----TDDYFYESAEKISFFFEEKAFGDDGNLKQPKELSINKVGHALHELDPVFKKFSRSE 118
               + DYF  S +KI FFFE+  F + GN   P E SINK+GHALH  DPVFK  + S 
Sbjct: 62  RAQGSTDYFLSSGDKIRFFFEKGVFDEKGNFLVPPEKSINKIGHALHAHDPVFKSITHSF 121

Query: 119 KTSNLLHSLGYKRPVDIQSMYIFKQPGIGGEVVPHQDNSFLITEP-STCTGLWLALEDAT 177
           K   L  SLG + PV +QSMYIFKQP  GGEV PHQD SFL TEP     G+W+A+EDAT
Sbjct: 122 KVQTLARSLGLQMPVVVQSMYIFKQPHFGGEVSPHQDASFLYTEPLGRVLGVWIAVEDAT 181

Query: 178 IINGCLWAIPGSHKNGLVRRFIRG----EEGVYFDRPPPSYDQNDFVPIEVKAGSLVLIH 233
           + NGCLW IPGSH +G+ RR +R       G  F    P+ D + FVP  V+ G+LVLIH
Sbjct: 182 LENGCLWFIPGSHTSGVSRRMVRAPVGSAPGTSFLGSEPARDNSLFVPTPVQRGALVLIH 241

Query: 234 GDLIHQSFENQSSKSRHAYSLHVVETDGCRWSQENW 269
           G+++H+S +N S +SR AY+ H++E  G  WS ENW
Sbjct: 242 GEVVHKSKQNLSDRSRQAYTFHLMEASGTTWSPENW 277

Isoform 1 has alpha-ketoglutarate-dependent dioxygenase activity. Does not show detectable activity towards fatty acid CoA thioesters. Is not expected to be active with phytanoyl CoA. Isoform 2 and isoform 3 probably lack enzyme activity.
Homo sapiens (taxid: 9606)
EC: 1EC: .EC: -EC: .EC: -EC: .EC: -

>sp\|Q0IIB1\|PHYD1_BOVIN Phytanoyl-CoA dioxygenase domain-containing protein 1 OS=Bos taurus GN=PHYHD1 PE=2 SV=1	Back alignment and function description

>sp\|Q5U3U0\|PHYD1_DANRE Phytanoyl-CoA dioxygenase domain-containing protein 1 OS=Danio rerio GN=phyhd1 PE=2 SV=1	Back alignment and function description

>sp\|Q9DB26\|PHYD1_MOUSE Phytanoyl-CoA dioxygenase domain-containing protein 1 OS=Mus musculus GN=Phyhd1 PE=2 SV=2	Back alignment and function description

>sp\|Q5BJP9\|PHYD1_RAT Phytanoyl-CoA dioxygenase domain-containing protein 1 OS=Rattus norvegicus GN=Phyhd1 PE=2 SV=1	Back alignment and function description

>sp\|Q9NAM7\|PHYD1_CAEEL Phytanoyl-CoA dioxygenase domain-containing protein 1 homolog OS=Caenorhabditis elegans GN=Y105C5B.9 PE=3 SV=1	Back alignment and function description

>sp\|P0C660\|PHYD1_CAEBR Phytanoyl-CoA dioxygenase domain-containing protein 1 homolog OS=Caenorhabditis briggsae GN=CBG00325 PE=3 SV=1	Back alignment and function description

>sp\|Q54XH6\|PHYD1_DICDI Phytanoyl-CoA dioxygenase domain-containing protein 1 homolog OS=Dictyostelium discoideum GN=phyhd1 PE=3 SV=1	Back alignment and function description

>sp\|O62515\|PAHX_CAEEL Probable phytanoyl-CoA dioxygenase OS=Caenorhabditis elegans GN=ZK550.6 PE=3 SV=2	Back alignment and function description

>sp\|O18778\|PAHX_BOVIN Phytanoyl-CoA dioxygenase, peroxisomal OS=Bos taurus GN=PHYH PE=2 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		269
224092111		282	predicted protein [Populus trichocarpa]	1.0	0.953	0.814	1e-129
225424246		283	PREDICTED: phytanoyl-CoA dioxygenase dom	1.0	0.950	0.803	1e-127
363807888		280	uncharacterized protein LOC100788875 [Gl	0.985	0.946	0.774	1e-122
449445411		274	PREDICTED: phytanoyl-CoA dioxygenase dom	0.951	0.934	0.804	1e-121
388515193		280	unknown [Medicago truncatula]	0.985	0.946	0.770	1e-120
356575959		280	PREDICTED: phytanoyl-CoA dioxygenase dom	0.985	0.946	0.763	1e-120
21593659		283	unknown [Arabidopsis thaliana]	1.0	0.950	0.747	1e-119
18379234		283	phytanoyl-CoA dioxygenase (PhyH)-like pr	1.0	0.950	0.743	1e-118
297814384		284	hypothetical protein ARALYDRAFT_484067 [	1.0	0.947	0.744	1e-117
388509426		280	unknown [Lotus japonicus]	0.985	0.946	0.770	1e-116

>gi\|224092111\|ref\|XP_002309477.1\| predicted protein [Populus trichocarpa] gi\|118486091\|gb\|ABK94889.1\| unknown [Populus trichocarpa] gi\|222855453\|gb\|EEE93000.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  465 bits (1197), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 219/269 (81%), Positives = 243/269 (90%)

Query: 1   MGLAGNLNSDNLNFFNSQGYVVLESFASDEEIEAMRKQMDHLLDGFDCSTSSVFSTTNQQ 60
           MG+ G L+SD  + FNSQGY+V+ESFA+ E+IE+M K+MD LLD FD +  SVFST NQ+
Sbjct: 1   MGITGTLSSDQFDSFNSQGYLVIESFANPEDIESMMKRMDKLLDDFDYTNVSVFSTKNQR 60

Query: 61  KVTDDYFYESAEKISFFFEEKAFGDDGNLKQPKELSINKVGHALHELDPVFKKFSRSEKT 120
           KVTDDYFY+SAE ISFFFEEKAFGDDG+LKQPK+LSINKVGHALHELDPVFK FS SEK 
Sbjct: 61  KVTDDYFYQSAENISFFFEEKAFGDDGSLKQPKQLSINKVGHALHELDPVFKGFSSSEKC 120

Query: 121 SNLLHSLGYKRPVDIQSMYIFKQPGIGGEVVPHQDNSFLITEPSTCTGLWLALEDATIIN 180
           S LL SLGYK+PV IQSMYIFKQPGIGGEVVPHQDNSFL TEP+TCTG+WLALEDAT++N
Sbjct: 121 SGLLSSLGYKKPVIIQSMYIFKQPGIGGEVVPHQDNSFLYTEPTTCTGMWLALEDATLLN 180

Query: 181 GCLWAIPGSHKNGLVRRFIRGEEGVYFDRPPPSYDQNDFVPIEVKAGSLVLIHGDLIHQS 240
           GCLWAIPGSHKNGLVRRF+RGE GVYFD+P PSYDQ DFVPIEVKAGSLVLIHGDLIHQS
Sbjct: 181 GCLWAIPGSHKNGLVRRFLRGENGVYFDQPSPSYDQKDFVPIEVKAGSLVLIHGDLIHQS 240

Query: 241 FENQSSKSRHAYSLHVVETDGCRWSQENW 269
           FENQSSKSRHAYS HVV+TDGC+W+ ENW
Sbjct: 241 FENQSSKSRHAYSWHVVDTDGCKWAPENW 269

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|225424246\|ref\|XP_002284469.1\| PREDICTED: phytanoyl-CoA dioxygenase domain-containing protein 1 [Vitis vinifera] gi\|297737693\|emb\|CBI26894.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|363807888\|ref\|NP_001242446.1\| uncharacterized protein LOC100788875 [Glycine max] gi\|255641531\|gb\|ACU21039.1\| unknown [Glycine max]	Back alignment and taxonomy information

>gi\|449445411\|ref\|XP_004140466.1\| PREDICTED: phytanoyl-CoA dioxygenase domain-containing protein 1-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|388515193\|gb\|AFK45658.1\| unknown [Medicago truncatula]	Back alignment and taxonomy information

>gi\|356575959\|ref\|XP_003556103.1\| PREDICTED: phytanoyl-CoA dioxygenase domain-containing protein 1-like [Glycine max]	Back alignment and taxonomy information

>gi\|21593659\|gb\|AAM65626.1\| unknown [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|18379234\|ref\|NP_565262.1\| phytanoyl-CoA dioxygenase (PhyH)-like protein [Arabidopsis thaliana] gi\|16323212\|gb\|AAL15340.1\| At2g01490/F2I9.11 [Arabidopsis thaliana] gi\|20197400\|gb\|AAC67325.2\| expressed protein [Arabidopsis thaliana] gi\|21436043\|gb\|AAM51599.1\| At2g01490/F2I9.11 [Arabidopsis thaliana] gi\|330250366\|gb\|AEC05460.1\| phytanoyl-CoA dioxygenase (PhyH)-like protein [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|297814384\|ref\|XP_002875075.1\| hypothetical protein ARALYDRAFT_484067 [Arabidopsis lyrata subsp. lyrata] gi\|297320913\|gb\|EFH51334.1\| hypothetical protein ARALYDRAFT_484067 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|388509426\|gb\|AFK42779.1\| unknown [Lotus japonicus]	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		269
TAIR\|locus:2049536		283	PAHX "AT2G01490" [Arabidopsis	1.0	0.950	0.721	1e-109
ZFIN\|ZDB-GENE-041114-159		291	phyhd1 "phytanoyl-CoA dioxygen	0.929	0.859	0.467	2.1e-61
UNIPROTKB\|Q5SRE7		291	PHYHD1 "Phytanoyl-CoA dioxygen	0.925	0.855	0.484	5.5e-61
UNIPROTKB\|Q0IIB1		291	PHYHD1 "Phytanoyl-CoA dioxygen	0.925	0.855	0.488	9e-61
MGI\|MGI:3612860		291	Phyhd1 "phytanoyl-CoA dioxygen	0.925	0.855	0.465	3.2e-58
RGD\|1310377		291	Phyhd1 "phytanoyl-CoA dioxygen	0.925	0.855	0.465	5.1e-58
DICTYBASE\|DDB_G0278961		281	DDB_G0278961 "phytanoyl-CoA di	0.925	0.886	0.447	1.1e-55
ASPGD\|ASPL0000073479		313	AN4647 [Emericella nidulans (t	0.676	0.581	0.439	9.8e-48
CGD\|CAL0004540		301	orf19.7316 [Candida albicans (	0.929	0.830	0.383	8.1e-44
UNIPROTKB\|Q5A3Z4		301	CaO19.7316 "Putative uncharact	0.929	0.830	0.383	8.1e-44

TAIR\|locus:2049536 PAHX "AT2G01490" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1084 (386.6 bits), Expect = 1.0e-109, P = 1.0e-109
 Identities = 194/269 (72%), Positives = 231/269 (85%)

Query:     1 MGLAGXXXXXXXXXXXXQGYVVLESFASDEEIEAMRKQMDHLLDGFDCSTSSVFSTTNQQ 60
             MG+ G            QGY+V+ESFAS++EI  +RK+MD LL+ FDCS SS+FST NQ+
Sbjct:     1 MGITGSLTPDQLDFFHSQGYLVIESFASEDEIRGLRKRMDELLNQFDCSVSSIFSTKNQK 60

Query:    61 KVTDDYFYESAEKISFFFEEKAFGDDGNLKQPKELSINKVGHALHELDPVFKKFSRSEKT 120
               TD+YF+ESAEKISFFFEEKAFGDDG LKQPK+LSINKVGHALHELDP++K F+ S K 
Sbjct:    61 HTTDNYFFESAEKISFFFEEKAFGDDGKLKQPKQLSINKVGHALHELDPLYKDFTYSSKF 120

Query:   121 SNLLHSLGYKRPVDIQSMYIFKQPGIGGEVVPHQDNSFLITEPSTCTGLWLALEDATIIN 180
             S+L  SLGY+RPV +QSMYIFKQPGIGGEVVPHQDNSF+ T+P +CTGLW+ALED+T++N
Sbjct:   121 SSLASSLGYRRPVVMQSMYIFKQPGIGGEVVPHQDNSFVYTDPQSCTGLWIALEDSTLVN 180

Query:   181 GCLWAIPGSHKNGLVRRFIRGEEGVYFDRPPPSYDQNDFVPIEVKAGSLVLIHGDLIHQS 240
             GCLWAIPGSHKNGLVRRFIRG+ G+ FD+P PSY+Q DFV IE+KAGSL+ IHGDLIHQS
Sbjct:   181 GCLWAIPGSHKNGLVRRFIRGDNGITFDQPSPSYEQKDFVSIEMKAGSLIAIHGDLIHQS 240

Query:   241 FENQSSKSRHAYSLHVVETDGCRWSQENW 269
             FEN SSKSRHAYSLHVVE+DGC+W+++NW
Sbjct:   241 FENLSSKSRHAYSLHVVESDGCKWAKDNW 269

GO:0048244 "phytanoyl-CoA dioxygenase activity" evidence=ISS;IMP

GO:0005886 "plasma membrane" evidence=IDA

ZFIN\|ZDB-GENE-041114-159 phyhd1 "phytanoyl-CoA dioxygenase domain containing 1" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5SRE7 PHYHD1 "Phytanoyl-CoA dioxygenase domain-containing protein 1" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|Q0IIB1 PHYHD1 "Phytanoyl-CoA dioxygenase domain-containing protein 1" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

MGI\|MGI:3612860 Phyhd1 "phytanoyl-CoA dioxygenase domain containing 1" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1310377 Phyhd1 "phytanoyl-CoA dioxygenase domain containing 1" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0278961 DDB_G0278961 "phytanoyl-CoA dioxygenase domain-containing protein" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

ASPGD\|ASPL0000073479 AN4647 [Emericella nidulans (taxid:162425)]	Back alignment and assigned GO terms

CGD\|CAL0004540 orf19.7316 [Candida albicans (taxid:5476)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5A3Z4 CaO19.7316 "Putative uncharacterized protein" [Candida albicans SC5314 (taxid:237561)]	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)
Q5U3U0	PHYD1_DANRE	1, ., -, ., -, ., -	0.4565	0.9702	0.8969	yes	no
Q5BJP9	PHYD1_RAT	1, ., -, ., -, ., -	0.4565	0.9702	0.8969	yes	no
Q9NAM7	PHYD1_CAEEL	1, ., -, ., -, ., -	0.4398	0.9479	0.8854	yes	no
Q54XH6	PHYD1_DICDI	1, ., -, ., -, ., -	0.4296	0.9739	0.9323	yes	no
Q9DB26	PHYD1_MOUSE	1, ., -, ., -, ., -	0.4565	0.9702	0.8969	yes	no
Q5SRE7	PHYD1_HUMAN	1, ., -, ., -, ., -	0.4746	0.9702	0.8969	yes	no
Q0IIB1	PHYD1_BOVIN	1, ., -, ., -, ., -	0.4746	0.9702	0.8969	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

Fail to connect to STRING server

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		269
pfam05721		213	pfam05721, PhyH, Phytanoyl-CoA dioxygenase (PhyH)	2e-54
COG5285		299	COG5285, COG5285, Protein involved in biosynthesis	5e-18
TIGR01762		288	TIGR01762, chlorin-enz, chlorinating enzyme	3e-06
TIGR02408		277	TIGR02408, ectoine_ThpD, ectoine hydroxylase	0.001

>gnl\|CDD\|218716 pfam05721, PhyH, Phytanoyl-CoA dioxygenase (PhyH)	Back alignment and domain information

 Score =  174 bits (443), Expect = 2e-54
 Identities = 91/244 (37%), Positives = 116/244 (47%), Gaps = 38/244 (15%)

Query: 15  FNSQGYVVLESFASDEEIEAMRKQMDHLLDGFDCSTSSVFSTTNQQKVTDDYFYESAEKI 74
           F   GY+V+E F S EE+ A+R + + LLD                        ES +  
Sbjct: 1   FREDGYLVIEGFLSPEEVAALRAEAERLLD---------------------RAAESGDDK 39

Query: 75  SFFFEEKAFGDDGNLKQPKELSINKVGHALHELDPVFKKFSRSEKTSNLLHSLGYKRPV- 133
             FF+EKA GD+       E SINK  H LH         +   +   +L S  Y     
Sbjct: 40  DDFFDEKAAGDE---TGLLEKSINKRDHFLHP-----FYLADLAR--AILGSPVYVALGL 89

Query: 134 --DIQSMYIFKQPGIGGEVVP-HQDNSFL-ITEPSTCTGLWLALEDATIINGCLWAIPGS 189
               Q + IFKQPG GGEV P HQD +FL          +W+AL+DAT  NGCL  IPGS
Sbjct: 90  QSMYQDLSIFKQPGTGGEVSPWHQDYTFLPTRPAELVVNVWIALDDATEENGCLRFIPGS 149

Query: 190 HK--NGLVRRFIRGEEGVYFDRPPPSYDQNDFVPIEVKAGSLVLIHGDLIHQSFENQSSK 247
           HK   G + R +  + G   D   P YD+   VP+ +KAG  VL H  L+H S  N+S K
Sbjct: 150 HKWEVGDLTRRLPYDPGHLNDDEAPKYDEEPAVPVPMKAGDAVLFHPRLLHGSGANRSDK 209

Query: 248 SRHA 251
           SR A
Sbjct: 210 SRRA 213

This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalyzing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues. Length = 213

>gnl\|CDD\|227609 COG5285, COG5285, Protein involved in biosynthesis of mitomycin antibiotics/polyketide fumonisin [Secondary metabolites biosynthesis, transport, and catabolism]	Back alignment and domain information

>gnl\|CDD\|130823 TIGR01762, chlorin-enz, chlorinating enzyme	Back alignment and domain information

>gnl\|CDD\|131461 TIGR02408, ectoine_ThpD, ectoine hydroxylase	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		269
KOG3290		286	consensus Peroxisomal phytanoyl-CoA hydroxylase [L	100.0
TIGR02408		277	ectoine_ThpD ectoine hydroxylase. Both ectoine and	100.0
TIGR01762		288	chlorin-enz chlorinating enzymes. This model repre	100.0
PF05721		211	PhyH: Phytanoyl-CoA dioxygenase (PhyH); InterPro:	99.97
COG5285		299	Protein involved in biosynthesis of mitomycin anti	99.94
PF07350		416	DUF1479: Protein of unknown function (DUF1479); In	99.1
smart00702		178	P4Hc Prolyl 4-hydroxylase alpha subunit homologues	98.35
PRK05467		226	Fe(II)-dependent oxygenase superfamily protein; Pr	98.33
PLN00052		310	prolyl 4-hydroxylase; Provisional	98.11
PF13640		100	2OG-FeII_Oxy_3: 2OG-Fe(II) oxygenase superfamily;	97.58
PF13759		101	2OG-FeII_Oxy_5: Putative 2OG-Fe(II) oxygenase; PDB	97.39
TIGR02466		201	conserved hypothetical protein. This family consis	97.34
COG3128		229	PiuC Uncharacterized iron-regulated protein [Funct	97.28
PF13532		194	2OG-FeII_Oxy_2: 2OG-Fe(II) oxygenase superfamily;	95.47
PRK15401		213	alpha-ketoglutarate-dependent dioxygenase AlkB; Pr	94.45
PHA02813		354	hypothetical protein; Provisional	92.83
PHA02869		418	C4L/C10L-like gene family protein; Provisional	89.51
PF12851		171	Tet_JBP: Oxygenase domain of the 2OGFeDO superfami	85.88
KOG3710		280	consensus EGL-Nine (EGLN) protein [Signal transduc	85.13
TIGR02409		366	carnitine_bodg gamma-butyrobetaine hydroxylase. Me	84.46
KOG1591		289	consensus Prolyl 4-hydroxylase alpha subunit [Amin	83.55
COG4340		226	Uncharacterized protein conserved in bacteria [Fun	82.7

>KOG3290 consensus Peroxisomal phytanoyl-CoA hydroxylase [Lipid transport and metabolism]	Back alignment and domain information

Probab=100.00  E-value=6.8e-41  Score=272.15  Aligned_cols=264  Identities=43%  Similarity=0.681  Sum_probs=228.2

Q ss_pred             CCCCHHHHHhhhhccEEEecCCCCHHHHHHHHHHHHHHHccCCCCCceeeecCcccccccchhcccccccceeeeccccC
Q 024285            5 GNLNSDNLNFFNSQGYVVLESFASDEEIEAMRKQMDHLLDGFDCSTSSVFSTTNQQKVTDDYFYESAEKISFFFEEKAFG   84 (269)
Q Consensus         5 ~~lt~~~~~~f~~~Gyvvl~~~l~~~~v~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~   84 (269)
                      ..|++.++..|+++||+++++|++.++++.|..++.+++++.+-.-+.+|.+.++.+..++||++|.+.+++|+|..++.
T Consensus         2 ~~l~~~~~~~f~~~Gflv~e~f~~~~e~~~L~~~~~~~~~~~~~~l~~~fst~~e~q~~~nyF~~s~dKi~~ffe~~~v~   81 (286)
T KOG3290|consen    2 GCLSPSQLVKFQTDGFLVIEGFLSAEEIDVLSQEQREFYNENDFLLHKIFSTQDEAQGFENYFLESCDKIRFFFEKGAVM   81 (286)
T ss_pred             CCCChhHHhhcccCceEEEeccccHHHHHHHHHHHHHHHHhCCceeeeccccHHHHhhHHHHHHHhcceeeecccccccc
Confidence            46899999999999999999999999999999999999998876555788888777888999999999999999999999


Q ss_pred             CCCCcccccccccccccccccccChHHHhhhcChhHHHHHHHhCCCCceeeccceeeecCCCCCCCCcccCCCCCccCCC
Q 024285           85 DDGNLKQPKELSINKVGHALHELDPVFKKFSRSEKTSNLLHSLGYKRPVDIQSMYIFKQPGIGGEVVPHQDNSFLITEPS  164 (269)
Q Consensus        85 ~~G~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~p~l~~~~~~l~g~~~~~~~~~~~~~~p~~~~~~~wH~D~~~~~~~~~  164 (269)
                      .+|.+..+...++|+++|.++..+|.|..+-.+.++..+...++-..+.+.++++++|+|+.|+.+..|||..|.+.+|.
T Consensus        82 kdg~l~kp~~k~~nK~gh~lhd~~p~~~~fty~~k~~~l~~~l~~~~Pvv~qsmyi~K~P~iGg~vt~HqD~~~~p~~P~  161 (286)
T KOG3290|consen   82 KDGSLAKPKEKSINKIGHKLHDLDPDFKLFTYSSKVQVLAVVLGLQGPVVAQSMYIFKPPDIGGEVTPHQDLTFFPWDPC  161 (286)
T ss_pred             cccccccCccccHHHhhhhhhhcCcchhheeeeccccceeeeeccCCceeeeEEEEecCCCCCCccCCcccceecccCch
Confidence            99999999999999999999999999998887777777777764333677788888899999999999999999999988


Q ss_pred             -ceeEEeEeeeeccCCCceEEEEcCCCCCCCccce-eeCCCCcc--ccCCCCCCCCCCeeeeeecCccEEEEeCccccCC
Q 024285          165 -TCTGLWLALEDATIINGCLWAIPGSHKNGLVRRF-IRGEEGVY--FDRPPPSYDQNDFVPIEVKAGSLVLIHGDLIHQS  240 (269)
Q Consensus       165 -~~v~~~i~L~d~~~~~G~l~vipGSH~~~~~~~~-~~~~~~~~--~~~~~~~~~~~~~v~~~~~~Gdvvl~~~~~~H~~  240 (269)
                       .++.+|+++.+++..||||.++||||+.....+. ...+++++  |....+-++......+.|++||.++||+.++|+|
T Consensus       162 d~~~~~W~Ame~~t~~NGCL~~iPGshk~~l~~~~yp~~sgg~~~~~~~~~~~~~q~~~~~v~mekg~tv~~h~~lvh~S  241 (286)
T KOG3290|consen  162 DSCVGAWTAMEDITLVNGCLQVIPGSHKGPLLFHRYPDWSGGVNMAYIGIQDYYPQSPRGHVEMEKGDTVFFHPLLVHGS  241 (286)
T ss_pred             hhhhhhhhhhhhhhhcCCceEeccccccCcceeeccCCcccccccceeecccCCccCCccceeecCCcEEEEeeeeeecC
Confidence             8889999999999999999999999999754332 22344443  3322233344567788899999999999999999


Q ss_pred             CCCCCCCCceEEEEEEEeCCCcccCCCC
Q 024285          241 FENQSSKSRHAYSLHVVETDGCRWSQEN  268 (269)
Q Consensus       241 ~~n~s~~~R~~~~~~~~~~~~~~~~~~~  268 (269)
                      ++|+|+..|.++..+|...+.++|...+
T Consensus       242 ~~NrSe~~R~a~s~h~~~~~~~ky~~~~  269 (286)
T KOG3290|consen  242 GANRSEGFRKAISCHVAETDNTKYSEVN  269 (286)
T ss_pred             CCCcccccccccccceeecCCceeecCC
Confidence            9999999999999999999878987765

>TIGR02408 ectoine_ThpD ectoine hydroxylase	Back alignment and domain information

>TIGR01762 chlorin-enz chlorinating enzymes	Back alignment and domain information

>PF05721 PhyH: Phytanoyl-CoA dioxygenase (PhyH); InterPro: IPR008775 This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins as well as a number of bacterial deoxygenases	Back alignment and domain information

>COG5285 Protein involved in biosynthesis of mitomycin antibiotics/polyketide fumonisin [Secondary metabolites biosynthesis, transport, and catabolism]	Back alignment and domain information

>PF07350 DUF1479: Protein of unknown function (DUF1479); InterPro: IPR010856 This family consists of several hypothetical Enterobacterial proteins, of around 420 residues in length	Back alignment and domain information

>smart00702 P4Hc Prolyl 4-hydroxylase alpha subunit homologues	Back alignment and domain information

>PRK05467 Fe(II)-dependent oxygenase superfamily protein; Provisional	Back alignment and domain information

>PLN00052 prolyl 4-hydroxylase; Provisional	Back alignment and domain information

>PF13640 2OG-FeII_Oxy_3: 2OG-Fe(II) oxygenase superfamily; PDB: 3DKQ_B 3GZE_D 3HQR_A 2Y34_A 2G1M_A 2G19_A 3OUI_A 3OUJ_A 2HBU_A 2Y33_A	Back alignment and domain information

>PF13759 2OG-FeII_Oxy_5: Putative 2OG-Fe(II) oxygenase; PDB: 3BVC_B 2RG4_A	Back alignment and domain information

>TIGR02466 conserved hypothetical protein	Back alignment and domain information

>COG3128 PiuC Uncharacterized iron-regulated protein [Function unknown]	Back alignment and domain information

>PF13532 2OG-FeII_Oxy_2: 2OG-Fe(II) oxygenase superfamily; PDB: 2IUW_A 3BTZ_A 3RZL_A 3RZH_A 3S5A_A 3RZG_A 3RZJ_A 3BUC_A 3H8X_A 3H8R_A	Back alignment and domain information

>PRK15401 alpha-ketoglutarate-dependent dioxygenase AlkB; Provisional	Back alignment and domain information

>PHA02813 hypothetical protein; Provisional	Back alignment and domain information

>PHA02869 C4L/C10L-like gene family protein; Provisional	Back alignment and domain information

>PF12851 Tet_JBP: Oxygenase domain of the 2OGFeDO superfamily ; InterPro: IPR024779 TETs are 2OG- and Fe(II)-dependent oxygenases that catalyse the conversion of 5 methyl-Cytosine (5-MC) to 5-hydroxymethyl-cytosine (hmC) in cultured cells and in vitro []	Back alignment and domain information

>KOG3710 consensus EGL-Nine (EGLN) protein [Signal transduction mechanisms]	Back alignment and domain information

>TIGR02409 carnitine_bodg gamma-butyrobetaine hydroxylase	Back alignment and domain information

>KOG1591 consensus Prolyl 4-hydroxylase alpha subunit [Amino acid transport and metabolism]	Back alignment and domain information

>COG4340 Uncharacterized protein conserved in bacteria [Function unknown]	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		269
2opw_A		291	Crystal Structure Of Human Phytanoyl-Coa Dioxygenas		5e-66
2a1x_A		308	Human Phytanoyl-Coa 2-Hydroxylase In Complex With I		5e-06

>pdb|2OPW|A Chain A, Crystal Structure Of Human Phytanoyl-Coa Dioxygenase Phyhd1 (Apo) Length = 291

Back alignment and structure

Iteration: 1

Score = 247 bits (630), Expect = 5e-66, Method: Compositional matrix adjust. Identities = 128/264 (48%), Positives = 168/264 (63%), Gaps = 15/264 (5%) Query: 19 GYVVLESFASDEEIEAMRKQMDHLLDGFD----CSTSSVFSTTNQQKV----TDDYFYES 70 G++VLE F S EE AM++++ ++ D C T FST ++++ + DYF S Sbjct: 16 GFLVLEGFLSAEECVAMQQRIGEIVAEMDVPLHCRTE--FSTQEEEQLRAQGSTDYFLSS 73 Query: 71 AEKISFFFEEKAFGDDGNLKQPKELSINKVGHALHELDPVFKKFSRSEKTSNLLHSLGYK 130 +KI FFFE+ F + GN P E SINK+GHALH DPVFK + S K L SLG + Sbjct: 74 GDKIRFFFEKGVFDEKGNFLVPPEKSINKIGHALHAHDPVFKSITHSFKVQTLARSLGLQ 133 Query: 131 RPVDIQSMYIFKQPGIGGEVVPHQDNSFLITEP-STCTGLWLALEDATIINGCLWAIPGS 189 PV +QSMYIFKQP GGEV PHQD SFL TEP G+W+A+EDAT+ NGCLW IPGS Sbjct: 134 MPVVVQSMYIFKQPHFGGEVSPHQDASFLYTEPLGRVLGVWIAVEDATLENGCLWFIPGS 193 Query: 190 HKNGLVRRFIRG----EEGVYFDRPPPSYDQNDFVPIEVKAGSLVLIHGDLIHQSFENQS 245 H +G+ RR +R G F P+ D + FVP V+ G+LVLIHG+++H+S +N S Sbjct: 194 HTSGVSRRMVRAPVGSAPGTSFLGSEPARDNSLFVPTPVQRGALVLIHGEVVHKSKQNLS 253 Query: 246 SKSRHAYSLHVVETDGCRWSQENW 269 +SR AY+ H++E G WS ENW Sbjct: 254 DRSRQAYTFHLMEASGTTWSPENW 277

PyMOL of 2opw

>pdb|2A1X|A Chain A, Human Phytanoyl-Coa 2-Hydroxylase In Complex With Iron And 2- Oxoglutarate Length = 308

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		269
2opw_A		291	Phyhd1 protein; double-stranded beta helix, oxygen	4e-94
2a1x_A		308	Phytanoyl-COA dioxygenase; beta jelly roll, double	3e-58
3emr_A		310	ECTD; double stranded beta helix, oxidoreductase;	7e-36
2rdq_A		288	1-deoxypentalenic acid 11-beta hydroxylase; Fe(II	5e-32
2fct_A		313	Syringomycin biosynthesis enzyme 2; mononuclear ir	7e-30
3gja_A		319	CYTC3; halogenase, beta barrel, biosynthetic prote	8e-25
3nnf_A		344	CURA; non-HAEM Fe(II)/alpha-ketoglutarate-dependen	3e-13
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-08
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-04

>2opw_A Phyhd1 protein; double-stranded beta helix, oxygenase, structural GE structural genomics consortium, SGC, oxidoreductase; 1.90A {Homo sapiens} PDB: 3obz_A* Length = 291	Back alignment and structure

 Score =  278 bits (711), Expect = 4e-94
 Identities = 129/276 (46%), Positives = 170/276 (61%), Gaps = 11/276 (3%)

Query: 5   GNLNSDNLNFFNSQGYVVLESFASDEEIEAMRKQMDHLLDGFDCSTS--SVFSTTNQQ-- 60
             L+   L  F   G++VLE F S EE  AM++++  ++   D      + FST  ++  
Sbjct: 2   ACLSPSQLQKFQQDGFLVLEGFLSAEECVAMQQRIGEIVAEMDVPLHCRTEFSTQEEEQL 61

Query: 61  --KVTDDYFYESAEKISFFFEEKAFGDDGNLKQPKELSINKVGHALHELDPVFKKFSRSE 118
             + + DYF  S +KI FFFE+  F + GN   P E SINK+GHALH  DPVFK  + S 
Sbjct: 62  RAQGSTDYFLSSGDKIRFFFEKGVFDEKGNFLVPPEKSINKIGHALHAHDPVFKSITHSF 121

Query: 119 KTSNLLHSLGYKRPVDIQSMYIFKQPGIGGEVVPHQDNSFLITEP-STCTGLWLALEDAT 177
           K   L  SLG + PV +QSMYIFKQP  GGEV PHQD SFL TEP     G+W+A+EDAT
Sbjct: 122 KVQTLARSLGLQMPVVVQSMYIFKQPHFGGEVSPHQDASFLYTEPLGRVLGVWIAVEDAT 181

Query: 178 IINGCLWAIPGSHKNGLVRRFIRGEEG----VYFDRPPPSYDQNDFVPIEVKAGSLVLIH 233
           + NGCLW IPGSH +G+ RR +R   G      F    P+ D + FVP  V+ G+LVLIH
Sbjct: 182 LENGCLWFIPGSHTSGVSRRMVRAPVGSAPGTSFLGSEPARDNSLFVPTPVQRGALVLIH 241

Query: 234 GDLIHQSFENQSSKSRHAYSLHVVETDGCRWSQENW 269
           G+++H+S +N S +SR AY+ H++E  G  WS ENW
Sbjct: 242 GEVVHKSKQNLSDRSRQAYTFHLMEASGTTWSPENW 277

PyMOL of 2opw

>2a1x_A Phytanoyl-COA dioxygenase; beta jelly roll, double-stranded beta-helix, structural GENO structural genomics consortium, SGC, oxidoreductase; HET: AKG; 2.50A {Homo sapiens} SCOP: b.82.2.9 Length = 308	Back alignment and structure

>3emr_A ECTD; double stranded beta helix, oxidoreductase; HET: MSE; 1.85A {Virgibacillus salexigens} Length = 310	Back alignment and structure

>2fct_A Syringomycin biosynthesis enzyme 2; mononuclear iron, cupin, halogenase, biosynthetic protein; HET: DSU AKG; 1.60A {Pseudomonas syringae PV} SCOP: b.82.2.9 PDB: 2fcu_A* 2fcv_A* Length = 313	Back alignment and structure

>3gja_A CYTC3; halogenase, beta barrel, biosynthetic protein; 2.20A {Streptomyces} PDB: 3gjb_A* Length = 319	Back alignment and structure

>3nnf_A CURA; non-HAEM Fe(II)/alpha-ketoglutarate-dependent enzymes, catal cryptic chlorination, biosynthetic protein; HET: AKG; 2.20A {Lyngbya majuscula} PDB: 3nnj_A 3nnl_A* 3nnm_A Length = 344	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		269
2opw_A		291	Phyhd1 protein; double-stranded beta helix, oxygen	100.0
2fct_A		313	Syringomycin biosynthesis enzyme 2; mononuclear ir	100.0
2a1x_A		308	Phytanoyl-COA dioxygenase; beta jelly roll, double	100.0
3emr_A		310	ECTD; double stranded beta helix, oxidoreductase;	100.0
3gja_A		319	CYTC3; halogenase, beta barrel, biosynthetic prote	100.0
2rdq_A		288	1-deoxypentalenic acid 11-beta hydroxylase; Fe(II	100.0
3nnf_A		344	CURA; non-HAEM Fe(II)/alpha-ketoglutarate-dependen	99.96
2dbn_A		461	Hypothetical protein YBIU; alpha/beta structure, s	99.59
2hbt_A		247	EGL nine homolog 1; prolyl hydroxylase, hypoxia in	98.61
2jig_A		224	Prolyl-4 hydroxylase; hydrolase; HET: PD2; 1.85A {	98.26
3dkq_A		243	PKHD-type hydroxylase SBAL_3634; putative oxygenas	97.98
3itq_A		216	Prolyl 4-hydroxylase, alpha subunit domain protei;	97.92
2rg4_A		216	Uncharacterized protein; rhodobacterales, oceanico	97.72
3kt7_A		633	PKHD-type hydroxylase TPA1; double-stranded beta h	97.0
1e5r_A		290	Proline oxidase; oxidoreductase, oxygenase, 2-oxog	88.37

>2opw_A Phyhd1 protein; double-stranded beta helix, oxygenase, structural GE structural genomics consortium, SGC, oxidoreductase; 1.90A {Homo sapiens} PDB: 3obz_A*	Back alignment and structure

Probab=100.00  E-value=3.8e-49  Score=341.62  Aligned_cols=265  Identities=48%  Similarity=0.846  Sum_probs=220.8

Q ss_pred             CCCCHHHHHhhhhccEEEecCCCCHHHHHHHHHHHHHHHccCCCC-C-ceeeecCcc--cc--cccchhcccccccceee
Q 024285            5 GNLNSDNLNFFNSQGYVVLESFASDEEIEAMRKQMDHLLDGFDCS-T-SSVFSTTNQ--QK--VTDDYFYESAEKISFFF   78 (269)
Q Consensus         5 ~~lt~~~~~~f~~~Gyvvl~~~l~~~~v~~l~~~~~~~~~~~~~~-~-~~~~~~~~~--~~--~~~~~~~~~~~~i~~~~   78 (269)
                      ..||++++++|+++|||||+++|++++|++++++++++++..... . ..+|.+...  ..  ..++||+.++..+++||
T Consensus         2 ~~Lt~e~~~~f~~dGyvvl~~~l~~e~v~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~y~l~~~~~~~~~~   81 (291)
T 2opw_A            2 ACLSPSQLQKFQQDGFLVLEGFLSAEECVAMQQRIGEIVAEMDVPLHCRTEFSTQEEEQLRAQGSTDYFLSSGDKIRFFF   81 (291)
T ss_dssp             CCCCHHHHHHHHHHSEEEETTSSCHHHHHHHHHHHHHHHHTCCCCGGGSSCCCSHHHHHHHHHHHHHHHHTTTTSEEEEE
T ss_pred             CcCCHHHHHHHHhCCEEEecCCCCHHHHHHHHHHHHHHHhhcccccCCcceecccccchhhccccccccccCCCceeeec
Confidence            479999999999999999999999999999999999998774211 1 123432100  00  23578888888999999


Q ss_pred             eccccCCCCCcccccccccccccccccccChHHHhhhcChhHHHHHHHhCCCCceeeccceeeecCCCCCCCCcccCCCC
Q 024285           79 EEKAFGDDGNLKQPKELSINKVGHALHELDPVFKKFSRSEKTSNLLHSLGYKRPVDIQSMYIFKQPGIGGEVVPHQDNSF  158 (269)
Q Consensus        79 ~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~p~l~~~~~~l~g~~~~~~~~~~~~~~p~~~~~~~wH~D~~~  158 (269)
                      ++++++++|.+..++...+|+++|.++..++.|.+++.+|+|.+++++|+|.++++++++++.|+|+.++.++||||..|
T Consensus        82 e~~~~~~~g~~~~~~~~~in~i~~~~~~~~~~f~~l~~~p~l~~~~~~l~g~~~~~~~~~~~~k~Pg~~~~~~wHqD~~~  161 (291)
T 2opw_A           82 EKGVFDEKGNFLVPPEKSINKIGHALHAHDPVFKSITHSFKVQTLARSLGLQMPVVVQSMYIFKQPHFGGEVSPHQDASF  161 (291)
T ss_dssp             CTTSBCTTSCBSSCGGGSEEEEEECHHHHCHHHHHHHTCHHHHHHHHHHTCSSEEEEEEEEECCCTTTBCCEEEECGGGT
T ss_pred             ccccccccCcccCchhhhhhhhhhHhhhhCHHHHHHhcCHHHHHHHHHhcCCCccchheeEEecCCCCCCCcCCeeCCcc
Confidence            99999999998877777788888878888999999999999999999998889999999999999998777899999999


Q ss_pred             CccCCC-ceeEEeEeeeeccCCCceEEEEcCCCCCCCccceeeCC-C--Cc-cccCCCCCCCCCCeeeeeecCccEEEEe
Q 024285          159 LITEPS-TCTGLWLALEDATIINGCLWAIPGSHKNGLVRRFIRGE-E--GV-YFDRPPPSYDQNDFVPIEVKAGSLVLIH  233 (269)
Q Consensus       159 ~~~~~~-~~v~~~i~L~d~~~~~G~l~vipGSH~~~~~~~~~~~~-~--~~-~~~~~~~~~~~~~~v~~~~~~Gdvvl~~  233 (269)
                      |+.+|. .++++||+|+|++++||||+|+||||+++....+.... +  +. .+..++..++....+.++++|||++|||
T Consensus       162 ~~~~p~~~~~~~wi~L~d~~~~nG~l~~vPGSH~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~aGd~~~f~  241 (291)
T 2opw_A          162 LYTEPLGRVLGVWIAVEDATLENGCLWFIPGSHTSGVSRRMVRAPVGSAPGTSFLGSEPARDNSLFVPTPVQRGALVLIH  241 (291)
T ss_dssp             SCEESSSCEEEEEEESSCBCTTTTCEEEETTCSSSCCSEEEEECC----CCEEEEECCCCCCGGGCEEECBCTTCEEEEE
T ss_pred             cccCCCCceEEEEEEcccCCCCCCCEEEECCccCCCcccccccCCCCCCCcceeeccccCCCcCCeeecccCCCcEEEEc
Confidence            987776 89999999999999999999999999997655443321 1  11 1222223344457899999999999999


Q ss_pred             CccccCCCCCCCCCCceEEEEEEEeCCCcccCCCCC
Q 024285          234 GDLIHQSFENQSSKSRHAYSLHVVETDGCRWSQENW  269 (269)
Q Consensus       234 ~~~~H~~~~n~s~~~R~~~~~~~~~~~~~~~~~~~~  269 (269)
                      ++++|+|++|.++.+|++++++|.+++++.|++++|
T Consensus       242 ~~~~H~s~~N~s~~~R~~~~~~~~~~~~~~~~~~~~  277 (291)
T 2opw_A          242 GEVVHKSKQNLSDRSRQAYTFHLMEASGTTWSPENW  277 (291)
T ss_dssp             TTCEEEECCBCSSSCCCEEEEEEEECTTCEECTTSS
T ss_pred             CCceecCCCCCCCCceEEEEEEEEcCCCCccCcccc
Confidence            999999999999999999999999987789999998

PyMOL of 2opw

>2fct_A Syringomycin biosynthesis enzyme 2; mononuclear iron, cupin, halogenase, biosynthetic protein; HET: DSU AKG; 1.60A {Pseudomonas syringae PV} SCOP: b.82.2.9 PDB: 2fcu_A* 2fcv_A*	Back alignment and structure

>2a1x_A Phytanoyl-COA dioxygenase; beta jelly roll, double-stranded beta-helix, structural GENO structural genomics consortium, SGC, oxidoreductase; HET: AKG; 2.50A {Homo sapiens} SCOP: b.82.2.9	Back alignment and structure

>3emr_A ECTD; double stranded beta helix, oxidoreductase; HET: MSE; 1.85A {Virgibacillus salexigens}	Back alignment and structure

>3gja_A CYTC3; halogenase, beta barrel, biosynthetic protein; 2.20A {Streptomyces} PDB: 3gjb_A*	Back alignment and structure

>3nnf_A CURA; non-HAEM Fe(II)/alpha-ketoglutarate-dependent enzymes, catal cryptic chlorination, biosynthetic protein; HET: AKG; 2.20A {Lyngbya majuscula} PDB: 3nnj_A 3nnl_A* 3nnm_A	Back alignment and structure

>2dbn_A Hypothetical protein YBIU; alpha/beta structure, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.70A {Escherichia coli} PDB: 2dbi_A 2csg_A*	Back alignment and structure

>2hbt_A EGL nine homolog 1; prolyl hydroxylase, hypoxia inducible factor, HIF, 2- oxoglutarate, oxygenase, oxidoreductase; HET: UN9; 1.60A {Homo sapiens} PDB: 2hbu_A* 2g1m_A* 3hqu_A* 3hqr_A* 2y33_A* 2y34_A* 2g19_A* 3ouj_A* 3ouh_A* 3oui_A*	Back alignment and structure

>2jig_A Prolyl-4 hydroxylase; hydrolase; HET: PD2; 1.85A {Chlamydomonas reinhardtii} PDB: 3gze_A 2v4a_A 2jij_A	Back alignment and structure

>3dkq_A PKHD-type hydroxylase SBAL_3634; putative oxygenase, structural genomics, JOI for structural genomics, JCSG; 2.26A {Shewanella baltica OS155}	Back alignment and structure

>3itq_A Prolyl 4-hydroxylase, alpha subunit domain protei; double-stranded beta helix, alpha-keto dependent non-heme iron oxygenase; 1.40A {Bacillus anthracis str}	Back alignment and structure

>2rg4_A Uncharacterized protein; rhodobacterales, oceanicola granulosus HTCC2516, Q2CBJ1_9RHO structural genomics, PSI-2; 1.90A {Oceanicola granulosus} PDB: 3bvc_A	Back alignment and structure

>3kt7_A PKHD-type hydroxylase TPA1; double-stranded beta helix fold, dioxygenase, iron, mRNP complex, prolyl hydroxylase; HET: AKG; 1.77A {Saccharomyces cerevisiae} PDB: 3kt1_A 3kt4_A 3mgu_A	Back alignment and structure

>1e5r_A Proline oxidase; oxidoreductase, oxygenase, 2-oxoglutarate dependent oxygenase; 2.30A {Streptomyces SP} SCOP: b.82.2.4 PDB: 1e5s_A	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		269
d2fcta1		308	b.82.2.9 (A:3-310) Syringomycin biosynthesis enzym	3e-18
d2a1xa1		296	b.82.2.9 (A:43-338) Phytanoyl-CoA dioxygenase, Phy	3e-15

>d2fcta1 b.82.2.9 (A:3-310) Syringomycin biosynthesis enzyme 2, SyrB2 {Pseudomonas syringae pv. syringae [TaxId: 321]} Length = 308	Back information, alignment and structure


class: All beta proteins
fold: Double-stranded beta-helix
superfamily: Clavaminate synthase-like
family: PhyH-like
domain: Syringomycin biosynthesis enzyme 2, SyrB2
species: Pseudomonas syringae pv. syringae [TaxId: 321]

 Score = 80.2 bits (196), Expect = 3e-18
 Identities = 44/290 (15%), Positives = 84/290 (28%), Gaps = 71/290 (24%)

Query: 6   NLNSDNLNFFNSQGYVVLESFASDEEIEAMRKQMDHLLDGFDCSTSSVFSTTNQQKVTDD 65
            L ++    F   G++      S EE++   K+                           
Sbjct: 4   ALTAEQRASFEKNGFIGPFDAYSPEEMKETWKRTRL------------------------ 39

Query: 66  YFYESAEKISFFFEEKAFGDDGNLKQPKELSINKVGHALHELDPVFKKFSRSEKTSNLLH 125
                 ++ +  +++      G          N   +  H  D          +  + + 
Sbjct: 40  ---RLLDRSAAAYQDLDAISGGT---------NIANYDRHLDDDFLASHICRPEICDRVE 87

Query: 126 SLGYKRPVDIQSMYIFKQPGIGGEVVPHQDNSF-----------LITEPSTCTGLWLALE 174
           S+     +  ++ +  K PG  G      D                 E      +W A  
Sbjct: 88  SILGPNVLCWRTEFFPKYPGDEGTDWHQADTFANASGKPQIIWPENEEFGGTITVWTAFT 147

Query: 175 DATIINGCLWAIPGSHKNGLV----------------------RRFIRGEEGVYFDRPPP 212
           DA I NGCL  IPG+  +                         R F   +          
Sbjct: 148 DANIANGCLQFIPGTQNSMNYDETKRMTYEPDANNSVVKDGVRRGFFGYDYRQLQIDENW 207

Query: 213 SYDQNDFVPIEVKAGSLVLIHGDLIHQSFEN--QSSKSRHAYSLHVVETD 260
             D+   VP+++KAG  ++    L+H S+ +  +S + R  ++   V + 
Sbjct: 208 KPDEASAVPMQMKAGQFIIFWSTLMHASYPHSGESQEMRMGFASRYVPSF 257

PyMOL of d2fcta1

>d2a1xa1 b.82.2.9 (A:43-338) Phytanoyl-CoA dioxygenase, PhyH {Human (Homo sapiens) [TaxId: 9606]} Length = 296	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		269
d2fcta1		308	Syringomycin biosynthesis enzyme 2, SyrB2 {Pseudom	100.0
d2a1xa1		296	Phytanoyl-CoA dioxygenase, PhyH {Human (Homo sapie	100.0
d2csga1		417	Hypothetical protein YbiU {Salmonella typhimurium	99.65
d2iuwa1		210	AlkB homolog 3 {Human (Homo sapiens) [TaxId: 9606]	96.01
d1e5ra_		290	Type II Proline 3-hydroxylase (proline oxidase) {S	86.91
d2bnma2		122	Hydroxypropylphosphonic acid epoxidase Fom4, C-ter	81.6
d1otja_		281	Taurine/alpha-ketoglutarate dioxygenase TauD {Esch	81.04

>d2fcta1 b.82.2.9 (A:3-310) Syringomycin biosynthesis enzyme 2, SyrB2 {Pseudomonas syringae pv. syringae [TaxId: 321]}	Back information, alignment and structure

class: All beta proteins
fold: Double-stranded beta-helix
superfamily: Clavaminate synthase-like
family: PhyH-like
domain: Syringomycin biosynthesis enzyme 2, SyrB2
species: Pseudomonas syringae pv. syringae [TaxId: 321]

Probab=100.00  E-value=9.7e-38  Score=269.78  Aligned_cols=219  Identities=21%  Similarity=0.275  Sum_probs=162.1

Q ss_pred             CCCCHHHHHhhhhccEEEecCCCCHHHHHHHHHHHHHHHccCCCCCceeeecCcccccccchhcccccccceeeeccccC
Q 024285            5 GNLNSDNLNFFNSQGYVVLESFASDEEIEAMRKQMDHLLDGFDCSTSSVFSTTNQQKVTDDYFYESAEKISFFFEEKAFG   84 (269)
Q Consensus         5 ~~lt~~~~~~f~~~Gyvvl~~~l~~~~v~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~   84 (269)
                      -.||+||+++|+++|||+++++|+++++++++++++..........   +...                     +  .. 
T Consensus         3 ~~Lt~eq~~~f~~~Gyl~i~~~~s~~ei~~i~~~~~~~~~~~~~~~---~~~~---------------------~--~~-   55 (308)
T d2fcta1           3 FALTAEQRASFEKNGFIGPFDAYSPEEMKETWKRTRLRLLDRSAAA---YQDL---------------------D--AI-   55 (308)
T ss_dssp             TCCCHHHHHHHHHHSEEEEEESSCHHHHHHHHHHHHHHHTCCTTCS---CCCC---------------------C--C--
T ss_pred             CCCCHHHHHHHHhCCEEECcCccCHHHHHHHHHHHHHHHhhccccc---cccc---------------------c--cc-
Confidence            4799999999999999999999999999999998876554322110   0000                     0  00 


Q ss_pred             CCCCcccccccccccccccccccChHHHhhhcChhHHHHHHHhCCCCceeeccceeeecCCCCCCCCcccCCCCCccC--
Q 024285           85 DDGNLKQPKELSINKVGHALHELDPVFKKFSRSEKTSNLLHSLGYKRPVDIQSMYIFKQPGIGGEVVPHQDNSFLITE--  162 (269)
Q Consensus        85 ~~G~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~p~l~~~~~~l~g~~~~~~~~~~~~~~p~~~~~~~wH~D~~~~~~~--  162 (269)
                       .+.      ..+  .....+..++.|.+++.+|+|++++++|+|.++.++++.++.|+|+... ++||||..||..+  
T Consensus        56 -~~~------~~~--~~~~~~~~~~~~~~l~~~p~il~~v~~llG~~~~~~~~~~~~k~p~~~~-~~wHqD~~y~~~~~~  125 (308)
T d2fcta1          56 -SGG------TNI--ANYDRHLDDDFLASHICRPEICDRVESILGPNVLCWRTEFFPKYPGDEG-TDWHQADTFANASGK  125 (308)
T ss_dssp             ----------CGG--GGBCGGGTCHHHHHHTTCHHHHHHHHHHHCSCEEEEEEEEEEECTTCCE-ECCBCCSSSCTTTSS
T ss_pred             -cCc------cce--eeehhhhcCHHHHHhhcCchhhhHHHHhhcccceeeecccccccccccc-cccccccccccCCCC
Confidence             000      000  0012345689999999999999999999999999999999999998754 7999999987542  


Q ss_pred             ----------CCceeEEeEeeeeccCCCceEEEEcCCCCCCCccceeeC-----CCC-c------------cc----cCC
Q 024285          163 ----------PSTCTGLWLALEDATIINGCLWAIPGSHKNGLVRRFIRG-----EEG-V------------YF----DRP  210 (269)
Q Consensus       163 ----------~~~~v~~~i~L~d~~~~~G~l~vipGSH~~~~~~~~~~~-----~~~-~------------~~----~~~  210 (269)
                                +...|++||||+|++++||||+|+||||+.+........     ... .            ..    ...
T Consensus       126 ~~~~~~~~~~~~~~vtvwiaL~D~~~enG~l~viPGSHk~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~  205 (308)
T d2fcta1         126 PQIIWPENEEFGGTITVWTAFTDANIANGCLQFIPGTQNSMNYDETKRMTYEPDANNSVVKDGVRRGFFGYDYRQLQIDE  205 (308)
T ss_dssp             CSEECCTTSCCCSCEEEEEESSCBCTTBTCEEEETTCTTSCCBCTTSCCCCCTTTCSSCEETTEEEEBTTBCGGGGBSST
T ss_pred             cccccCCCCCCCceEEEEEecccccccceeEEEeeCCccCCccccccccccCcccccccccccccccccccccccccccc
Confidence                      236799999999999999999999999998865431100     000 0            00    001


Q ss_pred             CCCCCCCCeeeeeecCccEEEEeCccccCCCCCC--CCCCceEEEEEEEeCC
Q 024285          211 PPSYDQNDFVPIEVKAGSLVLIHGDLIHQSFENQ--SSKSRHAYSLHVVETD  260 (269)
Q Consensus       211 ~~~~~~~~~v~~~~~~Gdvvl~~~~~~H~~~~n~--s~~~R~~~~~~~~~~~  260 (269)
                      ....++...+.++|+|||++|||++++|||++|.  |+++|.+++++|.+.+
T Consensus       206 ~~~~~~~~~v~~~lkaGdvlif~~~l~HgS~pN~~~S~~~R~~~~~rY~p~~  257 (308)
T d2fcta1         206 NWKPDEASAVPMQMKAGQFIIFWSTLMHASYPHSGESQEMRMGFASRYVPSF  257 (308)
T ss_dssp             TCCCCGGGCEEECBCTTEEEEEETTSEEEECCBCSSSSSCEEEEEEEEEETT
T ss_pred             cccccccceEEEeeCCCeEEEECCCccccCCCCCCCCCCceEEEEEEEecCc
Confidence            1122334678899999999999999999999997  5678999999999985

PyMOL of d2fcta1

>d2a1xa1 b.82.2.9 (A:43-338) Phytanoyl-CoA dioxygenase, PhyH {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2csga1 b.82.2.12 (A:3-419) Hypothetical protein YbiU {Salmonella typhimurium [TaxId: 90371]}	Back information, alignment and structure

>d2iuwa1 b.82.2.10 (A:70-279) AlkB homolog 3 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1e5ra_ b.82.2.4 (A:) Type II Proline 3-hydroxylase (proline oxidase) {Streptomyces sp. [TaxId: 1931]}	Back information, alignment and structure

>d2bnma2 b.82.1.10 (A:77-198) Hydroxypropylphosphonic acid epoxidase Fom4, C-terminal domain {Streptomyces wedmorensis [TaxId: 43759]}	Back information, alignment and structure

>d1otja_ b.82.2.5 (A:) Taurine/alpha-ketoglutarate dioxygenase TauD {Escherichia coli [TaxId: 562]}	Back information, alignment and structure