Psyllid ID: psy4131

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-

MSPSVTLSLFHSKHEPKMKYNTGGLTGWEQSYCSKIKLICLGIKLGSEVLSLLEATNVSVSTQGEDRLIRAHGQTLYEVFSLRQTGLKRIPDVVVWPVYITFGKYSEHSDTQISEKFDPAGNQTQISNVPIRRVNSILWLDEDNLVACIEAGIIGQDLERELNSRGYTSGHEPDSYEFSSLGGWVATRASGMKKNLYGNIEDLLVQVTMVTARGTLERPCRGPRVSSGPDFNHVILGSEAD

cccccccccccccccccccccccccccccccccccHHHHcccccccHHHHHHHHHccccccccHHHHHHHcccccHHHHHHHccccccccccEEEccccccEEEEEEcccEEEcccccccccccEEEEEEcccccccEEEEccccEEEEEccccHHHHHHHHHHccccccccccccccccHHHHHHHccccccccccccHHcEEEEEEEEcccEEEEcccccccccccccccccEEccccc

cccccccccccccccHHHHHHHccccccccccccccccccccccccHHHHHHHHHccccccccHHHHHHHcccccccccEEEccccccccccEEEEccccccEEEEccccccccccEEccccccEEEEEEcHHHHHEEEEcHHccEEEEcccccHHHHHHHHHHcccccccccccHHHEcccccHcccccccccEEEccEHHHEEEEEEEccccEEEEccccccccccccccEEEEccccc

mspsvtlslfhskhepkmkyntggltgweQSYCSKIKLICLGIKLGSEVLSLLEATNVSVSTQGEDRLIRAHGQTLYEVFSLRqtglkripdvvvwPVYITFgkysehsdtqisekfdpagnqtqisnvpirrvnsilwldednlVACIEAGIIGQDLERElnsrgytsghepdsyefsslggwvaTRASGMKKNLYGNIEDLLVQVTMVTargtlerpcrgprvssgpdfnhvilgsead

MSPSVTLSLfhskhepkmkyntgGLTGWEQSYCSKIKLICLGIKLGSEVLSLLEATNVSVSTQGEDRLIRAHGQTLYEVFSlrqtglkripdvVVWPVYITFGKYSEHSDTQISEKFdpagnqtqisnvpIRRVNSILWLDEDNLVACIEAGIIGQDLERELNSRGYTsghepdsyefssLGGWVATRASGMKKNLYGNIEDLLVQVTMVTARGtlerpcrgprvssgpdfnhvilgsead

******************KYNTGGLTGWEQSYCSKIKLICLGIKLGSEVLSLLEATNVSVSTQGEDRLIRAHGQTLYEVFSLRQTGLKRIPDVVVWPVYITFGKYSE*****************QISNVPIRRVNSILWLDEDNLVACIEAGIIGQDLERE**************YEFSSLGGWVATRASGMKKNLYGNIEDLLVQVTMVTARGTLE************************

*********FHSKHEPKMKYNTG************************EVLSLLEATNVSVSTQGEDRLIRAHGQTLYEVFSLRQTGLKRIPDVVVWPVYITFGKYSEHSDTQISEKFDPAGNQTQISNVPIRRVNSILWLDEDNLVACIEAGIIGQDLERELNSRGYTSGHEPDSYEFSSLGGWVATRASGMKKNLYGNIEDLLVQVTMVTARGTLERPCRGPRVSSGPDFNHVILGSEA*

*****TLSLFHSKHEPKMKYNTGGLTGWEQSYCSKIKLICLGIKLGSEVLSLLEATNVSVSTQGEDRLIRAHGQTLYEVFSLRQTGLKRIPDVVVWPVYITFGKYSEHSDTQISEKFDPAGNQTQISNVPIRRVNSILWLDEDNLVACIEAGIIGQDLERELNSRGYTSGHEPDSYEFSSLGGWVATRASGMKKNLYGNIEDLLVQVTMVTARGTLERPCRGPRVSSGPDFNHVILGS***

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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		241	2.2.26 [Sep-21-2011]
Q9V778		631	Alkyldihydroxyacetonephos	yes	N/A	0.742	0.283	0.532	9e-54
O00116		658	Alkyldihydroxyacetonephos	yes	N/A	0.780	0.285	0.458	5e-52
P97275		658	Alkyldihydroxyacetonephos	yes	N/A	0.780	0.285	0.449	3e-51
Q8C0I1		645	Alkyldihydroxyacetonephos	yes	N/A	0.780	0.291	0.449	3e-50
Q9EQR2		644	Alkyldihydroxyacetonephos	yes	N/A	0.780	0.291	0.449	1e-49
O45218		597	Alkyldihydroxyacetonephos	yes	N/A	0.800	0.323	0.429	1e-46
O96759		611	Alkyldihydroxyacetonephos	yes	N/A	0.692	0.273	0.356	1e-28
O97157		613	Alkyldihydroxyacetonephos	N/A	N/A	0.655	0.257	0.283	3e-20
Q46911		484	Uncharacterized FAD-linke	N/A	N/A	0.443	0.221	0.411	1e-17
Q8X7S0		484	Uncharacterized FAD-linke	N/A	N/A	0.439	0.219	0.415	1e-17

>sp\|Q9V778\|ADAS_DROME Alkyldihydroxyacetonephosphate synthase OS=Drosophila melanogaster GN=CG10253 PE=2 SV=1	Back alignment and function desciption

 Score =  210 bits (534), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 108/203 (53%), Positives = 133/203 (65%), Gaps = 24/203 (11%)

Query: 56  TNVSVSTQGEDRLIRAHGQTLYEVFSLRQTGLKRIPDVVVWP------------------ 97
           T V  S +G DRL+R HGQTL +++SL     +RIPD+VVWP                  
Sbjct: 124 TQVDYSAEGIDRLVRCHGQTLNDIYSLWHHKFRRIPDLVVWPRCHDEVVQLVRLANKHNV 183

Query: 98  VYITFGKYSEHSDTQISEKFDPAGNQTQ-ISNVPIRRVNSILWLDEDNLVACIEAGIIGQ 156
           + + FG       T +S       N+++ I  +   ++N +LWL+ +NL  C E+GI+GQ
Sbjct: 184 MLVPFG-----GGTSVSGAITCPQNESRMICALDTSQMNRLLWLNRENLTVCFESGIVGQ 238

Query: 157 DLERELNSRGYTSGHEPDSYEFSSLGGWVATRASGMKKNLYGNIEDLLVQVTMVTARGTL 216
           DLER L S G T GHEPDSYEFS+LGGWVATRASGMKKN+YGNIEDL+V+V MVT  GTL
Sbjct: 239 DLERVLRSEGLTVGHEPDSYEFSTLGGWVATRASGMKKNVYGNIEDLVVRVRMVTPSGTL 298

Query: 217 ERPCRGPRVSSGPDFNHVILGSE 239
           ER C  PRVS GPDFNHVILGSE
Sbjct: 299 ERECSAPRVSCGPDFNHVILGSE 321

Drosophila melanogaster (taxid: 7227)
EC: 2EC: .EC: 5EC: .EC: 1EC: .EC: 2EC: 6

>sp\|O00116\|ADAS_HUMAN Alkyldihydroxyacetonephosphate synthase, peroxisomal OS=Homo sapiens GN=AGPS PE=1 SV=1	Back alignment and function description

>sp\|P97275\|ADAS_CAVPO Alkyldihydroxyacetonephosphate synthase, peroxisomal OS=Cavia porcellus GN=AGPS PE=1 SV=1	Back alignment and function description

>sp\|Q8C0I1\|ADAS_MOUSE Alkyldihydroxyacetonephosphate synthase, peroxisomal OS=Mus musculus GN=Agps PE=1 SV=1	Back alignment and function description

>sp\|Q9EQR2\|ADAS_RAT Alkyldihydroxyacetonephosphate synthase, peroxisomal OS=Rattus norvegicus GN=Agps PE=2 SV=1	Back alignment and function description

>sp\|O45218\|ADAS_CAEEL Alkyldihydroxyacetonephosphate synthase OS=Caenorhabditis elegans GN=ads-1 PE=2 SV=1	Back alignment and function description

>sp\|O96759\|ADAS_DICDI Alkyldihydroxyacetonephosphate synthase OS=Dictyostelium discoideum GN=eapA PE=1 SV=1	Back alignment and function description

>sp\|O97157\|ADAS_TRYBB Alkyldihydroxyacetonephosphate synthase OS=Trypanosoma brucei brucei PE=3 SV=1	Back alignment and function description

>sp\|Q46911\|YGCU_ECOLI Uncharacterized FAD-linked oxidoreductase YgcU OS=Escherichia coli (strain K12) GN=ygcU PE=3 SV=4	Back alignment and function description

>sp\|Q8X7S0\|YGCU_ECO57 Uncharacterized FAD-linked oxidoreductase YgcU OS=Escherichia coli O157:H7 GN=ygcU PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		241
270012218		600	hypothetical protein TcasGA2_TC006332 [T	0.817	0.328	0.549	5e-59
332374582		600	unknown [Dendroctonus ponderosae]	0.767	0.308	0.525	5e-55
326922687		599	PREDICTED: alkyldihydroxyacetonephosphat	0.792	0.318	0.502	4e-54
449506760		621	PREDICTED: alkyldihydroxyacetonephosphat	0.788	0.305	0.504	4e-54
363735853		636	PREDICTED: alkyldihydroxyacetonephosphat	0.792	0.300	0.502	4e-54
242010624		565	predicted protein [Pediculus humanus cor	0.788	0.336	0.528	5e-54
118784292		626	AGAP004358-PA [Anopheles gambiae str. PE	0.780	0.300	0.523	3e-53
449266228		572	Alkyldihydroxyacetonephosphate synthase,	0.792	0.333	0.493	4e-53
170044873		609	alkyldihydroxyacetonephosphate synthase	0.780	0.308	0.504	1e-52
41056225		629	alkyldihydroxyacetonephosphate synthase,	0.746	0.286	0.509	1e-52

>gi\|270012218\|gb\|EFA08666.1\| hypothetical protein TcasGA2_TC006332 [Tribolium castaneum]	Back alignment and taxonomy information

 Score =  233 bits (594), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 116/211 (54%), Positives = 150/211 (71%), Gaps = 14/211 (6%)

Query: 44  KLGSEVLSLLEATNVSVSTQGEDRLIRAHGQTLYEVFSLRQTGLKRIPDVVVWPV----Y 99
           ++  E L+ +   ++S S +G DRLIRAHGQTL+++++LR +  +RIPD+VVWP      
Sbjct: 99  QISPENLARITNLDISYSLKGLDRLIRAHGQTLHDIYTLRTSFFERIPDIVVWPTCHSDV 158

Query: 100 ITFGKYSEHSD---------TQISEKFD-PAGNQTQISNVPIRRVNSILWLDEDNLVACI 149
           +   + ++ SD         T +S   + P G    I ++   ++N ILW+D +NLVAC 
Sbjct: 159 VKLVRLADESDMVVIPFGGGTAVSGAVECPTGESRTIISLDTSQMNRILWIDRENLVACC 218

Query: 150 EAGIIGQDLERELNSRGYTSGHEPDSYEFSSLGGWVATRASGMKKNLYGNIEDLLVQVTM 209
           E+GIIGQDLEREL   G+TSGHEPDSYEFSSLGGWVATRASGMKKNLYGNIEDLLV V M
Sbjct: 219 ESGIIGQDLERELRKLGFTSGHEPDSYEFSSLGGWVATRASGMKKNLYGNIEDLLVHVKM 278

Query: 210 VTARGTLERPCRGPRVSSGPDFNHVILGSEA 240
           VT +G LE+ C+ PR+S GPDFNHVI+GSE 
Sbjct: 279 VTPKGVLEKNCQVPRLSCGPDFNHVIMGSEG 309

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi\|332374582\|gb\|AEE62432.1\| unknown [Dendroctonus ponderosae]	Back alignment and taxonomy information

>gi\|326922687\|ref\|XP_003207578.1\| PREDICTED: alkyldihydroxyacetonephosphate synthase, peroxisomal-like [Meleagris gallopavo]	Back alignment and taxonomy information

>gi\|449506760\|ref\|XP_002196918.2\| PREDICTED: alkyldihydroxyacetonephosphate synthase, peroxisomal [Taeniopygia guttata]	Back alignment and taxonomy information

>gi\|363735853\|ref\|XP_421987.3\| PREDICTED: alkyldihydroxyacetonephosphate synthase, peroxisomal [Gallus gallus]	Back alignment and taxonomy information

>gi\|242010624\|ref\|XP_002426062.1\| predicted protein [Pediculus humanus corporis] gi\|212510084\|gb\|EEB13324.1\| predicted protein [Pediculus humanus corporis]	Back alignment and taxonomy information

>gi\|118784292\|ref\|XP_313642.2\| AGAP004358-PA [Anopheles gambiae str. PEST] gi\|116128437\|gb\|EAA09140.2\| AGAP004358-PA [Anopheles gambiae str. PEST]	Back alignment and taxonomy information

>gi\|449266228\|gb\|EMC77307.1\| Alkyldihydroxyacetonephosphate synthase, peroxisomal, partial [Columba livia]	Back alignment and taxonomy information

>gi\|170044873\|ref\|XP_001850055.1\| alkyldihydroxyacetonephosphate synthase [Culex quinquefasciatus] gi\|167867980\|gb\|EDS31363.1\| alkyldihydroxyacetonephosphate synthase [Culex quinquefasciatus]	Back alignment and taxonomy information

>gi\|41056225\|ref\|NP_956407.1\| alkyldihydroxyacetonephosphate synthase, peroxisomal [Danio rerio] gi\|28278019\|gb\|AAH45516.1\| Alkylglycerone phosphate synthase [Danio rerio] gi\|182889268\|gb\|AAI64864.1\| Agps protein [Danio rerio]	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		241
UNIPROTKB\|F1P5J7		638	AGPS "Uncharacterized protein"	0.809	0.305	0.516	4e-51
FB\|FBgn0033983		631	CG10253 [Drosophila melanogast	0.763	0.291	0.545	4.6e-50
ZFIN\|ZDB-GENE-031118-14		629	agps "alkylglycerone phosphate	0.775	0.297	0.522	5.8e-50
UNIPROTKB\|O00116		658	AGPS "Alkyldihydroxyacetonepho	0.809	0.296	0.483	3.7e-48
UNIPROTKB\|P97275		658	AGPS "Alkyldihydroxyacetonepho	0.809	0.296	0.473	1.2e-47
MGI\|MGI:2443065		645	Agps "alkylglycerone phosphate	0.809	0.302	0.473	1.1e-46
UNIPROTKB\|J9NZ69		699	AGPS "Uncharacterized protein"	0.809	0.278	0.473	2.1e-46
RGD\|620364		644	Agps "alkylglycerone phosphate	0.809	0.302	0.473	3.8e-46
WB\|WBGene00000081		597	ads-1 [Caenorhabditis elegans	0.796	0.321	0.432	6.4e-44
UNIPROTKB\|O45218		597	ads-1 "Alkyldihydroxyacetoneph	0.796	0.321	0.432	6.4e-44

UNIPROTKB\|F1P5J7 AGPS "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

 Score = 531 (192.0 bits), Expect = 4.0e-51, P = 4.0e-51
 Identities = 108/209 (51%), Positives = 142/209 (67%)

Query:    45 LGSEVLSLLEATNVSVSTQGEDRLIRAHGQTLYEVFSLRQTGLKRIPDVVVWPV-YITFG 103
             +  E L  L AT +S S   EDR+ RAHG  L+E+F LR+   KRIPD+VVWPV +    
Sbjct:   140 VNEEFLQDLRATKISYSQDAEDRVFRAHGHCLHEIFVLREGMFKRIPDIVVWPVCHEDVV 199

Query:   104 KYSE----HS--------DTQISEKFD-PAGNQTQISNVPIRRVNSILWLDEDNLVACIE 150
             K  E    H+         T +S   + P   +  I ++   ++N ILW+DE NL AC+E
Sbjct:   200 KIVELACKHNLCIIPFGGGTSVSPPLECPEEEKRTIVSLDTSQMNRILWIDEKNLTACVE 259

Query:   151 AGIIGQDLERELNSRGYTSGHEPDSYEFSSLGGWVATRASGMKKNLYGNIEDLLVQVTMV 210
             AGIIGQDLE++L+  G+ +GHEPDS EFSSLGGWVATRASGMKKN+YGNIEDL++ + MV
Sbjct:   260 AGIIGQDLEKQLSESGFCTGHEPDSMEFSSLGGWVATRASGMKKNIYGNIEDLVIHIKMV 319

Query:   211 TARGTLERPCRGPRVSSGPDFNHVILGSE 239
             T RG +E+ C+ PR+S+GPD +H I+GSE
Sbjct:   320 TPRGIVEKNCQVPRMSTGPDIHHFIMGSE 348

GO:0008762 "UDP-N-acetylmuramate dehydrogenase activity" evidence=IEA

GO:0050660 "flavin adenine dinucleotide binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005778 "peroxisomal membrane" evidence=IEA

GO:0008609 "alkylglycerone-phosphate synthase activity" evidence=IEA

GO:0008610 "lipid biosynthetic process" evidence=IEA

FB\|FBgn0033983 CG10253 [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-031118-14 agps "alkylglycerone phosphate synthase" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|O00116 AGPS "Alkyldihydroxyacetonephosphate synthase, peroxisomal" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|P97275 AGPS "Alkyldihydroxyacetonephosphate synthase, peroxisomal" [Cavia porcellus (taxid:10141)]	Back alignment and assigned GO terms

MGI\|MGI:2443065 Agps "alkylglycerone phosphate synthase" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|J9NZ69 AGPS "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

RGD\|620364 Agps "alkylglycerone phosphate synthase" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

WB\|WBGene00000081 ads-1 [Caenorhabditis elegans (taxid:6239)]	Back alignment and assigned GO terms

UNIPROTKB\|O45218 ads-1 "Alkyldihydroxyacetonephosphate synthase" [Caenorhabditis elegans (taxid:6239)]	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)
Q9V778	ADAS_DROME	2, ., 5, ., 1, ., 2, 6	0.5320	0.7427	0.2836	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Alignment Graph	Length	Definition	E-value
Query		241
pfam01565		139	pfam01565, FAD_binding_4, FAD binding domain	2e-23
COG0277		459	COG0277, GlcD, FAD/FMN-containing dehydrogenases [	4e-20
TIGR00387		413	TIGR00387, glcD, glycolate oxidase, subunit GlcD	1e-10
PLN02805		555	PLN02805, PLN02805, D-lactate dehydrogenase [cytoc	0.002

>gnl\|CDD\|216574 pfam01565, FAD_binding_4, FAD binding domain	Back alignment and domain information

 Score = 91.9 bits (229), Expect = 2e-23
 Identities = 30/88 (34%), Positives = 47/88 (53%)

Query: 131 IRRVNSILWLDEDNLVACIEAGIIGQDLERELNSRGYTSGHEPDSYEFSSLGGWVATRAS 190
           + R+N IL +D ++  A +EAG+   DL R L ++G   G EP S    ++GG +AT   
Sbjct: 50  LSRLNGILEIDPEDGTATVEAGVTLGDLVRALAAKGLLLGLEPGSGIPGTVGGAIATNGG 109

Query: 191 GMKKNLYGNIEDLLVQVTMVTARGTLER 218
           G     YG   D ++ + +V A G + R
Sbjct: 110 GYGSERYGLTRDNVLSLEVVLADGEVVR 137

This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyzes the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyzes the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidises the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan. Length = 139

>gnl\|CDD\|223354 COG0277, GlcD, FAD/FMN-containing dehydrogenases [Energy production and conversion]	Back alignment and domain information

>gnl\|CDD\|129482 TIGR00387, glcD, glycolate oxidase, subunit GlcD	Back alignment and domain information

>gnl\|CDD\|178402 PLN02805, PLN02805, D-lactate dehydrogenase [cytochrome]	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		241
PRK11230		499	glycolate oxidase subunit GlcD; Provisional	100.0
PLN02805		555	D-lactate dehydrogenase [cytochrome]	100.0
COG0277		459	GlcD FAD/FMN-containing dehydrogenases [Energy pro	100.0
PRK11183		564	D-lactate dehydrogenase; Provisional	99.97
KOG1232\|consensus		511		99.97
KOG1233\|consensus		613		99.96
TIGR00387		413	glcD glycolate oxidase, subunit GlcD. This protein	99.96
PRK11282		352	glcE glycolate oxidase FAD binding subunit; Provis	99.94
PLN02441		525	cytokinin dehydrogenase	99.93
PF01565		139	FAD_binding_4: FAD binding domain This is only a s	99.93
TIGR01679		419	bact_FAD_ox FAD-linked oxidoreductase. This model	99.89
TIGR01676		541	GLDHase galactonolactone dehydrogenase. This model	99.89
KOG1231\|consensus		505		99.88
TIGR01678		438	FAD_lactone_ox sugar 1,4-lactone oxidases. This mo	99.88
TIGR01677		557	pln_FAD_oxido plant-specific FAD-dependent oxidore	99.86
PLN02465		573	L-galactono-1,4-lactone dehydrogenase	99.8
PRK14652		302	UDP-N-acetylenolpyruvoylglucosamine reductase; Pro	99.64
PRK13906		307	murB UDP-N-acetylenolpyruvoylglucosamine reductase	99.64
PRK12436		305	UDP-N-acetylenolpyruvoylglucosamine reductase; Pro	99.6
PRK13905		298	murB UDP-N-acetylenolpyruvoylglucosamine reductase	99.53
TIGR00179		284	murB UDP-N-acetylenolpyruvoylglucosamine reductase	99.51
KOG4730\|consensus		518		99.49
PRK14653		297	UDP-N-acetylenolpyruvoylglucosamine reductase; Pro	99.31
KOG1262\|consensus		543		99.24
PRK14649		295	UDP-N-acetylenolpyruvoylglucosamine reductase; Pro	99.18
PRK13903		363	murB UDP-N-acetylenolpyruvoylglucosamine reductase	99.1
PRK14650		302	UDP-N-acetylenolpyruvoylglucosamine reductase; Pro	98.77
COG0812		291	MurB UDP-N-acetylmuramate dehydrogenase [Cell enve	98.74
PRK00046		334	murB UDP-N-acetylenolpyruvoylglucosamine reductase	98.66
PRK14648		354	UDP-N-acetylenolpyruvoylglucosamine reductase; Pro	98.56
PRK14651		273	UDP-N-acetylenolpyruvoylglucosamine reductase; Pro	98.41
PRK13904		257	murB UDP-N-acetylenolpyruvoylglucosamine reductase	98.17
PRK09799		258	putative oxidoreductase; Provisional	92.51
PF00941		171	FAD_binding_5: FAD binding domain in molybdopterin	92.28
TIGR02963		467	xanthine_xdhA xanthine dehydrogenase, small subuni	91.64
TIGR03312		257	Se_sel_red_FAD probable selenate reductase, FAD-bi	90.95
PRK09971		291	xanthine dehydrogenase subunit XdhB; Provisional	88.24
TIGR03199		264	pucC xanthine dehydrogenase C subunit. This gene h	86.32
TIGR03195		321	4hydrxCoA_B 4-hydroxybenzoyl-CoA reductase, beta s	84.72
PLN02906		1319	xanthine dehydrogenase	82.93

>PRK11230 glycolate oxidase subunit GlcD; Provisional	Back alignment and domain information

Probab=100.00  E-value=4.9e-35  Score=280.28  Aligned_cols=182  Identities=21%  Similarity=0.196  Sum_probs=166.4

Q ss_pred             cCCCHHHHHHHHh-cC-CceecChhhhhhhhcCCCccchhhcccCCccCCCceEEcce------------------EEEE
Q psy4131          43 IKLGSEVLSLLEA-TN-VSVSTQGEDRLIRAHGQTLYEVFSLRQTGLKRIPDVVVWPV------------------YITF  102 (241)
Q Consensus        43 ~~~~~~~~~~L~~-vg-~~V~~d~~~~~~ys~d~~~~~~~~l~~~~~~~~P~aVv~P~------------------v~~r  102 (241)
                      .+.+++++++|++ +| ++|++|++++..|++|.+.         .+...|.+||+|+                  |+||
T Consensus        15 ~~~~~~~~~~l~~~~g~~~v~~~~~~~~~y~~d~~~---------~~~~~p~~Vv~P~s~eeV~~iv~~a~~~~ipv~~r   85 (499)
T PRK11230         15 DVDRTSLLMALREHLPGLEILHTDEELIPYECDGLS---------AYRTRPLLVVLPKQMEQVQALLAVCHRLRVPVVAR   85 (499)
T ss_pred             cccHHHHHHHHHHhcCcceEEcCHHHHHHhccCccc---------ccCCCCCEEEeeCCHHHHHHHHHHHHHcCCeEEEE
Confidence            3456789999999 98 5899999999999999632         2567899999999                  9999


Q ss_pred             cCCCCCCCCCCCCccccCCCCCceEEEEcCCCCCeeEEeCCCCeEEeCccchHHHHHHHHHHcCCceeccCCCCCCceeh
Q psy4131         103 GKYSEHSDTQISEKFDPAGNQTQISNVPIRRVNSILWLDEDNLVACIEAGIIGQDLERELNSRGYTSGHEPDSYEFSSLG  182 (241)
Q Consensus       103 G~G~~~~~t~~~G~~~~~~~g~~gvvIdl~rmn~Il~id~~~~~v~VeaGv~~~~L~~~L~~~Gl~~~~~p~s~~~~tIG  182 (241)
                      |+|     |++.|+++|..+   +|+|||++||+|+++|+++.+|+||||+++.+|+++|+++|++++++|++...+|||
T Consensus        86 G~G-----t~~~gg~~~~~~---gividl~~ln~I~~id~~~~~v~VeaGv~~~~L~~~l~~~Gl~~~~~p~s~~~~tvG  157 (499)
T PRK11230         86 GAG-----TGLSGGALPLEK---GVLLVMARFNRILDINPVGRRARVQPGVRNLAISQAAAPHGLYYAPDPSSQIACSIG  157 (499)
T ss_pred             CCC-----cCcCCCcccCCC---cEEEEcccCCCceEEcCCCCEEEEcCCccHHHHHHHHHHcCCeeCCCCCccccceEc
Confidence            999     999999888654   599999999999999999999999999999999999999999999999888889999


Q ss_pred             hhhccCCCCCCCCccccccccEeEEEEEecCCcEEEcCCCCCCCcCCCcccccccCCCC
Q psy4131         183 GWVATRASGMKKNLYGNIEDLLVQVTMVTARGTLERPCRGPRVSSGPDFNHVILGSEAD  241 (241)
Q Consensus       183 G~ia~~g~G~~s~~yG~~~d~V~~levVl~dG~i~~~~~~~k~~~G~dl~~l~~GseGt  241 (241)
                      |++++|++|+.+.+||.++|+|+++|||++||++++++...++..||||.++|+|||||
T Consensus       158 G~ia~nagG~~~~~yG~~~d~v~~levVl~~G~i~~~~~~~~~~~g~dl~~l~~Gs~Gt  216 (499)
T PRK11230        158 GNVAENAGGVHCLKYGLTVHNLLKVEILTLDGEALTLGSDALDSPGFDLLALFTGSEGM  216 (499)
T ss_pred             ceeccCCCCccceeeCChhhheeEEEEEcCCCcEEEeCCccCCCCccchHhhhccCCCc
Confidence            99999999999999999999999999999999999988666667899999999999997

>PLN02805 D-lactate dehydrogenase [cytochrome]	Back alignment and domain information

>COG0277 GlcD FAD/FMN-containing dehydrogenases [Energy production and conversion]	Back alignment and domain information

>PRK11183 D-lactate dehydrogenase; Provisional	Back alignment and domain information

>KOG1232\|consensus	Back alignment and domain information

>KOG1233\|consensus	Back alignment and domain information

>TIGR00387 glcD glycolate oxidase, subunit GlcD	Back alignment and domain information

>PRK11282 glcE glycolate oxidase FAD binding subunit; Provisional	Back alignment and domain information

>PLN02441 cytokinin dehydrogenase	Back alignment and domain information

>PF01565 FAD_binding_4: FAD binding domain This is only a subset of the Pfam family; InterPro: IPR006094 Various enzymes use FAD as a co-factor, most of these enzymes are oxygen-dependent oxidoreductases, containing a covalently bound FAD group which is attached to a histidine via an 8-alpha-(N3-histidyl)-riboflavin linkage	Back alignment and domain information

>TIGR01679 bact_FAD_ox FAD-linked oxidoreductase	Back alignment and domain information

>TIGR01676 GLDHase galactonolactone dehydrogenase	Back alignment and domain information

>KOG1231\|consensus	Back alignment and domain information

>TIGR01678 FAD_lactone_ox sugar 1,4-lactone oxidases	Back alignment and domain information

>TIGR01677 pln_FAD_oxido plant-specific FAD-dependent oxidoreductase	Back alignment and domain information

>PLN02465 L-galactono-1,4-lactone dehydrogenase	Back alignment and domain information

>PRK14652 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional	Back alignment and domain information

>PRK13906 murB UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional	Back alignment and domain information

>PRK12436 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional	Back alignment and domain information

>PRK13905 murB UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional	Back alignment and domain information

>TIGR00179 murB UDP-N-acetylenolpyruvoylglucosamine reductase	Back alignment and domain information

>KOG4730\|consensus	Back alignment and domain information

>PRK14653 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional	Back alignment and domain information

>KOG1262\|consensus	Back alignment and domain information

>PRK14649 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional	Back alignment and domain information

>PRK13903 murB UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional	Back alignment and domain information

>PRK14650 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional	Back alignment and domain information

>COG0812 MurB UDP-N-acetylmuramate dehydrogenase [Cell envelope biogenesis, outer membrane]	Back alignment and domain information

>PRK00046 murB UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional	Back alignment and domain information

>PRK14648 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional	Back alignment and domain information

>PRK14651 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional	Back alignment and domain information

>PRK13904 murB UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional	Back alignment and domain information

>PRK09799 putative oxidoreductase; Provisional	Back alignment and domain information

>PF00941 FAD_binding_5: FAD binding domain in molybdopterin dehydrogenase; InterPro: IPR002346 Oxidoreductases, that also bind molybdopterin, have essentially no similarity outside this common domain	Back alignment and domain information

>TIGR02963 xanthine_xdhA xanthine dehydrogenase, small subunit	Back alignment and domain information

>TIGR03312 Se_sel_red_FAD probable selenate reductase, FAD-binding subunit	Back alignment and domain information

>PRK09971 xanthine dehydrogenase subunit XdhB; Provisional	Back alignment and domain information

>TIGR03199 pucC xanthine dehydrogenase C subunit	Back alignment and domain information

>TIGR03195 4hydrxCoA_B 4-hydroxybenzoyl-CoA reductase, beta subunit	Back alignment and domain information

>PLN02906 xanthine dehydrogenase	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		241
4bc7_A		658	Mammalian Alkyldihydroxyacetonephosphate Synthase:		2e-52
4bca_A		658	Mammalian Alkyldihydroxyacetonephosphate Synthase:		2e-52
4bby_A		658	Mammalian Alkyldihydroxyacetonephosphate Synthase:		2e-52
2uuu_A		584	Alkyldihydroxyacetonephosphate Synthase In P212121		9e-30

>pdb|4BC7|A Chain A, Mammalian Alkyldihydroxyacetonephosphate Synthase: Arg419his Mutant Length = 658

Back alignment and structure

Iteration: 1

Score = 201 bits (512), Expect = 2e-52, Method: Compositional matrix adjust. Identities = 98/218 (44%), Positives = 140/218 (64%), Gaps = 30/218 (13%) Query: 45 LGSEVLSLLEATNVSVSTQGEDRLIRAHGQTLYEVFSLRQTGLKRIPDVVVWPVYITFGK 104 + + L L+ TN+S S + +DR+ RAHG L+E+F LR+ +RIPD+V+WP Sbjct: 160 VNEDFLHELKKTNISYSQEADDRVFRAHGHCLHEIFLLREGMFERIPDIVLWPTC----- 214 Query: 105 YSEHSD----TQISEKFD------------------PAGNQTQISNVPIRRVNSILWLDE 142 H D ++ K++ PA I ++ ++N ILW+DE Sbjct: 215 ---HDDVVKIVNLACKYNLCIIPIGGGTSVSYGLMCPADETRTIISLDTSQMNRILWVDE 271 Query: 143 DNLVACIEAGIIGQDLERELNSRGYTSGHEPDSYEFSSLGGWVATRASGMKKNLYGNIED 202 +NL A +EAGI GQ+LER+L GY +GHEPDS EFS++GGW++TRASGMKKN+YGNIED Sbjct: 272 NNLTAHVEAGITGQELERQLKESGYCTGHEPDSLEFSTVGGWISTRASGMKKNIYGNIED 331 Query: 203 LLVQVTMVTARGTLERPCRGPRVSSGPDFNHVILGSEA 240 L+V + +VT RG +E+ C+GPR+S+GPD +H I+GSE Sbjct: 332 LVVHMKVVTPRGVIEKSCQGPRMSTGPDIHHFIMGSEG 369

PyMOL of 4bc7

>pdb|4BCA|A Chain A, Mammalian Alkyldihydroxyacetonephosphate Synthase: Tyr578phe Mutant Length = 658

Back alignment and structure

>pdb|4BBY|A Chain A, Mammalian Alkyldihydroxyacetonephosphate Synthase: Wild-Type Length = 658

Back alignment and structure

>pdb|2UUU|A Chain A, Alkyldihydroxyacetonephosphate Synthase In P212121 Length = 584

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		241
2uuu_A		584	Alkyldihydroxyacetonephosphate synthase; transfera	4e-58
4feh_A		481	Oxidoreductase DPRE1; alpha+beta, decaprenylphosph	3e-10
2vfr_A		422	Xylitol oxidase, alditol oxidase; FAD, sugar, poly	2e-09
1wvf_A		520	4-cresol dehydrogenase [hydroxylating] flavoprote	4e-09
3js8_A		540	Cholesterol oxidase; cholsterol, organic solvent s	6e-08
3pm9_A		476	Putative oxidoreductase; putative D-2-hydroxygluta	8e-08
1e8g_A		560	Vanillyl-alcohol oxidase; oxidoreductase, flavoenz	3e-07
2yvs_A		219	Glycolate oxidase subunit GLCE; oxidoreductase; 2.	1e-06
2i0k_A		561	Oxidoreductase; MIX alpha beta, covalent FAD, flav	3e-06
1f0x_A		571	DLDH, D-lactate dehydrogenase; oxidoreductase; HET	7e-05

>2uuu_A Alkyldihydroxyacetonephosphate synthase; transferase, lavoprotein, lipid synthesis, peroxisomal disor; HET: FAD PL3; 1.95A {Dictyostelium discoideum} PDB: 2uuv_A* Length = 584	Back alignment and structure

 Score =  192 bits (490), Expect = 4e-58
 Identities = 68/198 (34%), Positives = 109/198 (55%), Gaps = 24/198 (12%)

Query: 60  VSTQGEDRLIRAHGQTLYEVFSLRQTGLKRIPDVVVWP------------------VYIT 101
           +      R+    G++L ++  +R   +K  PD++V P                  V I 
Sbjct: 107 LKDDKLARITHTFGKSLRDLIRVRIGQVKNAPDLIVLPHSHEEVERLVQLAHKYNVVIIP 166

Query: 102 FGKYSEHSDTQISEKFDPAGNQTQISNVPIRRVNSILWLDEDNLVACIEAGIIGQDLERE 161
            G       + I    +P  N+    ++ +RR+N +LW+D   + ACI+ GI+G +LE++
Sbjct: 167 MG-----GGSNIVGAIEPVSNERFTVSIDMRRMNKVLWVDRREMTACIQVGIMGPELEKQ 221

Query: 162 LNSRGYTSGHEPDSYEFSSLGGWVATRASGMKKNLYGNIEDLLVQVTMVTARGTLERPCR 221
           L+ +G + GH+PDS+EFS+LGGW+AT +SG + + YG+IED+ V    VT  GTLE    
Sbjct: 222 LHKQGVSLGHDPDSFEFSTLGGWLATCSSGHQSDKYGDIEDMAVSFRTVTPTGTLELR-N 280

Query: 222 GPRVSSGPDFNHVILGSE 239
           G R  +G ++ H+ILGSE
Sbjct: 281 GARSGAGINYKHIILGSE 298

PyMOL of 2uuu

>4feh_A Oxidoreductase DPRE1; alpha+beta, decaprenylphosphoryl-beta-D-RIBO; HET: FAD; 2.04A {Mycobacterium tuberculosis} PDB: 4fdo_A* 4fdn_A* 4fdp_A* 4ff6_A* Length = 481	Back alignment and structure

>2vfr_A Xylitol oxidase, alditol oxidase; FAD, sugar, polyol, flavin, flavoprotein, oxidoreductase; HET: FAD; 1.1A {Streptomyces coelicolor} PDB: 2vfs_A* 2vft_A* 2vfu_A* 2vfv_A* Length = 422	Back alignment and structure

>1wvf_A 4-cresol dehydrogenase [hydroxylating] flavoprote subunit; flavoprotein, electron-transfer, FAD, oxidoreductase; HET: FAD; 1.30A {Pseudomonas putida} SCOP: d.58.32.1 d.145.1.1 PDB: 1wve_A* 1dii_A* 1diq_A* Length = 520	Back alignment and structure

>3js8_A Cholesterol oxidase; cholsterol, organic solvent stability, oxygen channel, FAD, flavoprotein, oxidoreductase; HET: FAD SUC; 1.54A {Chromobacterium SP} Length = 540	Back alignment and structure

>3pm9_A Putative oxidoreductase; putative D-2-hydroxyglutarate dehydrogenase, putative D-LACT dehydrogenase; HET: FAD; 2.57A {Rhodopseudomonas palustris} Length = 476	Back alignment and structure

>1e8g_A Vanillyl-alcohol oxidase; oxidoreductase, flavoenzyme, specificity; HET: FAD FCR; 2.1A {Penicillium simplicissimum} SCOP: d.58.32.1 d.145.1.1 PDB: 1e8f_A* 1e8h_A* 1qlt_A* 1qlu_A* 1vao_A* 1ahv_A* 1ahz_A* 1ahu_A* 2vao_A* 1w1j_A* 1dzn_A* 1w1l_A* 1e0y_A* 1w1k_A* 1w1m_A* Length = 560	Back alignment and structure

>2yvs_A Glycolate oxidase subunit GLCE; oxidoreductase; 2.00A {Thermus thermophilus} Length = 219	Back alignment and structure

>2i0k_A Oxidoreductase; MIX alpha beta, covalent FAD, flavoenzyme; HET: FAD; 1.60A {Brevibacterium sterolicum} SCOP: d.58.32.3 d.145.1.1 PDB: 1i19_A* Length = 561	Back alignment and structure

>1f0x_A DLDH, D-lactate dehydrogenase; oxidoreductase; HET: FAD; 1.90A {Escherichia coli} SCOP: d.58.32.2 d.145.1.1 Length = 571	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		241
4bby_A		658	Alkyldihydroxyacetonephosphate synthase, peroxiso;	100.0
3pm9_A		476	Putative oxidoreductase; putative D-2-hydroxygluta	100.0
2uuu_A		584	Alkyldihydroxyacetonephosphate synthase; transfera	100.0
1f0x_A		571	DLDH, D-lactate dehydrogenase; oxidoreductase; HET	99.97
1e8g_A		560	Vanillyl-alcohol oxidase; oxidoreductase, flavoenz	99.97
1wvf_A		520	4-cresol dehydrogenase [hydroxylating] flavoprote	99.96
2exr_A		524	Cytokinin dehydrogenase 7; AT5G21482.1, cytokinin	99.96
1w1o_A		534	Cytokinin dehydrogenase 1; flavin, oxidoreductase,	99.95
3tsh_A		500	Pollen allergen PHL P 4; flavoprotein, BI-covalent	99.93
2vfr_A		422	Xylitol oxidase, alditol oxidase; FAD, sugar, poly	99.9
1zr6_A		503	Glucooligosaccharide oxidase; alpha + beta, flavoe	99.89
3fw9_A		495	Reticuline oxidase; BI-covalent flavinylation, N-g	99.89
3rja_A		473	Carbohydrate oxidase; protein-substrate analogue c	99.89
2bvf_A		459	6-hydroxy-D-nicotine oxidase; autoflavinylation, e	99.89
1hsk_A		326	UDP-N-acetylenolpyruvoylglucosamine reductase; pep	99.89
4feh_A		481	Oxidoreductase DPRE1; alpha+beta, decaprenylphosph	99.88
2wdx_A		523	Putative hexose oxidase; oxidoreductase-antibiotic	99.87
3vte_A		518	Tetrahydrocannabinolic acid synthase; BI-covalent	99.87
3pop_A		501	GILR oxidase; FAD binding protein, gilvocarcin, gi	99.87
2ipi_A		521	Aclacinomycin oxidoreductase (aknox); anthracyclin	99.87
3tx1_A		322	UDP-N-acetylenolpyruvoylglucosamine reductase; str	99.86
2y3s_A		530	TAML; oxidoreductase; HET: FAD TIR; 1.67A {Strepto	99.85
3js8_A		540	Cholesterol oxidase; cholsterol, organic solvent s	99.84
2i0k_A		561	Oxidoreductase; MIX alpha beta, covalent FAD, flav	99.84
2yvs_A		219	Glycolate oxidase subunit GLCE; oxidoreductase; 2.	99.76
2gqt_A		268	UDP-N-acetylenolpyruvylglucosamine reductase; pept	99.57
3i99_A		357	UDP-N-acetylenolpyruvoylglucosamine reductase; str	99.55
1uxy_A		340	MURB, uridine diphospho-N-acetylenolpyruvylglucosa	99.53
1ffv_C		287	CUTM, flavoprotein of carbon monoxide dehydrogenas	96.95
2w3s_A		462	Xanthine dehydrogenase; XO, XDH, GOUT, iron, 2Fe-2	95.5
3nvz_B		305	Xanthine dehydrogenase/oxidase; hydroxylase, homod	94.26
1n62_C		288	Carbon monoxide dehydrogenase medium chain; CODH,	94.07
1t3q_C		288	Quinoline 2-oxidoreductase medium subunit; QOR, mo	93.35
3hrd_C		296	Nicotinate dehydrogenase FAD-subunit; selenium lig	87.25

>4bby_A Alkyldihydroxyacetonephosphate synthase, peroxiso; transferase, plasmalogen, flavin, peroxisome; HET: FAD; 1.90A {Cavia porcellus} PDB: 4bc9_A* 4bca_A* 4bc7_A*	Back alignment and structure

Probab=100.00  E-value=2.2e-41  Score=332.10  Aligned_cols=194  Identities=50%  Similarity=0.904  Sum_probs=181.0

Q ss_pred             cCCCHHHHHHHHhcCCceecChhhhhhhhcCCCccchhhcccCCccCCCceEEcce------------------EEEEcC
Q psy4131          43 IKLGSEVLSLLEATNVSVSTQGEDRLIRAHGQTLYEVFSLRQTGLKRIPDVVVWPV------------------YITFGK  104 (241)
Q Consensus        43 ~~~~~~~~~~L~~vg~~V~~d~~~~~~ys~d~~~~~~~~l~~~~~~~~P~aVv~P~------------------v~~rG~  104 (241)
                      ..++++++++|+++...+++|.++|..|+++.+++|++++|.+.++.+|++||+|+                  |+|||+
T Consensus       158 ~~~~~~~~~~l~~~~~~~~~~~~~r~~h~~g~s~~d~~~~~~g~~~~~P~aVV~P~s~eeV~~iv~~A~~~~ipVvprGg  237 (658)
T 4bby_A          158 SIVNEDFLHELKKTNISYSQEADDRVFRAHGHCLHEIFLLREGMFERIPDIVLWPTCHDDVVKIVNLACKYNLCIIPIGG  237 (658)
T ss_dssp             CCCCHHHHHHHHHHTCEEECCHHHHHHTSCCSCHHHHHHHHSSCCSCCCSEEEECCSHHHHHHHHHHHHHTTCEEEEESS
T ss_pred             CCCCHHHHHHHHHhcccccCchHHHhhhcCCCCHHHHHHHhCCcccCCcCEEEeeCCHHHHHHHHHHHHHCCCeEEEECC
Confidence            34789999999993335788999999999999999999999999999999999999                  999999


Q ss_pred             CCCCCCCCCCCccccCC-CCCceEEEEcCCCCCeeEEeCCCCeEEeCccchHHHHHHHHHHcCCceeccCCCCCCceehh
Q psy4131         105 YSEHSDTQISEKFDPAG-NQTQISNVPIRRVNSILWLDEDNLVACIEAGIIGQDLERELNSRGYTSGHEPDSYEFSSLGG  183 (241)
Q Consensus       105 G~~~~~t~~~G~~~~~~-~g~~gvvIdl~rmn~Il~id~~~~~v~VeaGv~~~~L~~~L~~~Gl~~~~~p~s~~~~tIGG  183 (241)
                      |     |++.|++++.. +.+++|+|||+|||+|++||+++++++||||+++.+|+++|+++|++||++|++...+||||
T Consensus       238 G-----Tsl~GG~~~~~~~~~ggVvLDlsrMnrIleiD~~~~~atVeaGv~~~~L~~~L~~~Gl~lp~dP~S~~~aTIGG  312 (658)
T 4bby_A          238 G-----TSVSYGLMCPADETRTIISLDTSQMNRILWVDENNLTAHVEAGITGQELERQLKESGYCTGHEPDSLEFSTVGG  312 (658)
T ss_dssp             C-----CCSSSTTCCCTTCCSCEEEEECTTCCCEEEEETTTTEEEEETTCBHHHHHHHHHHHTEECCCCCTTTTTCBHHH
T ss_pred             C-----cCCCCCCCCCCCCCCcEEEEECccCCCcEEEcCCCCEEEEecCchHHHHHHHHHHcCCccCCCCCCccccEEee
Confidence            9     99999886532 22457999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccCCCCCCCCccccccccEeEEEEEecCCcEEEcCCCCCCCcCCCcccccccCCCC
Q psy4131         184 WVATRASGMKKNLYGNIEDLLVQVTMVTARGTLERPCRGPRVSSGPDFNHVILGSEAD  241 (241)
Q Consensus       184 ~ia~~g~G~~s~~yG~~~d~V~~levVl~dG~i~~~~~~~k~~~G~dl~~l~~GseGt  241 (241)
                      ++++|++|+.+.+||.++|+|+++|||||||+++++++.+|+.+||||++||+|||||
T Consensus       313 ~iAtna~G~~s~rYG~~~d~VlgleVVlpdG~i~~~~~~~k~~aGyDL~~L~iGSEGT  370 (658)
T 4bby_A          313 WISTRASGMKKNIYGNIEDLVVHMKVVTPRGVIEKSCQGPRMSTGPDIHHFIMGSEGT  370 (658)
T ss_dssp             HHHHTCCCTTHHHHCCHHHHEEEEEEEETTEEEECSCCCSSCCSSSCTHHHHTTCTTS
T ss_pred             hhhcCCCCCCccCcCCHHHheeeEEEEeCCCcccccccccccCCCcCHHHHhccCCCc
Confidence            9999999999999999999999999999999999999999999999999999999998

PyMOL of 4bby

>3pm9_A Putative oxidoreductase; putative D-2-hydroxyglutarate dehydrogenase, putative D-LACT dehydrogenase; HET: FAD; 2.57A {Rhodopseudomonas palustris}	Back alignment and structure

>2uuu_A Alkyldihydroxyacetonephosphate synthase; transferase, lavoprotein, lipid synthesis, peroxisomal disor; HET: FAD PL3; 1.95A {Dictyostelium discoideum} PDB: 2uuv_A*	Back alignment and structure

>1f0x_A DLDH, D-lactate dehydrogenase; oxidoreductase; HET: FAD; 1.90A {Escherichia coli} SCOP: d.58.32.2 d.145.1.1	Back alignment and structure

>1e8g_A Vanillyl-alcohol oxidase; oxidoreductase, flavoenzyme, specificity; HET: FAD FCR; 2.1A {Penicillium simplicissimum} SCOP: d.58.32.1 d.145.1.1 PDB: 1e8f_A* 1e8h_A* 1qlt_A* 1qlu_A* 1vao_A* 1ahv_A* 1ahz_A* 1ahu_A* 2vao_A* 1w1j_A* 1dzn_A* 1w1l_A* 1e0y_A* 1w1k_A* 1w1m_A*	Back alignment and structure

>1wvf_A 4-cresol dehydrogenase [hydroxylating] flavoprote subunit; flavoprotein, electron-transfer, FAD, oxidoreductase; HET: FAD; 1.30A {Pseudomonas putida} SCOP: d.58.32.1 d.145.1.1 PDB: 1wve_A* 1dii_A* 1diq_A*	Back alignment and structure

>2exr_A Cytokinin dehydrogenase 7; AT5G21482.1, cytokinin oxidase/dehydrogenase, CKX, structura genomics, protein structure initiative; HET: MSE FAD; 1.70A {Arabidopsis thaliana} PDB: 2q4w_A*	Back alignment and structure

>1w1o_A Cytokinin dehydrogenase 1; flavin, oxidoreductase, flavoprotein, FAD; HET: NAG FAD; 1.7A {Zea mays} SCOP: d.58.32.4 d.145.1.1 PDB: 1w1q_A* 1w1r_A* 1w1s_A* 3dq0_A* 2qkn_A* 3c0p_A* 3bw7_A* 2qpm_A* 3kjm_A*	Back alignment and structure

>3tsh_A Pollen allergen PHL P 4; flavoprotein, BI-covalent flavinylation, oxidoreductase, Glu dehydrogenase, N-glycosylation, allergy, dehydrogenase; HET: FDA; 1.90A {Phleum pratense} PDB: 3tsj_A*	Back alignment and structure

>2vfr_A Xylitol oxidase, alditol oxidase; FAD, sugar, polyol, flavin, flavoprotein, oxidoreductase; HET: FAD; 1.1A {Streptomyces coelicolor} PDB: 2vfs_A* 2vft_A* 2vfu_A* 2vfv_A*	Back alignment and structure

>1zr6_A Glucooligosaccharide oxidase; alpha + beta, flavoenzyme, oxidoreductase; HET: NAG FAD; 1.55A {Acremonium strictum} PDB: 2axr_A* 3e0t_A* 3hsu_A*	Back alignment and structure

>3fw9_A Reticuline oxidase; BI-covalent flavinylation, N-glycosylation, alakloid biosynt oxidoreductase, alkaloid metabolism; HET: FAD SLX NAG MAN; 1.49A {Eschscholzia californica} PDB: 3d2h_A* 3d2d_A* 3d2j_A* 3gsy_A* 4ec3_A* 3fw8_A* 3fw7_A* 3fwa_A*	Back alignment and structure

>3rja_A Carbohydrate oxidase; protein-substrate analogue complex, FAD binding domain, BERB berberine-like domain, glucooligosaccharide oxidase; HET: FAD NAG ABL TRS; 2.10A {Microdochium nivale} PDB: 3rj8_A*	Back alignment and structure

>2bvf_A 6-hydroxy-D-nicotine oxidase; autoflavinylation, enantiomeric substrates, flavoenzymes, NI degradation; HET: FAD; 1.92A {Arthrobacter nicotinovorans} PDB: 2bvg_A* 2bvh_A*	Back alignment and structure

>1hsk_A UDP-N-acetylenolpyruvoylglucosamine reductase; peptidoglycan synthesis, cell WALL, cell division, oxidoreductase, NADP, flavoprotein, FAD; HET: FAD; 2.30A {Staphylococcus aureus} SCOP: d.145.1.2 d.146.1.1	Back alignment and structure

>4feh_A Oxidoreductase DPRE1; alpha+beta, decaprenylphosphoryl-beta-D-RIBO; HET: FAD; 2.04A {Mycobacterium tuberculosis} PDB: 4fdo_A* 4fdn_A* 4fdp_A* 4ff6_A* 4aut_A* 4f4q_A* 4g3t_A 4g3u_A	Back alignment and structure

>2wdx_A Putative hexose oxidase; oxidoreductase-antibiotic complex, glycopeptide; HET: FAD GHP 3MY 3FG OMY BMA NAG N1L T55; 2.30A {Nonomuraea SP} PDB: 2wdw_A*	Back alignment and structure

>3vte_A Tetrahydrocannabinolic acid synthase; BI-covalent flavinylation, oxidoreductase; HET: NAG FAD; 2.75A {Cannabis sativa}	Back alignment and structure

>3pop_A GILR oxidase; FAD binding protein, gilvocarcin, gilvocarcin biosynthesis, covalently bound FAD, oxidoreductase; HET: FAD; 1.65A {Streptomyces griseoflavus} PDB: 3pqb_A*	Back alignment and structure

>2ipi_A Aclacinomycin oxidoreductase (aknox); anthracycline, flavoenzyme, twinning, MAD; HET: AKY FAD; 1.65A {Streptomyces galilaeus}	Back alignment and structure

>3tx1_A UDP-N-acetylenolpyruvoylglucosamine reductase; structural genomics, center for structural genomics of infec diseases, csgid; HET: FAD; 2.69A {Listeria monocytogenes}	Back alignment and structure

>2y3s_A TAML; oxidoreductase; HET: FAD TIR; 1.67A {Streptomyces SP} PDB: 2y3r_A* 2y08_A* 2y4g_A*	Back alignment and structure

>3js8_A Cholesterol oxidase; cholsterol, organic solvent stability, oxygen channel, FAD, flavoprotein, oxidoreductase; HET: FAD SUC; 1.54A {Chromobacterium SP}	Back alignment and structure

>2i0k_A Oxidoreductase; MIX alpha beta, covalent FAD, flavoenzyme; HET: FAD; 1.60A {Brevibacterium sterolicum} SCOP: d.58.32.3 d.145.1.1 PDB: 1i19_A*	Back alignment and structure

>2yvs_A Glycolate oxidase subunit GLCE; oxidoreductase; 2.00A {Thermus thermophilus}	Back alignment and structure

>2gqt_A UDP-N-acetylenolpyruvylglucosamine reductase; peptidoglycan biosynthesis, enolpyruvyl-UDP-N- acetylglucosamine, flavin adenine dinucleotide; HET: FAD; 1.30A {Thermus caldophilus} PDB: 2gqu_A*	Back alignment and structure

>3i99_A UDP-N-acetylenolpyruvoylglucosamine reductase; structural genomics, center for structural of infectious diseases, csgid; HET: FAD; 2.20A {Vibrio cholerae}	Back alignment and structure

>1uxy_A MURB, uridine diphospho-N-acetylenolpyruvylglucosamine reductase; peptidoglycan synthesis, cell WALL, cell division, oxidoreductase, NADP; HET: FAD EPU; 1.80A {Escherichia coli} SCOP: d.145.1.2 d.146.1.1 PDB: 1mbb_A* 1mbt_A* 2q85_A* 2mbr_A*	Back alignment and structure

>1ffv_C CUTM, flavoprotein of carbon monoxide dehydrogenase; hydrolase; HET: ARO PCD FAD; 2.25A {Hydrogenophaga pseudoflava} SCOP: d.87.2.1 d.145.1.3 PDB: 1ffu_C*	Back alignment and structure

>2w3s_A Xanthine dehydrogenase; XO, XDH, GOUT, iron, 2Fe-2S, iron-sulfur, oxidoreductase, purine metabolism, molybdenum cofactor, hypoxanthine; HET: MPN FAD XAN; 2.60A {Rhodobacter capsulatus} PDB: 2w3r_A* 2w54_A* 2w55_A* 1jro_A* 1jrp_A*	Back alignment and structure

>3nvz_B Xanthine dehydrogenase/oxidase; hydroxylase, homodimer, xanthine oxidase, indole-3-aldehyde, oxidoreductase; HET: FAD MTE I3A; 1.60A {Bos taurus} PDB: 3eub_B* 3etr_B* 3ns1_B* 3nrz_B* 3rca_B* 3sr6_B* 3nvw_B* 3nvv_B* 3nvy_B*	Back alignment and structure

>1n62_C Carbon monoxide dehydrogenase medium chain; CODH, molybdenum, molybdopterin, oxidoreductase; HET: CUB MCN FAD; 1.09A {Oligotropha carboxidovorans} SCOP: d.87.2.1 d.145.1.3 PDB: 1n5w_C* 1n61_C* 1n60_C* 1n63_C* 1zxi_C*	Back alignment and structure

>1t3q_C Quinoline 2-oxidoreductase medium subunit; QOR, molybdenum, MCD; HET: FAD MCN; 1.80A {Pseudomonas putida} SCOP: d.87.2.1 d.145.1.3	Back alignment and structure

>3hrd_C Nicotinate dehydrogenase FAD-subunit; selenium ligand, iron, iron-sulfur, metal-binding, oxidoreductase; HET: MCN FAD; 2.20A {Eubacterium barkeri}	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		241
d1f0xa2		265	d.145.1.1 (A:9-273) D-lactate dehydrogenase {Esche	0.003

>d1f0xa2 d.145.1.1 (A:9-273) D-lactate dehydrogenase {Escherichia coli [TaxId: 562]} Length = 265	Back information, alignment and structure


class: Alpha and beta proteins (a+b)
fold: FAD-binding/transporter-associated domain-like
superfamily: FAD-binding/transporter-associated domain-like
family: FAD-linked oxidases, N-terminal domain
domain: D-lactate dehydrogenase
species: Escherichia coli [TaxId: 562]

 Score = 35.9 bits (82), Expect = 0.003
 Identities = 7/78 (8%), Positives = 21/78 (26%)

Query: 132 RRVNSILWLDEDNLVACIEAGIIGQDLERELNSRGYTSGHEPDSYEFSSLGGWVATRASG 191
            R++ +  L +   V       +    +               S   +S+ G +   + G
Sbjct: 94  LRLDKLHVLGKGEQVLAYPGTTLYSLEKALKPLGREPHSVIGSSCIGASVIGGICNNSGG 153

Query: 192 MKKNLYGNIEDLLVQVTM 209
                     ++ +   +
Sbjct: 154 SLVQRGPAYTEMSLFARI 171

PyMOL of d1f0xa2

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		241
d1wvfa2		236	Flavoprotein subunit of p-cresol methylhydroxylase	100.0
d1e8ga2		268	Vanillyl-alcohol oxidase {Fungus (Penicillium simp	99.97
d1w1oa2		206	Cytokinin dehydrogenase 1 {Maize (Zea mays) [TaxId	99.97
d1f0xa2		265	D-lactate dehydrogenase {Escherichia coli [TaxId:	99.96
d2i0ka2		216	Cholesterol oxidase {Brevibacterium sterolicum [Ta	99.84
d1hska1		194	Uridine diphospho-N-Acetylenolpyruvylglucosamine r	99.7
d1uxya1		198	Uridine diphospho-N-Acetylenolpyruvylglucosamine r	99.2
d1f0xa1		294	D-lactate dehydrogenase {Escherichia coli [TaxId:	94.08
d1ffvc2		177	Carbon monoxide (CO) dehydrogenase flavoprotein, N	93.87
d1jroa4		167	Xanthine dehydrogenase chain A, domain 3 {Rhodobac	92.6
d1v97a6		223	Xanthine oxidase, domain 3 (?) {Cow (Bos taurus) [	92.07
d1rm6b2		216	4-hydroxybenzoyl-CoA reductase beta subunit HrcB,	91.44
d1t3qc2		176	Quinoline 2-oxidoreductase medium subunit QorM {Ps	90.43
d1n62c2		177	Carbon monoxide (CO) dehydrogenase flavoprotein, N	87.05

>d1wvfa2 d.145.1.1 (A:7-242) Flavoprotein subunit of p-cresol methylhydroxylase {Pseudomonas putida [TaxId: 303]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: FAD-binding/transporter-associated domain-like
superfamily: FAD-binding/transporter-associated domain-like
family: FAD-linked oxidases, N-terminal domain
domain: Flavoprotein subunit of p-cresol methylhydroxylase
species: Pseudomonas putida [TaxId: 303]

Probab=100.00  E-value=1.6e-32  Score=236.47  Aligned_cols=176  Identities=15%  Similarity=0.130  Sum_probs=146.2

Q ss_pred             HHHHHHHh-cC-CceecChhhhhhhhcCCCccchhhcccCCccCCCceEEcce------------------EEEEcCCCC
Q psy4131          48 EVLSLLEA-TN-VSVSTQGEDRLIRAHGQTLYEVFSLRQTGLKRIPDVVVWPV------------------YITFGKYSE  107 (241)
Q Consensus        48 ~~~~~L~~-vg-~~V~~d~~~~~~ys~d~~~~~~~~l~~~~~~~~P~aVv~P~------------------v~~rG~G~~  107 (241)
                      +++++|++ +| ++|++|++++..|++|++..       ..+...|++||+|+                  ++++|+|  
T Consensus        14 ~~v~~l~~ivG~~~V~~~~~~~~~y~~d~~~~-------~~~~~~P~~Vv~P~s~eeV~~iv~~a~~~~~~i~~~g~G--   84 (236)
T d1wvfa2          14 KAVQKFRALLGDDNVLVESDQLVPYNKIMMPV-------ENAAHAPSAAVTATTVEQVQGVVKICNEHKIPIWTISTG--   84 (236)
T ss_dssp             HHHHHHHHHHCGGGEECSHHHHHHHHCCCSSS-------CGGGGCCSEEEECCSHHHHHHHHHHHHHHTCCEEEESSC--
T ss_pred             HHHHHHHHHcCCccEEECHHHHHHHhCccccc-------cccCcCCCEEEecCCHHHHHHHHHHHHcCCcceeccccc--
Confidence            68999999 99 58999999999999997542       12467899999999                  9999999  


Q ss_pred             CCCCCCCCcc-ccCCCCCceEEEEcCCCCCeeEEeCCCCeEEeCccchHHHHHHHHHHcCCceeccCCCCCCceehhhh-
Q psy4131         108 HSDTQISEKF-DPAGNQTQISNVPIRRVNSILWLDEDNLVACIEAGIIGQDLERELNSRGYTSGHEPDSYEFSSLGGWV-  185 (241)
Q Consensus       108 ~~~t~~~G~~-~~~~~g~~gvvIdl~rmn~Il~id~~~~~v~VeaGv~~~~L~~~L~~~Gl~~~~~p~s~~~~tIGG~i-  185 (241)
                         |++.++. .+...  ++|+|||++||+|+++|+++++|+||||++|.||+++|+++|+.+++.|+.  .+++||.+ 
T Consensus        85 ---~s~~~g~~~~~~~--~~ividl~~mn~i~~id~~~~~v~v~aG~~~~~l~~~l~~~g~~~~~~~~~--~~~~gG~i~  157 (236)
T d1wvfa2          85 ---RNFGYGSAAPVQR--GQVILDLKKMNKIIKIDPEMCYALVEPGVTFGQMYDYIQENNLPVMLSFSA--PSAIAGPVG  157 (236)
T ss_dssp             ---CCTTTTTTSCSST--TCEEEECTTCCCEEEEETTTTEEEECTTCCHHHHHHHHHHTTCSEECCCCS--SCTTCCHHH
T ss_pred             ---ccccccccccccc--eEEEeecccccchhhhcccccceehhhhhhhhhhHHHHhhhcccccccccc--ccccccccc
Confidence               8875443 44332  369999999999999999999999999999999999999999999887754  35566655 


Q ss_pred             ccCCCCCCCCccccccccEeEEEEEecCCcEEEcCC----------CCCCCcCCCcccccccCCCC
Q psy4131         186 ATRASGMKKNLYGNIEDLLVQVTMVTARGTLERPCR----------GPRVSSGPDFNHVILGSEAD  241 (241)
Q Consensus       186 a~~g~G~~s~~yG~~~d~V~~levVl~dG~i~~~~~----------~~k~~~G~dl~~l~~GseGt  241 (241)
                      +++++|.++.+||..+|+|+++|||+|||++++++.          ..+...||+|.++  |||||
T Consensus       158 ~~~~~G~~~~~yG~~~d~v~~levVl~~G~iv~~~~~~~~~~~~~~~~~~~~G~~~~~l--~SeGt  221 (236)
T d1wvfa2         158 NTMDRGVGYTPYGEHFMMQCGMEVVLANGDVYRTGMGGVPGSNTWQIFKWGYGPTLDGM--FTQAN  221 (236)
T ss_dssp             HHHTTCBCSSTTCBGGGGEEEEEEECTTSCEEECGGGGSTTCSCTTTCSCCSSCCCHHH--HTTSS
T ss_pred             cccccccccccccccccceeeeEEEcCCCcEEEeCCccCCCccHHHHHhcCcCcccccc--ccccc
Confidence            589999999999999999999999999999998643          2345667776655  48886

PyMOL of d1wvfa2

>d1e8ga2 d.145.1.1 (A:6-273) Vanillyl-alcohol oxidase {Fungus (Penicillium simplicissimum) [TaxId: 69488]}	Back information, alignment and structure

>d1w1oa2 d.145.1.1 (A:40-245) Cytokinin dehydrogenase 1 {Maize (Zea mays) [TaxId: 4577]}	Back information, alignment and structure

>d1f0xa2 d.145.1.1 (A:9-273) D-lactate dehydrogenase {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2i0ka2 d.145.1.1 (A:58-273) Cholesterol oxidase {Brevibacterium sterolicum [TaxId: 1702]}	Back information, alignment and structure

>d1hska1 d.145.1.2 (A:15-208) Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase (MurB), N-terminal domain {Staphylococcus aureus [TaxId: 1280]}	Back information, alignment and structure

>d1uxya1 d.145.1.2 (A:3-200) Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase (MurB), N-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1f0xa1 d.58.32.2 (A:274-567) D-lactate dehydrogenase {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1ffvc2 d.145.1.3 (C:1-177) Carbon monoxide (CO) dehydrogenase flavoprotein, N-terminal domain {Hydrogenophaga pseudoflava [TaxId: 47421]}	Back information, alignment and structure

>d1jroa4 d.145.1.3 (A:179-345) Xanthine dehydrogenase chain A, domain 3 {Rhodobacter capsulatus [TaxId: 1061]}	Back information, alignment and structure

>d1v97a6 d.145.1.3 (A:192-414) Xanthine oxidase, domain 3 (?) {Cow (Bos taurus) [TaxId: 9913]}	Back information, alignment and structure

>d1rm6b2 d.145.1.3 (B:1-216) 4-hydroxybenzoyl-CoA reductase beta subunit HrcB, N-terminal domain {Thauera aromatica [TaxId: 59405]}	Back information, alignment and structure

>d1t3qc2 d.145.1.3 (C:1-176) Quinoline 2-oxidoreductase medium subunit QorM {Pseudomonas putida [TaxId: 303]}	Back information, alignment and structure

>d1n62c2 d.145.1.3 (C:1-177) Carbon monoxide (CO) dehydrogenase flavoprotein, N-terminal domain {Oligotropha carboxidovorans, formerly Pseudomonas carboxydovorans [TaxId: 40137]}	Back information, alignment and structure