Psyllid ID: psy1771

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-------

MGTVLQWIVYKLGKCATHAIVFARLITPDSVDHGLHAFLVPIRDPKTLLPYPGVTVGDLEGTYTSPFRDPGKRFGSSLGALSTGRVSIIGFCVAYLSKAITIAVRYAGVRRQFGPPKQGSDSEPEELPVLEYELLQWRLFPHLAAVYMLRVFSDYFTREMGRFQMKLMEGGGDKDYLGAMGAEIHALSSAGKPLAGWIARDGIQECREACGGHGYLK

ccccccEEcccccccccEEEEEEEEEcccccccccEEEEEEEccccccccccccccccccccccccccccccHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHEEccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccc

ccccEEEccccccccccEEEEEEEEEcccccccccEEEEEEccccccccccccEEEccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccEEccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccc

MGTVLQWIVYKLGKCATHAIVFARlitpdsvdhglhaflvpirdpktllpypgvtvgdlegtytspfrdpgkrfgsslgalstgrVSIIGFCVAYLSKAITIAVRYAgvrrqfgppkqgsdsepeelpvLEYELLQWRLFPHLAAVYMLRVFSDYFTREMGRFQMKLmegggdkdylGAMGAEIHALSSAGKPLAGWIARDGIQECREacgghgylk

MGTVLQWIVYKLGKCATHAIVFARLITPDSVDHGLHAFLVpirdpktllpYPGVTVGDLEGTytspfrdpgkrfgSSLGALSTGRVSIIGFCVAYLSKAITIAVRYAGVRRQFGppkqgsdsepeELPVLEYELLQWRLFPHLAAVYMLRVFSDYFTREMGRFQMKLMEGGGDKDYLGAMGAEIHALSSAGKPLAGWIARDGIQECREACGGHGYLK

MGTVLQWIVYKLGKCATHAIVFARLITPDSVDHGLHAFLVPIRDPKTLLPYPGVTVGDLEGTYTSPFRDPGKRFGSSLGALSTGRVSIIGFCVAYLSKAITIAVRYAGVRRQFGPPKQGSDSepeelpvleyellQWRLFPHLAAVYMLRVFSDYFTREMGRFQMKLMEGGGDKDYLGAMGAEIHALSSAGKPLAGWIARDGIQECREACGGHGYLK

**TVLQWIVYKLGKCATHAIVFARLITPDSVDHGLHAFLVPIRDPKTLLPYPGVTVGDLEGTYTSPFRDPGKRFGSSLGALSTGRVSIIGFCVAYLSKAITIAVRYAGVRR****************PVLEYELLQWRLFPHLAAVYMLRVFSDYFTREMGRFQMKLMEGGGDKDYLGAMGAEIHALSSAGKPLAGWIARDGIQECREACGGH****

*GTVLQWIVYKLGKCATHAIVFARLITPDSVDHGLHAFLVPIRDPKTLLPYPGVTVGDLEGTYTSPFRDPGKRFGSSLGALSTGRVSIIGFCVAYLSKAITIAVRYAGVRR***************LPVLEYELLQWRLFPHLAAVYMLRVFSDYFTREMGRFQM**************MGAEIHALSSAGKPLAGWIARDGIQECREACGGHGYL*

MGTVLQWIVYKLGKCATHAIVFARLITPDSVDHGLHAFLVPIRDPKTLLPYPGVTVGDLEGTYTSPFRDPGKRFGSSLGALSTGRVSIIGFCVAYLSKAITIAVRYAGVRRQF************ELPVLEYELLQWRLFPHLAAVYMLRVFSDYFTREMGRFQMKLMEGGGDKDYLGAMGAEIHALSSAGKPLAGWIARDGIQECREACGGHGYLK

**TVLQWIVYKLGKCATHAIVFARLITPDSVDHGLHAFLVPIRDPKTLLPYPGVTVGDLEGTYTSPFRDPGKRFGSSLGALSTGRVSIIGFCVAYLSKAITIAVRYAGVRRQFGPPKQGSDSEPEELPVLEYELLQWRLFPHLAAVYMLRVFSDYFTREMGRFQMKLMEGGGDKDYLGAMGAEIHALSSAGKPLAGWIARDGIQECREACGGHGY**

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oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

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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		217	2.2.26 [Sep-21-2011]
O15254		700	Peroxisomal acyl-coenzyme	no	N/A	0.935	0.29	0.481	1e-55
Q9EPL9		700	Peroxisomal acyl-coenzyme	yes	N/A	0.926	0.287	0.481	1e-54
Q5RAU0		700	Peroxisomal acyl-coenzyme	yes	N/A	0.912	0.282	0.463	3e-52
Q63448		700	Peroxisomal acyl-coenzyme	yes	N/A	0.926	0.287	0.477	3e-46
Q9R0H0		661	Peroxisomal acyl-coenzyme	no	N/A	0.903	0.296	0.350	6e-30
P07872		661	Peroxisomal acyl-coenzyme	no	N/A	0.903	0.296	0.350	8e-30
O65201		692	Acyl-coenzyme A oxidase 2	yes	N/A	0.898	0.281	0.354	2e-27
Q9Z1N0		661	Peroxisomal acyl-coenzyme	no	N/A	0.903	0.296	0.346	3e-27
Q3SZP5		660	Peroxisomal acyl-coenzyme	no	N/A	0.903	0.296	0.334	4e-27
Q15067		660	Peroxisomal acyl-coenzyme	no	N/A	0.903	0.296	0.338	2e-26

>sp\|O15254\|ACOX3_HUMAN Peroxisomal acyl-coenzyme A oxidase 3 OS=Homo sapiens GN=ACOX3 PE=1 SV=2	Back alignment and function desciption

 Score =  216 bits (550), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 119/247 (48%), Positives = 147/247 (59%), Gaps = 44/247 (17%)

Query: 6   QWIVYKLGKCATHAIVFARLITPDSVDHGLHAFLVPIRDPKTLLPYPGVTVGDL------ 59
           ++ V  +GK ATHA+VFA+L  P    HGLH F+V IRDPKTLLP PGV VGD+      
Sbjct: 194 KFWVGNMGKTATHAVVFAKLCVPGDQCHGLHPFIVQIRDPKTLLPMPGVMVGDIGKKLGQ 253

Query: 60  -----------------------------EGTYTSPFRDPGKRFGSSLGALSTGRVSIIG 90
                                        EGTY SPF+D  +RFG+SLG+LS+GRVSI+ 
Sbjct: 254 NGLDNGFAMFHKVRVPRQSLLNRMGDVTPEGTYVSPFKDVRQRFGASLGSLSSGRVSIVS 313

Query: 91  FCVAYLSKAITIAVRYAGVRRQFGPPKQGSDSEPEELPVLEYELLQWRLFPHLAAVYMLR 150
             +  L  A+ IA+R++  RRQFGP      +E EE+PVLEY + QWRL P+LAAVY L 
Sbjct: 314 LAILNLKLAVAIALRFSATRRQFGP------TEEEEIPVLEYPMQQWRLLPYLAAVYALD 367

Query: 151 VFSDYFTREMGRFQMKLMEGGGDKDYLGA-MGAEIHALSSAGKPLAGWIARDGIQECREA 209
            FS     ++   Q  L    GD+    A +G EIHAL+SA KPLA W  + GIQECREA
Sbjct: 368 HFSKSLFLDLVELQRGL--ASGDRSARQAELGREIHALASASKPLASWTTQQGIQECREA 425

Query: 210 CGGHGYL 216
           CGGHGYL
Sbjct: 426 CGGHGYL 432

Oxidizes the CoA-esters of 2-methyl-branched fatty acids.
Homo sapiens (taxid: 9606)
EC: 1EC: .EC: 3EC: .EC: 3EC: .EC: 6

>sp\|Q9EPL9\|ACOX3_MOUSE Peroxisomal acyl-coenzyme A oxidase 3 OS=Mus musculus GN=Acox3 PE=2 SV=2	Back alignment and function description

>sp\|Q5RAU0\|ACOX3_PONAB Peroxisomal acyl-coenzyme A oxidase 3 OS=Pongo abelii GN=ACOX3 PE=2 SV=1	Back alignment and function description

>sp\|Q63448\|ACOX3_RAT Peroxisomal acyl-coenzyme A oxidase 3 OS=Rattus norvegicus GN=Acox3 PE=1 SV=1	Back alignment and function description

>sp\|Q9R0H0\|ACOX1_MOUSE Peroxisomal acyl-coenzyme A oxidase 1 OS=Mus musculus GN=Acox1 PE=1 SV=5	Back alignment and function description

>sp\|P07872\|ACOX1_RAT Peroxisomal acyl-coenzyme A oxidase 1 OS=Rattus norvegicus GN=Acox1 PE=1 SV=1	Back alignment and function description

>sp\|O65201\|ACOX2_ARATH Acyl-coenzyme A oxidase 2, peroxisomal OS=Arabidopsis thaliana GN=ACX2 PE=1 SV=2	Back alignment and function description

>sp\|Q9Z1N0\|ACOX1_CAVPO Peroxisomal acyl-coenzyme A oxidase 1 OS=Cavia porcellus GN=ACOX1 PE=2 SV=1	Back alignment and function description

>sp\|Q3SZP5\|ACOX1_BOVIN Peroxisomal acyl-coenzyme A oxidase 1 OS=Bos taurus GN=ACOX1 PE=2 SV=1	Back alignment and function description

>sp\|Q15067\|ACOX1_HUMAN Peroxisomal acyl-coenzyme A oxidase 1 OS=Homo sapiens GN=ACOX1 PE=1 SV=3	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		217
242013525		660	Acyl-coenzyme A oxidase 3, peroxisomal,	0.917	0.301	0.508	4e-65
66564429		676	PREDICTED: peroxisomal acyl-coenzyme A o	0.921	0.295	0.495	6e-63
380019947		676	PREDICTED: peroxisomal acyl-coenzyme A o	0.921	0.295	0.495	7e-63
383854203		674	PREDICTED: peroxisomal acyl-coenzyme A o	0.917	0.295	0.510	1e-62
340717901		674	PREDICTED: peroxisomal acyl-coenzyme A o	0.917	0.295	0.502	2e-62
328721038		714	PREDICTED: peroxisomal acyl-coenzyme A o	0.930	0.282	0.487	5e-62
193587201		687	PREDICTED: peroxisomal acyl-coenzyme A o	0.930	0.294	0.487	5e-62
307169905		650	Peroxisomal acyl-coenzyme A oxidase 3 [C	0.921	0.307	0.506	6e-62
350400106		674	PREDICTED: peroxisomal acyl-coenzyme A o	0.917	0.295	0.493	9e-62
332031099		713	Peroxisomal acyl-coenzyme A oxidase 3 [A	0.912	0.277	0.481	3e-60

>gi\|242013525\|ref\|XP_002427455.1\| Acyl-coenzyme A oxidase 3, peroxisomal, putative [Pediculus humanus corporis] gi\|212511841\|gb\|EEB14717.1\| Acyl-coenzyme A oxidase 3, peroxisomal, putative [Pediculus humanus corporis]	Back alignment and taxonomy information

 Score =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 124/244 (50%), Positives = 158/244 (64%), Gaps = 45/244 (18%)

Query: 9   VYKLGKCATHAIVFARLITPDSVDHGLHAFLVPIRDPKTLLPYPGVTVGDL--------- 59
           V  LGKC+THA+V+A+L+TPD  DHG + F+VP+RDPKTLLPYPG+TVGD+         
Sbjct: 190 VGNLGKCSTHAVVYAKLLTPDGKDHGHNWFVVPVRDPKTLLPYPGLTVGDMGEKIGLNGV 249

Query: 60  --------------------------EGTYTSPFRDPGKRFGSSLGALSTGRVSIIGFCV 93
                                     +G + S F+D  K+ G+SLGALS GRV I+  CV
Sbjct: 250 DNGFIFFNKYRIPKDNLLNKNGKITPDGKFISKFKDRRKQIGASLGALSGGRVMIMSICV 309

Query: 94  AYLSKAITIAVRYAGVRRQFGPPKQGSDSEPEELPVLEYELLQWRLFPHLAAVYMLRVFS 153
           AY S ++TIAVRY+ VR+QFG          EE+PVLEY+L QWRL P++A VY  ++FS
Sbjct: 310 AYFSMSVTIAVRYSAVRKQFG-------INDEEIPVLEYQLQQWRLIPYVAVVYAFKIFS 362

Query: 154 DYFTREMGRFQMKLMEGGGDKDYLGAMGAEIHALSSAGKPLAGWIARDGIQECREACGGH 213
           DYFT E+  FQ K   G   ++ L  +G EIH++SSAGKPL  WI++ GIQECREACGGH
Sbjct: 363 DYFTYELSWFQFKKFVG---EENLDELGVEIHSISSAGKPLFSWISQRGIQECREACGGH 419

Query: 214 GYLK 217
           GYLK
Sbjct: 420 GYLK 423

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi\|66564429\|ref\|XP_395486.2\| PREDICTED: peroxisomal acyl-coenzyme A oxidase 3-like [Apis mellifera]	Back alignment and taxonomy information

>gi\|380019947\|ref\|XP_003693862.1\| PREDICTED: peroxisomal acyl-coenzyme A oxidase 3-like [Apis florea]	Back alignment and taxonomy information

>gi\|383854203\|ref\|XP_003702611.1\| PREDICTED: peroxisomal acyl-coenzyme A oxidase 3-like [Megachile rotundata]	Back alignment and taxonomy information

>gi\|340717901\|ref\|XP_003397412.1\| PREDICTED: peroxisomal acyl-coenzyme A oxidase 3-like [Bombus terrestris]	Back alignment and taxonomy information

>gi\|328721038\|ref\|XP_003247197.1\| PREDICTED: peroxisomal acyl-coenzyme A oxidase 3-like isoform 3 [Acyrthosiphon pisum] gi\|328721041\|ref\|XP_003247198.1\| PREDICTED: peroxisomal acyl-coenzyme A oxidase 3-like isoform 4 [Acyrthosiphon pisum]	Back alignment and taxonomy information

>gi\|193587201\|ref\|XP_001947058.1\| PREDICTED: peroxisomal acyl-coenzyme A oxidase 3-like isoform 1 [Acyrthosiphon pisum] gi\|328721036\|ref\|XP_003247196.1\| PREDICTED: peroxisomal acyl-coenzyme A oxidase 3-like isoform 2 [Acyrthosiphon pisum] gi\|328721043\|ref\|XP_003247199.1\| PREDICTED: peroxisomal acyl-coenzyme A oxidase 3-like isoform 5 [Acyrthosiphon pisum]	Back alignment and taxonomy information

>gi\|307169905\|gb\|EFN62414.1\| Peroxisomal acyl-coenzyme A oxidase 3 [Camponotus floridanus]	Back alignment and taxonomy information

>gi\|350400106\|ref\|XP_003485741.1\| PREDICTED: peroxisomal acyl-coenzyme A oxidase 3-like [Bombus impatiens]	Back alignment and taxonomy information

>gi\|332031099\|gb\|EGI70676.1\| Peroxisomal acyl-coenzyme A oxidase 3 [Acromyrmex echinatior]	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		217
FB\|FBgn0032775		693	CG17544 [Drosophila melanogast	0.705	0.220	0.411	3.9e-41
ZFIN\|ZDB-GENE-040426-2163		692	acox3 "acyl-Coenzyme A oxidase	0.815	0.255	0.478	1.6e-34
UNIPROTKB\|D4A3R1		678	Acox3 "Acyl-coenzyme A oxidase	0.820	0.262	0.449	1.6e-34
UNIPROTKB\|O15254		700	ACOX3 "Peroxisomal acyl-coenzy	0.801	0.248	0.445	4.5e-33
UNIPROTKB\|E2R9W6		700	ACOX3 "Acyl-coenzyme A oxidase	0.815	0.252	0.468	1.2e-32
UNIPROTKB\|F1MQG3		633	ACOX3 "Acyl-coenzyme A oxidase	0.811	0.278	0.460	3.8e-32
MGI\|MGI:1933156		700	Acox3 "acyl-Coenzyme A oxidase	0.820	0.254	0.444	4.3e-32
FB\|FBgn0031813		724	CG9527 [Drosophila melanogaste	0.815	0.244	0.478	6.1e-32
WB\|WBGene00019060		667	F58F9.7 [Caenorhabditis elegan	0.778	0.253	0.365	1.7e-31
RGD\|69245		700	Acox3 "acyl-CoA oxidase 3, pri	0.820	0.254	0.428	5.1e-30

FB\|FBgn0032775 CG17544 [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

 Score = 295 (108.9 bits), Expect = 3.9e-41, Sum P(2) = 3.9e-41
 Identities = 65/158 (41%), Positives = 86/158 (54%)

Query:    60 EGTYTSPFRDPGKRFGSSLGALSTGRVSIIGFCVAYLSKAITIAVRYAGVRRQFGPPKQG 119
             EG Y S F +PGK  G++L + S GR+ I+      L  A  IAVRY+ VR+QFGP + G
Sbjct:   283 EGVYESVFTEPGKVLGAALESFSAGRIGIMQESANTLCSAAVIAVRYSAVRKQFGPERHG 342

Query:   120 SDSXXXXXXXXXXXXXQWRLFPHLAAVYMLRVFSDYFTREMGRFQMKLMEGGGDKDYLGA 179
              +              Q+R+FP+LAA  + ++ ++  T        +        D L  
Sbjct:   343 EEMAILEYQLH-----QYRIFPYLAAACVQKIATEELTSTYMEIIARSQADSNGFDVLTQ 397

Query:   180 MGAEIHALSSAGKPLAGWIARDGIQECREACGGHGYLK 217
               AEIHAL S+ KPL  W ARD IQE REACGGHGYL+
Sbjct:   398 NAAEIHALISSSKPLITWAARDAIQEAREACGGHGYLQ 435

GO:0016402 "pristanoyl-CoA oxidase activity" evidence=ISS

GO:0006635 "fatty acid beta-oxidation" evidence=IEA

GO:0005777 "peroxisome" evidence=IEA

GO:0003995 "acyl-CoA dehydrogenase activity" evidence=IEA

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

ZFIN\|ZDB-GENE-040426-2163 acox3 "acyl-Coenzyme A oxidase 3, pristanoyl" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|D4A3R1 Acox3 "Acyl-coenzyme A oxidase" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|O15254 ACOX3 "Peroxisomal acyl-coenzyme A oxidase 3" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|E2R9W6 ACOX3 "Acyl-coenzyme A oxidase" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|F1MQG3 ACOX3 "Acyl-coenzyme A oxidase" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

MGI\|MGI:1933156 Acox3 "acyl-Coenzyme A oxidase 3, pristanoyl" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

FB\|FBgn0031813 CG9527 [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

WB\|WBGene00019060 F58F9.7 [Caenorhabditis elegans (taxid:6239)]	Back alignment and assigned GO terms

RGD\|69245 Acox3 "acyl-CoA oxidase 3, pristanoyl" [Rattus norvegicus (taxid:10116)]	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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	1.3.3	LOW CONFIDENCE prediction!

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		217
cd01150		610	cd01150, AXO, Peroxisomal acyl-CoA oxidase	3e-82
PLN02443		664	PLN02443, PLN02443, acyl-coenzyme A oxidase	6e-40
PLN02636		686	PLN02636, PLN02636, acyl-coenzyme A oxidase	6e-35
PTZ00460		646	PTZ00460, PTZ00460, acyl-CoA dehydrogenase; Provis	3e-24
PLN02312		680	PLN02312, PLN02312, acyl-CoA oxidase	3e-24
cd00567		327	cd00567, ACAD, Acyl-CoA dehydrogenase	5e-21
COG1960		393	COG1960, CaiA, Acyl-CoA dehydrogenases [Lipid meta	7e-12
pfam00441		150	pfam00441, Acyl-CoA_dh_1, Acyl-CoA dehydrogenase,	7e-05
cd01158		373	cd01158, SCAD_SBCAD, Short chain acyl-CoA dehydrog	2e-04

>gnl\|CDD\|173839 cd01150, AXO, Peroxisomal acyl-CoA oxidase	Back alignment and domain information

 Score =  256 bits (655), Expect = 3e-82
 Identities = 112/246 (45%), Positives = 136/246 (55%), Gaps = 47/246 (19%)

Query: 7   WIVYKLGKCATHAIVFARLITPDSVDHGLHAFLVPIRDPKTLLPYPGVTVGDL------- 59
           W    LGK ATHA+VFA+LITP   +HGLHAF+VPIRDPKT  P PGVTVGD+       
Sbjct: 177 WWPGNLGKTATHAVVFAQLITPGK-NHGLHAFIVPIRDPKTHQPLPGVTVGDIGPKMGLN 235

Query: 60  ----------------------------EGTYTSPFRDPGKRFGSSLGALSTGRVSIIGF 91
                                       +GTY SPF+DP KR+G+ LG  S GRV +I  
Sbjct: 236 GVDNGFLQFRNVRIPRENLLNRFGDVSPDGTYVSPFKDPNKRYGAMLGTRSGGRVGLIYD 295

Query: 92  CVAYLSKAITIAVRYAGVRRQFGPPKQGSDSEPEELPVLEYELLQWRLFPHLAAVYMLRV 151
               L KA TIA+RY+ VRRQFGP    SD E     +L+Y+L Q+RLFP LAA Y    
Sbjct: 296 AAMSLKKAATIAIRYSAVRRQFGPK--PSDPEV---QILDYQLQQYRLFPQLAAAYAFHF 350

Query: 152 FSDYFTREMGRFQMKLMEGGGDKDYLGAMGAEIHALSSAGKPLAGWIARDGIQECREACG 211
            +            +L++G  +        AE+HALS+  K +A W A  GIQECREACG
Sbjct: 351 AAKSLVEMYHEIIKELLQGNSEL------LAELHALSAGLKAVATWTAAQGIQECREACG 404

Query: 212 GHGYLK 217
           GHGYL 
Sbjct: 405 GHGYLA 410

Peroxisomal acyl-CoA oxidases (AXO) catalyze the first set in the peroxisomal fatty acid beta-oxidation, the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. In a second oxidative half-reaction, the reduced FAD is reoxidized by molecular oxygen. AXO is generally a homodimer, but it has been reported to form a different type of oligomer in yeast. There are several subtypes of AXO's, based on substrate specificity. Palmitoyl-CoA oxidase acts on straight-chain fatty acids and prostanoids; whereas, the closely related Trihydroxycoprostanoly-CoA oxidase has the greatest activity for 2-methyl branched side chains of bile precursors. Pristanoyl-CoA oxidase, acts on 2-methyl branched fatty acids. AXO has an additional domain, C-terminal to the region with similarity to acyl-CoA dehydrogenases, which is included in this alignment. Length = 610

>gnl\|CDD\|178062 PLN02443, PLN02443, acyl-coenzyme A oxidase	Back alignment and domain information

>gnl\|CDD\|215342 PLN02636, PLN02636, acyl-coenzyme A oxidase	Back alignment and domain information

>gnl\|CDD\|185639 PTZ00460, PTZ00460, acyl-CoA dehydrogenase; Provisional	Back alignment and domain information

>gnl\|CDD\|215178 PLN02312, PLN02312, acyl-CoA oxidase	Back alignment and domain information

>gnl\|CDD\|173838 cd00567, ACAD, Acyl-CoA dehydrogenase	Back alignment and domain information

>gnl\|CDD\|224871 COG1960, CaiA, Acyl-CoA dehydrogenases [Lipid metabolism]	Back alignment and domain information

>gnl\|CDD\|201229 pfam00441, Acyl-CoA_dh_1, Acyl-CoA dehydrogenase, C-terminal domain	Back alignment and domain information

>gnl\|CDD\|173847 cd01158, SCAD_SBCAD, Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		217
KOG0139\|consensus		398		100.0
KOG0140\|consensus		408		100.0
TIGR03203		378	pimD_small pimeloyl-CoA dehydrogenase, small subun	100.0
PTZ00460		646	acyl-CoA dehydrogenase; Provisional	99.97
PLN02636		686	acyl-coenzyme A oxidase	99.97
cd01154		418	AidB Proteins involved in DNA damage response, sim	99.97
PRK11561		538	isovaleryl CoA dehydrogenase; Provisional	99.97
KOG0141\|consensus		421		99.97
TIGR03207		372	cyc_hxne_CoA_dh cyclohexanecarboxyl-CoA dehydrogen	99.97
PRK09463		777	fadE acyl-CoA dehydrogenase; Reviewed	99.97
cd01150		610	AXO Peroxisomal acyl-CoA oxidase. Peroxisomal acyl	99.97
PRK12341		381	putative acyl-CoA dehydrogenase; Provisional	99.97
PLN02312		680	acyl-CoA oxidase	99.97
cd01157		378	MCAD Medium chain acyl-CoA dehydrogenase. MCADs ar	99.97
COG1960		393	CaiA Acyl-CoA dehydrogenases [Lipid metabolism]	99.97
PRK13026		774	acyl-CoA dehydrogenase; Reviewed	99.96
cd01160		372	LCAD Long chain acyl-CoA dehydrogenase. LCAD is an	99.96
cd01162		375	IBD Isobutyryl-CoA dehydrogenase. Isobutyryl-CoA d	99.96
PRK03354		380	crotonobetainyl-CoA dehydrogenase; Validated	99.96
PTZ00456		622	acyl-CoA dehydrogenase; Provisional	99.96
cd01151		386	GCD Glutaryl-CoA dehydrogenase. Glutaryl-CoA dehyd	99.96
cd01161		409	VLCAD Very long chain acyl-CoA dehydrogenase. VLCA	99.96
PLN02519		404	isovaleryl-CoA dehydrogenase	99.96
cd01156		376	IVD Isovaleryl-CoA dehydrogenase. Isovaleryl-CoA d	99.96
cd01155		394	ACAD_FadE2 Acyl-CoA dehydrogenases similar to fadE	99.96
PTZ00461		410	isovaleryl-CoA dehydrogenase; Provisional	99.96
PLN02443		664	acyl-coenzyme A oxidase	99.96
PLN02526		412	acyl-coenzyme A oxidase	99.96
KOG0137\|consensus		634		99.95
cd01158		373	SCAD_SBCAD Short chain acyl-CoA dehydrogenases and	99.95
TIGR03204		395	pimC_large pimeloyl-CoA dehydrogenase, large subun	99.95
cd00567		327	ACAD Acyl-CoA dehydrogenase. Both mitochondrial ac	99.95
cd01153		407	ACAD_fadE5 Putative acyl-CoA dehydrogenases simila	99.95
PLN02876		822	acyl-CoA dehydrogenase	99.95
KOG0135\|consensus		661		99.94
cd01159		370	NcnH Naphthocyclinone hydroxylase. Naphthocyclinon	99.94
cd01163		377	DszC Dibenzothiophene (DBT) desulfurization enzyme	99.94
cd01152		380	ACAD_fadE6_17_26 Putative acyl-CoA dehydrogenases	99.94
KOG1469\|consensus		392		99.9
KOG0138\|consensus		432		99.9
PTZ00457		520	acyl-CoA dehydrogenase; Provisional	99.87
PF00441		150	Acyl-CoA_dh_1: Acyl-CoA dehydrogenase, C-terminal	99.78
TIGR02309		477	HpaB-1 4-hydroxyphenylacetate 3-monooxygenase, oxy	99.77
KOG0136\|consensus		670		99.76
PF08028		134	Acyl-CoA_dh_2: Acyl-CoA dehydrogenase, C-terminal	99.53
PF02770		52	Acyl-CoA_dh_M: Acyl-CoA dehydrogenase, middle doma	98.03
COG2368		493	Aromatic ring hydroxylase [Secondary metabolites b	97.85
TIGR02310		519	HpaB-2 4-hydroxyphenylacetate 3-monooxygenase, oxy	97.38
PF03241		205	HpaB: 4-hydroxyphenylacetate 3-hydroxylase C termi	94.53
PF11794		264	HpaB_N: 4-hydroxyphenylacetate 3-hydroxylase N ter	90.35
PTZ00457		520	acyl-CoA dehydrogenase; Provisional	88.22
KOG0137\|consensus		634		85.24

>KOG0139\|consensus	Back alignment and domain information

Probab=100.00  E-value=3.8e-39  Score=262.63  Aligned_cols=178  Identities=24%  Similarity=0.346  Sum_probs=167.2

Q ss_pred             CCcceeeeccCCCCCCcEEEEEEEeeeCCCCceeeeEEEEeeeCCCCCCCCCCceeeCC--------CCceeccCCC---
Q psy1771           1 MGTVLQWIVYKLGKCATHAIVFARLITPDSVDHGLHAFLVPIRDPKTLLPYPGVTVGDL--------EGTYTSPFRD---   69 (217)
Q Consensus         1 ~lnG~K~~is~~~~~A~~~~v~ar~~~~~~~~~~l~~flVp~~~~~~~~~~~Gv~i~~~--------~~~~~~~~~~---   69 (217)
                      ++||.|.|||| +..|+|++|+|.+ ++..+++|+++|+||+       ++||+++..+        ..++.+.|+|   
T Consensus       180 viNGsKmWItN-~~~A~~~lVfan~-d~~~~~Kgit~fiV~r-------d~~Gl~~~k~eDKLGmRaSsTcql~fedVrV  250 (398)
T KOG0139|consen  180 VINGSKMWITN-AGEADWFLVFANA-DPSKGYKGITCFIVPR-------DTPGLSLGKKEDKLGMRASSTCQLHFEDVRV  250 (398)
T ss_pred             EEecceeeecC-CcccceEEEEEec-ChhhccCceeEEEeeC-------CCCCcccCCccccccccccceeeEEeccccc
Confidence            58999999999 9999999999999 7888999999999999       9999999874        4567888887   


Q ss_pred             --------CCchhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcceecCCCCCCCCCCCCCCccchhHHHHHHhHH
Q psy1771          70 --------PGKRFGSSLGALSTGRVSIIGFCVAYLSKAITIAVRYAGVRRQFGPPKQGSDSEPEELPVLEYELLQWRLFP  141 (217)
Q Consensus        70 --------~~~g~~~~~~~l~~~r~~~aa~~~G~a~~al~~a~~~~~~R~~~~~~~~~~~~~~~~~~l~~~~~vq~~la~  141 (217)
                              +|.|++..++.|+-+|+.++++.+|.++.||+.++.|+++|.+||  +          +|.++|.+|++||+
T Consensus       251 pks~IlGe~G~GykyAm~~Ln~gRIgi~AqmlglaQ~c~d~tI~Y~q~R~~FG--k----------~l~d~Q~iQhqiA~  318 (398)
T KOG0139|consen  251 PKSSILGEYGKGYKYAIEVLNAGRIGIGAQMLGLAQGCFDETIPYAQERLQFG--K----------RLLDFQGLQHQIAD  318 (398)
T ss_pred             cchhhcccCCcchHHHHHhcCccceeehhhhhhhhHhHHHhhhHHHHHHHHhc--c----------hhhhHHHHHHHHHH
Confidence                    588999999999999999999999999999999999999999999  9          99999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCcccccchHHHHHHHhhhhhhhhHHHHHHHHHHHHHhcCCCCCC
Q psy1771         142 HLAAVYMLRVFSDYFTREMGRFQMKLMEGGGDKDYLGAMGAEIHALSSAGKPLAGWIARDGIQECREACGGHGYLK  217 (217)
Q Consensus       142 ~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aK~~a~e~a~~~~~~~~~~~G~~g~~~  217 (217)
                      +..++|++|+++|++++.                  .+.+.+..-+++|+|++++|.|..+++.|+|.+||.||++
T Consensus       319 ~~teiEaaRlL~ynaAr~------------------k~~G~pf~keAAMAKl~ase~A~~~t~qCiq~lGG~Gyt~  376 (398)
T KOG0139|consen  319 MATEIEAARLLVYNAARM------------------KDQGLPFVKEAAMAKLYASEVATKTTHQCIQWLGGVGYTK  376 (398)
T ss_pred             HHHHHHHHHHHHHHHHHH------------------HHcCCchHHHHHHHHHhhhhhhhHHHHHHHHHHhcccccc
Confidence            999999999999997754                  4578889999999999999999999999999999999985

>KOG0140\|consensus	Back alignment and domain information

>TIGR03203 pimD_small pimeloyl-CoA dehydrogenase, small subunit	Back alignment and domain information

>PTZ00460 acyl-CoA dehydrogenase; Provisional	Back alignment and domain information

>PLN02636 acyl-coenzyme A oxidase	Back alignment and domain information

>cd01154 AidB Proteins involved in DNA damage response, similar to the AidB gene product	Back alignment and domain information

>PRK11561 isovaleryl CoA dehydrogenase; Provisional	Back alignment and domain information

>KOG0141\|consensus	Back alignment and domain information

>TIGR03207 cyc_hxne_CoA_dh cyclohexanecarboxyl-CoA dehydrogenase	Back alignment and domain information

>PRK09463 fadE acyl-CoA dehydrogenase; Reviewed	Back alignment and domain information

>cd01150 AXO Peroxisomal acyl-CoA oxidase	Back alignment and domain information

>PRK12341 putative acyl-CoA dehydrogenase; Provisional	Back alignment and domain information

>PLN02312 acyl-CoA oxidase	Back alignment and domain information

>cd01157 MCAD Medium chain acyl-CoA dehydrogenase	Back alignment and domain information

>COG1960 CaiA Acyl-CoA dehydrogenases [Lipid metabolism]	Back alignment and domain information

>PRK13026 acyl-CoA dehydrogenase; Reviewed	Back alignment and domain information

>cd01160 LCAD Long chain acyl-CoA dehydrogenase	Back alignment and domain information

>cd01162 IBD Isobutyryl-CoA dehydrogenase	Back alignment and domain information

>PRK03354 crotonobetainyl-CoA dehydrogenase; Validated	Back alignment and domain information

>PTZ00456 acyl-CoA dehydrogenase; Provisional	Back alignment and domain information

>cd01151 GCD Glutaryl-CoA dehydrogenase	Back alignment and domain information

>cd01161 VLCAD Very long chain acyl-CoA dehydrogenase	Back alignment and domain information

>PLN02519 isovaleryl-CoA dehydrogenase	Back alignment and domain information

>cd01156 IVD Isovaleryl-CoA dehydrogenase	Back alignment and domain information

>cd01155 ACAD_FadE2 Acyl-CoA dehydrogenases similar to fadE2	Back alignment and domain information

>PTZ00461 isovaleryl-CoA dehydrogenase; Provisional	Back alignment and domain information

>PLN02443 acyl-coenzyme A oxidase	Back alignment and domain information

>PLN02526 acyl-coenzyme A oxidase	Back alignment and domain information

>KOG0137\|consensus	Back alignment and domain information

>cd01158 SCAD_SBCAD Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases	Back alignment and domain information

>TIGR03204 pimC_large pimeloyl-CoA dehydrogenase, large subunit	Back alignment and domain information

>cd00567 ACAD Acyl-CoA dehydrogenase	Back alignment and domain information

>cd01153 ACAD_fadE5 Putative acyl-CoA dehydrogenases similar to fadE5	Back alignment and domain information

>PLN02876 acyl-CoA dehydrogenase	Back alignment and domain information

>KOG0135\|consensus	Back alignment and domain information

>cd01159 NcnH Naphthocyclinone hydroxylase	Back alignment and domain information

>cd01163 DszC Dibenzothiophene (DBT) desulfurization enzyme C	Back alignment and domain information

>cd01152 ACAD_fadE6_17_26 Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	Back alignment and domain information

>KOG1469\|consensus	Back alignment and domain information

>KOG0138\|consensus	Back alignment and domain information

>PTZ00457 acyl-CoA dehydrogenase; Provisional	Back alignment and domain information

>PF00441 Acyl-CoA_dh_1: Acyl-CoA dehydrogenase, C-terminal domain; InterPro: IPR006090 Mammalian Co-A dehydrogenases (1	Back alignment and domain information

>TIGR02309 HpaB-1 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component	Back alignment and domain information

>KOG0136\|consensus	Back alignment and domain information

>PF08028 Acyl-CoA_dh_2: Acyl-CoA dehydrogenase, C-terminal domain; InterPro: IPR013107 Acyl Co-A dehydrogenases (1	Back alignment and domain information

>PF02770 Acyl-CoA_dh_M: Acyl-CoA dehydrogenase, middle domain; InterPro: IPR006091 Acyl-CoA dehydrogenases (1	Back alignment and domain information

>COG2368 Aromatic ring hydroxylase [Secondary metabolites biosynthesis, transport, and catabolism]	Back alignment and domain information

>TIGR02310 HpaB-2 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component	Back alignment and domain information

>PF03241 HpaB: 4-hydroxyphenylacetate 3-hydroxylase C terminal; InterPro: IPR024719 This C-terminal domain is found in HpaB, which encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli []	Back alignment and domain information

>PF11794 HpaB_N: 4-hydroxyphenylacetate 3-hydroxylase N terminal; InterPro: IPR024674 This domain is found in the N terminus of HpaB, which encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli []	Back alignment and domain information

>PTZ00457 acyl-CoA dehydrogenase; Provisional	Back alignment and domain information

>KOG0137\|consensus	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		217
1is2_A		661	Crystal Structure Of Peroxisomal Acyl-coa Oxidase-i		4e-27
2fon_A		683	X-Ray Crystal Structure Of Leacx1, An Acyl-Coa Oxid		3e-23
1w07_A		659	Arabidopsis Thaliana Acyl-Coa Oxidase 1 Length = 65		2e-22
1jqi_A		388	Crystal Structure Of Rat Short Chain Acyl-Coa Dehyd		3e-04

>pdb|1IS2|A Chain A, Crystal Structure Of Peroxisomal Acyl-coa Oxidase-ii From Rat Liver Length = 661

Back alignment and structure

Iteration: 1

Score = 117 bits (293), Expect = 4e-27, Method: Composition-based stats. Identities = 84/248 (33%), Positives = 108/248 (43%), Gaps = 52/248 (20%) Query: 3 TVLQWIVYKLGKCATHAIVFARLITPDSVDHGLHAFLVPIRDPKTLLPYPGVTVGDL--- 59 T ++W LGK + HAIV A+LIT +GLHAF+VPIR+ T P PG+TVGD+ Sbjct: 171 TSIKWWPGGLGKTSNHAIVLAQLITQGEC-YGLHAFVVPIREIGTHKPLPGITVGDIGPK 229 Query: 60 --------------------------------EGTYTSPFRDPGKRFGSSLGALSTGRVS 87 +GTY P + + G + R Sbjct: 230 FGYEEMDNGYLKMDNYRIPRENMLMKYAQVKPDGTYVKPLSNK-----LTYGTMVFVRSF 284 Query: 88 IIGFCVAYLSKAITIAVRYAGVRRQFGPPKQGSDSXXXXXXXXXXXXXQWRLFPHLAAVY 147 ++G LSKA TIA+RY+ VRRQ KQ Q++LFP LA Y Sbjct: 285 LVGNAAQSLSKACTIAIRYSAVRRQ-SEIKQSEPEPQILDFQTQ----QYKLFPLLATAY 339 Query: 148 MLRVFSDYFTREMGRFQMKLMEGGGDKDYLGAMGAEIHALSSAGKPLAGWIARDGIQECR 207 Y R + G GD L E+HAL++ K W A GI+ECR Sbjct: 340 AFHFVGRYMKETYLRINESI--GQGDLSEL----PELHALTAGLKAFTTWTANAGIEECR 393 Query: 208 EACGGHGY 215 ACGGHGY Sbjct: 394 MACGGHGY 401

PyMOL of 1is2

>pdb|2FON|A Chain A, X-Ray Crystal Structure Of Leacx1, An Acyl-Coa Oxidase From Lycopersicon Esculentum (Tomato) Length = 683

Back alignment and structure

>pdb|1W07|A Chain A, Arabidopsis Thaliana Acyl-Coa Oxidase 1 Length = 659

Back alignment and structure

>pdb|1JQI|A Chain A, Crystal Structure Of Rat Short Chain Acyl-Coa Dehydrogenase Complexed With Acetoacetyl-Coa Length = 388

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		217
2ddh_A		661	Acyl-COA oxidase; beta barrel, alpha UP-DOWN bundl	1e-65
1w07_A		659	Acyl-COA oxidase; oxidoreductase, peroxisomal beta	3e-64
2uxw_A		607	VERY-long-chain specific acyl-COA dehydrogenase; f	5e-09
3owa_A		597	Acyl-COA dehydrogenase; structural genomics, cente	1e-07
2z1q_A		577	Acyl-COA dehydrogenase; FAD, structural genomics,	1e-07
2dvl_A		372	Acyl-COA dehydrogenase; structural genomics, NPPSF	3e-07
2vig_A		391	Short-chain specific acyl-COA dehydrogenase,; fatt	8e-07
1buc_A		383	Butyryl-COA dehydrogenase; acyl-COA dehydrogenase	1e-06
3mpi_A		397	Glutaryl-COA dehydrogenase; alpha-beta fold, oxido	1e-06
2d29_A		387	Acyl-COA dehydrogenase; structural genomics, NPPSF	2e-06
1rx0_A		393	Acyl-COA dehydrogenase family member 8, mitochondr	3e-06
1ukw_A		379	Acyl-COA dehydrogenase; oxidoreductase, riken stru	4e-06
2jif_A		404	Short/branched chain specific acyl-COA dehydrogen;	4e-06
3pfd_A		393	Acyl-COA dehydrogenase; structural genomics, seatt	6e-06
3mxl_A		395	Nitrososynthase; flavin monooxygenase, acyl-COA de	2e-05
3nf4_A		387	Acyl-COA dehydrogenase; seattle structural genomic	2e-05
3ii9_A		396	Glutaryl-COA dehydrogenase; slipchip, microfluidic	3e-05
3m9v_A		439	FAD-dependent oxidoreductase; KIJD3, fatty acyl-CO	8e-05
1egd_A		396	Medium chain acyl-COA dehydrogenase; flavoprotein,	2e-04
1ivh_A		394	Isovaleryl-COA dehydrogenase; oxidoreductase, acyl	2e-04
1r2j_A		366	Protein FKBI; polyketide synthase, polyketide, acy	4e-04
2ix5_A		436	Acyl-coenzyme A oxidase 4, peroxisomal; FAD, ACX4,	4e-04
3p4t_A		403	Putative acyl-COA dehydrogenase; ssgcid, structura	4e-04
3sf6_A		403	Glutaryl-COA dehydrogenase; ssgcid, NIH, niaid, SB	5e-04
3swo_A		399	Glutaryl-COA dehydrogenase; ssgcid, glutaryl-COA d	6e-04
3r7k_A		403	Probable acyl COA dehydrogenase; ssgcid, structura	9e-04

>2ddh_A Acyl-COA oxidase; beta barrel, alpha UP-DOWN bundle, oxidoreductase; HET: FAD HXD; 2.07A {Rattus norvegicus} SCOP: a.29.3.2 a.29.3.2 e.6.1.2 PDB: 1is2_A* Length = 661	Back alignment and structure

 Score =  212 bits (542), Expect = 1e-65
 Identities = 79/241 (32%), Positives = 108/241 (44%), Gaps = 52/241 (21%)

Query: 12  LGKCATHAIVFARLITPDSVDHGLHAFLVPIRDPKTLLPYPGVTVGDL------------ 59
           LGK + HAIV A+LIT     +GLHAF+VPIR+  T  P PG+TVGD+            
Sbjct: 180 LGKTSNHAIVLAQLIT-QGECYGLHAFVVPIREIGTHKPLPGITVGDIGPKFGYEEMDNG 238

Query: 60  -----------------------EGTYTSPFRDPGKRFGSSLGALSTGRVSIIGFCVAYL 96
                                  +GTY  P  +       + G +   R  ++G     L
Sbjct: 239 YLKMDNYRIPRENMLMKYAQVKPDGTYVKPLSNK-----LTYGTMVFVRSFLVGNAAQSL 293

Query: 97  SKAITIAVRYAGVRRQFGPPKQGSDSEPEELPVLEYELLQWRLFPHLAAVYMLRVFSDYF 156
           SKA TIA+RY+ VRRQ    +        E  +L+++  Q++LFP LA  Y       Y 
Sbjct: 294 SKACTIAIRYSAVRRQSEIKQSE-----PEPQILDFQTQQYKLFPLLATAYAFHFVGRYM 348

Query: 157 TREMGRFQMKLMEGGGDKDYLGAMGAEIHALSSAGKPLAGWIARDGIQECREACGGHGYL 216
                R    + +G   +        E+HAL++  K    W A  GI+ECR ACGGHGY 
Sbjct: 349 KETYLRINESIGQGDLSE------LPELHALTAGLKAFTTWTANAGIEECRMACGGHGYS 402

Query: 217 K 217
            
Sbjct: 403 H 403

PyMOL of 2ddh

>1w07_A Acyl-COA oxidase; oxidoreductase, peroxisomal beta-oxidation, FAD cofactor; HET: FAD; 2.0A {Arabidopsis thaliana} SCOP: a.29.3.2 a.29.3.2 e.6.1.2 PDB: 2fon_A* Length = 659	Back alignment and structure

>2uxw_A VERY-long-chain specific acyl-COA dehydrogenase; fatty acid metabolism, transit peptide, disease mutation, LI metabolism, coenzyme A dehydrogenase; HET: FAD TH3; 1.45A {Homo sapiens} PDB: 3b96_A* Length = 607	Back alignment and structure

>3owa_A Acyl-COA dehydrogenase; structural genomics, center for structural genomics of infec diseases, csgid, alpha-structure, beta-barrel; HET: MSE FAD 1PE; 1.97A {Bacillus anthracis} Length = 597	Back alignment and structure

>2z1q_A Acyl-COA dehydrogenase; FAD, structural genomics, NPPSFA, Na project on protein structural and functional analyses; HET: FAD; 2.30A {Thermus thermophilus} Length = 577	Back alignment and structure

>2dvl_A Acyl-COA dehydrogenase; structural genomics, NPPSFA, national project on protein STR and functional analyses; HET: FAD; 2.50A {Thermus thermophilus} Length = 372	Back alignment and structure

>2vig_A Short-chain specific acyl-COA dehydrogenase,; fatty acid metabolism, FAD, polymorphism, flavoprotein, mitochondrion, disease mutation; HET: FAD COS; 1.9A {Homo sapiens} PDB: 1jqi_A* Length = 391	Back alignment and structure

>1buc_A Butyryl-COA dehydrogenase; acyl-COA dehydrogenase short-chain acyl-COA dehydrogenase, flavoprotein, oxidoreductase; HET: CAA FAD; 2.50A {Megasphaera elsdenii} SCOP: a.29.3.1 e.6.1.1 Length = 383	Back alignment and structure

>3mpi_A Glutaryl-COA dehydrogenase; alpha-beta fold, oxidoreductase; HET: FAD GRA; 2.05A {Desulfococcus multivorans} PDB: 3mpj_A* Length = 397	Back alignment and structure

>2d29_A Acyl-COA dehydrogenase; structural genomics, NPPSFA, national project protein structural and functional analyses; HET: FAD; 1.65A {Thermus thermophilus} SCOP: a.29.3.1 e.6.1.1 PDB: 1ws9_A 2cx9_A* Length = 387	Back alignment and structure

>1rx0_A Acyl-COA dehydrogenase family member 8, mitochondrial; flavoprotein, coenzyme A, oxidoreductase; HET: FAD 2MC; 1.77A {Homo sapiens} SCOP: a.29.3.1 e.6.1.1 Length = 393	Back alignment and structure

>1ukw_A Acyl-COA dehydrogenase; oxidoreductase, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: FAD; 2.40A {Thermus thermophilus} SCOP: a.29.3.1 e.6.1.1 Length = 379	Back alignment and structure

>2jif_A Short/branched chain specific acyl-COA dehydrogen; mitochondrion, oxidoreductase, transit peptide, fatty acid metabolism, FAD, flavoprotein; HET: FAD COS; 2.0A {Homo sapiens} Length = 404	Back alignment and structure

>3pfd_A Acyl-COA dehydrogenase; structural genomics, seattle structural genomics center for infectious disease, ssgcid; HET: FDA; 2.10A {Mycobacterium thermoresistibile} Length = 393	Back alignment and structure

>3mxl_A Nitrososynthase; flavin monooxygenase, acyl-COA dehydrogenas oxidoreductase; 3.15A {Micromonospora carbonacea} Length = 395	Back alignment and structure

>3nf4_A Acyl-COA dehydrogenase; seattle structural genomics center for infectious disease, S FAD, FADH, tuberculosis, oxidoredu; HET: FAD; 2.35A {Mycobacterium thermoresistibile} Length = 387	Back alignment and structure

>3ii9_A Glutaryl-COA dehydrogenase; slipchip, microfluidics, screening, optimization, protein crystallization, structural genomics; HET: PGE PG4; 1.74A {Burkholderia pseudomallei 1710B} PDB: 3eon_A* 3eom_A* 3gqt_A* 3gnc_A* 3d6b_A Length = 396	Back alignment and structure

>3m9v_A FAD-dependent oxidoreductase; KIJD3, fatty acyl-COA dehydrogenase family, kijanose, kijani FAD, flavoprotein; HET: TYD; 2.05A {Actinomadura kijaniata} Length = 439	Back alignment and structure

>1egd_A Medium chain acyl-COA dehydrogenase; flavoprotein, electron transfer; HET: FAD; 2.40A {Homo sapiens} SCOP: a.29.3.1 e.6.1.1 PDB: 1egc_A* 1ege_A* 1t9g_A* 2a1t_A* 1udy_A* 3mdd_A* 3mde_A* Length = 396	Back alignment and structure

>1ivh_A Isovaleryl-COA dehydrogenase; oxidoreductase, acyl-COA dehydrogenase, flavoprotein, isovaleric acidemia; HET: FAD COS; 2.60A {Homo sapiens} SCOP: a.29.3.1 e.6.1.1 Length = 394	Back alignment and structure

>1r2j_A Protein FKBI; polyketide synthase, polyketide, acyl-COA dehydrogenase, , aldehyde dehydrogenase, oxidoreductase; HET: FAD; 2.10A {Streptomyces hygroscopicus} SCOP: a.29.3.1 e.6.1.1 Length = 366	Back alignment and structure

>2ix5_A Acyl-coenzyme A oxidase 4, peroxisomal; FAD, ACX4, flavin, peroxisome, glyoxysome, fatty acid metabo lipid metabolism, acyl-COA oxidase; HET: CAA FAD; 2.7A {Arabidopsis thaliana} PDB: 2ix6_A* Length = 436	Back alignment and structure

>3p4t_A Putative acyl-COA dehydrogenase; ssgcid, structural genomics, seattle structural genomics CEN infectious disease, oxidoreductase; HET: FAO; 1.70A {Mycobacterium smegmatis} PDB: 3oib_A* Length = 403	Back alignment and structure

>3sf6_A Glutaryl-COA dehydrogenase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, structu genomics; HET: FDA; 1.70A {Mycobacterium smegmatis} Length = 403	Back alignment and structure

>3swo_A Glutaryl-COA dehydrogenase; ssgcid, glutaryl-COA dehdrogenase, mycobacerium smegmatis, S genomics; HET: FDA; 1.45A {Mycobacterium smegmatis} Length = 399	Back alignment and structure

>3r7k_A Probable acyl COA dehydrogenase; ssgcid, structural genomics, seattle structural genomics CEN infectious disease, oxidoreductase; HET: FDA; 2.50A {Mycobacterium abscessus} Length = 403	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		217
1buc_A		383	Butyryl-COA dehydrogenase; acyl-COA dehydrogenase	99.97
2jif_A		404	Short/branched chain specific acyl-COA dehydrogen;	99.97
1ukw_A		379	Acyl-COA dehydrogenase; oxidoreductase, riken stru	99.97
2vig_A		391	Short-chain specific acyl-COA dehydrogenase,; fatt	99.97
2pg0_A		385	Acyl-COA dehydrogenase; GK1316, geobacillus kausto	99.97
2d29_A		387	Acyl-COA dehydrogenase; structural genomics, NPPSF	99.97
1egd_A		396	Medium chain acyl-COA dehydrogenase; flavoprotein,	99.97
3pfd_A		393	Acyl-COA dehydrogenase; structural genomics, seatt	99.97
1ivh_A		394	Isovaleryl-COA dehydrogenase; oxidoreductase, acyl	99.97
3r7k_A		403	Probable acyl COA dehydrogenase; ssgcid, structura	99.97
3p4t_A		403	Putative acyl-COA dehydrogenase; ssgcid, structura	99.97
4hr3_A		415	Putative acyl-COA dehydrogenase; ssgcid, seattle s	99.97
1rx0_A		393	Acyl-COA dehydrogenase family member 8, mitochondr	99.97
3ii9_A		396	Glutaryl-COA dehydrogenase; slipchip, microfluidic	99.97
2dvl_A		372	Acyl-COA dehydrogenase; structural genomics, NPPSF	99.97
1r2j_A		366	Protein FKBI; polyketide synthase, polyketide, acy	99.97
2wbi_A		428	Acyl-COA dehydrogenase family member 11; human, ph	99.97
3nf4_A		387	Acyl-COA dehydrogenase; seattle structural genomic	99.97
2uxw_A		607	VERY-long-chain specific acyl-COA dehydrogenase; f	99.97
2z1q_A		577	Acyl-COA dehydrogenase; FAD, structural genomics,	99.97
3owa_A		597	Acyl-COA dehydrogenase; structural genomics, cente	99.97
3mpi_A		397	Glutaryl-COA dehydrogenase; alpha-beta fold, oxido	99.97
2ix5_A		436	Acyl-coenzyme A oxidase 4, peroxisomal; FAD, ACX4,	99.97
3sf6_A		403	Glutaryl-COA dehydrogenase; ssgcid, NIH, niaid, SB	99.97
3swo_A		399	Glutaryl-COA dehydrogenase; ssgcid, glutaryl-COA d	99.97
2eba_A		385	Putative glutaryl-COA dehydrogenase; thermus therm	99.97
1siq_A		392	GCD, glutaryl-COA dehydrogenase; acyl-COA dehydrog	99.96
3mkh_A		438	Nitroalkane oxidase; oxidoreductase flavoenzyme, a	99.96
2jbr_A		422	P-hydroxyphenylacetate hydroxylase C2 oxygenase C;	99.96
2rfq_A		394	3-HSA hydroxylase, oxygenase; rhodococcus SP. RHA1	99.96
2ddh_A		661	Acyl-COA oxidase; beta barrel, alpha UP-DOWN bundl	99.95
2c12_A		439	Nitroalkane oxidase; oxidoreductase, flavoenzyme,	99.95
2or0_A		414	Hydroxylase; APC7385, rhodococcus SP. RHA1, struct	99.95
3djl_A		541	Protein AIDB; alpha helix, beta-barrel, FAD, flavo	99.95
1w07_A		659	Acyl-COA oxidase; oxidoreductase, peroxisomal beta	99.95
3mxl_A		395	Nitrososynthase; flavin monooxygenase, acyl-COA de	99.95
3m9v_A		439	FAD-dependent oxidoreductase; KIJD3, fatty acyl-CO	99.95
2yyk_A		481	4-hydroxyphenylacetate-3-hydroxylase; structurome,	99.89
1u8v_A		490	Gamma-aminobutyrate metabolism dehydratase/isomera	99.87
3hwc_A		515	Chlorophenol-4-monooxygenase component 2; beta bar	99.85
4g5e_A		517	2,4,6-trichlorophenol 4-monooxygenase; oxidoreduct	99.83
3owa_A		597	Acyl-COA dehydrogenase; structural genomics, cente	86.44

>1buc_A Butyryl-COA dehydrogenase; acyl-COA dehydrogenase short-chain acyl-COA dehydrogenase, flavoprotein, oxidoreductase; HET: CAA FAD; 2.50A {Megasphaera elsdenii} SCOP: a.29.3.1 e.6.1.1	Back alignment and structure

Probab=99.97  E-value=2e-31  Score=228.59  Aligned_cols=178  Identities=25%  Similarity=0.324  Sum_probs=157.4

Q ss_pred             CCcceeeeccCCCCCCcEEEEEEEeeeCCCCceeeeEEEEeeeCCCCCCCCCCceeeCC--------CCceeccCCC---
Q psy1771           1 MGTVLQWIVYKLGKCATHAIVFARLITPDSVDHGLHAFLVPIRDPKTLLPYPGVTVGDL--------EGTYTSPFRD---   69 (217)
Q Consensus         1 ~lnG~K~~is~~~~~A~~~~v~ar~~~~~~~~~~l~~flVp~~~~~~~~~~~Gv~i~~~--------~~~~~~~~~~---   69 (217)
                      +|||+|.|+|+ +.+|||++|+|+++ +++++.++++|+||+       +.|||++.+.        .+++++.|+|   
T Consensus       153 ~lnG~K~~~s~-~~~Ad~~~v~a~~~-~~~~~~g~~~flV~~-------~~~Gv~v~~~~~~~g~~~~~~~~v~f~~v~V  223 (383)
T 1buc_A          153 TLNGSKIFITN-GGAADIYIVFAMTD-KSKGNHGITAFILED-------GTPGFTYGKKEDKMGIHTSQTMELVFQDVKV  223 (383)
T ss_dssp             EEEEEEEEEET-TTTCSEEEEEEESC-SSSSTTSEEEEEEET-------TCTTEEEEEECCCSSCTTSCEEEEEEEEEEE
T ss_pred             EEEEEEeccCC-CCcCCEEEEEEEeC-CCCCCCceEEEEEEC-------CCCCeEecCccccccccCCceeEEEEccEEe
Confidence            48999999999 99999999999983 444567899999998       8999999752        3456777765   


Q ss_pred             --------CCchhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcceecCCCCCCCCCCCCCCccchhHHHHHHhHH
Q psy1771          70 --------PGKRFGSSLGALSTGRVSIIGFCVAYLSKAITIAVRYAGVRRQFGPPKQGSDSEPEELPVLEYELLQWRLFP  141 (217)
Q Consensus        70 --------~~~g~~~~~~~l~~~r~~~aa~~~G~a~~al~~a~~~~~~R~~~~~~~~~~~~~~~~~~l~~~~~vq~~la~  141 (217)
                              +++|+..++..++..|+..++.++|+++++++.+++|+++|++||  +          |+.++|.+|++|++
T Consensus       224 p~~~~lg~~g~g~~~~~~~l~~~r~~~aa~~~G~a~~al~~~~~ya~~R~~fG--~----------~i~~~q~vq~~la~  291 (383)
T 1buc_A          224 PAENMLGEEGKGFKIAMMTLDGGRIGVAAQALGIAEAALADAVEYSKQRVQFG--K----------PLCKFQSISFKLAD  291 (383)
T ss_dssp             CGGGEESCTTBHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEETT--E----------EGGGSHHHHHHHHH
T ss_pred             CHHHcCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCeeCC--c----------chhhhHHHHHHHHH
Confidence                    467888888889999999999999999999999999999999999  9          99999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCcccccchHHHHHHHhhhhhhhhHHHHHHHHHHHHHhcCCCCCC
Q psy1771         142 HLAAVYMLRVFSDYFTREMGRFQMKLMEGGGDKDYLGAMGAEIHALSSAGKPLAGWIARDGIQECREACGGHGYLK  217 (217)
Q Consensus       142 ~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aK~~a~e~a~~~~~~~~~~~G~~g~~~  217 (217)
                      |.++++++|++++++++.++.                  +.+....++++|.++++.+.++++.++|++||.||++
T Consensus       292 ~~~~~~~ar~~~~~aa~~~~~------------------g~~~~~~~~~aK~~a~~~a~~~~~~a~q~~Gg~g~~~  349 (383)
T 1buc_A          292 MKMQIEAARNLVYKAACKKQE------------------GKPFTVDAAIAKRVASDVAMRVTTEAVQIFGGYGYSE  349 (383)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH------------------TCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGGGST
T ss_pred             HHHHHHHHHHHHHHHHHHHhC------------------CCchHHHHHHHHHHHHHHHHHHHHHHHHhcCCeecCC
Confidence            999999999999999987652                  1224567899999999999999999999999999974

PyMOL of 1buc

>2jif_A Short/branched chain specific acyl-COA dehydrogen; mitochondrion, oxidoreductase, transit peptide, fatty acid metabolism, FAD, flavoprotein; HET: FAD COS; 2.0A {Homo sapiens}	Back alignment and structure

>1ukw_A Acyl-COA dehydrogenase; oxidoreductase, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: FAD; 2.40A {Thermus thermophilus} SCOP: a.29.3.1 e.6.1.1	Back alignment and structure

>2vig_A Short-chain specific acyl-COA dehydrogenase,; fatty acid metabolism, FAD, polymorphism, flavoprotein, mitochondrion, disease mutation; HET: FAD COS; 1.9A {Homo sapiens} PDB: 1jqi_A*	Back alignment and structure

>2pg0_A Acyl-COA dehydrogenase; GK1316, geobacillus kaustophilus HTA structural genomics, PSI, protein structure initiative; HET: FAD; 1.80A {Geobacillus kaustophilus}	Back alignment and structure

>2d29_A Acyl-COA dehydrogenase; structural genomics, NPPSFA, national project protein structural and functional analyses; HET: FAD; 1.65A {Thermus thermophilus} SCOP: a.29.3.1 e.6.1.1 PDB: 1ws9_A 2cx9_A*	Back alignment and structure

>1egd_A Medium chain acyl-COA dehydrogenase; flavoprotein, electron transfer; HET: FAD; 2.40A {Homo sapiens} SCOP: a.29.3.1 e.6.1.1 PDB: 1egc_A* 1ege_A* 1t9g_A* 2a1t_A* 1udy_A* 3mdd_A* 3mde_A*	Back alignment and structure

>3pfd_A Acyl-COA dehydrogenase; structural genomics, seattle structural genomics center for infectious disease, ssgcid; HET: FDA; 2.10A {Mycobacterium thermoresistibile}	Back alignment and structure

>1ivh_A Isovaleryl-COA dehydrogenase; oxidoreductase, acyl-COA dehydrogenase, flavoprotein, isovaleric acidemia; HET: FAD COS; 2.60A {Homo sapiens} SCOP: a.29.3.1 e.6.1.1	Back alignment and structure

>3r7k_A Probable acyl COA dehydrogenase; ssgcid, structural genomics, seattle structural genomics CEN infectious disease, oxidoreductase; HET: FDA; 2.50A {Mycobacterium abscessus}	Back alignment and structure

>3p4t_A Putative acyl-COA dehydrogenase; ssgcid, structural genomics, seattle structural genomics CEN infectious disease, oxidoreductase; HET: FAO; 1.70A {Mycobacterium smegmatis} PDB: 3oib_A*	Back alignment and structure

>4hr3_A Putative acyl-COA dehydrogenase; ssgcid, seattle structural genomics center for infectious DI niaid; HET: FAD; 1.80A {Mycobacterium abscessus}	Back alignment and structure

>1rx0_A Acyl-COA dehydrogenase family member 8, mitochondrial; flavoprotein, coenzyme A, oxidoreductase; HET: FAD 2MC; 1.77A {Homo sapiens} SCOP: a.29.3.1 e.6.1.1	Back alignment and structure

>3ii9_A Glutaryl-COA dehydrogenase; slipchip, microfluidics, screening, optimization, protein crystallization, structural genomics; HET: PGE PG4; 1.74A {Burkholderia pseudomallei 1710B} PDB: 3eon_A* 3eom_A* 3gqt_A* 3gnc_A* 3d6b_A	Back alignment and structure

>2dvl_A Acyl-COA dehydrogenase; structural genomics, NPPSFA, national project on protein STR and functional analyses; HET: FAD; 2.50A {Thermus thermophilus}	Back alignment and structure

>1r2j_A Protein FKBI; polyketide synthase, polyketide, acyl-COA dehydrogenase, , aldehyde dehydrogenase, oxidoreductase; HET: FAD; 2.10A {Streptomyces hygroscopicus} SCOP: a.29.3.1 e.6.1.1	Back alignment and structure

>2wbi_A Acyl-COA dehydrogenase family member 11; human, phosphoprotein, oxidoreducta; HET: FAD; 2.80A {Homo sapiens}	Back alignment and structure

>3nf4_A Acyl-COA dehydrogenase; seattle structural genomics center for infectious disease, S FAD, FADH, tuberculosis, oxidoredu; HET: FAD; 2.35A {Mycobacterium thermoresistibile}	Back alignment and structure

>2uxw_A VERY-long-chain specific acyl-COA dehydrogenase; fatty acid metabolism, transit peptide, disease mutation, LI metabolism, coenzyme A dehydrogenase; HET: FAD TH3; 1.45A {Homo sapiens} PDB: 3b96_A*	Back alignment and structure

>2z1q_A Acyl-COA dehydrogenase; FAD, structural genomics, NPPSFA, Na project on protein structural and functional analyses; HET: FAD; 2.30A {Thermus thermophilus}	Back alignment and structure

>3owa_A Acyl-COA dehydrogenase; structural genomics, center for structural genomics of infec diseases, csgid, alpha-structure, beta-barrel; HET: MSE FAD 1PE; 1.97A {Bacillus anthracis}	Back alignment and structure

>3mpi_A Glutaryl-COA dehydrogenase; alpha-beta fold, oxidoreductase; HET: FAD GRA; 2.05A {Desulfococcus multivorans} PDB: 3mpj_A*	Back alignment and structure

>2ix5_A Acyl-coenzyme A oxidase 4, peroxisomal; FAD, ACX4, flavin, peroxisome, glyoxysome, fatty acid metabo lipid metabolism, acyl-COA oxidase; HET: CAA FAD; 2.7A {Arabidopsis thaliana} PDB: 2ix6_A*	Back alignment and structure

>3sf6_A Glutaryl-COA dehydrogenase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, structu genomics; HET: FDA; 1.70A {Mycobacterium smegmatis}	Back alignment and structure

>3swo_A Glutaryl-COA dehydrogenase; ssgcid, glutaryl-COA dehdrogenase, mycobacerium smegmatis, S genomics; HET: FDA; 1.45A {Mycobacterium smegmatis}	Back alignment and structure

>2eba_A Putative glutaryl-COA dehydrogenase; thermus thermophilius, FAD, STRU genomics, NPPSFA; HET: FAD; 2.21A {Thermus thermophilus}	Back alignment and structure

>1siq_A GCD, glutaryl-COA dehydrogenase; acyl-COA dehydrogenase, decarboxylation, flavin protein, oxidoreductase; HET: FAD; 2.10A {Homo sapiens} SCOP: a.29.3.1 e.6.1.1 PDB: 2r0n_A* 1sir_A* 2r0m_A*	Back alignment and structure

>3mkh_A Nitroalkane oxidase; oxidoreductase flavoenzyme, acyl-COA dehydrogen flavoprotein, oxidoreductase; HET: FAD; 2.00A {Podospora anserina}	Back alignment and structure

>2jbr_A P-hydroxyphenylacetate hydroxylase C2 oxygenase C; flavoenzyme hydroxylase, oxidoreductase; 2.3A {Acinetobacter baumannii} PDB: 2jbs_A* 2jbt_A*	Back alignment and structure

>2rfq_A 3-HSA hydroxylase, oxygenase; rhodococcus SP. RHA1, structural genomics protein structure initiative, midwest center for structural genomics, MCSG; HET: 1PS; 1.65A {Rhodococcus SP} PDB: 3aff_A 3afe_A	Back alignment and structure

>2ddh_A Acyl-COA oxidase; beta barrel, alpha UP-DOWN bundle, oxidoreductase; HET: FAD HXD; 2.07A {Rattus norvegicus} SCOP: a.29.3.2 a.29.3.2 e.6.1.2 PDB: 1is2_A*	Back alignment and structure

>2c12_A Nitroalkane oxidase; oxidoreductase, flavoenzyme, acyl-COA dehydrogenase, long cell EDGE, FAD, inhibitor, flavoprotein; HET: SPM FAD PE4; 2.07A {Fusarium oxysporum} SCOP: a.29.3.1 e.6.1.1 PDB: 2c0u_A* 2zaf_A* 2reh_A* 3d9g_A* 3d9f_A* 3d9d_A* 3d9e_A* 3fcj_A*	Back alignment and structure

>2or0_A Hydroxylase; APC7385, rhodococcus SP. RHA1, structu genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; HET: MSE; 2.10A {Rhodococcus SP}	Back alignment and structure

>3djl_A Protein AIDB; alpha helix, beta-barrel, FAD, flavoprotein, oxidoreductase; HET: FAD; 1.70A {Escherichia coli} PDB: 3u33_A*	Back alignment and structure

>1w07_A Acyl-COA oxidase; oxidoreductase, peroxisomal beta-oxidation, FAD cofactor; HET: FAD; 2.0A {Arabidopsis thaliana} SCOP: a.29.3.2 a.29.3.2 e.6.1.2 PDB: 2fon_A*	Back alignment and structure

>3mxl_A Nitrososynthase; flavin monooxygenase, acyl-COA dehydrogenas oxidoreductase; 3.15A {Micromonospora carbonacea}	Back alignment and structure

>3m9v_A FAD-dependent oxidoreductase; KIJD3, fatty acyl-COA dehydrogenase family, kijanose, kijani FAD, flavoprotein; HET: TYD; 2.05A {Actinomadura kijaniata}	Back alignment and structure

>2yyk_A 4-hydroxyphenylacetate-3-hydroxylase; structurome, riken spring-8 center, oxygnase component, 4- hydroxyphenylacetate 3-monooxygenase; 1.60A {Thermus thermophilus} PDB: 2yyl_A* 2yym_A* 2yyi_A* 2yyg_A* 2yyj_A*	Back alignment and structure

>1u8v_A Gamma-aminobutyrate metabolism dehydratase/isomerase; ALFA-helixes, beta-strands, lyase; HET: FAD; 1.60A {Clostridium aminobutyricum} SCOP: a.29.3.1 e.6.1.1	Back alignment and structure

>3hwc_A Chlorophenol-4-monooxygenase component 2; beta barrel, helix bundle, oxidoreductase; 2.50A {Burkholderia cepacia}	Back alignment and structure

>4g5e_A 2,4,6-trichlorophenol 4-monooxygenase; oxidoreductase; 2.50A {Cupriavidus necator JMP134}	Back alignment and structure

>3owa_A Acyl-COA dehydrogenase; structural genomics, center for structural genomics of infec diseases, csgid, alpha-structure, beta-barrel; HET: MSE FAD 1PE; 1.97A {Bacillus anthracis}	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		217
d2ddha1		183	a.29.3.2 (A:278-460) Peroxisomal acyl-CoA oxidase-	1e-21
d1w07a1		189	a.29.3.2 (A:273-461) Acyl-coenzyme A oxidase 1, do	3e-17
d2ddha3		267	e.6.1.2 (A:1-267) Peroxisomal acyl-CoA oxidase-II,	4e-07
d1w07a3		271	e.6.1.2 (A:2-272) Acyl-coenzyme A oxidase 1, domai	3e-06

>d2ddha1 a.29.3.2 (A:278-460) Peroxisomal acyl-CoA oxidase-II, domains 3 and 4 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 183	Back information, alignment and structure


class: All alpha proteins
fold: Bromodomain-like
superfamily: Acyl-CoA dehydrogenase C-terminal domain-like
family: acyl-CoA oxidase C-terminal domains
domain: Peroxisomal acyl-CoA oxidase-II, domains 3 and 4
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 85.7 bits (211), Expect = 1e-21
 Identities = 46/133 (34%), Positives = 64/133 (48%), Gaps = 11/133 (8%)

Query: 85  RVSIIGFCVAYLSKAITIAVRYAGVRRQFGPPKQGSDSEPEELPVLEYELLQWRLFPHLA 144
           R  ++G     LSKA TIA+RY+ VRRQ    +        E  +L+++  Q++LFP LA
Sbjct: 5   RSFLVGNAAQSLSKACTIAIRYSAVRRQSEIKQSE-----PEPQILDFQTQQYKLFPLLA 59

Query: 145 AVYMLRVFSDYFTREMGRFQMKLMEGGGDKDYLGAMGAEIHALSSAGKPLAGWIARDGIQ 204
             Y       Y      R    + +G   +        E+HAL++  K    W A  GI+
Sbjct: 60  TAYAFHFVGRYMKETYLRINESIGQGDLSE------LPELHALTAGLKAFTTWTANAGIE 113

Query: 205 ECREACGGHGYLK 217
           ECR ACGGHGY  
Sbjct: 114 ECRMACGGHGYSH 126

PyMOL of d2ddha1

>d1w07a1 a.29.3.2 (A:273-461) Acyl-coenzyme A oxidase 1, domains 3 and 4 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 189	Back information, alignment and structure

>d2ddha3 e.6.1.2 (A:1-267) Peroxisomal acyl-CoA oxidase-II, domains 1 and 2 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 267	Back information, alignment and structure

>d1w07a3 e.6.1.2 (A:2-272) Acyl-coenzyme A oxidase 1, domains 1 and 2 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 271	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		217
d1siqa1		154	Glutaryl-CoA dehydrogenase GCDH {Human (Homo sapie	99.87
d1ivha1		151	Isovaleryl-CoA dehydrogenase, C-domain {Human (Hom	99.87
d2d29a1		153	Acyl-CoA dehydrogenase {Thermus thermophilus [TaxI	99.87
d3mdea1		154	Medium chain acyl-CoA dehydrogenase, C-domain {Pig	99.86
d1jqia1		153	Butyryl-CoA dehydrogenase, C-domain {Rat (Rattus n	99.86
d1rx0a1		153	Isobutyryl-CoA dehydrogenase {Human (Homo sapiens)	99.86
d2c12a1		170	Nitroalkane oxidase {Fusarium oxysporum [TaxId: 55	99.85
d1r2ja1		153	Protein FkbI {Streptomyces hygroscopicus [TaxId: 1	99.85
d1ukwa1		152	Medium chain acyl-CoA dehydrogenase, C-domain {The	99.85
d1w07a1		189	Acyl-coenzyme A oxidase 1, domains 3 and 4 {Thale	99.84
d1buca1		151	Butyryl-CoA dehydrogenase, C-domain {Megasphaera e	99.84
d2ddha1		183	Peroxisomal acyl-CoA oxidase-II, domains 3 and 4 {	99.78
d2ddha3		267	Peroxisomal acyl-CoA oxidase-II, domains 1 and 2 {	99.08
d1buca2		232	Butyryl-CoA dehydrogenase, NM domains {Megasphaera	99.02
d1ukwa2		227	Medium chain acyl-CoA dehydrogenase, NM domains {T	98.93
d1rx0a2		231	Isobutyryl-CoA dehydrogenase {Human (Homo sapiens)	98.92
d1w07a3		271	Acyl-coenzyme A oxidase 1, domains 1 and 2 {Thale	98.9
d1siqa2		236	Glutaryl-CoA dehydrogenase GCDH {Human (Homo sapie	98.87
d1jqia2		231	Butyryl-CoA dehydrogenase, NM domains {Rat (Rattus	98.79
d3mdea2		231	Medium chain acyl-CoA dehydrogenase, NM domains {P	98.76
d1ivha2		236	Isovaleryl-coa dehydrogenase, NM domains {Human (H	98.72
d2d29a2		233	Acyl-CoA dehydrogenase {Thermus thermophilus [TaxI	98.72
d1r2ja2		210	Protein FkbI {Streptomyces hygroscopicus [TaxId: 1	98.65
d2c12a2		259	Nitroalkane oxidase {Fusarium oxysporum [TaxId: 55	98.49
d1u8va2		275	4-hydroxybutyryl-CoA dehydratase AbfD, NM domains	98.41
d1u8va1		215	4-hydroxybutyryl-CoA dehydratase AbfD, C-terminal	93.48

>d1siqa1 a.29.3.1 (A:239-392) Glutaryl-CoA dehydrogenase GCDH {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: All alpha proteins
fold: Bromodomain-like
superfamily: Acyl-CoA dehydrogenase C-terminal domain-like
family: Medium chain acyl-CoA dehydrogenase-like, C-terminal domain
domain: Glutaryl-CoA dehydrogenase GCDH
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=3e-22  Score=149.12  Aligned_cols=111  Identities=23%  Similarity=0.174  Sum_probs=102.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcceecCCCCCCCCCCCCCCccchhHHHHHHhHHHHHHHHHHHHHHHHH
Q psy1771          77 SLGALSTGRVSIIGFCVAYLSKAITIAVRYAGVRRQFGPPKQGSDSEPEELPVLEYELLQWRLFPHLAAVYMLRVFSDYF  156 (217)
Q Consensus        77 ~~~~l~~~r~~~aa~~~G~a~~al~~a~~~~~~R~~~~~~~~~~~~~~~~~~l~~~~~vq~~la~~~~~~~~~r~~~~~~  156 (217)
                      .+..|+.+|+.+++.++|.++++++.+++|+++|++||  +          ||+++|.||++|++|.+++++++++++++
T Consensus         4 ~~~~Ln~~R~~iaa~~lG~a~~~l~~a~~ya~~R~~fG--~----------pl~~~q~v~~~la~~~~~~~~~r~~~~~a   71 (154)
T d1siqa1           4 PFGCLNNARYGIAWGVLGASEFCLHTARQYALDRMQFG--V----------PLARNQLIQKKLADMLTEITLGLHACLQL   71 (154)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEETT--E----------EGGGSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcc--c----------hhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999999999  9          99999999999999999999999999998


Q ss_pred             HHHHHHHHHHHhhCCCCCcccccchHHHHHHHhhhhhhhhHHHHHHHHHHHHHhcCCCCCC
Q psy1771         157 TREMGRFQMKLMEGGGDKDYLGAMGAEIHALSSAGKPLAGWIARDGIQECREACGGHGYLK  217 (217)
Q Consensus       157 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aK~~a~e~a~~~~~~~~~~~G~~g~~~  217 (217)
                      ++.+|                  .+.....+++++|+++++.+.++++.++|++||.||++
T Consensus        72 a~~~d------------------~~~~~~~~~~~aK~~a~~~a~~~~~~a~qi~Gg~G~~~  114 (154)
T d1siqa1          72 GRLKD------------------QDKAAPEMVSLLKRNNCGKALDIARQARDMLGGNGISD  114 (154)
T ss_dssp             HHHHH------------------TTCCCHHHHHHHHHHHHHHHHHHHHHHHHHTGGGGGSG
T ss_pred             HHhhh------------------hcchhhHHHHHHHHHhhhHHHHHHHHHHHHhhcCCCCC
Confidence            87765                  23445677899999999999999999999999999974

PyMOL of d1siqa1

>d1ivha1 a.29.3.1 (A:242-392) Isovaleryl-CoA dehydrogenase, C-domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2d29a1 a.29.3.1 (A:235-387) Acyl-CoA dehydrogenase {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d3mdea1 a.29.3.1 (A:242-395) Medium chain acyl-CoA dehydrogenase, C-domain {Pig (Sus scrofa) [TaxId: 9823]}	Back information, alignment and structure

>d1jqia1 a.29.3.1 (A:235-387) Butyryl-CoA dehydrogenase, C-domain {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d1rx0a1 a.29.3.1 (A:241-393) Isobutyryl-CoA dehydrogenase {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2c12a1 a.29.3.1 (A:261-430) Nitroalkane oxidase {Fusarium oxysporum [TaxId: 5507]}	Back information, alignment and structure

>d1r2ja1 a.29.3.1 (A:213-365) Protein FkbI {Streptomyces hygroscopicus [TaxId: 1912]}	Back information, alignment and structure

>d1ukwa1 a.29.3.1 (A:259-410) Medium chain acyl-CoA dehydrogenase, C-domain {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1w07a1 a.29.3.2 (A:273-461) Acyl-coenzyme A oxidase 1, domains 3 and 4 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1buca1 a.29.3.1 (A:233-383) Butyryl-CoA dehydrogenase, C-domain {Megasphaera elsdenii [TaxId: 907]}	Back information, alignment and structure

>d2ddha1 a.29.3.2 (A:278-460) Peroxisomal acyl-CoA oxidase-II, domains 3 and 4 {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d2ddha3 e.6.1.2 (A:1-267) Peroxisomal acyl-CoA oxidase-II, domains 1 and 2 {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d1buca2 e.6.1.1 (A:1-232) Butyryl-CoA dehydrogenase, NM domains {Megasphaera elsdenii [TaxId: 907]}	Back information, alignment and structure

>d1ukwa2 e.6.1.1 (A:32-258) Medium chain acyl-CoA dehydrogenase, NM domains {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1rx0a2 e.6.1.1 (A:10-240) Isobutyryl-CoA dehydrogenase {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1w07a3 e.6.1.2 (A:2-272) Acyl-coenzyme A oxidase 1, domains 1 and 2 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1siqa2 e.6.1.1 (A:3-238) Glutaryl-CoA dehydrogenase GCDH {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1jqia2 e.6.1.1 (A:4-234) Butyryl-CoA dehydrogenase, NM domains {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d3mdea2 e.6.1.1 (A:11-241) Medium chain acyl-CoA dehydrogenase, NM domains {Pig (Sus scrofa) [TaxId: 9823]}	Back information, alignment and structure

>d1ivha2 e.6.1.1 (A:6-241) Isovaleryl-coa dehydrogenase, NM domains {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2d29a2 e.6.1.1 (A:2-234) Acyl-CoA dehydrogenase {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1r2ja2 e.6.1.1 (A:3-212) Protein FkbI {Streptomyces hygroscopicus [TaxId: 1912]}	Back information, alignment and structure

>d2c12a2 e.6.1.1 (A:2-260) Nitroalkane oxidase {Fusarium oxysporum [TaxId: 5507]}	Back information, alignment and structure

>d1u8va2 e.6.1.1 (A:1-275) 4-hydroxybutyryl-CoA dehydratase AbfD, NM domains {Clostridium aminobutyricum [TaxId: 33953]}	Back information, alignment and structure

>d1u8va1 a.29.3.1 (A:276-490) 4-hydroxybutyryl-CoA dehydratase AbfD, C-terminal domain {Clostridium aminobutyricum [TaxId: 33953]}	Back information, alignment and structure