Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionQ8IXH6
DateThu Apr 26 09:34:36 BST 2012
Unique Job ID544235acab21f8f4

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3npeA_
Top template information
PDB header:oxidoreductase
Chain: A: PDB Molecule:9-cis-epoxycarotenoid dioxygenase 1, chloroplastic;
PDBTitle: structure of vp14 in complex with oxygen
Confidence and coverage
Confidence: 36.6% Coverage: 9%
19 residues ( 9% of your sequence) have been modelled with 36.6% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
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Warning: 57% of your sequence is predicted disordered. Disordered regions cannot be meaningfully predicted.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MFQRLSSLFFSTPSPPEDPDCPRAFVSEEDEVDGWLIIDLPDSYAAPPSPGAAPAPAGRP
Secondary structure 
SS confidence 
Disorder  ??
???????
???
???????????????????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  PPAPSLMDESWFVTPPACFTAEGPGLGPARLQSSPLEDLLIEHPSMSVYVTGSTIVLEPG
Secondary structure 
SS confidence 
Disorder  ?????????
?????????????????
???????????
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  SPSPLPDAALPDGDLSEGELTPARREPRAARHAAPLPARAALLEKAGQVRRLQRARQRAE
Secondary structure 
SS confidence 
Disorder  ????????????????????????????????
??
???
Disorder confidence 
 
   .........190.........200.........210.........220
Sequence  RHALSAKAVQRQNRARESRPRRSKNQSSFIYQPCQRQFNY
Secondary structure 
SS confidence 
Disorder  ?????
???????
????
?
????
Disorder confidence 
 

Confidence Key
High(9)                    Low (0)
?Disordered
Alpha helix
Beta strand

Domain analysis 

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

RankAligned region

PDB 3npe chain A

3D model

Region: 27 - 45
Aligned: 19
Modelled: 19
Confidence: 36.6%
Identity: 26%
PDB header:oxidoreductase
Chain: A: PDB Molecule:9-cis-epoxycarotenoid dioxygenase 1, chloroplastic;
PDBTitle: structure of vp14 in complex with oxygen

Phyre2

PDB 3r8k chain B

3D model

Region: 1 - 34
Aligned: 34
Modelled: 34
Confidence: 34.5%
Identity: 15%
PDB header:apoptosis
Chain: B: PDB Molecule:heme-binding protein 2;
PDBTitle: crystal structure of human soul protein (hexagonal form)

Phyre2

PDB 3fsn chain A

3D model

Region: 22 - 40
Aligned: 17
Modelled: 19
Confidence: 30.4%
Identity: 18%
PDB header:isomerase
Chain: A: PDB Molecule:retinal pigment epithelium-specific 65 kda protein;
PDBTitle: crystal structure of rpe65 at 2.14 angstrom resolution

Phyre2

PDB 2biw chain C

3D model

Region: 29 - 45
Aligned: 17
Modelled: 17
Confidence: 29.0%
Identity: 29%
PDB header:oxidoreductase
Chain: C: PDB Molecule:apocarotenoid-cleaving oxygenase;
PDBTitle: crystal structure of apocarotenoid cleavage oxygenase from2 synechocystis, native enzyme

Phyre2

PDB 2gov chain A domain 1

3D model

Region: 1 - 34
Aligned: 34
Modelled: 34
Confidence: 28.4%
Identity: 3%
Fold: Probable bacterial effector-binding domain
Superfamily: Probable bacterial effector-binding domain
Family: SOUL heme-binding protein

Phyre2

PDB 2o5a chain A domain 1

3D model

Region: 28 - 42
Aligned: 15
Modelled: 15
Confidence: 21.2%
Identity: 47%
Fold: Nucleotidyltransferase
Superfamily: Nucleotidyltransferase
Family: Iojap/YbeB-like

Phyre2

PDB 1sgv chain A domain 2

3D model

Region: 32 - 46
Aligned: 15
Modelled: 15
Confidence: 20.4%
Identity: 27%
Fold: Pseudouridine synthase
Superfamily: Pseudouridine synthase
Family: Pseudouridine synthase II TruB

Phyre2

PDB 3ups chain A

3D model

Region: 28 - 42
Aligned: 15
Modelled: 15
Confidence: 20.2%
Identity: 27%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:iojap-like protein;
PDBTitle: crystal structure of iojap-like protein from zymomonas mobilis

Phyre2

PDB 2id1 chain A domain 1

3D model

Region: 28 - 42
Aligned: 15
Modelled: 15
Confidence: 19.1%
Identity: 33%
Fold: Nucleotidyltransferase
Superfamily: Nucleotidyltransferase
Family: Iojap/YbeB-like

Phyre2

PDB 2cfu chain A domain 2

3D model

Region: 24 - 39
Aligned: 16
Modelled: 16
Confidence: 17.6%
Identity: 25%
Fold: Metallo-hydrolase/oxidoreductase
Superfamily: Metallo-hydrolase/oxidoreductase
Family: Alkylsulfatase-like

Phyre2

PDB 1ee8 chain A domain 2

3D model

Region: 31 - 77
Aligned: 22
Modelled: 22
Confidence: 17.3%
Identity: 23%
Fold: N-terminal domain of MutM-like DNA repair proteins
Superfamily: N-terminal domain of MutM-like DNA repair proteins
Family: N-terminal domain of MutM-like DNA repair proteins

Phyre2

PDB 1xk5 chain A

3D model

Region: 34 - 77
Aligned: 20
Modelled: 21
Confidence: 14.5%
Identity: 30%
PDB header:transport protein
Chain: A: PDB Molecule:snurportin-1;
PDBTitle: crystal structure of the m3g-cap-binding domain of2 snurportin1 in complex with a m3gpppg-cap dinucleotide

Phyre2

PDB 2cfu chain A

3D model

Region: 24 - 39
Aligned: 16
Modelled: 16
Confidence: 13.3%
Identity: 25%
PDB header:hydrolase
Chain: A: PDB Molecule:sdsa1;
PDBTitle: crystal structure of sdsa1, an alkylsulfatase from2 pseudomonas aeruginosa, in complex with 1-decane-sulfonic-3 acid.

Phyre2

PDB 2i82 chain D

3D model

Region: 31 - 56
Aligned: 26
Modelled: 26
Confidence: 12.8%
Identity: 12%
PDB header:lyase/rna
Chain: D: PDB Molecule:ribosomal large subunit pseudouridine synthase a;
PDBTitle: crystal structure of pseudouridine synthase rlua: indirect2 sequence readout through protein-induced rna structure

Phyre2

PDB 1oa8 chain A

3D model

Region: 76 - 102
Aligned: 23
Modelled: 27
Confidence: 12.7%
Identity: 30%
Fold: AXH domain
Superfamily: AXH domain
Family: AXH domain

Phyre2

PDB 1k82 chain D

3D model

Region: 32 - 77
Aligned: 21
Modelled: 21
Confidence: 11.9%
Identity: 38%
PDB header:hydrolase/dna
Chain: D: PDB Molecule:formamidopyrimidine-dna glycosylase;
PDBTitle: crystal structure of e.coli formamidopyrimidine-dna2 glycosylase (fpg) covalently trapped with dna

Phyre2

PDB 1q1o chain A

3D model

Region: 30 - 39
Aligned: 10
Modelled: 10
Confidence: 11.5%
Identity: 20%
Fold: beta-Grasp (ubiquitin-like)
Superfamily: CAD & PB1 domains
Family: PB1 domain

Phyre2

PDB 3km5 chain B

3D model

Region: 17 - 76
Aligned: 60
Modelled: 60
Confidence: 11.4%
Identity: 8%
PDB header:cell invasion
Chain: B: PDB Molecule:lysine specific cysteine protease;
PDBTitle: crystal structure analysis of the k2 cleaved adhesin domain of lys-2 gingipain (kgp)

Phyre2

PDB 3gjx chain E

3D model

Region: 37 - 77
Aligned: 18
Modelled: 18
Confidence: 11.1%
Identity: 28%
PDB header:protein transport
Chain: E: PDB Molecule:snurportin-1;
PDBTitle: crystal structure of the nuclear export complex crm1-2 snurportin1-rangtp

Phyre2

PDB 3ce8 chain A

3D model

Region: 96 - 107
Aligned: 12
Modelled: 12
Confidence: 10.5%
Identity: 42%
PDB header:unknown function
Chain: A: PDB Molecule:putative pii-like nitrogen regulatory protein;
PDBTitle: crystal structure of a duf3240 family protein (sbal_0098) from2 shewanella baltica os155 at 2.40 a resolution

Phyre2
1
c3npeA_
2
c3r8kB_
3
c3fsnA_
4
c2biwC_
5
d2gova1
6
d2o5aa1
7
d1sgva2
8
c3upsA_
9
d2id1a1
10
d2cfua2
11
d1ee8a2
12
c1xk5A_
13
c2cfuA_
14
c2i82D_
15
d1oa8a_
16
c1k82D_
17
d1q1oa_
18
c3km5B_
19
c3gjxE_
20
c3ce8A_
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3npeA_
36.6 26 PDB header:oxidoreductase
Chain: A: PDB Molecule:9-cis-epoxycarotenoid dioxygenase 1, chloroplastic;
PDBTitle: structure of vp14 in complex with oxygen
2c3r8kB_
34.5 15 PDB header:apoptosis
Chain: B: PDB Molecule:heme-binding protein 2;
PDBTitle: crystal structure of human soul protein (hexagonal form)
3c3fsnA_
30.4 18 PDB header:isomerase
Chain: A: PDB Molecule:retinal pigment epithelium-specific 65 kda protein;
PDBTitle: crystal structure of rpe65 at 2.14 angstrom resolution
4c2biwC_
29.0 29 PDB header:oxidoreductase
Chain: C: PDB Molecule:apocarotenoid-cleaving oxygenase;
PDBTitle: crystal structure of apocarotenoid cleavage oxygenase from2 synechocystis, native enzyme
5d2gova1
28.4 3 Fold:Probable bacterial effector-binding domain
Superfamily:Probable bacterial effector-binding domain
Family:SOUL heme-binding protein
6d2o5aa1
21.2 47 Fold:Nucleotidyltransferase
Superfamily:Nucleotidyltransferase
Family:Iojap/YbeB-like
7d1sgva2
20.4 27 Fold:Pseudouridine synthase
Superfamily:Pseudouridine synthase
Family:Pseudouridine synthase II TruB
8c3upsA_
20.2 27 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:iojap-like protein;
PDBTitle: crystal structure of iojap-like protein from zymomonas mobilis
9d2id1a1
19.1 33 Fold:Nucleotidyltransferase
Superfamily:Nucleotidyltransferase
Family:Iojap/YbeB-like
10d2cfua2
17.6 25 Fold:Metallo-hydrolase/oxidoreductase
Superfamily:Metallo-hydrolase/oxidoreductase
Family:Alkylsulfatase-like
11d1ee8a2
17.3 23 Fold:N-terminal domain of MutM-like DNA repair proteins
Superfamily:N-terminal domain of MutM-like DNA repair proteins
Family:N-terminal domain of MutM-like DNA repair proteins
12c1xk5A_
14.5 30 PDB header:transport protein
Chain: A: PDB Molecule:snurportin-1;
PDBTitle: crystal structure of the m3g-cap-binding domain of2 snurportin1 in complex with a m3gpppg-cap dinucleotide
13c2cfuA_
13.3 25 PDB header:hydrolase
Chain: A: PDB Molecule:sdsa1;
PDBTitle: crystal structure of sdsa1, an alkylsulfatase from2 pseudomonas aeruginosa, in complex with 1-decane-sulfonic-3 acid.
14c2i82D_
12.8 12 PDB header:lyase/rna
Chain: D: PDB Molecule:ribosomal large subunit pseudouridine synthase a;
PDBTitle: crystal structure of pseudouridine synthase rlua: indirect2 sequence readout through protein-induced rna structure
15d1oa8a_
12.7 30 Fold:AXH domain
Superfamily:AXH domain
Family:AXH domain
16c1k82D_
11.9 38 PDB header:hydrolase/dna
Chain: D: PDB Molecule:formamidopyrimidine-dna glycosylase;
PDBTitle: crystal structure of e.coli formamidopyrimidine-dna2 glycosylase (fpg) covalently trapped with dna
17d1q1oa_
11.5 20 Fold:beta-Grasp (ubiquitin-like)
Superfamily:CAD & PB1 domains
Family:PB1 domain
18c3km5B_
11.4 8 PDB header:cell invasion
Chain: B: PDB Molecule:lysine specific cysteine protease;
PDBTitle: crystal structure analysis of the k2 cleaved adhesin domain of lys-2 gingipain (kgp)
19c3gjxE_
11.1 28 PDB header:protein transport
Chain: E: PDB Molecule:snurportin-1;
PDBTitle: crystal structure of the nuclear export complex crm1-2 snurportin1-rangtp
20c3ce8A_
10.5 42 PDB header:unknown function
Chain: A: PDB Molecule:putative pii-like nitrogen regulatory protein;
PDBTitle: crystal structure of a duf3240 family protein (sbal_0098) from2 shewanella baltica os155 at 2.40 a resolution
21c3hxrA_
not modelled 10.1 19 PDB header:structural protein
Chain: A: PDB Molecule:nucleoporin nup120;
PDBTitle: nucleoporin nup120 from s.cerevisiae (aa 1-757)
22d2apoa2
not modelled 9.9 21 Fold:Pseudouridine synthase
Superfamily:Pseudouridine synthase
Family:Pseudouridine synthase II TruB
23d3proc2
not modelled 9.6 67 Fold:Alpha-lytic protease prodomain-like
Superfamily:Alpha-lytic protease prodomain
Family:Alpha-lytic protease prodomain
24d1sr4a_
not modelled 9.4 43 Fold:beta-Trefoil
Superfamily:Ricin B-like lectins
Family:Ricin B-like
25c1sr4A_
not modelled 9.4 43 PDB header:toxin
Chain: A: PDB Molecule:cytolethal distending toxin subunit a;
PDBTitle: crystal structure of the haemophilus ducreyi cytolethal2 distending toxin
26c2i7fB_
not modelled 9.3 50 PDB header:oxidoreductase
Chain: B: PDB Molecule:ferredoxin component of dioxygenase;
PDBTitle: sphingomonas yanoikuyae b1 ferredoxin
27d1p5dx4
not modelled 8.8 29 Fold:TBP-like
Superfamily:Phosphoglucomutase, C-terminal domain
Family:Phosphoglucomutase, C-terminal domain
28d1v9ka_
not modelled 8.7 24 Fold:Pseudouridine synthase
Superfamily:Pseudouridine synthase
Family:Pseudouridine synthase RsuA/RluD
29d1k3xa2
not modelled 8.2 18 Fold:N-terminal domain of MutM-like DNA repair proteins
Superfamily:N-terminal domain of MutM-like DNA repair proteins
Family:N-terminal domain of MutM-like DNA repair proteins
30c3i0uA_
not modelled 8.2 59 PDB header:lyase
Chain: A: PDB Molecule:phosphothreonine lyase ospf;
PDBTitle: structure of the type iii effector/phosphothreonine lyase ospf from2 shigella flexneri
31c1k8wA_
not modelled 8.0 29 PDB header:lyase/rna
Chain: A: PDB Molecule:trna pseudouridine synthase b;
PDBTitle: crystal structure of the e. coli pseudouridine synthase2 trub bound to a t stem-loop rna
32c3zv0D_
not modelled 7.7 44 PDB header:cell cycle
Chain: D: PDB Molecule:h/aca ribonucleoprotein complex subunit 4;
PDBTitle: structure of the shq1p-cbf5p complex
33d1aisb1
not modelled 7.6 43 Fold:Cyclin-like
Superfamily:Cyclin-like
Family:Transcription factor IIB (TFIIB), core domain
34d1xzwa1
not modelled 7.6 67 Fold:Immunoglobulin-like beta-sandwich
Superfamily:Purple acid phosphatase, N-terminal domain
Family:Purple acid phosphatase, N-terminal domain
35c3fkaD_
not modelled 7.1 17 PDB header:unknown function
Chain: D: PDB Molecule:uncharacterized ntf-2 like protein;
PDBTitle: crystal structure of a ntf-2 like protein of unknown function2 (spo1084) from silicibacter pomeroyi dss-3 at 1.69 a resolution
36d1usra_
not modelled 7.0 29 Fold:6-bladed beta-propeller
Superfamily:Sialidases
Family:Sialidases (neuraminidases)
37d1pqsa_
not modelled 6.9 22 Fold:beta-Grasp (ubiquitin-like)
Superfamily:CAD & PB1 domains
Family:PB1 domain
38c2fugC_
not modelled 6.9 44 PDB header:oxidoreductase
Chain: C: PDB Molecule:nadh-quinone oxidoreductase chain 3;
PDBTitle: crystal structure of the hydrophilic domain of respiratory complex i2 from thermus thermophilus
39c3dukD_
not modelled 6.7 12 PDB header:unknown function
Chain: D: PDB Molecule:ntf2-like protein of unknown function;
PDBTitle: crystal structure of a ntf2-like protein of unknown function2 (mfla_0564) from methylobacillus flagellatus kt at 2.200 a resolution
40c3s63B_
not modelled 6.5 25 PDB header:lipid binding protein
Chain: B: PDB Molecule:saposin-like protein;
PDBTitle: saposin-like protein na-slp-1
41d1wjfa_
not modelled 6.2 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:N-terminal Zn binding domain of HIV integrase
Family:N-terminal Zn binding domain of HIV integrase
42d2ey4a2
not modelled 6.1 18 Fold:Pseudouridine synthase
Superfamily:Pseudouridine synthase
Family:Pseudouridine synthase II TruB
43d1wfwa_
not modelled 5.9 19 Fold:SH3-like barrel
Superfamily:SH3-domain
Family:SH3-domain
44d1e0ea_
not modelled 5.9 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:N-terminal Zn binding domain of HIV integrase
Family:N-terminal Zn binding domain of HIV integrase
45d1r3ea2
not modelled 5.9 21 Fold:Pseudouridine synthase
Superfamily:Pseudouridine synthase
Family:Pseudouridine synthase II TruB
46c2eouA_
not modelled 5.8 100 PDB header:transcription
Chain: A: PDB Molecule:zinc finger protein 473;
PDBTitle: solution structure of the c2h2 type zinc finger (region 370-2 400) of human zinc finger protein 473
47d1d0qa_
not modelled 5.8 50 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:DNA primase zinc finger
48c3hefB_
not modelled 5.8 28 PDB header:viral protein
Chain: B: PDB Molecule:gene 1 protein;
PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit
49c2v0xB_
not modelled 5.7 22 PDB header:cell cycle
Chain: B: PDB Molecule:lamina-associated polypeptide 2 isoforms
PDBTitle: the dimerization domain of lap2alpha
50c2gu1A_
not modelled 5.7 36 PDB header:hydrolase
Chain: A: PDB Molecule:zinc peptidase;
PDBTitle: crystal structure of a zinc containing peptidase from2 vibrio cholerae
51c3m1hB_
not modelled 5.7 14 PDB header:cell invasion
Chain: B: PDB Molecule:lysine specific cysteine protease;
PDBTitle: crystal structure analysis of the k3 cleaved adhesin domain of lys-2 gingipain (kgp) from porphyromonas gingivalis w83
52c3cs5B_
not modelled 5.7 86 PDB header:photosynthesis
Chain: B: PDB Molecule:phycobilisome degradation protein nbla;
PDBTitle: nbla protein from synechococcus elongatus pcc 7942
53d1xe0a_
not modelled 5.6 32 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily:Nucleoplasmin-like core domain
Family:Nucleoplasmin-like core domain
54d1v3ea_
not modelled 5.5 29 Fold:6-bladed beta-propeller
Superfamily:Sialidases
Family:Sialidases (neuraminidases)
55d3d32a1
not modelled 5.5 24 Fold:beta-Grasp (ubiquitin-like)
Superfamily:Ubiquitin-like
Family:GABARAP-like
56c2jeuA_
not modelled 5.5 50 PDB header:transcription
Chain: A: PDB Molecule:regulatory protein e2;
PDBTitle: transcription activator structure reveals redox control of2 a replication initiation reaction
57d2f2fa1
not modelled 5.4 43 Fold:beta-Trefoil
Superfamily:Ricin B-like lectins
Family:Ricin B-like
58c2c2xB_
not modelled 5.4 26 PDB header:oxidoreductase
Chain: B: PDB Molecule:methylenetetrahydrofolate dehydrogenase-
PDBTitle: three dimensional structure of bifunctional2 methylenetetrahydrofolate dehydrogenase-cyclohydrolase3 from mycobacterium tuberculosis
59d3e9la1
not modelled 5.4 28 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Prp8 beta-finger domain-like
60d1wj6a_
not modelled 5.3 27 Fold:beta-Grasp (ubiquitin-like)
Superfamily:CAD & PB1 domains
Family:PB1 domain

Binding site prediction 

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If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite