Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	M	I	I	F	R	Y	L	I	I	I	I	L	S	V	Y	M	T	G	C	T	N	N	N	L	K	K	E	D	I	P	E	D	M	F	A	I	I	Y	G	S	D	S	I	K	K	Y	E	H	G	Q	M	E	L	T	K	N	I	N	S
Secondary structure
SS confidence
Disorder		?	?															?	?			?	?	?	?	?	?	?	?	?	?	?	?	?	?		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?						?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	C	I	E	A	L	V	F	L	S	E	E	D	P	E	K	Y	S	D	Y	I	N	D	Y	H	K	I	A	E	G	Y	R	F	L	D	D	N	R	T	F	M	N	K	D	S	I	E	L	L	V	R	G	L	N	V	K	K	D	V	L
Secondary structure
SS confidence
Disorder													?																											?	?																	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.
Sequence		C	S	R	V	K	F	E	S	F	Q	H	L	K	N	K	F	Q
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

Rank Aligned region

PDB 2wl8 chain D Region: 71 - 95 Aligned: 25 Modelled: 25 Confidence: 25.0% Identity: 12% PDB header:protein transport Chain: D: PDB Molecule:peroxisomal biogenesis factor 19; PDBTitle: x-ray crystal structure of pex19p Phyre2 PDB 1q2z chain A Region: 61 - 98 Aligned: 38 Modelled: 38 Confidence: 18.6% Identity: 11% Fold: alpha-alpha superhelix Superfamily: C-terminal domain of Ku80 Family: C-terminal domain of Ku80 Phyre2 PDB 2jee chain A Region: 104 - 114 Aligned: 11 Modelled: 11 Confidence: 15.0% Identity: 36% PDB header:cell cycle Chain: A: PDB Molecule:yiiu; PDBTitle: xray structure of e. coli yiiu Phyre2 PDB 1faf chain A Region: 68 - 98 Aligned: 30 Modelled: 31 Confidence: 14.6% Identity: 7% Fold: Long alpha-hairpin Superfamily: Chaperone J-domain Family: Chaperone J-domain Phyre2 PDB 2pi8 chain A domain 1 Region: 59 - 89 Aligned: 31 Modelled: 31 Confidence: 13.5% Identity: 19% Fold: Double psi beta-barrel Superfamily: Barwin-like endoglucanases Family: MLTA-like Phyre2 PDB 2cwo chain D Region: 48 - 121 Aligned: 67 Modelled: 74 Confidence: 12.4% Identity: 19% PDB header:rna binding protein Chain: D: PDB Molecule:rna silencing suppressor; PDBTitle: crystal structure of rna silencing suppressor p21 from beet yellows2 virus Phyre2 PDB 3dve chain B Region: 90 - 102 Aligned: 13 Modelled: 13 Confidence: 11.0% Identity: 23% PDB header:membrane protein Chain: B: PDB Molecule:voltage-dependent n-type calcium channel subunit alpha-1b; PDBTitle: crystal structure of ca2+/cam-cav2.2 iq domain complex Phyre2 PDB 2pjw chain V Region: 76 - 96 Aligned: 21 Modelled: 21 Confidence: 8.7% Identity: 33% PDB header:endocytosis/exocytosis Chain: V: PDB Molecule:vacuolar protein sorting-associated protein 27; PDBTitle: the vps27/hse1 complex is a gat domain-based scaffold for2 ubiquitin-dependent sorting Phyre2 PDB 1k3v chain A Region: 72 - 87 Aligned: 16 Modelled: 16 Confidence: 8.3% Identity: 19% PDB header:virus Chain: A: PDB Molecule:capsid protein vp2; PDBTitle: porcine parvovirus capsid Phyre2 PDB 1k3v chain A Region: 72 - 87 Aligned: 16 Modelled: 16 Confidence: 8.3% Identity: 19% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: ssDNA viruses Family: Parvoviridae-like VP Phyre2 PDB 1c8d chain A Region: 72 - 87 Aligned: 16 Modelled: 16 Confidence: 7.7% Identity: 13% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: ssDNA viruses Family: Parvoviridae-like VP Phyre2 PDB 2wx4 chain C Region: 16 - 23 Aligned: 8 Modelled: 8 Confidence: 7.4% Identity: 50% PDB header:structural protein Chain: C: PDB Molecule:decapping protein 1; PDBTitle: asymmetric trimer of the drosophila melanogaster dcp1 c-2 terminal domain Phyre2 PDB 1kl1 chain A Region: 66 - 116 Aligned: 50 Modelled: 51 Confidence: 7.1% Identity: 16% Fold: PLP-dependent transferase-like Superfamily: PLP-dependent transferases Family: GABA-aminotransferase-like Phyre2 PDB 2nw8 chain A domain 1 Region: 63 - 82 Aligned: 20 Modelled: 20 Confidence: 7.1% Identity: 20% Fold: Indolic compounds 2,3-dioxygenase-like Superfamily: Indolic compounds 2,3-dioxygenase-like Family: Bacterial tryptophan 2,3-dioxygenase Phyre2 PDB 2nox chain P Region: 55 - 82 Aligned: 28 Modelled: 28 Confidence: 6.9% Identity: 21% PDB header:oxidoreductase Chain: P: PDB Molecule:tryptophan 2,3-dioxygenase; PDBTitle: crystal structure of tryptophan 2,3-dioxygenase from ralstonia2 metallidurans Phyre2 PDB 2elb chain A domain 1 Region: 25 - 118 Aligned: 94 Modelled: 94 Confidence: 6.8% Identity: 7% Fold: BAR/IMD domain-like Superfamily: BAR/IMD domain-like Family: BAR domain Phyre2 PDB 1s58 chain A Region: 72 - 87 Aligned: 16 Modelled: 16 Confidence: 6.3% Identity: 25% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: ssDNA viruses Family: Parvoviridae-like VP Phyre2 PDB 3dvj chain B Region: 90 - 99 Aligned: 10 Modelled: 10 Confidence: 5.8% Identity: 30% PDB header:membrane protein Chain: B: PDB Molecule:voltage-dependent n-type calcium channel subunit alpha-1b; PDBTitle: crystal structure of ca2+/cam-cav2.2 iq domain (without cloning2 artifact, hm to tv) complex Phyre2 PDB 2nw7 chain C Region: 63 - 82 Aligned: 20 Modelled: 20 Confidence: 5.7% Identity: 20% PDB header:oxidoreductase Chain: C: PDB Molecule:tryptophan 2,3-dioxygenase; PDBTitle: crystal structure of tryptophan 2,3-dioxygenase (tdo) from2 xanthomonas campestris in complex with ferric heme.3 northeast structural genomics target xcr13 Phyre2 PDB 1fpv chain A Region: 72 - 87 Aligned: 16 Modelled: 16 Confidence: 5.7% Identity: 13% PDB header:virus Chain: A: PDB Molecule:feline panleukopenia virus (strain b) viral PDBTitle: structure determination of feline panleukopenia virus empty2 particles Phyre2 1 c2wl8D_ 2 d1q2za_ 3 c2jeeA_ 4 d1fafa_ 5 d2pi8a1 6 c2cwoD_ 7 c3dveB_ 8 c2pjwV_ 9 c1k3vA_ 10 d1k3va_ 11 d1c8da_ 12 c2wx4C_ 13 d1kl1a_ 14 d2nw8a1 15 c2noxP_ 16 d2elba1 17 d1s58a_ 18 c3dvjB_ 19 c2nw7C_ 20 c1fpvA_ 21 22 23

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 c2wl8D_ 25.0 12 PDB header:protein transport Chain: D: PDB Molecule:peroxisomal biogenesis factor 19; PDBTitle: x-ray crystal structure of pex19p 2 d1q2za_ 18.6 11 Fold:alpha-alpha superhelix Superfamily:C-terminal domain of Ku80 Family:C-terminal domain of Ku80 3 c2jeeA_ 15.0 36 PDB header:cell cycle Chain: A: PDB Molecule:yiiu; PDBTitle: xray structure of e. coli yiiu 4 d1fafa_ 14.6 7 Fold:Long alpha-hairpin Superfamily:Chaperone J-domain Family:Chaperone J-domain 5 d2pi8a1 13.5 19 Fold:Double psi beta-barrel Superfamily:Barwin-like endoglucanases Family:MLTA-like 6 c2cwoD_ 12.4 19 PDB header:rna binding protein Chain: D: PDB Molecule:rna silencing suppressor; PDBTitle: crystal structure of rna silencing suppressor p21 from beet yellows2 virus 7 c3dveB_ 11.0 23 PDB header:membrane protein Chain: B: PDB Molecule:voltage-dependent n-type calcium channel subunit alpha-1b; PDBTitle: crystal structure of ca2+/cam-cav2.2 iq domain complex 8 c2pjwV_ 8.7 33 PDB header:endocytosis/exocytosis Chain: V: PDB Molecule:vacuolar protein sorting-associated protein 27; PDBTitle: the vps27/hse1 complex is a gat domain-based scaffold for2 ubiquitin-dependent sorting 9 c1k3vA_ 8.3 19 PDB header:virus Chain: A: PDB Molecule:capsid protein vp2; PDBTitle: porcine parvovirus capsid 10 d1k3va_ 8.3 19 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:ssDNA viruses Family:Parvoviridae-like VP 11 d1c8da_ 7.7 13 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:ssDNA viruses Family:Parvoviridae-like VP 12 c2wx4C_ 7.4 50 PDB header:structural protein Chain: C: PDB Molecule:decapping protein 1; PDBTitle: asymmetric trimer of the drosophila melanogaster dcp1 c-2 terminal domain 13 d1kl1a_ 7.1 16 Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:GABA-aminotransferase-like 14 d2nw8a1 7.1 20 Fold:Indolic compounds 2,3-dioxygenase-like Superfamily:Indolic compounds 2,3-dioxygenase-like Family:Bacterial tryptophan 2,3-dioxygenase 15 c2noxP_ 6.9 21 PDB header:oxidoreductase Chain: P: PDB Molecule:tryptophan 2,3-dioxygenase; PDBTitle: crystal structure of tryptophan 2,3-dioxygenase from ralstonia2 metallidurans 16 d2elba1 6.8 7 Fold:BAR/IMD domain-like Superfamily:BAR/IMD domain-like Family:BAR domain 17 d1s58a_ 6.3 25 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:ssDNA viruses Family:Parvoviridae-like VP 18 c3dvjB_ 5.8 30 PDB header:membrane protein Chain: B: PDB Molecule:voltage-dependent n-type calcium channel subunit alpha-1b; PDBTitle: crystal structure of ca2+/cam-cav2.2 iq domain (without cloning2 artifact, hm to tv) complex 19 c2nw7C_ 5.7 20 PDB header:oxidoreductase Chain: C: PDB Molecule:tryptophan 2,3-dioxygenase; PDBTitle: crystal structure of tryptophan 2,3-dioxygenase (tdo) from2 xanthomonas campestris in complex with ferric heme.3 northeast structural genomics target xcr13 20 c1fpvA_ 5.7 13 PDB header:virus Chain: A: PDB Molecule:feline panleukopenia virus (strain b) viral PDBTitle: structure determination of feline panleukopenia virus empty2 particles 21 d2ae0x1 not modelled 5.4 19 Fold:Double psi beta-barrel Superfamily:Barwin-like endoglucanases Family:MLTA-like 22 c3nttA_ not modelled 5.3 25 PDB header:virus Chain: A: PDB Molecule:capsid protein; PDBTitle: structural insights of adeno-associated virus 5. a gene therapy vector2 for cystic fibrosis 23 c3kieF_ not modelled 5.2 19 PDB header:virus Chain: F: PDB Molecule:capsid protein vp1; PDBTitle: crystal structure of adeno-associated virus serotype 3b

Binding site prediction

Due to computational demand, binding site predictions are not run for batch jobs

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

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Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group Imperial College London Lawrence Kelley, Benjamin Jefferys Disclaimer Terms and Conditions	Component software Template detection: HHpred 1.51 Secondary structure prediction: Psi-pred 2.5 Disorder prediction: Disopred 2.4 Transmembrane prediction: Memsat_SVM Multi-template modelling and ab initio: Poing 1.0