Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	S	L	T	T	H	Y	R	R	S	Q	L	I	A	L	P	V	P	G	G	K	A	K	V	E	Y	C	Y	A	V	N	V	P	G	D	R	E	I	V	T	H	S	F	A	E	W	A	V	G	D	F	N	R	Q	K	E	T	V	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.
Sequence		C	D	K	L	T	A	G	S	K	I	T	T	E	C	P	S	E	S	F	V	G	S	R	K	H	N	G	L	S	T	S	A	K	V	M	S	M	N	A	S	A	R	S	N	S	F	V	V	N	S	G	K
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 3jwd chain A Region: 61 - 79 Aligned: 19 Modelled: 19 Confidence: 18.5% Identity: 63% PDB header:viral protein Chain: A: PDB Molecule:hiv-1 gp120 envelope glycoprotein; PDBTitle: structure of hiv-1 gp120 with gp41-interactive region: layered2 architecture and basis of conformational mobility Phyre2 PDB 3ngb chain I Region: 61 - 79 Aligned: 19 Modelled: 19 Confidence: 15.5% Identity: 58% PDB header:viral protein/immune system Chain: I: PDB Molecule:envelope glycoprotein gp160; PDBTitle: crystal structure of broadly and potently neutralizing antibody vrc012 in complex with hiv-1 gp120 Phyre2 PDB 1oe1 chain A domain 2 Region: 4 - 46 Aligned: 40 Modelled: 43 Confidence: 14.9% Identity: 18% Fold: Cupredoxin-like Superfamily: Cupredoxins Family: Multidomain cupredoxins Phyre2 PDB 4a02 chain A Region: 9 - 51 Aligned: 43 Modelled: 43 Confidence: 11.6% Identity: 19% PDB header:chitin binding protein Chain: A: PDB Molecule:chitin binding protein; PDBTitle: x-ray crystallographic structure of efcbm33a Phyre2 PDB 2bf1 chain A Region: 35 - 44 Aligned: 10 Modelled: 10 Confidence: 10.9% Identity: 30% PDB header:virus protein Chain: A: PDB Molecule:exterior membrane glycoprotein gp120; PDBTitle: structure of an unliganded and fully-glycosylated siv gp1202 envelope glycoprotein Phyre2 PDB 1tvc chain A domain 1 Region: 7 - 75 Aligned: 64 Modelled: 69 Confidence: 10.3% Identity: 20% Fold: Reductase/isomerase/elongation factor common domain Superfamily: Riboflavin synthase domain-like Family: Ferredoxin reductase FAD-binding domain-like Phyre2 PDB 2b4c chain G domain 1 Region: 4 - 44 Aligned: 27 Modelled: 27 Confidence: 8.1% Identity: 41% Fold: gp120 core Superfamily: gp120 core Family: gp120 core Phyre2 PDB 2fgy chain A Region: 16 - 38 Aligned: 20 Modelled: 23 Confidence: 6.7% Identity: 55% PDB header:lyase Chain: A: PDB Molecule:carboxysome shell polypeptide; PDBTitle: beta carbonic anhydrase from the carboxysomal shell of2 halothiobacillus neapolitanus (csosca) Phyre2 PDB 1gvh chain A domain 2 Region: 13 - 79 Aligned: 63 Modelled: 67 Confidence: 6.3% Identity: 14% Fold: Reductase/isomerase/elongation factor common domain Superfamily: Riboflavin synthase domain-like Family: Ferredoxin reductase FAD-binding domain-like Phyre2 PDB 1fqj chain C Region: 67 - 79 Aligned: 13 Modelled: 13 Confidence: 6.3% Identity: 54% PDB header:signaling protein Chain: C: PDB Molecule:retinal rod rhodopsin-sensitive cgmp 3',5'- PDBTitle: crystal structure of the heterotrimeric complex of the rgs2 domain of rgs9, the gamma subunit of phosphodiesterase and3 the gt/i1 chimera alpha subunit [(rgs9)-(pdegamma)-4 (gt/i1alpha)-(gdp)-(alf4-)-(mg2+)] Phyre2 PDB 1w07 chain A domain 3 Region: 54 - 112 Aligned: 52 Modelled: 59 Confidence: 5.4% Identity: 23% Fold: Acyl-CoA dehydrogenase NM domain-like Superfamily: Acyl-CoA dehydrogenase NM domain-like Family: acyl-CoA oxidase N-terminal domains Phyre2 PDB 2bem chain A Region: 9 - 51 Aligned: 43 Modelled: 43 Confidence: 5.0% Identity: 21% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: E-set domains of sugar-utilizing enzymes Phyre2 1 c3jwdA_ 2 c3ngbI_ 3 d1oe1a2 4 c4a02A_ 5 c2bf1A_ 6 d1tvca1 7 d2b4cg1 8 c2fgyA_ 9 d1gvha2 10 c1fqjC_ 11 d1w07a3 12 d2bema_

Detailed template information

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

1 c3jwdA_ 18.5 63 PDB header:viral protein Chain: A: PDB Molecule:hiv-1 gp120 envelope glycoprotein; PDBTitle: structure of hiv-1 gp120 with gp41-interactive region: layered2 architecture and basis of conformational mobility 2 c3ngbI_ 15.5 58 PDB header:viral protein/immune system Chain: I: PDB Molecule:envelope glycoprotein gp160; PDBTitle: crystal structure of broadly and potently neutralizing antibody vrc012 in complex with hiv-1 gp120 3 d1oe1a2 14.9 18 Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Multidomain cupredoxins 4 c4a02A_ 11.6 19 PDB header:chitin binding protein Chain: A: PDB Molecule:chitin binding protein; PDBTitle: x-ray crystallographic structure of efcbm33a 5 c2bf1A_ 10.9 30 PDB header:virus protein Chain: A: PDB Molecule:exterior membrane glycoprotein gp120; PDBTitle: structure of an unliganded and fully-glycosylated siv gp1202 envelope glycoprotein 6 d1tvca1 10.3 20 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Riboflavin synthase domain-like Family:Ferredoxin reductase FAD-binding domain-like 7 d2b4cg1 8.1 41 Fold:gp120 core Superfamily:gp120 core Family:gp120 core 8 c2fgyA_ 6.7 55 PDB header:lyase Chain: A: PDB Molecule:carboxysome shell polypeptide; PDBTitle: beta carbonic anhydrase from the carboxysomal shell of2 halothiobacillus neapolitanus (csosca) 9 d1gvha2 6.3 14 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Riboflavin synthase domain-like Family:Ferredoxin reductase FAD-binding domain-like 10 c1fqjC_ 6.3 54 PDB header:signaling protein Chain: C: PDB Molecule:retinal rod rhodopsin-sensitive cgmp 3',5'- PDBTitle: crystal structure of the heterotrimeric complex of the rgs2 domain of rgs9, the gamma subunit of phosphodiesterase and3 the gt/i1 chimera alpha subunit [(rgs9)-(pdegamma)-4 (gt/i1alpha)-(gdp)-(alf4-)-(mg2+)] 11 d1w07a3 5.4 23 Fold:Acyl-CoA dehydrogenase NM domain-like Superfamily:Acyl-CoA dehydrogenase NM domain-like Family:acyl-CoA oxidase N-terminal domains 12 d2bema_ 5.0 21 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:E-set domains of sugar-utilizing enzymes

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

Transmembrane helix prediction

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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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