Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	I	L	F	V	C	S	L	L	L	L	S	G	C	S	H	M	A	N	D	S	W	S	G	Q	D	K	A	Q	H	F	I	A	S	A	M	L	S	A	A	G	N	E	Y	S	Q	H	Q	G	M	S	R	D	R	S	A	M	F	G
Secondary structure
SS confidence
Disorder		?	?																		?	?	?	?	?																									?				?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.
Sequence		L	M	F	S	V	S	L	G	A	S	K	E	L	W	D	S	R	P	E	G	S	G	W	S	W	K	D	L	A	W	D	V	A	G	A	S	T	G	Y	T	V	W	Q	L	T	R	H
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 3bvh chain E Region: 12 - 33 Aligned: 22 Modelled: 22 Confidence: 9.1% Identity: 18% PDB header:blood clotting Chain: E: PDB Molecule:fibrinogen beta chain; PDBTitle: crystal structure of recombinant gammad364a fibrinogen fragment d with2 the peptide ligand gly-pro-arg-pro-amide Phyre2 PDB 2rqx chain A Region: 14 - 28 Aligned: 15 Modelled: 15 Confidence: 8.4% Identity: 27% PDB header:signaling protein Chain: A: PDB Molecule:polymyxin b resistance protein; PDBTitle: solution nmr structure of pmrd from klebsiella pneumoniae Phyre2 PDB 2ozl chain B domain 1 Region: 67 - 101 Aligned: 35 Modelled: 35 Confidence: 7.0% Identity: 17% Fold: Thiamin diphosphate-binding fold (THDP-binding) Superfamily: Thiamin diphosphate-binding fold (THDP-binding) Family: Branched-chain alpha-keto acid dehydrogenase Pyr module Phyre2 PDB 1qs0 chain B domain 1 Region: 67 - 101 Aligned: 35 Modelled: 32 Confidence: 6.5% Identity: 9% Fold: Thiamin diphosphate-binding fold (THDP-binding) Superfamily: Thiamin diphosphate-binding fold (THDP-binding) Family: Branched-chain alpha-keto acid dehydrogenase Pyr module Phyre2 PDB 2bjo chain A Region: 79 - 107 Aligned: 29 Modelled: 29 Confidence: 6.3% Identity: 14% PDB header:oxidoreductase Chain: A: PDB Molecule:organic hydroperoxide resistance protein ohrb; PDBTitle: crystal structure of the organic hydroperoxide resistance2 protein ohrb of bacillus subtilis Phyre2 PDB 2hpc chain H Region: 12 - 33 Aligned: 22 Modelled: 22 Confidence: 5.7% Identity: 18% PDB header:blood clotting Chain: H: PDB Molecule:fibrinogen beta chain; PDBTitle: crystal structure of fragment d from human fibrinogen complexed with2 gly-pro-arg-pro-amide. Phyre2 PDB 2j61 chain B Region: 14 - 33 Aligned: 20 Modelled: 20 Confidence: 5.4% Identity: 20% PDB header:lectin Chain: B: PDB Molecule:ficolin-2; PDBTitle: l-ficolin complexed to n-acetylglucosamine (forme c) Phyre2 1 c3bvhE_ 2 c2rqxA_ 3 d2ozlb1 4 d1qs0b1 5 c2bjoA_ 6 c2hpcH_ 7 c2j61B_

Detailed template information

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

1 c3bvhE_ 9.1 18 PDB header:blood clotting Chain: E: PDB Molecule:fibrinogen beta chain; PDBTitle: crystal structure of recombinant gammad364a fibrinogen fragment d with2 the peptide ligand gly-pro-arg-pro-amide 2 c2rqxA_ 8.4 27 PDB header:signaling protein Chain: A: PDB Molecule:polymyxin b resistance protein; PDBTitle: solution nmr structure of pmrd from klebsiella pneumoniae 3 d2ozlb1 7.0 17 Fold:Thiamin diphosphate-binding fold (THDP-binding) Superfamily:Thiamin diphosphate-binding fold (THDP-binding) Family:Branched-chain alpha-keto acid dehydrogenase Pyr module 4 d1qs0b1 6.5 9 Fold:Thiamin diphosphate-binding fold (THDP-binding) Superfamily:Thiamin diphosphate-binding fold (THDP-binding) Family:Branched-chain alpha-keto acid dehydrogenase Pyr module 5 c2bjoA_ 6.3 14 PDB header:oxidoreductase Chain: A: PDB Molecule:organic hydroperoxide resistance protein ohrb; PDBTitle: crystal structure of the organic hydroperoxide resistance2 protein ohrb of bacillus subtilis 6 c2hpcH_ 5.7 18 PDB header:blood clotting Chain: H: PDB Molecule:fibrinogen beta chain; PDBTitle: crystal structure of fragment d from human fibrinogen complexed with2 gly-pro-arg-pro-amide. 7 c2j61B_ 5.4 20 PDB header:lectin Chain: B: PDB Molecule:ficolin-2; PDBTitle: l-ficolin complexed to n-acetylglucosamine (forme c)

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

---

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