Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	G	I	L	S	W	I	I	F	G	L	I	A	G	I	L	A	K	W	I	M	P	G	K	D	G	G	G	F	F	M	T	I	L	L	G	I	V	G	A	V	V	G	G	W	I	S	T	L	F	G	F	G	K	V	D	G	F	N	F
Secondary structure
SS confidence
Disorder		?	?																																																					?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.
Sequence		G	S	F	V	V	A	V	I	G	A	I	V	V	L	F	I	Y	R	K	I	K	S
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 1l7v chain A Region: 9 - 79 Aligned: 68 Modelled: 71 Confidence: 92.7% Identity: 16% Fold: ABC transporter involved in vitamin B12 uptake, BtuC Superfamily: ABC transporter involved in vitamin B12 uptake, BtuC Family: ABC transporter involved in vitamin B12 uptake, BtuC Phyre2 PDB 2nq2 chain A Region: 9 - 80 Aligned: 68 Modelled: 72 Confidence: 88.7% Identity: 19% PDB header:metal transport Chain: A: PDB Molecule:hypothetical abc transporter permease protein PDBTitle: an inward-facing conformation of a putative metal-chelate2 type abc transporter. Phyre2 PDB 2ap8 chain A Region: 34 - 46 Aligned: 13 Modelled: 13 Confidence: 19.3% Identity: 46% PDB header:antibiotic Chain: A: PDB Molecule:bombinin h4; PDBTitle: solution structure of bombinin h4 in dpc micelles Phyre2 PDB 2ap7 chain A Region: 34 - 46 Aligned: 13 Modelled: 13 Confidence: 19.1% Identity: 46% PDB header:antibiotic Chain: A: PDB Molecule:bombinin h2; PDBTitle: solution structure of bombinin h2 in dpc micelles Phyre2 PDB 1xoo chain A Region: 8 - 18 Aligned: 11 Modelled: 11 Confidence: 12.0% Identity: 45% PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin; PDBTitle: nmr structure of g1s mutant of influenza hemagglutinin2 fusion peptide in dpc micelles at ph 5 Phyre2 PDB 2l4g chain A Region: 8 - 19 Aligned: 12 Modelled: 12 Confidence: 11.6% Identity: 42% PDB header:viral protein Chain: A: PDB Molecule:haemagglutinin; PDBTitle: influenza haemagglutinin fusion peptide mutant g13a Phyre2 PDB 2kxa chain A Region: 8 - 16 Aligned: 9 Modelled: 9 Confidence: 11.2% Identity: 56% PDB header:viral protein, immune system Chain: A: PDB Molecule:haemagglutinin ha2 chain peptide; PDBTitle: the hemagglutinin fusion peptide (h1 subtype) at ph 7.4 Phyre2 PDB 1ibo chain A Region: 8 - 18 Aligned: 11 Modelled: 11 Confidence: 11.0% Identity: 45% PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin ha2 chain peptide; PDBTitle: nmr structure of hemagglutinin fusion peptide in dpc2 micelles at ph 7.4 Phyre2 PDB 1ibn chain A Region: 8 - 18 Aligned: 11 Modelled: 11 Confidence: 11.0% Identity: 45% PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin ha2 chain peptide; PDBTitle: nmr structure of hemagglutinin fusion peptide in dpc2 micelles at ph 5 Phyre2 PDB 1xop chain A Region: 8 - 18 Aligned: 11 Modelled: 11 Confidence: 10.9% Identity: 45% PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin; PDBTitle: nmr structure of g1v mutant of influenza hemagglutinin2 fusion peptide in dpc micelles at ph 5 Phyre2 PDB 2jrd chain A Region: 8 - 18 Aligned: 11 Modelled: 11 Confidence: 7.0% Identity: 45% PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin; PDBTitle: influenza hemagglutinin fusion domain mutant f9a Phyre2 PDB 3c1i chain A Region: 1 - 82 Aligned: 82 Modelled: 82 Confidence: 6.5% Identity: 23% PDB header:transport protein Chain: A: PDB Molecule:ammonia channel; PDBTitle: substrate binding, deprotonation and selectivity at the2 periplasmic entrance of the e. coli ammonia channel amtb Phyre2 PDB 2kpe chain A Region: 4 - 21 Aligned: 18 Modelled: 18 Confidence: 6.3% Identity: 33% PDB header:membrane protein Chain: A: PDB Molecule:glycophorin-a; PDBTitle: refined structure of glycophorin a transmembrane segment dimer in dpc2 micelles Phyre2 PDB 2kpe chain B Region: 4 - 21 Aligned: 18 Modelled: 18 Confidence: 6.3% Identity: 33% PDB header:membrane protein Chain: B: PDB Molecule:glycophorin-a; PDBTitle: refined structure of glycophorin a transmembrane segment dimer in dpc2 micelles Phyre2 1 d1l7va_ 2 c2nq2A_ 3 c2ap8A_ 4 c2ap7A_ 5 c1xooA_ 6 c2l4gA_ 7 c2kxaA_ 8 c1iboA_ 9 c1ibnA_ 10 c1xopA_ 11 c2jrdA_ 12 c3c1iA_ 13 c2kpeA_ 14 c2kpeB_

Detailed template information

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

1 d1l7va_ 92.7 16 Fold:ABC transporter involved in vitamin B12 uptake, BtuC Superfamily:ABC transporter involved in vitamin B12 uptake, BtuC Family:ABC transporter involved in vitamin B12 uptake, BtuC 2 c2nq2A_ 88.7 19 PDB header:metal transport Chain: A: PDB Molecule:hypothetical abc transporter permease protein PDBTitle: an inward-facing conformation of a putative metal-chelate2 type abc transporter. 3 c2ap8A_ 19.3 46 PDB header:antibiotic Chain: A: PDB Molecule:bombinin h4; PDBTitle: solution structure of bombinin h4 in dpc micelles 4 c2ap7A_ 19.1 46 PDB header:antibiotic Chain: A: PDB Molecule:bombinin h2; PDBTitle: solution structure of bombinin h2 in dpc micelles 5 c1xooA_ 12.0 45 PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin; PDBTitle: nmr structure of g1s mutant of influenza hemagglutinin2 fusion peptide in dpc micelles at ph 5 6 c2l4gA_ 11.6 42 PDB header:viral protein Chain: A: PDB Molecule:haemagglutinin; PDBTitle: influenza haemagglutinin fusion peptide mutant g13a 7 c2kxaA_ 11.2 56 PDB header:viral protein, immune system Chain: A: PDB Molecule:haemagglutinin ha2 chain peptide; PDBTitle: the hemagglutinin fusion peptide (h1 subtype) at ph 7.4 8 c1iboA_ 11.0 45 PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin ha2 chain peptide; PDBTitle: nmr structure of hemagglutinin fusion peptide in dpc2 micelles at ph 7.4 9 c1ibnA_ 11.0 45 PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin ha2 chain peptide; PDBTitle: nmr structure of hemagglutinin fusion peptide in dpc2 micelles at ph 5 10 c1xopA_ 10.9 45 PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin; PDBTitle: nmr structure of g1v mutant of influenza hemagglutinin2 fusion peptide in dpc micelles at ph 5 11 c2jrdA_ 7.0 45 PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin; PDBTitle: influenza hemagglutinin fusion domain mutant f9a 12 c3c1iA_ 6.5 23 PDB header:transport protein Chain: A: PDB Molecule:ammonia channel; PDBTitle: substrate binding, deprotonation and selectivity at the2 periplasmic entrance of the e. coli ammonia channel amtb 13 c2kpeA_ 6.3 33 PDB header:membrane protein Chain: A: PDB Molecule:glycophorin-a; PDBTitle: refined structure of glycophorin a transmembrane segment dimer in dpc2 micelles 14 c2kpeB_ 6.3 33 PDB header:membrane protein Chain: B: PDB Molecule:glycophorin-a; PDBTitle: refined structure of glycophorin a transmembrane segment dimer in dpc2 micelles

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