Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	V	A	D	P	T	T	T	L	Q	V	K	N	T	G	S	L	S	V	N	R	Y	G	W	I	N	I	W	M	A	I	L	G	Q	F	F	T	L	F	P	L	F	F	E	S	C	L	I	L	L	K	T	W	L	E	I	F	P	D	N
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?					?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.
Sequence		A	G	I	L	R	I	Y	L	L	Q	F	S	A	I	V	G	Y	K	T	R	R	A	A
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 2y94 chain C Region: 42 - 51 Aligned: 10 Modelled: 10 Confidence: 13.6% Identity: 60% PDB header:transferase Chain: C: PDB Molecule:5'-amp-activated protein kinase catalytic subunit alpha-1; PDBTitle: structure of an active form of mammalian ampk Phyre2 PDB 1ejx chain B Region: 5 - 19 Aligned: 15 Modelled: 15 Confidence: 12.3% Identity: 27% Fold: beta-clip Superfamily: Urease, beta-subunit Family: Urease, beta-subunit Phyre2 PDB 4ubp chain B Region: 5 - 19 Aligned: 15 Modelled: 15 Confidence: 12.0% Identity: 40% Fold: beta-clip Superfamily: Urease, beta-subunit Family: Urease, beta-subunit Phyre2 PDB 3qb2 chain A Region: 38 - 67 Aligned: 30 Modelled: 30 Confidence: 11.4% Identity: 23% PDB header:hydrolase inhibitor Chain: A: PDB Molecule:immunity factor for spn; PDBTitle: the crystal structure of immunity factor for spn (ifs) Phyre2 PDB 1e9y chain A domain 1 Region: 5 - 19 Aligned: 15 Modelled: 15 Confidence: 10.3% Identity: 33% Fold: beta-clip Superfamily: Urease, beta-subunit Family: Urease, beta-subunit Phyre2 PDB 3izx chain E Region: 59 - 83 Aligned: 25 Modelled: 25 Confidence: 9.6% Identity: 28% PDB header:virus Chain: E: PDB Molecule:viral structural protein 5; PDBTitle: 3.1 angstrom cryoem structure of cytoplasmic polyhedrosis virus Phyre2 PDB 2i5n chain H domain 2 Region: 24 - 32 Aligned: 9 Modelled: 9 Confidence: 9.3% Identity: 44% Fold: Single transmembrane helix Superfamily: Photosystem II reaction centre subunit H, transmembrane region Family: Photosystem II reaction centre subunit H, transmembrane region Phyre2 PDB 3iz3 chain D Region: 59 - 83 Aligned: 25 Modelled: 25 Confidence: 9.1% Identity: 28% PDB header:virus Chain: D: PDB Molecule:viral structural protein 5; PDBTitle: cryoem structure of cytoplasmic polyhedrosis virus Phyre2 PDB 3pnt chain D Region: 38 - 67 Aligned: 30 Modelled: 30 Confidence: 8.4% Identity: 23% PDB header:hydrolase/hydrolase inhibitor Chain: D: PDB Molecule:immunity factor for spn; PDBTitle: crystal structure of the streptococcus pyogenes nad+ glycohydrolase2 spn in complex with ifs, the immunity factor for spn Phyre2 PDB 2xb0 chain X Region: 18 - 34 Aligned: 17 Modelled: 17 Confidence: 8.1% Identity: 12% PDB header:hydrolase Chain: X: PDB Molecule:chromo domain-containing protein 1; PDBTitle: dna-binding domain from saccharomyces cerevisiae chromatin-2 remodelling protein chd1 Phyre2 PDB 2e9x chain F Region: 40 - 66 Aligned: 27 Modelled: 27 Confidence: 6.1% Identity: 22% PDB header:replication Chain: F: PDB Molecule:dna replication complex gins protein psf2; PDBTitle: the crystal structure of human gins core complex Phyre2 PDB 3qga chain D Region: 5 - 19 Aligned: 15 Modelled: 15 Confidence: 5.9% Identity: 40% PDB header:hydrolase Chain: D: PDB Molecule:fusion of urease beta and gamma subunits; PDBTitle: 3.0 a model of iron containing urease urea2b2 from helicobacter2 mustelae Phyre2 PDB 1l3a chain C Region: 8 - 25 Aligned: 18 Modelled: 18 Confidence: 5.7% Identity: 17% Fold: ssDNA-binding transcriptional regulator domain Superfamily: ssDNA-binding transcriptional regulator domain Family: Plant transcriptional regulator PBF-2 Phyre2 1 c2y94C_ 2 d1ejxb_ 3 d4ubpb_ 4 c3qb2A_ 5 d1e9ya1 6 c3izxE_ 7 d2i5nh2 8 c3iz3D_ 9 c3pntD_ 10 c2xb0X_ 11 c2e9xF_ 12 c3qgaD_ 13 d1l3ac_

Detailed template information

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

1 c2y94C_ 13.6 60 PDB header:transferase Chain: C: PDB Molecule:5'-amp-activated protein kinase catalytic subunit alpha-1; PDBTitle: structure of an active form of mammalian ampk 2 d1ejxb_ 12.3 27 Fold:beta-clip Superfamily:Urease, beta-subunit Family:Urease, beta-subunit 3 d4ubpb_ 12.0 40 Fold:beta-clip Superfamily:Urease, beta-subunit Family:Urease, beta-subunit 4 c3qb2A_ 11.4 23 PDB header:hydrolase inhibitor Chain: A: PDB Molecule:immunity factor for spn; PDBTitle: the crystal structure of immunity factor for spn (ifs) 5 d1e9ya1 10.3 33 Fold:beta-clip Superfamily:Urease, beta-subunit Family:Urease, beta-subunit 6 c3izxE_ 9.6 28 PDB header:virus Chain: E: PDB Molecule:viral structural protein 5; PDBTitle: 3.1 angstrom cryoem structure of cytoplasmic polyhedrosis virus 7 d2i5nh2 9.3 44 Fold:Single transmembrane helix Superfamily:Photosystem II reaction centre subunit H, transmembrane region Family:Photosystem II reaction centre subunit H, transmembrane region 8 c3iz3D_ 9.1 28 PDB header:virus Chain: D: PDB Molecule:viral structural protein 5; PDBTitle: cryoem structure of cytoplasmic polyhedrosis virus 9 c3pntD_ 8.4 23 PDB header:hydrolase/hydrolase inhibitor Chain: D: PDB Molecule:immunity factor for spn; PDBTitle: crystal structure of the streptococcus pyogenes nad+ glycohydrolase2 spn in complex with ifs, the immunity factor for spn 10 c2xb0X_ 8.1 12 PDB header:hydrolase Chain: X: PDB Molecule:chromo domain-containing protein 1; PDBTitle: dna-binding domain from saccharomyces cerevisiae chromatin-2 remodelling protein chd1 11 c2e9xF_ 6.1 22 PDB header:replication Chain: F: PDB Molecule:dna replication complex gins protein psf2; PDBTitle: the crystal structure of human gins core complex 12 c3qgaD_ 5.9 40 PDB header:hydrolase Chain: D: PDB Molecule:fusion of urease beta and gamma subunits; PDBTitle: 3.0 a model of iron containing urease urea2b2 from helicobacter2 mustelae 13 d1l3ac_ 5.7 17 Fold:ssDNA-binding transcriptional regulator domain Superfamily:ssDNA-binding transcriptional regulator domain Family:Plant transcriptional regulator PBF-2

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