Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	T	L	T	T	G	V	V	L	L	R	W	Q	L	L	S	A	V	M	M	F	L	A	S	T	L	N	I	R	F	R	R	S	D	Y	V	G	L	A	V	I	S	S	G	L	G	V	V	S	A	C	W	F	A	M	G	L	L	G
Secondary structure
SS confidence
Disorder		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.
Sequence		I	T	M	A	D	I	T	A	I	W	H	N	I	E	S	V	M	I	E	E	M	N	Q	T	P	P	Q	W	P	M	I	L	T
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 1szi chain A Region: 57 - 88 Aligned: 32 Modelled: 32 Confidence: 63.0% Identity: 22% Fold: Four-helical up-and-down bundle Superfamily: Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain Family: Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain Phyre2 PDB 2cj9 chain A Region: 22 - 89 Aligned: 44 Modelled: 48 Confidence: 12.5% Identity: 30% PDB header:ligase Chain: A: PDB Molecule:seryl-trna synthetase; PDBTitle: crystal structure of methanosarcina barkeri seryl-trna2 synthetase complexed with an analog of seryladenylate Phyre2 PDB 1tdp chain A Region: 71 - 83 Aligned: 13 Modelled: 13 Confidence: 12.5% Identity: 31% Fold: Bromodomain-like Superfamily: Bacteriocin immunity protein-like Family: Carnobacteriocin B2 immunity protein Phyre2 PDB 3mko chain A Region: 58 - 88 Aligned: 22 Modelled: 30 Confidence: 9.3% Identity: 23% PDB header:viral protein Chain: A: PDB Molecule:glycoprotein c; PDBTitle: crystal structure of the lymphocytic choriomeningitis virus membrane2 fusion glycoprotein gp2 in its postfusion conformation Phyre2 PDB 2qnl chain A Region: 62 - 88 Aligned: 27 Modelled: 27 Confidence: 9.1% Identity: 22% PDB header:signaling protein Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a putative dna damage-inducible protein2 (chu_0679) from cytophaga hutchinsonii atcc 33406 at 1.50 a3 resolution Phyre2 PDB 3cs5 chain B Region: 71 - 83 Aligned: 13 Modelled: 13 Confidence: 6.3% Identity: 31% PDB header:photosynthesis Chain: B: PDB Molecule:phycobilisome degradation protein nbla; PDBTitle: nbla protein from synechococcus elongatus pcc 7942 Phyre2 PDB 2axt chain H domain 1 Region: 44 - 77 Aligned: 34 Modelled: 34 Confidence: 5.6% Identity: 21% Fold: Single transmembrane helix Superfamily: Photosystem II 10 kDa phosphoprotein PsbH Family: PsbH-like Phyre2 1 d1szia_ 2 c2cj9A_ 3 d1tdpa_ 4 c3mkoA_ 5 c2qnlA_ 6 c3cs5B_ 7 d2axth1

Detailed template information

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

1 d1szia_ 63.0 22 Fold:Four-helical up-and-down bundle Superfamily:Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain Family:Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain 2 c2cj9A_ 12.5 30 PDB header:ligase Chain: A: PDB Molecule:seryl-trna synthetase; PDBTitle: crystal structure of methanosarcina barkeri seryl-trna2 synthetase complexed with an analog of seryladenylate 3 d1tdpa_ 12.5 31 Fold:Bromodomain-like Superfamily:Bacteriocin immunity protein-like Family:Carnobacteriocin B2 immunity protein 4 c3mkoA_ 9.3 23 PDB header:viral protein Chain: A: PDB Molecule:glycoprotein c; PDBTitle: crystal structure of the lymphocytic choriomeningitis virus membrane2 fusion glycoprotein gp2 in its postfusion conformation 5 c2qnlA_ 9.1 22 PDB header:signaling protein Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a putative dna damage-inducible protein2 (chu_0679) from cytophaga hutchinsonii atcc 33406 at 1.50 a3 resolution 6 c3cs5B_ 6.3 31 PDB header:photosynthesis Chain: B: PDB Molecule:phycobilisome degradation protein nbla; PDBTitle: nbla protein from synechococcus elongatus pcc 7942 7 d2axth1 5.6 21 Fold:Single transmembrane helix Superfamily:Photosystem II 10 kDa phosphoprotein PsbH Family:PsbH-like

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