Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	M	K	V	I	F	T	S	N	R	F	I	D	F	L	I	R	L	L	I	T	A	I	V	I	S	P	V	I	I	W	S	W	D	T	V	K	E	T	T	A	D	G	M	L	A	A	A	F	V	I	L	Y	S	G	V	L	L	F	I
Secondary structure
SS confidence
Disorder		?	?	?			?	?																															?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.
Sequence		L	Y	F	C	F	S	A	L	T	D	L	Q	K	P	D	E	R	K	S	D	E	R	N	E	D	E
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 3rko chain F Region: 41 - 83 Aligned: 42 Modelled: 43 Confidence: 21.7% Identity: 14% PDB header:oxidoreductase Chain: F: PDB Molecule:nadh-quinone oxidoreductase subunit j; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 1utc chain A domain 2 Region: 27 - 33 Aligned: 7 Modelled: 7 Confidence: 18.2% Identity: 43% Fold: 7-bladed beta-propeller Superfamily: Clathrin heavy-chain terminal domain Family: Clathrin heavy-chain terminal domain Phyre2 PDB 1bpo chain A Region: 27 - 33 Aligned: 7 Modelled: 7 Confidence: 17.9% Identity: 43% PDB header:membrane protein Chain: A: PDB Molecule:protein (clathrin); PDBTitle: clathrin heavy-chain terminal domain and linker Phyre2 PDB 1c9l chain A Region: 27 - 33 Aligned: 7 Modelled: 7 Confidence: 17.3% Identity: 43% PDB header:endocytosis/exocytosis Chain: A: PDB Molecule:clathrin; PDBTitle: peptide-in-groove interactions link target proteins to the2 b-propeller of clathrin Phyre2 PDB 3qnq chain D Region: 40 - 81 Aligned: 42 Modelled: 42 Confidence: 16.7% Identity: 5% PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system Phyre2 PDB 1xi4 chain D Region: 27 - 33 Aligned: 7 Modelled: 7 Confidence: 13.7% Identity: 43% PDB header:endocytosis/exocytosis Chain: D: PDB Molecule:clathrin heavy chain; PDBTitle: clathrin d6 coat Phyre2 PDB 2q04 chain C Region: 23 - 34 Aligned: 12 Modelled: 12 Confidence: 10.8% Identity: 25% PDB header:transferase Chain: C: PDB Molecule:acetoin utilization protein; PDBTitle: crystal structure of acetoin utilization protein (zp_00540088.1) from2 exiguobacterium sibiricum 255-15 at 2.33 a resolution Phyre2 PDB 2k59 chain B Region: 12 - 29 Aligned: 18 Modelled: 18 Confidence: 6.6% Identity: 28% PDB header:transport protein Chain: B: PDB Molecule:neuronal acetylcholine receptor subunit beta-2; PDBTitle: nmr structures of the second transmembrane domain of the2 neuronal acetylcholine receptor beta 2 subunit Phyre2 PDB 3c8e chain B Region: 27 - 41 Aligned: 15 Modelled: 15 Confidence: 5.9% Identity: 20% PDB header:transferase Chain: B: PDB Molecule:yghu, glutathione s-transferase homologue; PDBTitle: crystal structure analysis of yghu from e. coli Phyre2 PDB 1qhk chain A Region: 26 - 37 Aligned: 12 Modelled: 12 Confidence: 5.8% Identity: 25% Fold: MbtH/L9 domain-like Superfamily: L9 N-domain-like Family: N-terminal domain of RNase HI Phyre2 PDB 3bsu chain F Region: 26 - 37 Aligned: 12 Modelled: 12 Confidence: 5.6% Identity: 8% PDB header:hydrolase/rna/dna Chain: F: PDB Molecule:ribonuclease h1; PDBTitle: hybrid-binding domain of human rnase h1 in complex with 12-2 mer rna/dna Phyre2 1 c3rkoF_ 2 d1utca2 3 c1bpoA_ 4 c1c9lA_ 5 c3qnqD_ 6 c1xi4D_ 7 c2q04C_ 8 c2k59B_ 9 c3c8eB_ 10 d1qhka_ 11 c3bsuF_

Detailed template information

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

1 c3rkoF_ 21.7 14 PDB header:oxidoreductase Chain: F: PDB Molecule:nadh-quinone oxidoreductase subunit j; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 2 d1utca2 18.2 43 Fold:7-bladed beta-propeller Superfamily:Clathrin heavy-chain terminal domain Family:Clathrin heavy-chain terminal domain 3 c1bpoA_ 17.9 43 PDB header:membrane protein Chain: A: PDB Molecule:protein (clathrin); PDBTitle: clathrin heavy-chain terminal domain and linker 4 c1c9lA_ 17.3 43 PDB header:endocytosis/exocytosis Chain: A: PDB Molecule:clathrin; PDBTitle: peptide-in-groove interactions link target proteins to the2 b-propeller of clathrin 5 c3qnqD_ 16.7 5 PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system 6 c1xi4D_ 13.7 43 PDB header:endocytosis/exocytosis Chain: D: PDB Molecule:clathrin heavy chain; PDBTitle: clathrin d6 coat 7 c2q04C_ 10.8 25 PDB header:transferase Chain: C: PDB Molecule:acetoin utilization protein; PDBTitle: crystal structure of acetoin utilization protein (zp_00540088.1) from2 exiguobacterium sibiricum 255-15 at 2.33 a resolution 8 c2k59B_ 6.6 28 PDB header:transport protein Chain: B: PDB Molecule:neuronal acetylcholine receptor subunit beta-2; PDBTitle: nmr structures of the second transmembrane domain of the2 neuronal acetylcholine receptor beta 2 subunit 9 c3c8eB_ 5.9 20 PDB header:transferase Chain: B: PDB Molecule:yghu, glutathione s-transferase homologue; PDBTitle: crystal structure analysis of yghu from e. coli 10 d1qhka_ 5.8 25 Fold:MbtH/L9 domain-like Superfamily:L9 N-domain-like Family:N-terminal domain of RNase HI 11 c3bsuF_ 5.6 8 PDB header:hydrolase/rna/dna Chain: F: PDB Molecule:ribonuclease h1; PDBTitle: hybrid-binding domain of human rnase h1 in complex with 12-2 mer rna/dna

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