Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	Y	E	V	L	L	L	G	L	L	V	G	V	A	N	Y	C	F	R	Y	L	P	L	R	L	R	V	G	N	A	R	P	T	K	R	G	A	V	G	I	L	L	D	T	I	G	I	A	S	I	C	A	L	L	V	V	S	T	A
Secondary structure
SS confidence
Disorder		?	?																										?	?	?	?	?	?	?	?	?										?													?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.
Sequence		P	E	V	M	H	D	T	R	R	F	V	P	T	L	V	G	F	A	V	L	G	A	S	F	Y	K	T	R	S	I	I	I	P	T	L	L	S	A	L	A	Y	G	L	A	W	K	V	M	A	I	I
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 1vf5 chain C domain 3 Region: 31 - 51 Aligned: 21 Modelled: 21 Confidence: 9.1% Identity: 10% Fold: Single transmembrane helix Superfamily: Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor Family: Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor Phyre2 PDB 1tdj chain A domain 3 Region: 33 - 48 Aligned: 16 Modelled: 16 Confidence: 8.6% Identity: 38% Fold: Ferredoxin-like Superfamily: ACT-like Family: Allosteric threonine deaminase C-terminal domain Phyre2 PDB 1mu2 chain A domain 2 Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 8.3% Identity: 46% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: Reverse transcriptase Phyre2 PDB 2zd1 chain B domain 1 Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 7.0% Identity: 38% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: Reverse transcriptase Phyre2 PDB 2opq chain A Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 6.3% Identity: 38% PDB header:transferase Chain: A: PDB Molecule:reverse transcriptase/ribonuclease h; PDBTitle: crystal structure of l100i mutant hiv-1 reverse2 transcriptase in complex with gw420867x. Phyre2 1 d1vf5c3 2 d1tdja3 3 d1mu2a2 4 d2zd1b1 5 c2opqA_

Detailed template information

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

1 d1vf5c3 9.1 10 Fold:Single transmembrane helix Superfamily:Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor Family:Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor 2 d1tdja3 8.6 38 Fold:Ferredoxin-like Superfamily:ACT-like Family:Allosteric threonine deaminase C-terminal domain 3 d1mu2a2 8.3 46 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Reverse transcriptase 4 d2zd1b1 7.0 38 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Reverse transcriptase 5 c2opqA_ 6.3 38 PDB header:transferase Chain: A: PDB Molecule:reverse transcriptase/ribonuclease h; PDBTitle: crystal structure of l100i mutant hiv-1 reverse2 transcriptase in complex with gw420867x.

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