Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	Y	V	S	R	R	L	L	I	T	C	L	L	L	V	S	A	C	V	V	A	G	I	W	G	L	R	S	G	A	V	T	L	E	T	S	Q	V	F	A	A	L	M	G	D	A	P	R	S	M	T	M	V	V	T	E	W	R	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																							?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		P	R	V	L	M	A	L	L	I	G	A	A	L	G	V	S	G	A	I	F	Q	S	L	M	R	N	P	L	G	S	P	D	V	M	G	F	N	T	G	A	W	S	G	V	L	V	A	M	V	L	F	G	Q	D	L	T	A	I	A	L
Secondary structure
SS confidence
Disorder																																																						?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		S	A	M	V	G	G	I	V	T	S	L	L	V	W	L	L	A	W	R	N	G	I	D	T	F	R	L	I	I	I	G	I	G	V	R	A	M	L	V	A	F	N	T	W	L	L	L	K	A	S	L	E	T	A	L	T	A	G	L	W
Secondary structure
SS confidence
Disorder																				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		N	A	G	S	L	N	G	L	T	W	A	K	T	S	P	S	A	P	I	I	I	L	M	L	I	A	A	A	L	L	V	R	R	M	R	L	L	E	M	G	D	D	T	A	C	A	L	G	V	S	V	E	R	S	R	L	L	M	M	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		V	A	V	V	L	T	A	A	A	T	A	L	A	G	P	I	S	F	I	A	L	V	A	P	H	I	A	R	R	I	S	G	T	A	R	W	G	L	T	Q	A	A	L	C	G	A	L	L	L	L	A	A	D	L	C	A	Q	Q	L	F
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330
Sequence		M	P	Y	Q	L	P	V	G	V	V	T	V	S	L	G	G	I	Y	L	I	V	L	L	I	Q	E	S	R	K	K
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: 5 - 325 Aligned: 313 Modelled: 321 Confidence: 100.0% Identity: 31% 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: 8 - 326 Aligned: 306 Modelled: 319 Confidence: 100.0% Identity: 27% 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 2b2h chain A Region: 57 - 231 Aligned: 166 Modelled: 171 Confidence: 60.8% Identity: 13% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) Phyre2 PDB 1yce chain D Region: 75 - 116 Aligned: 42 Modelled: 42 Confidence: 16.2% Identity: 19% PDB header:membrane protein Chain: D: PDB Molecule:subunit c; PDBTitle: structure of the rotor ring of f-type na+-atpase from ilyobacter2 tartaricus Phyre2 PDB 3lrc chain C Region: 190 - 329 Aligned: 140 Modelled: 140 Confidence: 12.1% Identity: 7% PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) Phyre2 PDB 2w5j chain M Region: 75 - 115 Aligned: 41 Modelled: 41 Confidence: 10.0% Identity: 20% PDB header:hydrolase Chain: M: PDB Molecule:atp synthase c chain, chloroplastic; PDBTitle: structure of the c14-rotor ring of the proton translocating2 chloroplast atp synthase Phyre2 PDB 1q1h chain A Region: 220 - 241 Aligned: 22 Modelled: 22 Confidence: 9.9% Identity: 23% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Transcription factor E/IIe-alpha, N-terminal domain Phyre2 PDB 1q1h chain A Region: 220 - 241 Aligned: 22 Modelled: 22 Confidence: 9.9% Identity: 23% PDB header:transcription Chain: A: PDB Molecule:transcription factor e; PDBTitle: an extended winged helix domain in general transcription2 factor e/iie alpha Phyre2 PDB 3k3g chain A Region: 61 - 330 Aligned: 249 Modelled: 253 Confidence: 8.9% Identity: 15% PDB header:transport protein Chain: A: PDB Molecule:urea transporter; PDBTitle: crystal structure of the urea transporter from desulfovibrio vulgaris2 bound to 1,3-dimethylurea Phyre2 PDB 2xq2 chain A Region: 11 - 210 Aligned: 183 Modelled: 193 Confidence: 6.0% Identity: 12% PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt Phyre2 1 d1l7va_ 2 c2nq2A_ 3 c2b2hA_ 4 c1yceD_ 5 c3lrcC_ 6 c2w5jM_ 7 d1q1ha_ 8 c1q1hA_ 9 c3k3gA_ 10 c2xq2A_

Detailed template information

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

1 d1l7va_ 100.0 31 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_ 100.0 27 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 c2b2hA_ 60.8 13 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) 4 c1yceD_ 16.2 19 PDB header:membrane protein Chain: D: PDB Molecule:subunit c; PDBTitle: structure of the rotor ring of f-type na+-atpase from ilyobacter2 tartaricus 5 c3lrcC_ 12.1 7 PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) 6 c2w5jM_ 10.0 20 PDB header:hydrolase Chain: M: PDB Molecule:atp synthase c chain, chloroplastic; PDBTitle: structure of the c14-rotor ring of the proton translocating2 chloroplast atp synthase 7 d1q1ha_ 9.9 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcription factor E/IIe-alpha, N-terminal domain 8 c1q1hA_ 9.9 23 PDB header:transcription Chain: A: PDB Molecule:transcription factor e; PDBTitle: an extended winged helix domain in general transcription2 factor e/iie alpha 9 c3k3gA_ 8.9 15 PDB header:transport protein Chain: A: PDB Molecule:urea transporter; PDBTitle: crystal structure of the urea transporter from desulfovibrio vulgaris2 bound to 1,3-dimethylurea 10 c2xq2A_ 6.0 12 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt

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