Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	G	E	L	I	W	V	L	S	L	L	A	V	A	I	V	L	F	A	T	G	R	V	R	M	D	A	V	A	L	F	V	I	V	A	F	A	L	S	G	T	L	T	V	P	E	V	F	S	G	F	S	D	P	N	V	V	L	I
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	A	L	F	I	I	G	D	G	L	V	R	T	G	V	A	T	V	M	G	T	W	L	V	K	V	A	G	N	S	E	I	K	M	L	V	L	L	M	L	T	V	A	G	L	G	A	F	M	S	S	T	G	V	V	A	I	F	I	P
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	V	L	S	V	A	M	R	M	Q	T	S	P	S	R	L	M	M	P	L	S	F	A	G	L	I	S	G	M	M	T	L	V	A	T	P	P	N	L	V	V	N	S	E	L	L	R	E	G	Y	H	G	F	S	F	F	S	V	T	P
Secondary structure
SS confidence
Disorder										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	G	L	V	V	L	V	L	G	I	L	Y	M	L	V	M	R	F	M	L	K	G	D	T	Q	T	P	Q	R	E	G	W	T	R	R	T	F	R	D	L	I	R	E	Y	R	L	T	G	R	A	R	R	L	A	I	R	P	G	S	P
Secondary structure
SS confidence
Disorder																							?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		M	I	G	Q	R	L	D	D	L	K	L	R	E	R	Y	G	A	N	V	I	G	V	E	R	W	R	R	F	R	R	V	I	V	N	V	N	G	V	S	E	F	R	A	R	D	V	L	L	I	D	M	S	A	A	D	V	D	L	R	Q
Secondary structure
SS confidence
Disorder											?	?	?	?											?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		F	C	S	E	Q	L	L	E	P	M	V	L	R	G	E	Y	F	S	D	Q	A	L	D	V	G	M	A	E	I	S	L	I	P	E	S	E	L	I	G	K	S	V	R	E	I	G	F	R	T	R	Y	G	L	N	V	V	G	L	K	R
Secondary structure
SS confidence
Disorder				?	?	?					?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		N	G	V	A	L	E	G	S	L	A	D	E	P	L	L	L	G	D	I	I	L	V	V	G	N	W	K	L	I	G	M	L	A	K	Q	G	R	D	F	V	A	L	N	L	P	E	E	V	S	E	A	S	P	A	H	S	Q	A	P	H
Secondary structure
SS confidence
Disorder				?	?	?	?	?																																				?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		A	I	F	C	L	V	L	M	V	A	L	M	L	T	D	E	I	P	N	P	V	A	A	I	I	A	C	L	L	M	G	K	F	R	C	I	D	A	E	S	A	Y	K	S	I	H	W	P	S	I	I	L	I	V	G	M	M	P	F	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510	.	.	.	.	.	.	.	.	.	520	.	.	.	.	.	.	.	.	.	530	.	.	.	.	.	.	.	.	.	540
Sequence		V	A	L	Q	K	T	G	G	V	A	L	A	V	K	G	L	M	D	I	G	G	G	Y	G	P	H	M	M	L	G	C	L	F	V	L	S	A	V	I	G	L	F	I	S	N	T	A	T	A	V	L	M	A	P	I	A	L	A	A	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	550	.	.	.	.	.	.	.	.	.	560	.	.	.	.	.	.	.	.	.	570	.	.	.	.	.	.	.	.	.	580	.	.	.	.	.	.	.	.	.	590	.	.	.	.	.	.	.	.	.	600
Sequence		K	T	M	G	V	S	P	Y	P	F	A	M	V	V	A	M	A	A	S	A	A	F	M	T	P	V	S	S	P	V	N	T	L	V	L	G	P	G	N	Y	S	F	S	D	F	V	K	L	G	V	P	F	T	I	I	V	M	A	V	C
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	610
Sequence		V	V	M	I	P	M	L	F	P	F
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 2fy8 chain A domain 2 Region: 319 - 395 Aligned: 77 Modelled: 77 Confidence: 99.4% Identity: 25% Fold: TrkA C-terminal domain-like Superfamily: TrkA C-terminal domain-like Family: TrkA C-terminal domain-like Phyre2 PDB 1vct chain A domain 2 Region: 320 - 394 Aligned: 75 Modelled: 75 Confidence: 99.4% Identity: 21% Fold: TrkA C-terminal domain-like Superfamily: TrkA C-terminal domain-like Family: TrkA C-terminal domain-like Phyre2 PDB 2bkn chain A Region: 320 - 394 Aligned: 75 Modelled: 75 Confidence: 99.3% Identity: 21% PDB header:membrane protein Chain: A: PDB Molecule:hypothetical protein ph0236; PDBTitle: structure analysis of unknown function protein Phyre2 PDB 1lnq chain C Region: 216 - 394 Aligned: 169 Modelled: 179 Confidence: 98.9% Identity: 17% PDB header:metal transport Chain: C: PDB Molecule:potassium channel related protein; PDBTitle: crystal structure of mthk at 3.3 a Phyre2 PDB 2fy8 chain A Region: 320 - 394 Aligned: 75 Modelled: 75 Confidence: 98.9% Identity: 25% PDB header:transport protein Chain: A: PDB Molecule:calcium-gated potassium channel mthk; PDBTitle: crystal structure of mthk rck domain in its ligand-free gating-ring2 form Phyre2 PDB 3jxo chain B Region: 321 - 394 Aligned: 71 Modelled: 74 Confidence: 98.8% Identity: 17% PDB header:transport protein Chain: B: PDB Molecule:trka-n domain protein; PDBTitle: crystal structure of an octomeric two-subunit trka k+ channel ring2 gating assembly, tm1088a:tm1088b, from thermotoga maritima Phyre2 PDB 3l4b chain G Region: 328 - 394 Aligned: 63 Modelled: 67 Confidence: 97.4% Identity: 16% PDB header:transport protein Chain: G: PDB Molecule:trka k+ channel protien tm1088b; PDBTitle: crystal structure of an octomeric two-subunit trka k+ channel ring2 gating assembly, tm1088a:tm1088b, from thermotoga maritima Phyre2 PDB 3u6n chain C Region: 331 - 397 Aligned: 67 Modelled: 67 Confidence: 97.0% Identity: 12% PDB header:transport protein Chain: C: PDB Molecule:high-conductance ca2+-activated k+ channel protein; PDBTitle: open structure of the bk channel gating ring Phyre2 PDB 3mt5 chain A Region: 331 - 385 Aligned: 55 Modelled: 55 Confidence: 95.5% Identity: 13% PDB header:membrane protein, transport protein Chain: A: PDB Molecule:potassium large conductance calcium-activated channel, PDBTitle: crystal structure of the human bk gating apparatus Phyre2 PDB 3naf chain A Region: 331 - 395 Aligned: 65 Modelled: 65 Confidence: 72.3% Identity: 14% PDB header:ion transport Chain: A: PDB Molecule:calcium-activated potassium channel subunit alpha-1; PDBTitle: structure of the intracellular gating ring from the human high-2 conductance ca2+ gated k+ channel (bk channel) Phyre2 PDB 1l7v chain A Region: 7 - 199 Aligned: 174 Modelled: 193 Confidence: 20.0% Identity: 13% 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: 56 - 200 Aligned: 127 Modelled: 145 Confidence: 13.1% Identity: 16% 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 2c2x chain B Region: 328 - 371 Aligned: 44 Modelled: 44 Confidence: 12.9% Identity: 11% PDB header:oxidoreductase Chain: B: PDB Molecule:methylenetetrahydrofolate dehydrogenase- PDBTitle: three dimensional structure of bifunctional2 methylenetetrahydrofolate dehydrogenase-cyclohydrolase3 from mycobacterium tuberculosis Phyre2 1 d2fy8a2 2 d1vcta2 3 c2bknA_ 4 c1lnqC_ 5 c2fy8A_ 6 c3jxoB_ 7 c3l4bG_ 8 c3u6nC_ 9 c3mt5A_ 10 c3nafA_ 11 d1l7va_ 12 c2nq2A_ 13 c2c2xB_

Detailed template information

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

1 d2fy8a2 99.4 25 Fold:TrkA C-terminal domain-like Superfamily:TrkA C-terminal domain-like Family:TrkA C-terminal domain-like 2 d1vcta2 99.4 21 Fold:TrkA C-terminal domain-like Superfamily:TrkA C-terminal domain-like Family:TrkA C-terminal domain-like 3 c2bknA_ 99.3 21 PDB header:membrane protein Chain: A: PDB Molecule:hypothetical protein ph0236; PDBTitle: structure analysis of unknown function protein 4 c1lnqC_ 98.9 17 PDB header:metal transport Chain: C: PDB Molecule:potassium channel related protein; PDBTitle: crystal structure of mthk at 3.3 a 5 c2fy8A_ 98.9 25 PDB header:transport protein Chain: A: PDB Molecule:calcium-gated potassium channel mthk; PDBTitle: crystal structure of mthk rck domain in its ligand-free gating-ring2 form 6 c3jxoB_ 98.8 17 PDB header:transport protein Chain: B: PDB Molecule:trka-n domain protein; PDBTitle: crystal structure of an octomeric two-subunit trka k+ channel ring2 gating assembly, tm1088a:tm1088b, from thermotoga maritima 7 c3l4bG_ 97.4 16 PDB header:transport protein Chain: G: PDB Molecule:trka k+ channel protien tm1088b; PDBTitle: crystal structure of an octomeric two-subunit trka k+ channel ring2 gating assembly, tm1088a:tm1088b, from thermotoga maritima 8 c3u6nC_ 97.0 12 PDB header:transport protein Chain: C: PDB Molecule:high-conductance ca2+-activated k+ channel protein; PDBTitle: open structure of the bk channel gating ring 9 c3mt5A_ 95.5 13 PDB header:membrane protein, transport protein Chain: A: PDB Molecule:potassium large conductance calcium-activated channel, PDBTitle: crystal structure of the human bk gating apparatus 10 c3nafA_ 72.3 14 PDB header:ion transport Chain: A: PDB Molecule:calcium-activated potassium channel subunit alpha-1; PDBTitle: structure of the intracellular gating ring from the human high-2 conductance ca2+ gated k+ channel (bk channel) 11 d1l7va_ 20.0 13 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 12 c2nq2A_ 13.1 16 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. 13 c2c2xB_ 12.9 11 PDB header:oxidoreductase Chain: B: PDB Molecule:methylenetetrahydrofolate dehydrogenase- PDBTitle: three dimensional structure of bifunctional2 methylenetetrahydrofolate dehydrogenase-cyclohydrolase3 from mycobacterium tuberculosis

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