Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	E	L	L	F	P	G	W	L	A	G	I	M	L	A	C	A	A	G	P	L	G	S	F	V	V	W	R	R	M	S	Y	F	G	D	T	L	A	H	A	S	L	L	G	V	A	F	G	L	L	L	D	V	N	P	F	Y	A	V
Secondary structure
SS confidence
Disorder		?																																		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	A	V	T	L	L	L	A	G	G	L	V	W	L	E	K	R	P	Q	L	A	I	D	T	L	L	G	I	M	A	H	S	A	L	S	L	G	L	V	V	V	S	L	M	S	N	I	R	V	D	L	M	A	Y	L	F	G	D	L	L
Secondary structure
SS confidence
Disorder																	?	?	?	?	?	?																								?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	V	T	P	E	D	L	I	S	I	A	I	G	V	V	I	V	V	A	I	L	F	W	Q	W	R	N	L	L	S	M	T	I	S	P	D	L	A	F	V	D	G	V	K	L	Q	R	V	K	L	L	L	M	L	V	T	A	L	T	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		G	V	A	M	K	F	V	G	A	L	I	I	T	S	L	L	I	I	P	A	A	T	A	R	R	F	A	R	T	P	E	Q	M	A	G	V	A	V	L	V	G	M	V	A	V	T	G	G	L	T	F	S	A	V	Y	D	T	P	A	G
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.
Sequence		P	S	V	V	L	C	A	A	L	L	F	I	L	S	M	M	K	K	Q	A	S
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 2nq2 chain A Region: 2 - 257 Aligned: 255 Modelled: 256 Confidence: 100.0% Identity: 15% 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 1l7v chain A Region: 2 - 257 Aligned: 254 Modelled: 256 Confidence: 100.0% Identity: 17% 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 1q1h chain A Region: 154 - 175 Aligned: 22 Modelled: 22 Confidence: 26.0% 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 1q1h chain A Region: 154 - 175 Aligned: 22 Modelled: 22 Confidence: 26.0% 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 2b2h chain A Region: 3 - 168 Aligned: 165 Modelled: 166 Confidence: 21.3% Identity: 15% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) Phyre2 PDB 3cmw chain A Region: 152 - 166 Aligned: 15 Modelled: 15 Confidence: 7.6% Identity: 27% PDB header:recombination/dna Chain: A: PDB Molecule:protein reca; PDBTitle: mechanism of homologous recombination from the reca-2 ssdna/dsdna structures Phyre2 PDB 3qnq chain D Region: 123 - 164 Aligned: 42 Modelled: 42 Confidence: 5.9% Identity: 7% 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 2pil chain A Region: 1 - 32 Aligned: 32 Modelled: 32 Confidence: 5.8% Identity: 25% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 1 c2nq2A_ 2 d1l7va_ 3 c1q1hA_ 4 d1q1ha_ 5 c2b2hA_ 6 c3cmwA_ 7 c3qnqD_ 8 d2pila_

Detailed template information

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

1 c2nq2A_ 100.0 15 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. 2 d1l7va_ 100.0 17 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 3 c1q1hA_ 26.0 23 PDB header:transcription Chain: A: PDB Molecule:transcription factor e; PDBTitle: an extended winged helix domain in general transcription2 factor e/iie alpha 4 d1q1ha_ 26.0 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcription factor E/IIe-alpha, N-terminal domain 5 c2b2hA_ 21.3 15 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) 6 c3cmwA_ 7.6 27 PDB header:recombination/dna Chain: A: PDB Molecule:protein reca; PDBTitle: mechanism of homologous recombination from the reca-2 ssdna/dsdna structures 7 c3qnqD_ 5.9 7 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 8 d2pila_ 5.8 25 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin

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