Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		V	G	L	G	E	G	S	A	L	P	V	G	V	P	V	P	W	P	S	A	T	P	P	T	G	W	L	K	C	N	G	A	A	F	S	A	E	E	Y	P	E	L	A	K	A	Y	P	T	N	K	L	P	D	L	R	G	E	F	I	R
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	W	D	D	G	R	G	I	D	T	G	R	S	I	L	S	I	Q	G	Y	A	T	E	D	H	A	H	G	L	P	S	R	S	T	I	V	T	D	A	T	I	N	F	Y	F	D	E	I	W	V	N	S	G	T	D	I	I	K	R	G
Secondary structure
SS confidence
Disorder							?	?	?												?			?		?			?			?	?	?	?	?	?	?	?	?			?	?	?	?	?	?	?	?	?	?			?	?			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.
Sequence		N	T	N	D	A	G	L	P	A	P	D	Y	G	T	F	K	T	Y	K	Q	S	V	D	G	L	G	A	A	A	S	E	T	R	P	R	N	I	A	F	N	Y	I	V	R	A	A
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 1pdi chain Q Region: 7 - 165 Aligned: 159 Modelled: 159 Confidence: 100.0% Identity: 25% PDB header:structural protein Chain: Q: PDB Molecule:short tail fiber protein; PDBTitle: fitting of the c-terminal part of the short tail fibers2 into the cryo-em reconstruction of t4 baseplate Phyre2 PDB 2xgf chain A Region: 7 - 166 Aligned: 160 Modelled: 160 Confidence: 100.0% Identity: 34% PDB header:viral protein Chain: A: PDB Molecule:long tail fiber protein p37; PDBTitle: structure of the bacteriophage t4 long tail fibre needle-2 shaped receptor-binding tip Phyre2 PDB 1ocy chain A Region: 7 - 165 Aligned: 159 Modelled: 159 Confidence: 100.0% Identity: 24% Fold: Receptor-binding domain of short tail fibre protein gp12 Superfamily: Receptor-binding domain of short tail fibre protein gp12 Family: Receptor-binding domain of short tail fibre protein gp12 Phyre2 PDB 1h6w chain A Region: 7 - 55 Aligned: 49 Modelled: 49 Confidence: 99.8% Identity: 33% PDB header:structural protein Chain: A: PDB Molecule:bacteriophage t4 short tail fibre; PDBTitle: crystal structure of a heat- and protease-stable fragment2 of the bacteriophage t4 short fibre Phyre2 PDB 2fkk chain A Region: 10 - 166 Aligned: 134 Modelled: 140 Confidence: 98.3% Identity: 14% PDB header:viral protein Chain: A: PDB Molecule:baseplate structural protein gp10; PDBTitle: crystal structure of the c-terminal domain of the bacteriophage t42 gene product 10 Phyre2 PDB 2fl8 chain N Region: 10 - 166 Aligned: 134 Modelled: 140 Confidence: 98.2% Identity: 14% PDB header:virus/viral protein Chain: N: PDB Molecule:baseplate structural protein gp10; PDBTitle: fitting of the gp10 trimer structure into the cryoem map of the2 bacteriophage t4 baseplate in the hexagonal conformation. Phyre2 PDB 1atx chain A Region: 12 - 34 Aligned: 20 Modelled: 23 Confidence: 33.0% Identity: 35% Fold: Defensin-like Superfamily: Defensin-like Family: Defensin Phyre2 PDB 1m5h chain A domain 2 Region: 12 - 57 Aligned: 40 Modelled: 46 Confidence: 7.3% Identity: 25% Fold: Ferredoxin-like Superfamily: Formylmethanofuran:tetrahydromethanopterin formyltransferase Family: Formylmethanofuran:tetrahydromethanopterin formyltransferase Phyre2 PDB 1el6 chain A Region: 3 - 25 Aligned: 23 Modelled: 23 Confidence: 6.2% Identity: 22% Fold: Baseplate structural protein gp11 Superfamily: Baseplate structural protein gp11 Family: Baseplate structural protein gp11 Phyre2 PDB 1s48 chain A Region: 23 - 42 Aligned: 20 Modelled: 20 Confidence: 5.7% Identity: 5% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: RNA-dependent RNA-polymerase Phyre2 PDB 1v0d chain A Region: 23 - 31 Aligned: 9 Modelled: 9 Confidence: 5.5% Identity: 56% PDB header:hydrolase Chain: A: PDB Molecule:dna fragmentation factor 40 kda subunit; PDBTitle: crystal structure of caspase-activated dnase (cad) Phyre2 PDB 1v0d chain A Region: 23 - 31 Aligned: 9 Modelled: 9 Confidence: 5.5% Identity: 56% Fold: His-Me finger endonucleases Superfamily: His-Me finger endonucleases Family: Caspase-activated DNase, CAD (DffB, DFF40) Phyre2 1 c1pdiQ_ 2 c2xgfA_ 3 d1ocya_ 4 c1h6wA_ 5 c2fkkA_ 6 c2fl8N_ 7 d1atxa_ 8 d1m5ha2 9 d1el6a_ 10 d1s48a_ 11 c1v0dA_ 12 d1v0da_

Detailed template information

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

1 c1pdiQ_ 100.0 25 PDB header:structural protein Chain: Q: PDB Molecule:short tail fiber protein; PDBTitle: fitting of the c-terminal part of the short tail fibers2 into the cryo-em reconstruction of t4 baseplate 2 c2xgfA_ 100.0 34 PDB header:viral protein Chain: A: PDB Molecule:long tail fiber protein p37; PDBTitle: structure of the bacteriophage t4 long tail fibre needle-2 shaped receptor-binding tip 3 d1ocya_ 100.0 24 Fold:Receptor-binding domain of short tail fibre protein gp12 Superfamily:Receptor-binding domain of short tail fibre protein gp12 Family:Receptor-binding domain of short tail fibre protein gp12 4 c1h6wA_ 99.8 33 PDB header:structural protein Chain: A: PDB Molecule:bacteriophage t4 short tail fibre; PDBTitle: crystal structure of a heat- and protease-stable fragment2 of the bacteriophage t4 short fibre 5 c2fkkA_ 98.3 14 PDB header:viral protein Chain: A: PDB Molecule:baseplate structural protein gp10; PDBTitle: crystal structure of the c-terminal domain of the bacteriophage t42 gene product 10 6 c2fl8N_ 98.2 14 PDB header:virus/viral protein Chain: N: PDB Molecule:baseplate structural protein gp10; PDBTitle: fitting of the gp10 trimer structure into the cryoem map of the2 bacteriophage t4 baseplate in the hexagonal conformation. 7 d1atxa_ 33.0 35 Fold:Defensin-like Superfamily:Defensin-like Family:Defensin 8 d1m5ha2 7.3 25 Fold:Ferredoxin-like Superfamily:Formylmethanofuran:tetrahydromethanopterin formyltransferase Family:Formylmethanofuran:tetrahydromethanopterin formyltransferase 9 d1el6a_ 6.2 22 Fold:Baseplate structural protein gp11 Superfamily:Baseplate structural protein gp11 Family:Baseplate structural protein gp11 10 d1s48a_ 5.7 5 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 11 c1v0dA_ 5.5 56 PDB header:hydrolase Chain: A: PDB Molecule:dna fragmentation factor 40 kda subunit; PDBTitle: crystal structure of caspase-activated dnase (cad) 12 d1v0da_ 5.5 56 Fold:His-Me finger endonucleases Superfamily:His-Me finger endonucleases Family:Caspase-activated DNase, CAD (DffB, DFF40)

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

---

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