Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	F	S	N	H	A	D	M	M	L	T	Q	I	A	I	G	L	C	F	T	L	L	Y	F	V	V	F	R	T	L	I	L	Q	F	N	M	C	T	P	G	R	E	D	A	E	V	K	L	Y	S	K	A	E	Y	K	A	S	R	G	Q
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																																												?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	T	A	A	E	P	K	K	E	L	D	Q	A	A	G	I	L	Q	A	L	G	G	V	G	N	I	S	S	I	N	N	C	A	T	R	L	R	I	A	L	H	D	M	S	Q	T	L	D	D	E	V	F	K	K	L	G	A	H	G	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?																																				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.
Sequence		F	R	S	G	D	A	I	Q	V	I	I	G	L	H	V	S	Q	L	R	E	Q	L	D	S	L	I	N	S	H	Q	S	A	E	N	V	A	I	T	E	A	V
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 1iba chain A Region: 72 - 150 Aligned: 78 Modelled: 79 Confidence: 99.9% Identity: 33% PDB header:phoshphotransferase Chain: A: PDB Molecule:glucose permease; PDBTitle: glucose permease (domain iib), nmr, 11 structures Phyre2 PDB 3bp8 chain C domain 1 Region: 72 - 147 Aligned: 75 Modelled: 76 Confidence: 99.9% Identity: 35% Fold: Homing endonuclease-like Superfamily: Glucose permease domain IIB Family: Glucose permease domain IIB Phyre2 PDB 3ipj chain B Region: 64 - 154 Aligned: 90 Modelled: 91 Confidence: 99.9% Identity: 28% PDB header:transferase Chain: B: PDB Molecule:pts system, iiabc component; PDBTitle: the crystal structure of one domain of the pts system, iiabc component2 from clostridium difficile Phyre2 PDB 2rdd chain B Region: 16 - 33 Aligned: 18 Modelled: 18 Confidence: 72.7% Identity: 17% PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. Phyre2 PDB 3arc chain T Region: 9 - 24 Aligned: 16 Modelled: 16 Confidence: 33.9% Identity: 25% PDB header:electron transport, photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution Phyre2 PDB 3hd7 chain A Region: 6 - 30 Aligned: 25 Modelled: 25 Confidence: 32.8% Identity: 8% PDB header:exocytosis Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1 Phyre2 PDB 3dtu chain B domain 2 Region: 4 - 29 Aligned: 26 Modelled: 26 Confidence: 26.2% Identity: 12% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 3mk7 chain F Region: 9 - 27 Aligned: 19 Modelled: 19 Confidence: 19.0% Identity: 26% PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase Phyre2 PDB 2dla chain B Region: 67 - 108 Aligned: 41 Modelled: 42 Confidence: 18.0% Identity: 17% PDB header:replication Chain: B: PDB Molecule:397aa long hypothetical protein; PDBTitle: primase large subunit amino terminal domain from pyrococcus horikoshii Phyre2 PDB 3a0b chain T Region: 9 - 24 Aligned: 16 Modelled: 16 Confidence: 16.4% Identity: 25% PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 1iij chain A Region: 2 - 33 Aligned: 32 Modelled: 32 Confidence: 12.8% Identity: 19% PDB header:signaling protein Chain: A: PDB Molecule:erbb-2 receptor protein-tyrosine kinase; PDBTitle: solution structure of the neu/erbb-2 membrane spanning2 segment Phyre2 PDB 2cfu chain A domain 2 Region: 58 - 88 Aligned: 31 Modelled: 31 Confidence: 12.8% Identity: 19% Fold: Metallo-hydrolase/oxidoreductase Superfamily: Metallo-hydrolase/oxidoreductase Family: Alkylsulfatase-like Phyre2 PDB 2zjs chain E Region: 11 - 31 Aligned: 16 Modelled: 21 Confidence: 12.5% Identity: 50% PDB header:protein transport/immune system Chain: E: PDB Molecule:preprotein translocase sece subunit; PDBTitle: crystal structure of secye translocon from thermus thermophilus with a2 fab fragment Phyre2 PDB 3tix chain B Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 11.3% Identity: 8% PDB header:gene regulation/protein binding Chain: B: PDB Molecule:chromo domain-containing protein 1; PDBTitle: crystal structure of the chp1-tas3 complex core Phyre2 PDB 1fft chain B domain 2 Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 10.8% Identity: 8% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 3bz1 chain T Region: 9 - 24 Aligned: 16 Modelled: 16 Confidence: 10.4% Identity: 25% PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer Phyre2 PDB 3prq chain T Region: 9 - 24 Aligned: 16 Modelled: 16 Confidence: 10.4% Identity: 25% PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 1 of 2). this file contains first monomer of psii3 dimer Phyre2 PDB 3bz2 chain T Region: 9 - 24 Aligned: 16 Modelled: 16 Confidence: 10.4% Identity: 25% PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 22 of 2). this file contains second monomer of psii dimer Phyre2 PDB 3prr chain T Region: 9 - 24 Aligned: 16 Modelled: 16 Confidence: 10.4% Identity: 25% PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 2 of 2). this file contains second monomer of psii3 dimer Phyre2 PDB 1s5l chain T Region: 9 - 24 Aligned: 16 Modelled: 16 Confidence: 10.3% Identity: 25% PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii psbt protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 1 c1ibaA_ 2 d3bp8c1 3 c3ipjB_ 4 c2rddB_ 5 c3arct_ 6 c3hd7A_ 7 d3dtub2 8 c3mk7F_ 9 c2dlaB_ 10 c3a0bT_ 11 c1iijA_ 12 d2cfua2 13 c2zjsE_ 14 c3tixB_ 15 d1fftb2 16 c3bz1T_ 17 c3prqT_ 18 c3bz2T_ 19 c3prrT_ 20 c1s5lT_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36

Detailed template information

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

1 c1ibaA_ 99.9 33 PDB header:phoshphotransferase Chain: A: PDB Molecule:glucose permease; PDBTitle: glucose permease (domain iib), nmr, 11 structures 2 d3bp8c1 99.9 35 Fold:Homing endonuclease-like Superfamily:Glucose permease domain IIB Family:Glucose permease domain IIB 3 c3ipjB_ 99.9 28 PDB header:transferase Chain: B: PDB Molecule:pts system, iiabc component; PDBTitle: the crystal structure of one domain of the pts system, iiabc component2 from clostridium difficile 4 c2rddB_ 72.7 17 PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. 5 c3arct_ 33.9 25 PDB header:electron transport, photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 6 c3hd7A_ 32.8 8 PDB header:exocytosis Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1 7 d3dtub2 26.2 12 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 8 c3mk7F_ 19.0 26 PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase 9 c2dlaB_ 18.0 17 PDB header:replication Chain: B: PDB Molecule:397aa long hypothetical protein; PDBTitle: primase large subunit amino terminal domain from pyrococcus horikoshii 10 c3a0bT_ 16.4 25 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of br-substituted photosystem ii complex 11 c1iijA_ 12.8 19 PDB header:signaling protein Chain: A: PDB Molecule:erbb-2 receptor protein-tyrosine kinase; PDBTitle: solution structure of the neu/erbb-2 membrane spanning2 segment 12 d2cfua2 12.8 19 Fold:Metallo-hydrolase/oxidoreductase Superfamily:Metallo-hydrolase/oxidoreductase Family:Alkylsulfatase-like 13 c2zjsE_ 12.5 50 PDB header:protein transport/immune system Chain: E: PDB Molecule:preprotein translocase sece subunit; PDBTitle: crystal structure of secye translocon from thermus thermophilus with a2 fab fragment 14 c3tixB_ 11.3 8 PDB header:gene regulation/protein binding Chain: B: PDB Molecule:chromo domain-containing protein 1; PDBTitle: crystal structure of the chp1-tas3 complex core 15 d1fftb2 10.8 8 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 16 c3bz1T_ 10.4 25 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer 17 c3prqT_ 10.4 25 PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 1 of 2). this file contains first monomer of psii3 dimer 18 c3bz2T_ 10.4 25 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 22 of 2). this file contains second monomer of psii dimer 19 c3prrT_ 10.4 25 PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 2 of 2). this file contains second monomer of psii3 dimer 20 c1s5lT_ 10.3 25 PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii psbt protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 21 c1s5lt_ not modelled 10.3 25 PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii psbt protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 22 c3kziT_ not modelled 10.2 25 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of monomeric form of cyanobacterial photosystem ii 23 c3arcT_ not modelled 10.2 25 PDB header:electron transport, photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 24 d2axtt1 not modelled 10.2 25 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein T, PsbT Family:PsbT-like 25 c3a0bt_ not modelled 10.2 25 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of br-substituted photosystem ii complex 26 c3a0ht_ not modelled 10.2 25 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of i-substituted photosystem ii complex 27 c2axtT_ not modelled 10.2 25 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center t protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 28 c2axtt_ not modelled 10.2 25 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center t protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 29 c3a0hT_ not modelled 10.2 25 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of i-substituted photosystem ii complex 30 c2cfuA_ not modelled 10.1 19 PDB header:hydrolase Chain: A: PDB Molecule:sdsa1; PDBTitle: crystal structure of sdsa1, an alkylsulfatase from2 pseudomonas aeruginosa, in complex with 1-decane-sulfonic-3 acid. 31 c3zqsB_ not modelled 8.0 17 PDB header:ligase Chain: B: PDB Molecule:e3 ubiquitin-protein ligase fancl; PDBTitle: human fancl central domain 32 c3d22A_ not modelled 6.9 14 PDB header:oxidoreductase Chain: A: PDB Molecule:thioredoxin h-type; PDBTitle: crystal structure of a poplar thioredoxin h mutant,2 pttrxh4c61s 33 d1fzda_ not modelled 6.7 22 Fold:Fibrinogen C-terminal domain-like Superfamily:Fibrinogen C-terminal domain-like Family:Fibrinogen C-terminal domain-like 34 d1t57a_ not modelled 5.9 24 Fold:Pyruvate kinase C-terminal domain-like Superfamily:PK C-terminal domain-like Family:MTH1675-like 35 c3qd1X_ not modelled 5.8 45 PDB header:sugar binding protein Chain: X: PDB Molecule:platelet binding protein gspb; PDBTitle: gspb plus alpha-2,3-sialyl (1-thioethyl)galactose 36 d3pvia_ not modelled 5.5 30 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:Restriction endonuclease PvuII

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