Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	S	K	R	R	F	S	L	P	R	L	D	I	T	G	M	W	V	F	S	L	G	V	W	F	H	I	V	A	R	L	V	Y	S	K	P	W	M	A	F	F	L	A	E	L	I	A	A	I	L	V	L	F	G	A	Y	Q	V	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.
Sequence		D	A	W	I	A	R	V	S	R	E	E	R	E	A	L	E	A	R	Q	Q	A	M	M	E	G	Q	Q	E	G	G	H	V	S	H
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 3mp7 chain B Region: 32 - 64 Aligned: 33 Modelled: 33 Confidence: 45.5% Identity: 27% PDB header:protein transport Chain: B: PDB Molecule:preprotein translocase subunit sece; PDBTitle: lateral opening of a translocon upon entry of protein suggests the2 mechanism of insertion into membranes Phyre2 PDB 3cjl chain A Region: 26 - 62 Aligned: 36 Modelled: 32 Confidence: 35.6% Identity: 19% PDB header:unknown function Chain: A: PDB Molecule:domain of unknown function; PDBTitle: crystal structure of a protein of unknown function (eca1910) from2 pectobacterium atrosepticum scri1043 at 2.20 a resolution Phyre2 PDB 2pv4 chain A domain 1 Region: 53 - 69 Aligned: 17 Modelled: 17 Confidence: 15.1% Identity: 35% Fold: Sama2622-like Superfamily: Sama2622-like Family: Sama2622-like Phyre2 PDB 1q90 chain N Region: 38 - 55 Aligned: 18 Modelled: 18 Confidence: 14.1% Identity: 28% Fold: Single transmembrane helix Superfamily: PetN subunit of the cytochrome b6f complex Family: PetN subunit of the cytochrome b6f complex Phyre2 PDB 1vf5 chain H Region: 38 - 55 Aligned: 18 Modelled: 18 Confidence: 12.8% Identity: 22% PDB header:photosynthesis Chain: H: PDB Molecule:protein pet n; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus Phyre2 PDB 1vf5 chain U Region: 38 - 55 Aligned: 18 Modelled: 18 Confidence: 12.8% Identity: 22% PDB header:photosynthesis Chain: U: PDB Molecule:protein pet n; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus Phyre2 PDB 2d2c chain U Region: 38 - 55 Aligned: 18 Modelled: 18 Confidence: 12.8% Identity: 22% PDB header:photosynthesis Chain: U: PDB Molecule:cytochrome b6-f complex subunit viii; PDBTitle: crystal structure of cytochrome b6f complex with dbmib from2 m. laminosus Phyre2 PDB 2e74 chain H domain 1 Region: 38 - 55 Aligned: 18 Modelled: 18 Confidence: 12.8% Identity: 22% Fold: Single transmembrane helix Superfamily: PetN subunit of the cytochrome b6f complex Family: PetN subunit of the cytochrome b6f complex Phyre2 PDB 2d2c chain H Region: 38 - 55 Aligned: 18 Modelled: 18 Confidence: 12.8% Identity: 22% PDB header:photosynthesis Chain: H: PDB Molecule:cytochrome b6-f complex subunit viii; PDBTitle: crystal structure of cytochrome b6f complex with dbmib from2 m. laminosus Phyre2 PDB 1xme chain B domain 2 Region: 30 - 53 Aligned: 24 Modelled: 24 Confidence: 12.6% Identity: 46% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 2e76 chain H Region: 38 - 55 Aligned: 18 Modelled: 18 Confidence: 11.6% Identity: 22% PDB header:photosynthesis Chain: H: PDB Molecule:cytochrome b6-f complex subunit 8; PDBTitle: crystal structure of the cytochrome b6f complex with tridecyl-2 stigmatellin (tds) from m.laminosus Phyre2 PDB 2e74 chain H Region: 38 - 55 Aligned: 18 Modelled: 18 Confidence: 11.6% Identity: 22% PDB header:photosynthesis Chain: H: PDB Molecule:cytochrome b6-f complex subunit 8; PDBTitle: crystal structure of the cytochrome b6f complex from m.laminosus Phyre2 PDB 2e75 chain H Region: 38 - 55 Aligned: 18 Modelled: 18 Confidence: 11.6% Identity: 22% PDB header:photosynthesis Chain: H: PDB Molecule:cytochrome b6-f complex subunit 8; PDBTitle: crystal structure of the cytochrome b6f complex with 2-nonyl-4-2 hydroxyquinoline n-oxide (nqno) from m.laminosus Phyre2 PDB 2zu8 chain A Region: 14 - 27 Aligned: 14 Modelled: 14 Confidence: 9.6% Identity: 21% PDB header:transferase Chain: A: PDB Molecule:mannosyl-3-phosphoglycerate synthase; PDBTitle: crystal structure of mannosyl-3-phosphoglycerate synthase2 from pyrococcus horikoshii Phyre2 PDB 3lr4 chain A Region: 13 - 19 Aligned: 7 Modelled: 7 Confidence: 9.4% Identity: 57% PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: periplasmic domain of the riss sensor protein from burkholderia2 pseudomallei, barium phased at low ph Phyre2 PDB 2gjh chain A Region: 84 - 94 Aligned: 11 Modelled: 11 Confidence: 8.9% Identity: 64% PDB header:de novo protein Chain: A: PDB Molecule:designed protein; PDBTitle: nmr structure of cfr (c-terminal fragment of2 computationally designed novel-topology protein top7) Phyre2 PDB 1wmh chain B Region: 5 - 32 Aligned: 23 Modelled: 28 Confidence: 8.1% Identity: 30% Fold: beta-Grasp (ubiquitin-like) Superfamily: CAD & PB1 domains Family: PB1 domain Phyre2 PDB 1ckk chain B Region: 1 - 10 Aligned: 10 Modelled: 10 Confidence: 7.1% Identity: 50% PDB header:calmodulin-peptide complex Chain: B: PDB Molecule:protein (rat ca2+/calmodulin dependent protein PDBTitle: calmodulin/rat ca2+/calmodulin dependent protein kinase2 fragment Phyre2 PDB 2pu9 chain B domain 1 Region: 7 - 17 Aligned: 11 Modelled: 11 Confidence: 6.8% Identity: 27% Fold: SH3-like barrel Superfamily: Electron transport accessory proteins Family: Ferredoxin thioredoxin reductase (FTR), alpha (variable) chain Phyre2 PDB 1jb0 chain K Region: 43 - 53 Aligned: 11 Modelled: 11 Confidence: 6.3% Identity: 36% PDB header:photosynthesis Chain: K: PDB Molecule:photosystem 1 reaction centre subunit x; PDBTitle: crystal structure of photosystem i: a photosynthetic reaction center2 and core antenna system from cyanobacteria Phyre2 1 c3mp7B_ 2 c3cjlA_ 3 d2pv4a1 4 d1q90n_ 5 c1vf5H_ 6 c1vf5U_ 7 c2d2cU_ 8 d2e74h1 9 c2d2cH_ 10 d1xmeb2 11 c2e76H_ 12 c2e74H_ 13 c2e75H_ 14 c2zu8A_ 15 c3lr4A_ 16 c2gjhA_ 17 d1wmhb_ 18 c1ckkB_ 19 d2pu9b1 20 c1jb0K_ 21 22 23 24

Detailed template information

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

1 c3mp7B_ 45.5 27 PDB header:protein transport Chain: B: PDB Molecule:preprotein translocase subunit sece; PDBTitle: lateral opening of a translocon upon entry of protein suggests the2 mechanism of insertion into membranes 2 c3cjlA_ 35.6 19 PDB header:unknown function Chain: A: PDB Molecule:domain of unknown function; PDBTitle: crystal structure of a protein of unknown function (eca1910) from2 pectobacterium atrosepticum scri1043 at 2.20 a resolution 3 d2pv4a1 15.1 35 Fold:Sama2622-like Superfamily:Sama2622-like Family:Sama2622-like 4 d1q90n_ 14.1 28 Fold:Single transmembrane helix Superfamily:PetN subunit of the cytochrome b6f complex Family:PetN subunit of the cytochrome b6f complex 5 c1vf5H_ 12.8 22 PDB header:photosynthesis Chain: H: PDB Molecule:protein pet n; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus 6 c1vf5U_ 12.8 22 PDB header:photosynthesis Chain: U: PDB Molecule:protein pet n; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus 7 c2d2cU_ 12.8 22 PDB header:photosynthesis Chain: U: PDB Molecule:cytochrome b6-f complex subunit viii; PDBTitle: crystal structure of cytochrome b6f complex with dbmib from2 m. laminosus 8 d2e74h1 12.8 22 Fold:Single transmembrane helix Superfamily:PetN subunit of the cytochrome b6f complex Family:PetN subunit of the cytochrome b6f complex 9 c2d2cH_ 12.8 22 PDB header:photosynthesis Chain: H: PDB Molecule:cytochrome b6-f complex subunit viii; PDBTitle: crystal structure of cytochrome b6f complex with dbmib from2 m. laminosus 10 d1xmeb2 12.6 46 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 11 c2e76H_ 11.6 22 PDB header:photosynthesis Chain: H: PDB Molecule:cytochrome b6-f complex subunit 8; PDBTitle: crystal structure of the cytochrome b6f complex with tridecyl-2 stigmatellin (tds) from m.laminosus 12 c2e74H_ 11.6 22 PDB header:photosynthesis Chain: H: PDB Molecule:cytochrome b6-f complex subunit 8; PDBTitle: crystal structure of the cytochrome b6f complex from m.laminosus 13 c2e75H_ 11.6 22 PDB header:photosynthesis Chain: H: PDB Molecule:cytochrome b6-f complex subunit 8; PDBTitle: crystal structure of the cytochrome b6f complex with 2-nonyl-4-2 hydroxyquinoline n-oxide (nqno) from m.laminosus 14 c2zu8A_ 9.6 21 PDB header:transferase Chain: A: PDB Molecule:mannosyl-3-phosphoglycerate synthase; PDBTitle: crystal structure of mannosyl-3-phosphoglycerate synthase2 from pyrococcus horikoshii 15 c3lr4A_ 9.4 57 PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: periplasmic domain of the riss sensor protein from burkholderia2 pseudomallei, barium phased at low ph 16 c2gjhA_ 8.9 64 PDB header:de novo protein Chain: A: PDB Molecule:designed protein; PDBTitle: nmr structure of cfr (c-terminal fragment of2 computationally designed novel-topology protein top7) 17 d1wmhb_ 8.1 30 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 18 c1ckkB_ 7.1 50 PDB header:calmodulin-peptide complex Chain: B: PDB Molecule:protein (rat ca2+/calmodulin dependent protein PDBTitle: calmodulin/rat ca2+/calmodulin dependent protein kinase2 fragment 19 d2pu9b1 6.8 27 Fold:SH3-like barrel Superfamily:Electron transport accessory proteins Family:Ferredoxin thioredoxin reductase (FTR), alpha (variable) chain 20 c1jb0K_ 6.3 36 PDB header:photosynthesis Chain: K: PDB Molecule:photosystem 1 reaction centre subunit x; PDBTitle: crystal structure of photosystem i: a photosynthetic reaction center2 and core antenna system from cyanobacteria 21 d1jb0k_ not modelled 6.3 36 Fold:Photosystem I reaction center subunit X, PsaK Superfamily:Photosystem I reaction center subunit X, PsaK Family:Photosystem I reaction center subunit X, PsaK 22 c2wvmA_ not modelled 6.2 29 PDB header:transferase Chain: A: PDB Molecule:mannosyl-3-phosphoglycerate synthase; PDBTitle: h309a mutant of mannosyl-3-phosphoglycerate synthase from2 thermus thermophilus hb27 in complex with3 gdp-alpha-d-mannose and mg(ii) 23 d1td6a_ not modelled 5.8 33 Fold:Hypothetical protein MPN330 Superfamily:Hypothetical protein MPN330 Family:Hypothetical protein MPN330 24 c2w0cT_ not modelled 5.7 50 PDB header:virus Chain: T: PDB Molecule:protein p6; PDBTitle: x-ray structure of the entire lipid-containing2 bacteriophage pm2

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