Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	Y	L	N	T	T	D	C	S	L	F	L	A	E	R	S	K	F	M	T	K	Y	A	L	I	G	L	L	A	V	C	A	T	V	L	C	F	S	L	I	F	R	E	R	L	C	E	L	N	I	H	R	G	N	T	V	V	Q	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?									?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.
Sequence		T	L	A	Y	E	A	R	K
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 2ii8 chain F Region: 44 - 67 Aligned: 24 Modelled: 24 Confidence: 56.5% Identity: 29% PDB header:signaling protein Chain: F: PDB Molecule:anabaena sensory rhodopsin transducer protein; PDBTitle: anabaena sensory rhodopsin transducer Phyre2 PDB 1nc7 chain A Region: 43 - 68 Aligned: 26 Modelled: 26 Confidence: 55.5% Identity: 27% Fold: Hypothetical protein TM1070 Superfamily: Hypothetical protein TM1070 Family: Hypothetical protein TM1070 Phyre2 PDB 2krx chain A Region: 43 - 57 Aligned: 15 Modelled: 15 Confidence: 11.1% Identity: 27% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:asl3597 protein; PDBTitle: solution nmr structure of asl3597 from nostoc sp. pcc7120. northeast2 structural genomics consortium target id nsr244. Phyre2 PDB 3arc chain L Region: 27 - 42 Aligned: 16 Modelled: 16 Confidence: 8.7% Identity: 44% PDB header:electron transport, photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution Phyre2 PDB 3jrt chain A Region: 32 - 42 Aligned: 11 Modelled: 11 Confidence: 6.3% Identity: 36% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:integron cassette protein vpc_cass2; PDBTitle: structure from the mobile metagenome of v. paracholerae:2 integron cassette protein vpc_cass2 Phyre2 PDB 1q90 chain M Region: 12 - 48 Aligned: 31 Modelled: 37 Confidence: 5.6% Identity: 39% Fold: Single transmembrane helix Superfamily: PetM subunit of the cytochrome b6f complex Family: PetM subunit of the cytochrome b6f complex Phyre2 PDB 2vvy chain C Region: 1 - 51 Aligned: 47 Modelled: 50 Confidence: 5.4% Identity: 30% PDB header:viral protein Chain: C: PDB Molecule:protein b15; PDBTitle: structure of vaccinia virus protein b14 Phyre2 1 c2ii8F_ 2 d1nc7a_ 3 c2krxA_ 4 c3arcl_ 5 c3jrtA_ 6 d1q90m_ 7 c2vvyC_

Detailed template information

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

1 c2ii8F_ 56.5 29 PDB header:signaling protein Chain: F: PDB Molecule:anabaena sensory rhodopsin transducer protein; PDBTitle: anabaena sensory rhodopsin transducer 2 d1nc7a_ 55.5 27 Fold:Hypothetical protein TM1070 Superfamily:Hypothetical protein TM1070 Family:Hypothetical protein TM1070 3 c2krxA_ 11.1 27 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:asl3597 protein; PDBTitle: solution nmr structure of asl3597 from nostoc sp. pcc7120. northeast2 structural genomics consortium target id nsr244. 4 c3arcl_ 8.7 44 PDB header:electron transport, photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 5 c3jrtA_ 6.3 36 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:integron cassette protein vpc_cass2; PDBTitle: structure from the mobile metagenome of v. paracholerae:2 integron cassette protein vpc_cass2 6 d1q90m_ 5.6 39 Fold:Single transmembrane helix Superfamily:PetM subunit of the cytochrome b6f complex Family:PetM subunit of the cytochrome b6f complex 7 c2vvyC_ 5.4 30 PDB header:viral protein Chain: C: PDB Molecule:protein b15; PDBTitle: structure of vaccinia virus protein b14

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