Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	T	S	K	T	V	A	K	L	L	F	V	V	G	A	L	V	Y	L	V	G	L	W	I	S	C	P	L	L	S	G	K	G	Y	F	L	G	V	L	M	T	A	T	F	G	N	Y	A	Y	L	R	A	E	K	L	G	Q	L	D
Secondary structure
SS confidence
Disorder		?	?	?	?																																																						?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.
Sequence		D	F	F	T	H	I	C	Q	L	V	A	L	I	T	I	G	L	L	F	I	G	V	L	N	A	P	I	N	T	Y	E	M	V	I	Y	P	I	A	F	F	V	C	L	F	G	Q	M	R	L	F	R	S	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 1jva chain A domain 2 Region: 16 - 24 Aligned: 9 Modelled: 9 Confidence: 35.4% Identity: 67% Fold: Homing endonuclease-like Superfamily: Homing endonucleases Family: Intein endonuclease Phyre2 PDB 1q90 chain L Region: 5 - 24 Aligned: 20 Modelled: 20 Confidence: 21.9% Identity: 25% Fold: Single transmembrane helix Superfamily: PetL subunit of the cytochrome b6f complex Family: PetL subunit of the cytochrome b6f complex Phyre2 PDB 1q90 chain L Region: 5 - 24 Aligned: 20 Modelled: 20 Confidence: 21.9% Identity: 25% PDB header:photosynthesis Chain: L: PDB Molecule:cytochrome b6f complex subunit petl; PDBTitle: structure of the cytochrome b6f (plastohydroquinone : plastocyanin2 oxidoreductase) from chlamydomonas reinhardtii Phyre2 PDB 1b24 chain A Region: 13 - 27 Aligned: 15 Modelled: 15 Confidence: 21.0% Identity: 47% PDB header:intron-encoded Chain: A: PDB Molecule:protein (i-dmoi); PDBTitle: i-dmoi, intron-encoded endonuclease Phyre2 PDB 1b24 chain A domain 1 Region: 13 - 23 Aligned: 11 Modelled: 11 Confidence: 18.6% Identity: 55% Fold: Homing endonuclease-like Superfamily: Homing endonucleases Family: Group I mobile intron endonuclease Phyre2 PDB 2i5n chain L domain 1 Region: 28 - 83 Aligned: 56 Modelled: 56 Confidence: 14.3% Identity: 13% Fold: Bacterial photosystem II reaction centre, L and M subunits Superfamily: Bacterial photosystem II reaction centre, L and M subunits Family: Bacterial photosystem II reaction centre, L and M subunits Phyre2 PDB 3a0b chain X Region: 86 - 96 Aligned: 11 Modelled: 11 Confidence: 11.1% Identity: 9% PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 3a0b chain X Region: 86 - 96 Aligned: 11 Modelled: 11 Confidence: 11.1% Identity: 9% PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 3a0h chain X Region: 86 - 96 Aligned: 11 Modelled: 11 Confidence: 11.1% Identity: 9% PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of i-substituted photosystem ii complex Phyre2 PDB 3a0h chain X Region: 86 - 96 Aligned: 11 Modelled: 11 Confidence: 11.1% Identity: 9% PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of i-substituted photosystem ii complex Phyre2 PDB 2k21 chain A Region: 36 - 63 Aligned: 26 Modelled: 28 Confidence: 10.5% Identity: 31% PDB header:membrane protein Chain: A: PDB Molecule:potassium voltage-gated channel subfamily e PDBTitle: nmr structure of human kcne1 in lmpg micelles at ph 6.0 and2 40 degree c Phyre2 PDB 3rko chain F Region: 39 - 59 Aligned: 21 Modelled: 21 Confidence: 9.8% Identity: 19% PDB header:oxidoreductase Chain: F: PDB Molecule:nadh-quinone oxidoreductase subunit j; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 1m56 chain D Region: 53 - 85 Aligned: 33 Modelled: 33 Confidence: 9.8% Identity: 18% Fold: Single transmembrane helix Superfamily: Bacterial aa3 type cytochrome c oxidase subunit IV Family: Bacterial aa3 type cytochrome c oxidase subunit IV Phyre2 PDB 1s5l chain X Region: 86 - 96 Aligned: 11 Modelled: 11 Confidence: 9.6% Identity: 9% PDB header:photosynthesis Chain: X: PDB Molecule:photosystem ii psbx protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 1qle chain D Region: 53 - 85 Aligned: 33 Modelled: 33 Confidence: 8.8% Identity: 15% Fold: Single transmembrane helix Superfamily: Bacterial aa3 type cytochrome c oxidase subunit IV Family: Bacterial aa3 type cytochrome c oxidase subunit IV Phyre2 PDB 1eys chain M Region: 28 - 83 Aligned: 56 Modelled: 56 Confidence: 8.5% Identity: 21% Fold: Bacterial photosystem II reaction centre, L and M subunits Superfamily: Bacterial photosystem II reaction centre, L and M subunits Family: Bacterial photosystem II reaction centre, L and M subunits Phyre2 PDB 2j8c chain M domain 1 Region: 27 - 84 Aligned: 58 Modelled: 58 Confidence: 8.2% Identity: 12% Fold: Bacterial photosystem II reaction centre, L and M subunits Superfamily: Bacterial photosystem II reaction centre, L and M subunits Family: Bacterial photosystem II reaction centre, L and M subunits Phyre2 PDB 2hac chain A Region: 27 - 54 Aligned: 23 Modelled: 23 Confidence: 7.0% Identity: 48% PDB header:membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd3 zeta chain; PDBTitle: structure of zeta-zeta transmembrane dimer Phyre2 PDB 2e0i chain D Region: 23 - 35 Aligned: 13 Modelled: 13 Confidence: 7.0% Identity: 23% PDB header:lyase Chain: D: PDB Molecule:432aa long hypothetical deoxyribodipyrimidine photolyase; PDBTitle: crystal structure of archaeal photolyase from sulfolobus tokodaii with2 two fad molecules: implication of a novel light-harvesting cofactor Phyre2 PDB 2j8c chain L domain 1 Region: 28 - 83 Aligned: 56 Modelled: 56 Confidence: 6.6% Identity: 18% Fold: Bacterial photosystem II reaction centre, L and M subunits Superfamily: Bacterial photosystem II reaction centre, L and M subunits Family: Bacterial photosystem II reaction centre, L and M subunits Phyre2 1 d1jvaa2 2 d1q90l_ 3 c1q90L_ 4 c1b24A_ 5 d1b24a1 6 d2i5nl1 7 c3a0bx_ 8 c3a0bX_ 9 c3a0hx_ 10 c3a0hX_ 11 c2k21A_ 12 c3rkoF_ 13 d1m56d_ 14 c1s5lx_ 15 d1qled_ 16 d1eysm_ 17 d2j8cm1 18 c2hacA_ 19 c2e0iD_ 20 d2j8cl1 21 22 23

Detailed template information

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

1 d1jvaa2 35.4 67 Fold:Homing endonuclease-like Superfamily:Homing endonucleases Family:Intein endonuclease 2 d1q90l_ 21.9 25 Fold:Single transmembrane helix Superfamily:PetL subunit of the cytochrome b6f complex Family:PetL subunit of the cytochrome b6f complex 3 c1q90L_ 21.9 25 PDB header:photosynthesis Chain: L: PDB Molecule:cytochrome b6f complex subunit petl; PDBTitle: structure of the cytochrome b6f (plastohydroquinone : plastocyanin2 oxidoreductase) from chlamydomonas reinhardtii 4 c1b24A_ 21.0 47 PDB header:intron-encoded Chain: A: PDB Molecule:protein (i-dmoi); PDBTitle: i-dmoi, intron-encoded endonuclease 5 d1b24a1 18.6 55 Fold:Homing endonuclease-like Superfamily:Homing endonucleases Family:Group I mobile intron endonuclease 6 d2i5nl1 14.3 13 Fold:Bacterial photosystem II reaction centre, L and M subunits Superfamily:Bacterial photosystem II reaction centre, L and M subunits Family:Bacterial photosystem II reaction centre, L and M subunits 7 c3a0bx_ 11.1 9 PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of br-substituted photosystem ii complex 8 c3a0bX_ 11.1 9 PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of br-substituted photosystem ii complex 9 c3a0hx_ 11.1 9 PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of i-substituted photosystem ii complex 10 c3a0hX_ 11.1 9 PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of i-substituted photosystem ii complex 11 c2k21A_ 10.5 31 PDB header:membrane protein Chain: A: PDB Molecule:potassium voltage-gated channel subfamily e PDBTitle: nmr structure of human kcne1 in lmpg micelles at ph 6.0 and2 40 degree c 12 c3rkoF_ 9.8 19 PDB header:oxidoreductase Chain: F: PDB Molecule:nadh-quinone oxidoreductase subunit j; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 13 d1m56d_ 9.8 18 Fold:Single transmembrane helix Superfamily:Bacterial aa3 type cytochrome c oxidase subunit IV Family:Bacterial aa3 type cytochrome c oxidase subunit IV 14 c1s5lx_ 9.6 9 PDB header:photosynthesis Chain: X: PDB Molecule:photosystem ii psbx protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 15 d1qled_ 8.8 15 Fold:Single transmembrane helix Superfamily:Bacterial aa3 type cytochrome c oxidase subunit IV Family:Bacterial aa3 type cytochrome c oxidase subunit IV 16 d1eysm_ 8.5 21 Fold:Bacterial photosystem II reaction centre, L and M subunits Superfamily:Bacterial photosystem II reaction centre, L and M subunits Family:Bacterial photosystem II reaction centre, L and M subunits 17 d2j8cm1 8.2 12 Fold:Bacterial photosystem II reaction centre, L and M subunits Superfamily:Bacterial photosystem II reaction centre, L and M subunits Family:Bacterial photosystem II reaction centre, L and M subunits 18 c2hacA_ 7.0 48 PDB header:membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd3 zeta chain; PDBTitle: structure of zeta-zeta transmembrane dimer 19 c2e0iD_ 7.0 23 PDB header:lyase Chain: D: PDB Molecule:432aa long hypothetical deoxyribodipyrimidine photolyase; PDBTitle: crystal structure of archaeal photolyase from sulfolobus tokodaii with2 two fad molecules: implication of a novel light-harvesting cofactor 20 d2j8cl1 6.6 18 Fold:Bacterial photosystem II reaction centre, L and M subunits Superfamily:Bacterial photosystem II reaction centre, L and M subunits Family:Bacterial photosystem II reaction centre, L and M subunits 21 c2jobA_ not modelled 5.7 20 PDB header:lipid binding protein Chain: A: PDB Molecule:antilipopolysaccharide factor; PDBTitle: solution structure of an antilipopolysaccharide factor from2 shrimp and its possible lipid a binding site 22 d2i5nm1 not modelled 5.6 23 Fold:Bacterial photosystem II reaction centre, L and M subunits Superfamily:Bacterial photosystem II reaction centre, L and M subunits Family:Bacterial photosystem II reaction centre, L and M subunits 23 c2j4dA_ not modelled 5.2 31 PDB header:dna-binding protein Chain: A: PDB Molecule:cryptochrome dash; PDBTitle: cryptochrome 3 from arabidopsis thaliana

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