Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	E	N	K	S	N	P	E	L	K	I	R	S	T	E	R	D	Y	K	Y	I	S	R	I	T	G	R	Y	A	G	L	S	L	V	F	L	T	A	G	I	V	L	W	T	V	M	D	I	I	F	D	A	C	I	D	S	W	K	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?							?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		D	P	E	L	N	N	S	S	Y	M	W	N	I	L	I	Y	A	I	P	Y	T	L	Y	A	L	A	A	G	F	L	V	T	F	F	S	V	P	N	V	R	I	N	I	R	K	Y	R	D	I	P	A	E	M	S	Y	A	P	G	E	H
Secondary structure
SS confidence
Disorder																																																										?	?	?	?
Disorder confidence
		.	.	.	.	.	.
Sequence		I	K	G	G	Q	E
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 3bz1 chain L Region: 25 - 42 Aligned: 18 Modelled: 18 Confidence: 34.5% Identity: 33% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer Phyre2 PDB 3kzi chain L Region: 25 - 42 Aligned: 18 Modelled: 18 Confidence: 34.5% Identity: 33% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of monomeric form of cyanobacterial photosystem ii Phyre2 PDB 1s5l chain L Region: 25 - 42 Aligned: 18 Modelled: 18 Confidence: 34.5% Identity: 33% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 1s5l chain L Region: 25 - 42 Aligned: 18 Modelled: 18 Confidence: 34.5% Identity: 33% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 3prr chain L Region: 25 - 42 Aligned: 18 Modelled: 18 Confidence: 34.5% Identity: 33% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; 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 2axt chain L domain 1 Region: 25 - 42 Aligned: 18 Modelled: 18 Confidence: 34.5% Identity: 33% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein L, PsbL Family: PsbL-like Phyre2 PDB 3arc chain L Region: 25 - 42 Aligned: 18 Modelled: 18 Confidence: 34.5% Identity: 33% 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 2axt chain L Region: 25 - 42 Aligned: 18 Modelled: 18 Confidence: 34.5% Identity: 33% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus Phyre2 PDB 2axt chain L Region: 25 - 42 Aligned: 18 Modelled: 18 Confidence: 34.5% Identity: 33% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus Phyre2 PDB 3prq chain L Region: 25 - 42 Aligned: 18 Modelled: 18 Confidence: 34.5% Identity: 33% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; 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 L Region: 25 - 42 Aligned: 18 Modelled: 18 Confidence: 34.5% Identity: 33% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 22 of 2). this file contains second monomer of psii dimer Phyre2 PDB 3a0b chain L Region: 25 - 42 Aligned: 18 Modelled: 18 Confidence: 30.6% Identity: 33% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 3a0h chain L Region: 25 - 42 Aligned: 18 Modelled: 18 Confidence: 30.6% Identity: 33% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex Phyre2 PDB 3a0h chain L Region: 25 - 42 Aligned: 18 Modelled: 18 Confidence: 30.6% Identity: 33% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex Phyre2 PDB 3a0b chain L Region: 25 - 42 Aligned: 18 Modelled: 18 Confidence: 29.1% Identity: 33% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 2fok chain A domain 1 Region: 55 - 90 Aligned: 19 Modelled: 19 Confidence: 19.8% Identity: 47% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Restriction endonuclease FokI, N-terminal (recognition) domain Phyre2 PDB 3hos chain A Region: 61 - 74 Aligned: 14 Modelled: 14 Confidence: 17.4% Identity: 29% PDB header:transferase, dna binding protein/dna Chain: A: PDB Molecule:transposable element mariner, complete cds; PDBTitle: crystal structure of the mariner mos1 paired end complex with mg Phyre2 PDB 2f7t chain A Region: 61 - 74 Aligned: 14 Modelled: 14 Confidence: 15.9% Identity: 29% PDB header:dna binding protein Chain: A: PDB Molecule:mos1 transposase; PDBTitle: crystal structure of the catalytic domain of mos1 mariner2 transposase Phyre2 PDB 3n1b chain A Region: 43 - 73 Aligned: 30 Modelled: 31 Confidence: 14.2% Identity: 23% PDB header:transport protein Chain: A: PDB Molecule:vacuolar protein sorting-associated protein 54; PDBTitle: c-terminal domain of vps54 subunit of the garp complex Phyre2 PDB 2e29 chain A domain 1 Region: 59 - 74 Aligned: 16 Modelled: 16 Confidence: 11.1% Identity: 25% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: GUCT domain Phyre2 1 c3bz1L_ 2 c3kziL_ 3 c1s5ll_ 4 c1s5lL_ 5 c3prrL_ 6 d2axtl1 7 c3arcL_ 8 c2axtl_ 9 c2axtL_ 10 c3prqL_ 11 c3bz2L_ 12 c3a0bl_ 13 c3a0hl_ 14 c3a0hL_ 15 c3a0bL_ 16 d2foka1 17 c3hosA_ 18 c2f7tA_ 19 c3n1bA_ 20 d2e29a1 21 22 23 24 25 26 27 28 29 30

Detailed template information

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

1 c3bz1L_ 34.5 33 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer 2 c3kziL_ 34.5 33 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of monomeric form of cyanobacterial photosystem ii 3 c1s5ll_ 34.5 33 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 4 c1s5lL_ 34.5 33 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 5 c3prrL_ 34.5 33 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 2 of 2). this file contains second monomer of psii3 dimer 6 d2axtl1 34.5 33 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein L, PsbL Family:PsbL-like 7 c3arcL_ 34.5 33 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 8 c2axtl_ 34.5 33 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 9 c2axtL_ 34.5 33 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 10 c3prqL_ 34.5 33 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 1 of 2). this file contains first monomer of psii3 dimer 11 c3bz2L_ 34.5 33 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 22 of 2). this file contains second monomer of psii dimer 12 c3a0bl_ 30.6 33 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex 13 c3a0hl_ 30.6 33 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex 14 c3a0hL_ 30.6 33 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex 15 c3a0bL_ 29.1 33 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex 16 d2foka1 19.8 47 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Restriction endonuclease FokI, N-terminal (recognition) domain 17 c3hosA_ 17.4 29 PDB header:transferase, dna binding protein/dna Chain: A: PDB Molecule:transposable element mariner, complete cds; PDBTitle: crystal structure of the mariner mos1 paired end complex with mg 18 c2f7tA_ 15.9 29 PDB header:dna binding protein Chain: A: PDB Molecule:mos1 transposase; PDBTitle: crystal structure of the catalytic domain of mos1 mariner2 transposase 19 c3n1bA_ 14.2 23 PDB header:transport protein Chain: A: PDB Molecule:vacuolar protein sorting-associated protein 54; PDBTitle: c-terminal domain of vps54 subunit of the garp complex 20 d2e29a1 11.1 25 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:GUCT domain 21 c3f2kB_ not modelled 10.8 29 PDB header:transferase Chain: B: PDB Molecule:histone-lysine n-methyltransferase setmar; PDBTitle: structure of the transposase domain of human histone-lysine2 n-methyltransferase setmar 22 d1nb5i_ not modelled 9.2 7 Fold:Cystatin-like Superfamily:Cystatin/monellin Family:Cystatins 23 d1d2zb_ not modelled 7.7 40 Fold:DEATH domain Superfamily:DEATH domain Family:DEATH domain, DD 24 d1eu3a1 not modelled 7.1 29 Fold:OB-fold Superfamily:Bacterial enterotoxins Family:Superantigen toxins, N-terminal domain 25 c2rlfA_ not modelled 6.3 21 PDB header:proton transport Chain: A: PDB Molecule:matrix protein 2; PDBTitle: proton channel m2 from influenza a in complex with2 inhibitor rimantadine 26 d2ihoa2 not modelled 6.2 71 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:MOA C-terminal domain-like 27 d1stfi_ not modelled 6.0 11 Fold:Cystatin-like Superfamily:Cystatin/monellin Family:Cystatins 28 d2jnwa1 not modelled 6.0 21 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:XPF/Rad1/Mus81 nuclease 29 c1yceD_ not modelled 5.7 19 PDB header:membrane protein Chain: D: PDB Molecule:subunit c; PDBTitle: structure of the rotor ring of f-type na+-atpase from ilyobacter2 tartaricus 30 c3zv0A_ not modelled 5.3 13 PDB header:cell cycle Chain: A: PDB Molecule:protein shq1; PDBTitle: structure of the shq1p-cbf5p complex

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