Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	A	I	T	E	S	K	P	T	R	R	W	A	M	P	D	T	L	V	I	I	F	F	V	A	I	L	T	S	L	A	T	W	V	V	P	V	G	M	F	D	S	Q	E	V	Q	Y	Q	V	D	G	Q	T	K	T	R	K	V	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?																															?	?	?	?	?	?	?	?	?	?	?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		D	P	H	S	F	R	I	L	T	N	E	A	G	E	P	E	Y	H	R	V	Q	L	F	T	T	G	D	E	R	P	G	L	M	N	F	P	F	E	G	L	T	S	G	S	K	Y	G	T	A	V	G	I	I	M	F	M	L	V	I	G
Secondary structure
SS confidence
Disorder															?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?										?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	A	F	G	I	V	M	R	T	G	T	I	D	N	G	I	L	A	L	I	R	H	T	R	G	N	E	I	L	F	I	P	A	L	F	I	L	F	S	L	G	G	A	V	F	G	M	G	E	E	A	V	A	F	A	I	I	I	A	P
Secondary structure
SS confidence
Disorder																																												?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	M	V	R	L	G	Y	D	S	I	T	T	V	L	V	T	Y	I	A	T	Q	I	G	F	A	S	S	W	M	N	P	F	C	V	V	V	A	Q	G	I	A	G	V	P	V	L	S	G	S	G	L	R	I	V	V	W	V	I	A	T
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		L	I	G	L	I	F	T	M	V	Y	A	S	R	V	K	K	N	P	L	L	S	R	V	H	E	S	D	R	F	F	R	E	K	Q	A	D	V	E	Q	R	P	F	T	F	G	D	W	L	V	L	I	V	L	T	A	V	M	V	W	V
Secondary structure
SS confidence
Disorder																													?		?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		I	W	G	V	I	V	N	A	W	F	I	P	E	I	A	S	Q	F	F	T	M	G	L	V	I	G	I	I	G	V	V	F	R	L	N	G	M	T	V	N	T	M	A	S	S	F	T	E	G	A	R	M	M	I	A	P	A	L	L	V
Secondary structure
SS confidence
Disorder							?	?	?																									?	?	?		?	?															?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		G	F	A	K	G	I	L	L	L	V	G	N	G	E	A	G	D	A	S	V	L	N	T	I	L	N	S	I	A	N	A	I	S	G	L	D	N	A	V	A	A	W	F	M	L	L	F	Q	A	V	F	N	F	F	V	T	S	G	S	G
Secondary structure
SS confidence
Disorder														?	?	?	?	?															?	?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		Q	A	A	L	T	M	P	L	L	A	P	L	G	D	L	V	G	V	N	R	Q	V	T	V	L	A	F	Q	F	G	D	G	F	S	H	I	I	Y	P	T	S	A	S	L	M	A	T	L	G	V	C	R	V	D	F	R	N	W	L	K
Secondary structure
SS confidence
Disorder																	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.
Sequence		V	G	A	T	L	L	G	L	L	F	I	M	S	S	V	V	V	I	G	A	Q	L	M	G	Y	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 3qnq chain D Region: 129 - 270 Aligned: 134 Modelled: 142 Confidence: 46.1% Identity: 12% PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system Phyre2 PDB 2voy chain E Region: 112 - 131 Aligned: 20 Modelled: 20 Confidence: 20.1% Identity: 15% PDB header:hydrolase Chain: E: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus Phyre2 PDB 2knc chain A Region: 229 - 268 Aligned: 40 Modelled: 40 Confidence: 12.1% Identity: 10% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 3eh4 chain A Region: 228 - 312 Aligned: 85 Modelled: 85 Confidence: 10.4% Identity: 13% PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c oxidase subunit 1; PDBTitle: structure of the reduced form of cytochrome ba3 oxidase from thermus2 thermophilus Phyre2 PDB 1jb0 chain F Region: 489 - 505 Aligned: 17 Modelled: 17 Confidence: 9.4% Identity: 24% Fold: Single transmembrane helix Superfamily: Subunit III of photosystem I reaction centre, PsaF Family: Subunit III of photosystem I reaction centre, PsaF Phyre2 PDB 1eys chain H Region: 3 - 17 Aligned: 15 Modelled: 15 Confidence: 9.1% Identity: 7% PDB header:electron transport Chain: H: PDB Molecule:photosynthetic reaction center; PDBTitle: crystal structure of photosynthetic reaction center from a2 thermophilic bacterium, thermochromatium tepidum Phyre2 PDB 2wsf chain F Region: 489 - 505 Aligned: 17 Modelled: 17 Confidence: 8.5% Identity: 12% PDB header:photosynthesis Chain: F: PDB Molecule:photosystem i reaction center subunit iii, PDBTitle: improved model of plant photosystem i Phyre2 PDB 2yvx chain D Region: 12 - 201 Aligned: 148 Modelled: 158 Confidence: 8.1% Identity: 15% PDB header:transport protein Chain: D: PDB Molecule:mg2+ transporter mgte; PDBTitle: crystal structure of magnesium transporter mgte Phyre2 PDB 2j01 chain C domain 1 Region: 3 - 19 Aligned: 17 Modelled: 17 Confidence: 7.1% Identity: 18% Fold: Ribosomal protein L1 Superfamily: Ribosomal protein L1 Family: Ribosomal protein L1 Phyre2 PDB 3mk7 chain F Region: 229 - 310 Aligned: 82 Modelled: 82 Confidence: 6.5% Identity: 6% PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase Phyre2 PDB 1wrg chain A Region: 18 - 35 Aligned: 18 Modelled: 18 Confidence: 6.4% Identity: 28% PDB header:membrane protein Chain: A: PDB Molecule:light-harvesting protein b-880, beta chain; PDBTitle: light-harvesting complex 1 beta subunit from wild-type2 rhodospirillum rubrum Phyre2 PDB 1nee chain A domain 1 Region: 5 - 18 Aligned: 14 Modelled: 14 Confidence: 6.4% Identity: 29% Fold: Ribosome binding domain-like Superfamily: Translation initiation factor 2 beta, aIF2beta, N-terminal domain Family: Translation initiation factor 2 beta, aIF2beta, N-terminal domain Phyre2 PDB 1lgh chain B Region: 18 - 35 Aligned: 18 Modelled: 18 Confidence: 6.3% Identity: 22% Fold: Light-harvesting complex subunits Superfamily: Light-harvesting complex subunits Family: Light-harvesting complex subunits Phyre2 PDB 3kys chain B Region: 11 - 19 Aligned: 9 Modelled: 9 Confidence: 6.3% Identity: 33% PDB header:transcription/protein binding Chain: B: PDB Molecule:65 kda yes-associated protein; PDBTitle: crystal structure of human yap and tead complex Phyre2 PDB 1k8g chain A domain 2 Region: 12 - 17 Aligned: 6 Modelled: 6 Confidence: 5.7% Identity: 17% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Single strand DNA-binding domain, SSB Phyre2 PDB 2voy chain B Region: 5 - 32 Aligned: 28 Modelled: 28 Confidence: 5.7% Identity: 29% PDB header:hydrolase Chain: B: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus Phyre2 PDB 1nee chain A Region: 5 - 18 Aligned: 14 Modelled: 14 Confidence: 5.6% Identity: 29% PDB header:translation Chain: A: PDB Molecule:probable translation initiation factor 2 beta PDBTitle: structure of archaeal translation factor aif2beta from2 methanobacterium thermoautrophicum Phyre2 PDB 2b2h chain A Region: 129 - 279 Aligned: 151 Modelled: 151 Confidence: 5.5% Identity: 10% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) Phyre2 PDB 2o01 chain F Region: 493 - 505 Aligned: 13 Modelled: 13 Confidence: 5.4% Identity: 15% PDB header:photosynthesis Chain: F: PDB Molecule:photosystem i reaction center subunit iii, PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution Phyre2 PDB 2gyc chain 2 Region: 3 - 19 Aligned: 17 Modelled: 17 Confidence: 5.4% Identity: 24% PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l1; PDBTitle: structure of the 50s subunit of a secm-stalled e. coli2 ribosome complex obtained by fitting atomic models for rna3 and protein components into cryo-em map emd-1143 Phyre2 1 c3qnqD_ 2 c2voyE_ 3 c2kncA_ 4 c3eh4A_ 5 d1jb0f_ 6 c1eysH_ 7 c2wsfF_ 8 c2yvxD_ 9 d2j01c1 10 c3mk7F_ 11 c1wrgA_ 12 d1neea1 13 d1lghb_ 14 c3kysB_ 15 d1k8ga2 16 c2voyB_ 17 c1neeA_ 18 c2b2hA_ 19 c2o01F_ 20 c2gyc2_ 21 22 23 24

Detailed template information

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

1 c3qnqD_ 46.1 12 PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system 2 c2voyE_ 20.1 15 PDB header:hydrolase Chain: E: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus 3 c2kncA_ 12.1 10 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 4 c3eh4A_ 10.4 13 PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c oxidase subunit 1; PDBTitle: structure of the reduced form of cytochrome ba3 oxidase from thermus2 thermophilus 5 d1jb0f_ 9.4 24 Fold:Single transmembrane helix Superfamily:Subunit III of photosystem I reaction centre, PsaF Family:Subunit III of photosystem I reaction centre, PsaF 6 c1eysH_ 9.1 7 PDB header:electron transport Chain: H: PDB Molecule:photosynthetic reaction center; PDBTitle: crystal structure of photosynthetic reaction center from a2 thermophilic bacterium, thermochromatium tepidum 7 c2wsfF_ 8.5 12 PDB header:photosynthesis Chain: F: PDB Molecule:photosystem i reaction center subunit iii, PDBTitle: improved model of plant photosystem i 8 c2yvxD_ 8.1 15 PDB header:transport protein Chain: D: PDB Molecule:mg2+ transporter mgte; PDBTitle: crystal structure of magnesium transporter mgte 9 d2j01c1 7.1 18 Fold:Ribosomal protein L1 Superfamily:Ribosomal protein L1 Family:Ribosomal protein L1 10 c3mk7F_ 6.5 6 PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase 11 c1wrgA_ 6.4 28 PDB header:membrane protein Chain: A: PDB Molecule:light-harvesting protein b-880, beta chain; PDBTitle: light-harvesting complex 1 beta subunit from wild-type2 rhodospirillum rubrum 12 d1neea1 6.4 29 Fold:Ribosome binding domain-like Superfamily:Translation initiation factor 2 beta, aIF2beta, N-terminal domain Family:Translation initiation factor 2 beta, aIF2beta, N-terminal domain 13 d1lghb_ 6.3 22 Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits 14 c3kysB_ 6.3 33 PDB header:transcription/protein binding Chain: B: PDB Molecule:65 kda yes-associated protein; PDBTitle: crystal structure of human yap and tead complex 15 d1k8ga2 5.7 17 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Single strand DNA-binding domain, SSB 16 c2voyB_ 5.7 29 PDB header:hydrolase Chain: B: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus 17 c1neeA_ 5.6 29 PDB header:translation Chain: A: PDB Molecule:probable translation initiation factor 2 beta PDBTitle: structure of archaeal translation factor aif2beta from2 methanobacterium thermoautrophicum 18 c2b2hA_ 5.5 10 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) 19 c2o01F_ 5.4 15 PDB header:photosynthesis Chain: F: PDB Molecule:photosystem i reaction center subunit iii, PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution 20 c2gyc2_ 5.4 24 PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l1; PDBTitle: structure of the 50s subunit of a secm-stalled e. coli2 ribosome complex obtained by fitting atomic models for rna3 and protein components into cryo-em map emd-1143 21 c2vdaB_ not modelled 5.2 29 PDB header:protein transport Chain: B: PDB Molecule:maltoporin; PDBTitle: solution structure of the seca-signal peptide complex 22 d1fftb2 not modelled 5.2 6 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 23 d1jb7a2 not modelled 5.2 17 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Single strand DNA-binding domain, SSB 24 d1wiia_ not modelled 5.1 7 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Putative zinc binding domain

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