Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	R	T	L	K	P	L	I	L	N	T	S	A	L	T	L	T	L	I	L	I	Y	T	G	I	S	A	H	D	K	L	T	W	L	M	E	V	T	P	V	I	I	V	V	Q	L	L	L	A	T	A	R	R	Y	P	L	T	P	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	Y	T	L	I	F	L	H	A	I	I	L	M	V	G	G	Q	Y	T	Y	A	K	V	P	V	G	F	E	V	Q	E	W	L	G	L	S	R	N	P	Y	D	K	L	G	H	F	F	Q	G	L	V	P	A	L	V	A	R	E	I	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	R	G	M	Y	V	R	G	R	K	M	V	A	F	L	V	C	C	V	A	L	A	I	S	A	M	Y	E	L	I	E	W	W	A	A	L	A	M	G	Q	G	A	D	D	F	L	G	T	Q	G	D	Q	W	D	T	Q	S	D	M	F
Secondary structure
SS confidence
Disorder						?	?	?																																								?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.
Sequence		C	A	L	L	G	A	L	T	T	V	I	F	L	A	R	F	H	C	R	Q	L	R	R	F	G	L	I	T	G
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 3shp chain A Region: 169 - 177 Aligned: 9 Modelled: 9 Confidence: 55.1% Identity: 56% PDB header:transferase Chain: A: PDB Molecule:putative acetyltransferase sthe_0691; PDBTitle: crystal structure of putative acetyltransferase from sphaerobacter2 thermophilus dsm 20745 Phyre2 PDB 1ceu chain A Region: 84 - 113 Aligned: 30 Modelled: 30 Confidence: 26.4% Identity: 17% PDB header:viral protein Chain: A: PDB Molecule:protein (hiv-1 regulatory protein n-terminal PDBTitle: nmr structure of the (1-51) n-terminal domain of the hiv-12 regulatory protein Phyre2 PDB 2d9r chain A domain 1 Region: 75 - 97 Aligned: 21 Modelled: 21 Confidence: 14.6% Identity: 24% Fold: Double-split beta-barrel Superfamily: AF2212/PG0164-like Family: PG0164-like Phyre2 PDB 1ifl chain A Region: 159 - 199 Aligned: 41 Modelled: 41 Confidence: 10.2% Identity: 10% PDB header:virus Chain: A: PDB Molecule:inovirus; PDBTitle: molecular models and structural comparisons of native and2 mutant class i filamentous bacteriophages ff (fd, f1, m13),3 if1 and ike Phyre2 PDB 2df7 chain H Region: 74 - 81 Aligned: 8 Modelled: 8 Confidence: 10.2% Identity: 50% PDB header:virus like particle Chain: H: PDB Molecule:structural polyprotein vp2; PDBTitle: crystal structure of infectious bursal disease virus vp2 subviral2 particle Phyre2 PDB 2k6l chain A Region: 164 - 171 Aligned: 8 Modelled: 8 Confidence: 10.0% Identity: 38% PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: the solution structure of xacb0070 from xanthonomas2 axonopodis pv citri reveals this new protein is a member of3 the rhh family of transcriptional repressors Phyre2 PDB 2df7 chain A domain 1 Region: 74 - 81 Aligned: 8 Modelled: 8 Confidence: 9.7% Identity: 50% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Birnaviridae-like VP Phyre2 PDB 1m8l chain A Region: 82 - 113 Aligned: 32 Modelled: 32 Confidence: 9.6% Identity: 13% PDB header:viral protein Chain: A: PDB Molecule:vpr protein; PDBTitle: nmr structure of the hiv-1 regulatory protein vpr Phyre2 PDB 1yu8 chain X domain 1 Region: 86 - 103 Aligned: 18 Modelled: 18 Confidence: 9.4% Identity: 17% Fold: VHP, Villin headpiece domain Superfamily: VHP, Villin headpiece domain Family: VHP, Villin headpiece domain Phyre2 PDB 3nqz chain B Region: 76 - 101 Aligned: 22 Modelled: 24 Confidence: 9.4% Identity: 23% PDB header:hydrolase Chain: B: PDB Molecule:secreted metalloprotease mcp02; PDBTitle: crystal structure of the autoprocessed vibriolysin mcp-02 with e369a2 mutation Phyre2 PDB 1und chain A Region: 86 - 103 Aligned: 18 Modelled: 18 Confidence: 9.4% Identity: 17% Fold: VHP, Villin headpiece domain Superfamily: VHP, Villin headpiece domain Family: VHP, Villin headpiece domain Phyre2 PDB 1unc chain A Region: 86 - 103 Aligned: 18 Modelled: 18 Confidence: 9.0% Identity: 11% Fold: VHP, Villin headpiece domain Superfamily: VHP, Villin headpiece domain Family: VHP, Villin headpiece domain Phyre2 PDB 1yq1 chain A Region: 75 - 125 Aligned: 51 Modelled: 51 Confidence: 8.8% Identity: 14% PDB header:transferase Chain: A: PDB Molecule:glutathione s-transferase; PDBTitle: structural genomics of caenorhabditis elegans: glutathione2 s-transferase Phyre2 PDB 1t0z chain A Region: 170 - 178 Aligned: 9 Modelled: 9 Confidence: 8.7% Identity: 33% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Scorpion toxin-like Family: Long-chain scorpion toxins Phyre2 PDB 1u4g chain A Region: 76 - 101 Aligned: 22 Modelled: 26 Confidence: 8.0% Identity: 18% Fold: Zincin-like Superfamily: Metalloproteases ("zincins"), catalytic domain Family: Thermolysin-like Phyre2 PDB 1b33 chain N Region: 83 - 91 Aligned: 9 Modelled: 9 Confidence: 7.8% Identity: 33% Fold: Allophycocyanin linker chain (domain) Superfamily: Allophycocyanin linker chain (domain) Family: Allophycocyanin linker chain (domain) Phyre2 PDB 3ide chain D Region: 74 - 80 Aligned: 7 Modelled: 7 Confidence: 7.6% Identity: 29% PDB header:virus like particle Chain: D: PDB Molecule:capsid protein vp2; PDBTitle: structure of ipnv subviral particle Phyre2 PDB 1xcr chain A domain 1 Region: 75 - 84 Aligned: 10 Modelled: 10 Confidence: 7.5% Identity: 50% Fold: AF0104/ALDC/Ptd012-like Superfamily: AF0104/ALDC/Ptd012-like Family: PTD012-like Phyre2 PDB 1zdb chain A Region: 144 - 150 Aligned: 7 Modelled: 7 Confidence: 7.2% Identity: 29% PDB header:igg binding domain Chain: A: PDB Molecule:mini protein a domain, z38; PDBTitle: phage-selected mini protein a domain, z38, nmr, minimized2 mean structure Phyre2 PDB 1s28 chain A Region: 94 - 104 Aligned: 11 Modelled: 11 Confidence: 7.1% Identity: 36% Fold: Secretion chaperone-like Superfamily: Type III secretory system chaperone-like Family: Type III secretory system chaperone Phyre2 1 c3shpA_ 2 c1ceuA_ 3 d2d9ra1 4 c1iflA_ 5 c2df7H_ 6 c2k6lA_ 7 d2df7a1 8 c1m8lA_ 9 d1yu8x1 10 c3nqzB_ 11 d1unda_ 12 d1unca_ 13 c1yq1A_ 14 d1t0za_ 15 d1u4ga_ 16 d1b33n_ 17 c3ideD_ 18 d1xcra1 19 c1zdbA_ 20 d1s28a_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38

Detailed template information

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

1 c3shpA_ 55.1 56 PDB header:transferase Chain: A: PDB Molecule:putative acetyltransferase sthe_0691; PDBTitle: crystal structure of putative acetyltransferase from sphaerobacter2 thermophilus dsm 20745 2 c1ceuA_ 26.4 17 PDB header:viral protein Chain: A: PDB Molecule:protein (hiv-1 regulatory protein n-terminal PDBTitle: nmr structure of the (1-51) n-terminal domain of the hiv-12 regulatory protein 3 d2d9ra1 14.6 24 Fold:Double-split beta-barrel Superfamily:AF2212/PG0164-like Family:PG0164-like 4 c1iflA_ 10.2 10 PDB header:virus Chain: A: PDB Molecule:inovirus; PDBTitle: molecular models and structural comparisons of native and2 mutant class i filamentous bacteriophages ff (fd, f1, m13),3 if1 and ike 5 c2df7H_ 10.2 50 PDB header:virus like particle Chain: H: PDB Molecule:structural polyprotein vp2; PDBTitle: crystal structure of infectious bursal disease virus vp2 subviral2 particle 6 c2k6lA_ 10.0 38 PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: the solution structure of xacb0070 from xanthonomas2 axonopodis pv citri reveals this new protein is a member of3 the rhh family of transcriptional repressors 7 d2df7a1 9.7 50 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Birnaviridae-like VP 8 c1m8lA_ 9.6 13 PDB header:viral protein Chain: A: PDB Molecule:vpr protein; PDBTitle: nmr structure of the hiv-1 regulatory protein vpr 9 d1yu8x1 9.4 17 Fold:VHP, Villin headpiece domain Superfamily:VHP, Villin headpiece domain Family:VHP, Villin headpiece domain 10 c3nqzB_ 9.4 23 PDB header:hydrolase Chain: B: PDB Molecule:secreted metalloprotease mcp02; PDBTitle: crystal structure of the autoprocessed vibriolysin mcp-02 with e369a2 mutation 11 d1unda_ 9.4 17 Fold:VHP, Villin headpiece domain Superfamily:VHP, Villin headpiece domain Family:VHP, Villin headpiece domain 12 d1unca_ 9.0 11 Fold:VHP, Villin headpiece domain Superfamily:VHP, Villin headpiece domain Family:VHP, Villin headpiece domain 13 c1yq1A_ 8.8 14 PDB header:transferase Chain: A: PDB Molecule:glutathione s-transferase; PDBTitle: structural genomics of caenorhabditis elegans: glutathione2 s-transferase 14 d1t0za_ 8.7 33 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Scorpion toxin-like Family:Long-chain scorpion toxins 15 d1u4ga_ 8.0 18 Fold:Zincin-like Superfamily:Metalloproteases ("zincins"), catalytic domain Family:Thermolysin-like 16 d1b33n_ 7.8 33 Fold:Allophycocyanin linker chain (domain) Superfamily:Allophycocyanin linker chain (domain) Family:Allophycocyanin linker chain (domain) 17 c3ideD_ 7.6 29 PDB header:virus like particle Chain: D: PDB Molecule:capsid protein vp2; PDBTitle: structure of ipnv subviral particle 18 d1xcra1 7.5 50 Fold:AF0104/ALDC/Ptd012-like Superfamily:AF0104/ALDC/Ptd012-like Family:PTD012-like 19 c1zdbA_ 7.2 29 PDB header:igg binding domain Chain: A: PDB Molecule:mini protein a domain, z38; PDBTitle: phage-selected mini protein a domain, z38, nmr, minimized2 mean structure 20 d1s28a_ 7.1 36 Fold:Secretion chaperone-like Superfamily:Type III secretory system chaperone-like Family:Type III secretory system chaperone 21 c2h2wA_ not modelled 7.0 24 PDB header:transferase Chain: A: PDB Molecule:homoserine o-succinyltransferase; PDBTitle: crystal structure of homoserine o-succinyltransferase (ec 2.3.1.46)2 (homoserine o-transsuccinylase) (hts) (tm0881) from thermotoga3 maritima at 2.52 a resolution 22 c2k6nA_ not modelled 6.9 22 PDB header:structural protein Chain: A: PDB Molecule:supervillin; PDBTitle: solution structure of human supervillin headpiece, minimized2 average 23 c3zqoK_ not modelled 6.6 29 PDB header:dna-binding protein Chain: K: PDB Molecule:terminase small subunit; PDBTitle: crystal structure of the small terminase oligomerization2 core domain from a spp1-like bacteriophage (crystal form 3) 24 d1oz9a_ not modelled 6.4 21 Fold:Zincin-like Superfamily:Metalloproteases ("zincins"), catalytic domain Family:Predicted metal-dependent hydrolase 25 c3nixF_ not modelled 6.4 20 PDB header:oxidoreductase Chain: F: PDB Molecule:flavoprotein/dehydrogenase; PDBTitle: crystal structure of flavoprotein/dehydrogenase from cytophaga2 hutchinsonii. northeast structural genomics consortium target chr43. 26 d1kqfc_ not modelled 6.2 12 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Formate dehydrogenase N, cytochrome (gamma) subunit 27 d1oqva_ not modelled 6.0 11 Fold:Pili subunits Superfamily:Pili subunits Family:TcpA-like pilin 28 c2cj0A_ not modelled 5.9 22 PDB header:oxidoreductase Chain: A: PDB Molecule:chloroperoxidase; PDBTitle: chloroperoxidase complexed with nitrate 29 d1qzpa_ not modelled 5.9 17 Fold:VHP, Villin headpiece domain Superfamily:VHP, Villin headpiece domain Family:VHP, Villin headpiece domain 30 d1n2fa_ not modelled 5.9 19 Fold:OsmC-like Superfamily:OsmC-like Family:Ohr/OsmC resistance proteins 31 d1ujsa_ not modelled 5.7 20 Fold:VHP, Villin headpiece domain Superfamily:VHP, Villin headpiece domain Family:VHP, Villin headpiece domain 32 d1yu5x1 not modelled 5.7 17 Fold:VHP, Villin headpiece domain Superfamily:VHP, Villin headpiece domain Family:VHP, Villin headpiece domain 33 c2l3xA_ not modelled 5.6 39 PDB header:protein binding Chain: A: PDB Molecule:ablim2 protein; PDBTitle: villin head piece domain of human ablim2 34 c2jmhA_ not modelled 5.5 57 PDB header:allergen Chain: A: PDB Molecule:mite allergen blo t 5; PDBTitle: nmr solution structure of blo t 5, a major mite allergen2 from blomia tropicalis 35 c1vjqB_ not modelled 5.5 21 PDB header:structural genomics, de novo protein Chain: B: PDB Molecule:designed protein; PDBTitle: designed protein based on backbone conformation of2 procarboxypeptidase-a (1aye) with sidechains chosen for maximal3 predicted stability. 36 d2d8ca1 not modelled 5.2 33 Fold:SAM domain-like Superfamily:SAM/Pointed domain Family:SAM (sterile alpha motif) domain 37 c3gd9A_ not modelled 5.1 38 PDB header:hydrolase Chain: A: PDB Molecule:laminaripentaose-producing beta-1,3-guluase PDBTitle: crystal structure of laminaripentaose-producing beta-1,3-2 glucanase in complex with laminaritetraose 38 d1edla_ not modelled 5.1 29 Fold:immunoglobulin/albumin-binding domain-like Superfamily:Bacterial immunoglobulin/albumin-binding domains Family:Immunoglobulin-binding protein A modules

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