Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	Q	F	Y	V	H	V	R	L	F	E	D	T	A	E	Q	T	K	K	F	E	E	L	M	L	N	F	L	Y	Q	K	T	V	K	E	S	D	D	S	C	C	R	L	I	P	E	G	Y	I	L	K	S	T	M	N	C	Q	Q	I
Secondary structure
SS confidence
Disorder		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.
Sequence		L	D	Q	T	F	S	I	A	N	S	A	G	V	D	A	N	I	F	V	C	K	F	E	Q	S	A	C	L	L	P	S	A	S	L	V	G	N	D	F	V	H	Y	D	L	T	P	K	P	I	K	L	D	S
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 1gff chain 2 Region: 63 - 99 Aligned: 37 Modelled: 37 Confidence: 26.1% Identity: 30% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: ssDNA viruses Family: Microviridae-like VP Phyre2 PDB 1dx5 chain I domain 2 Region: 46 - 57 Aligned: 12 Modelled: 12 Confidence: 23.2% Identity: 58% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: EGF/Laminin Family: EGF-type module Phyre2 PDB 1i8l chain C Region: 64 - 83 Aligned: 20 Modelled: 20 Confidence: 17.0% Identity: 25% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 PDB 1j8i chain A Region: 37 - 95 Aligned: 46 Modelled: 59 Confidence: 15.7% Identity: 33% Fold: IL8-like Superfamily: Interleukin 8-like chemokines Family: Interleukin 8-like chemokines Phyre2 PDB 2rh2 chain A domain 1 Region: 41 - 53 Aligned: 13 Modelled: 13 Confidence: 15.1% Identity: 54% Fold: SH3-like barrel Superfamily: Electron transport accessory proteins Family: R67 dihydrofolate reductase Phyre2 PDB 1gpm chain A domain 3 Region: 100 - 108 Aligned: 9 Modelled: 9 Confidence: 11.6% Identity: 56% Fold: Alpha-lytic protease prodomain-like Superfamily: GMP synthetase C-terminal dimerisation domain Family: GMP synthetase C-terminal dimerisation domain Phyre2 PDB 2wfu chain A Region: 39 - 43 Aligned: 5 Modelled: 5 Confidence: 10.3% Identity: 100% PDB header:signaling protein Chain: A: PDB Molecule:probable insulin-like peptide 5 a chain; PDBTitle: crystal structure of dilp5 variant db Phyre2 PDB 2wfv chain A Region: 39 - 43 Aligned: 5 Modelled: 5 Confidence: 10.0% Identity: 100% PDB header:signaling protein Chain: A: PDB Molecule:probable insulin-like peptide 5 a chain; PDBTitle: crystal structure of dilp5 variant c4 Phyre2 PDB 1v5s chain A Region: 53 - 99 Aligned: 47 Modelled: 47 Confidence: 9.6% Identity: 23% Fold: TBP-like Superfamily: KA1-like Family: Kinase associated domain 1, KA1 Phyre2 PDB 4htc chain I Region: 94 - 108 Aligned: 15 Modelled: 15 Confidence: 9.4% Identity: 53% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Leech antihemostatic proteins Family: Hirudin-like Phyre2 PDB 1wvo chain A Region: 43 - 55 Aligned: 13 Modelled: 13 Confidence: 9.3% Identity: 54% PDB header:transferase Chain: A: PDB Molecule:sialic acid synthase; PDBTitle: solution structure of rsgi ruh-029, an antifreeze protein2 like domain in human n-acetylneuraminic acid phosphate3 synthase gene. Phyre2 PDB 1tyk chain A Region: 38 - 43 Aligned: 6 Modelled: 6 Confidence: 8.6% Identity: 83% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: omega toxin-like Family: Spider toxins Phyre2 PDB 1m3w chain D Region: 16 - 25 Aligned: 10 Modelled: 10 Confidence: 8.5% Identity: 70% PDB header:de novo protein Chain: D: PDB Molecule:h10h24; PDBTitle: crystal structure of a molecular maquette scaffold Phyre2 PDB 1m3w chain C Region: 16 - 25 Aligned: 10 Modelled: 10 Confidence: 8.5% Identity: 70% PDB header:de novo protein Chain: C: PDB Molecule:h10h24; PDBTitle: crystal structure of a molecular maquette scaffold Phyre2 PDB 1m3w chain B Region: 16 - 25 Aligned: 10 Modelled: 10 Confidence: 8.5% Identity: 70% PDB header:de novo protein Chain: B: PDB Molecule:h10h24; PDBTitle: crystal structure of a molecular maquette scaffold Phyre2 PDB 1m3w chain A Region: 16 - 25 Aligned: 10 Modelled: 10 Confidence: 8.5% Identity: 70% PDB header:de novo protein Chain: A: PDB Molecule:h10h24; PDBTitle: crystal structure of a molecular maquette scaffold Phyre2 PDB 1g3p chain A domain 2 Region: 68 - 90 Aligned: 23 Modelled: 23 Confidence: 8.4% Identity: 35% Fold: N-terminal domains of the minor coat protein g3p Superfamily: N-terminal domains of the minor coat protein g3p Family: N-terminal domains of the minor coat protein g3p Phyre2 PDB 1ev7 chain A Region: 30 - 51 Aligned: 22 Modelled: 22 Confidence: 7.5% Identity: 36% Fold: Restriction endonuclease-like Superfamily: Restriction endonuclease-like Family: Restriction endonuclease NaeI Phyre2 PDB 2op5 chain A domain 1 Region: 57 - 67 Aligned: 11 Modelled: 11 Confidence: 7.2% Identity: 55% Fold: Ferredoxin-like Superfamily: Dimeric alpha+beta barrel Family: Marine metagenome family DABB1 Phyre2 PDB 2ywc chain C Region: 100 - 108 Aligned: 9 Modelled: 9 Confidence: 7.1% Identity: 78% PDB header:ligase Chain: C: PDB Molecule:gmp synthase [glutamine-hydrolyzing]; PDBTitle: crystal structure of gmp synthetase from thermus thermophilus in2 complex with xmp Phyre2 1 d1gff2_ 2 d1dx5i2 3 d1i8lc_ 4 d1j8ia_ 5 d2rh2a1 6 d1gpma3 7 c2wfuA_ 8 c2wfvA_ 9 d1v5sa_ 10 d4htci_ 11 c1wvoA_ 12 d1tyka_ 13 c1m3wD_ 14 c1m3wC_ 15 c1m3wB_ 16 c1m3wA_ 17 d1g3pa2 18 d1ev7a_ 19 d2op5a1 20 c2ywcC_ 21 22 23 24 25 26 27 28 29 30

Detailed template information

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

1 d1gff2_ 26.1 30 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:ssDNA viruses Family:Microviridae-like VP 2 d1dx5i2 23.2 58 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:EGF/Laminin Family:EGF-type module 3 d1i8lc_ 17.0 25 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 4 d1j8ia_ 15.7 33 Fold:IL8-like Superfamily:Interleukin 8-like chemokines Family:Interleukin 8-like chemokines 5 d2rh2a1 15.1 54 Fold:SH3-like barrel Superfamily:Electron transport accessory proteins Family:R67 dihydrofolate reductase 6 d1gpma3 11.6 56 Fold:Alpha-lytic protease prodomain-like Superfamily:GMP synthetase C-terminal dimerisation domain Family:GMP synthetase C-terminal dimerisation domain 7 c2wfuA_ 10.3 100 PDB header:signaling protein Chain: A: PDB Molecule:probable insulin-like peptide 5 a chain; PDBTitle: crystal structure of dilp5 variant db 8 c2wfvA_ 10.0 100 PDB header:signaling protein Chain: A: PDB Molecule:probable insulin-like peptide 5 a chain; PDBTitle: crystal structure of dilp5 variant c4 9 d1v5sa_ 9.6 23 Fold:TBP-like Superfamily:KA1-like Family:Kinase associated domain 1, KA1 10 d4htci_ 9.4 53 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Leech antihemostatic proteins Family:Hirudin-like 11 c1wvoA_ 9.3 54 PDB header:transferase Chain: A: PDB Molecule:sialic acid synthase; PDBTitle: solution structure of rsgi ruh-029, an antifreeze protein2 like domain in human n-acetylneuraminic acid phosphate3 synthase gene. 12 d1tyka_ 8.6 83 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:omega toxin-like Family:Spider toxins 13 c1m3wD_ 8.5 70 PDB header:de novo protein Chain: D: PDB Molecule:h10h24; PDBTitle: crystal structure of a molecular maquette scaffold 14 c1m3wC_ 8.5 70 PDB header:de novo protein Chain: C: PDB Molecule:h10h24; PDBTitle: crystal structure of a molecular maquette scaffold 15 c1m3wB_ 8.5 70 PDB header:de novo protein Chain: B: PDB Molecule:h10h24; PDBTitle: crystal structure of a molecular maquette scaffold 16 c1m3wA_ 8.5 70 PDB header:de novo protein Chain: A: PDB Molecule:h10h24; PDBTitle: crystal structure of a molecular maquette scaffold 17 d1g3pa2 8.4 35 Fold:N-terminal domains of the minor coat protein g3p Superfamily:N-terminal domains of the minor coat protein g3p Family:N-terminal domains of the minor coat protein g3p 18 d1ev7a_ 7.5 36 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:Restriction endonuclease NaeI 19 d2op5a1 7.2 55 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:Marine metagenome family DABB1 20 c2ywcC_ 7.1 78 PDB header:ligase Chain: C: PDB Molecule:gmp synthase [glutamine-hydrolyzing]; PDBTitle: crystal structure of gmp synthetase from thermus thermophilus in2 complex with xmp 21 d2dexx2 not modelled 7.1 47 Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Peptidylarginine deiminase Pad4, N-terminal domain 22 d1p8ba_ not modelled 6.4 46 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:omega toxin-like Family:Albumin 1 23 c1h8lA_ not modelled 6.4 19 PDB header:carboxypeptidase Chain: A: PDB Molecule:carboxypeptidase gp180 residues 503-882; PDBTitle: duck carboxypeptidase d domain ii in complex with gemsa 24 d1kqha_ not modelled 6.2 71 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:omega toxin-like Family:Spider toxins 25 d1c8aa2 not modelled 6.1 38 Fold:beta-clip Superfamily:AFP III-like domain Family:AFP III-like domain 26 d1opsa_ not modelled 5.8 38 Fold:beta-clip Superfamily:AFP III-like domain Family:AFP III-like domain 27 d1bmlc1 not modelled 5.6 54 Fold:beta-Grasp (ubiquitin-like) Superfamily:Staphylokinase/streptokinase Family:Staphylokinase/streptokinase 28 c1y96D_ not modelled 5.5 24 PDB header:rna binding protein Chain: D: PDB Molecule:gem-associated protein 7; PDBTitle: crystal structure of the gemin6/gemin7 heterodimer from the2 human smn complex 29 d1bo0a_ not modelled 5.3 28 Fold:IL8-like Superfamily:Interleukin 8-like chemokines Family:Interleukin 8-like chemokines 30 d1xn8a_ not modelled 5.2 35 Fold:Hypothetical protein YqbG Superfamily:Hypothetical protein YqbG Family:Hypothetical protein YqbG

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