Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	V	S	K	Y	V	A	I	F	S	F	V	F	I	Q	L	I	S	V	G	K	V	F	A	N	A	D	E	W	M	T	T	F	R	E	N	I	A	Q	T	W	Q	Q	P	E	H	Y	D	L	Y	I	P	A	I	T	W	H	A	R
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		F	A	Y	D	K	E	K	T	D	R	Y	N	E	R	P	W	G	G	G	F	G	L	S	R	W	D	E	K	G	N	W	H	G	L	Y	A	M	A	F	K	D	S	W	N	K	W	E	P	I	A	G	Y	G	W	E	S	T	W	R	P
Secondary structure
SS confidence
Disorder																													?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	A	D	E	N	F	H	L	G	L	G	F	T	A	G	V	T	A	R	D	N	W	N	Y	I	P	L	P	V	L	L	P	L	A	S	V	G	Y	G	P	V	T	F	Q	M	T	Y	I	P	G	T	Y	N	N	G	N	V	Y	F	A
Secondary structure
SS confidence
Disorder			?
Disorder confidence
		.	.	.	.	.	.
Sequence		W	M	R	F	Q	F
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 1thq chain A Region: 32 - 186 Aligned: 145 Modelled: 155 Confidence: 100.0% Identity: 99% Fold: Transmembrane beta-barrels Superfamily: OMPA-like Family: Outer membrane enzyme PagP Phyre2 PDB 1c8n chain A Region: 158 - 183 Aligned: 26 Modelled: 26 Confidence: 42.4% Identity: 23% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Tombusviridae-like VP Phyre2 PDB 4sbv chain C Region: 158 - 183 Aligned: 26 Modelled: 26 Confidence: 42.0% Identity: 27% PDB header:virus Chain: C: PDB Molecule:southern bean mosaic virus coat protein; PDBTitle: the refinement of southern bean mosaic virus in reciprocal2 space Phyre2 PDB 4sbv chain C Region: 158 - 183 Aligned: 26 Modelled: 26 Confidence: 42.0% Identity: 27% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Tombusviridae-like VP Phyre2 PDB 4sbv chain A Region: 158 - 183 Aligned: 26 Modelled: 26 Confidence: 40.0% Identity: 27% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Tombusviridae-like VP Phyre2 PDB 1f2n chain C Region: 131 - 183 Aligned: 53 Modelled: 53 Confidence: 39.9% Identity: 21% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Tombusviridae-like VP Phyre2 PDB 2vq0 chain A domain 1 Region: 158 - 183 Aligned: 26 Modelled: 26 Confidence: 38.2% Identity: 23% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Tombusviridae-like VP Phyre2 PDB 1x35 chain C Region: 158 - 183 Aligned: 26 Modelled: 26 Confidence: 35.0% Identity: 23% PDB header:virus Chain: C: PDB Molecule:coat protein; PDBTitle: recombinant t=3 capsid of a site specific mutant of semv cp Phyre2 PDB 1smv chain A Region: 158 - 183 Aligned: 26 Modelled: 26 Confidence: 34.3% Identity: 23% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Tombusviridae-like VP Phyre2 PDB 2izw chain C Region: 158 - 183 Aligned: 26 Modelled: 26 Confidence: 31.7% Identity: 31% PDB header:virus Chain: C: PDB Molecule:ryegrass mottle virus coat protein; PDBTitle: crystal structure of ryegrass mottle virus Phyre2 PDB 1c8n chain C Region: 158 - 183 Aligned: 26 Modelled: 26 Confidence: 30.5% Identity: 23% PDB header:virus Chain: C: PDB Molecule:coat protein; PDBTitle: tobacco necrosis virus Phyre2 PDB 1c8n chain C Region: 158 - 183 Aligned: 26 Modelled: 26 Confidence: 30.5% Identity: 23% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Tombusviridae-like VP Phyre2 PDB 1f2n chain A Region: 158 - 183 Aligned: 26 Modelled: 26 Confidence: 30.5% Identity: 15% PDB header:virus Chain: A: PDB Molecule:capsid protein; PDBTitle: rice yellow mottle virus Phyre2 PDB 1f2n chain A Region: 158 - 183 Aligned: 26 Modelled: 26 Confidence: 30.5% Identity: 15% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Tombusviridae-like VP Phyre2 PDB 1ng0 chain C Region: 158 - 183 Aligned: 26 Modelled: 26 Confidence: 29.1% Identity: 19% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Tombusviridae-like VP Phyre2 PDB 1ng0 chain A Region: 158 - 183 Aligned: 26 Modelled: 26 Confidence: 26.8% Identity: 19% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Tombusviridae-like VP Phyre2 PDB 1ng0 chain A Region: 158 - 183 Aligned: 26 Modelled: 26 Confidence: 26.8% Identity: 19% PDB header:virus Chain: A: PDB Molecule:coat protein; PDBTitle: the three-dimensional structure of cocksfoot mottle virus2 at 2.7a resolution Phyre2 PDB 1smv chain C Region: 158 - 183 Aligned: 26 Modelled: 26 Confidence: 24.7% Identity: 23% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Tombusviridae-like VP Phyre2 PDB 2tbv chain C Region: 158 - 181 Aligned: 24 Modelled: 24 Confidence: 24.3% Identity: 29% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Tombusviridae-like VP Phyre2 PDB 2axt chain Z domain 1 Region: 8 - 33 Aligned: 24 Modelled: 26 Confidence: 19.7% Identity: 33% Fold: Transmembrane helix hairpin Superfamily: PsbZ-like Family: PsbZ-like Phyre2 1 d1thqa_ 2 d1c8na_ 3 c4sbvC_ 4 d4sbvc_ 5 d4sbva_ 6 d1f2nc_ 7 d2vq0a1 8 c1x35C_ 9 d1smva_ 10 c2izwC_ 11 c1c8nC_ 12 d1c8nc_ 13 c1f2nA_ 14 d1f2na_ 15 d1ng0c_ 16 d1ng0a_ 17 c1ng0A_ 18 d1smvc_ 19 d2tbvc_ 20 d2axtz1 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54

Detailed template information

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

1 d1thqa_ 100.0 99 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane enzyme PagP 2 d1c8na_ 42.4 23 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Tombusviridae-like VP 3 c4sbvC_ 42.0 27 PDB header:virus Chain: C: PDB Molecule:southern bean mosaic virus coat protein; PDBTitle: the refinement of southern bean mosaic virus in reciprocal2 space 4 d4sbvc_ 42.0 27 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Tombusviridae-like VP 5 d4sbva_ 40.0 27 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Tombusviridae-like VP 6 d1f2nc_ 39.9 21 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Tombusviridae-like VP 7 d2vq0a1 38.2 23 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Tombusviridae-like VP 8 c1x35C_ 35.0 23 PDB header:virus Chain: C: PDB Molecule:coat protein; PDBTitle: recombinant t=3 capsid of a site specific mutant of semv cp 9 d1smva_ 34.3 23 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Tombusviridae-like VP 10 c2izwC_ 31.7 31 PDB header:virus Chain: C: PDB Molecule:ryegrass mottle virus coat protein; PDBTitle: crystal structure of ryegrass mottle virus 11 c1c8nC_ 30.5 23 PDB header:virus Chain: C: PDB Molecule:coat protein; PDBTitle: tobacco necrosis virus 12 d1c8nc_ 30.5 23 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Tombusviridae-like VP 13 c1f2nA_ 30.5 15 PDB header:virus Chain: A: PDB Molecule:capsid protein; PDBTitle: rice yellow mottle virus 14 d1f2na_ 30.5 15 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Tombusviridae-like VP 15 d1ng0c_ 29.1 19 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Tombusviridae-like VP 16 d1ng0a_ 26.8 19 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Tombusviridae-like VP 17 c1ng0A_ 26.8 19 PDB header:virus Chain: A: PDB Molecule:coat protein; PDBTitle: the three-dimensional structure of cocksfoot mottle virus2 at 2.7a resolution 18 d1smvc_ 24.7 23 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Tombusviridae-like VP 19 d2tbvc_ 24.3 29 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Tombusviridae-like VP 20 d2axtz1 19.7 33 Fold:Transmembrane helix hairpin Superfamily:PsbZ-like Family:PsbZ-like 21 c2zahC_ not modelled 16.6 38 PDB header:virus Chain: C: PDB Molecule:coat protein; PDBTitle: x-ray structure of melon necrotic spot virus 22 d1m3ya1 not modelled 15.5 38 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Group II dsDNA viruses VP Family:Major capsid protein vp54 23 d1opoa_ not modelled 12.2 23 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Tombusviridae-like VP 24 c1opoB_ not modelled 12.2 23 PDB header:virus Chain: B: PDB Molecule:coat protein; PDBTitle: the structure of carnation mottle virus 25 d1bev1_ not modelled 12.2 23 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Picornaviridae-like VP (VP1, VP2, VP3 and VP4) 26 d1cov1_ not modelled 10.7 22 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Picornaviridae-like VP (VP1, VP2, VP3 and VP4) 27 d1igqa_ not modelled 9.7 26 Fold:SH3-like barrel Superfamily:C-terminal domain of transcriptional repressors Family:Transcriptional repressor protein KorB 28 c1m4xC_ not modelled 8.3 38 PDB header:virus Chain: C: PDB Molecule:pbcv-1 virus capsid; PDBTitle: pbcv-1 virus capsid, quasi-atomic model 29 d1p2za1 not modelled 8.3 26 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Group II dsDNA viruses VP Family:Adenovirus hexon 30 c1j5qB_ not modelled 8.3 38 PDB header:viral protein Chain: B: PDB Molecule:major capsid protein; PDBTitle: the structure and evolution of the major capsid protein of a large,2 lipid-containing, dna virus. 31 d2d8za2 not modelled 8.1 56 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 32 d1igub_ not modelled 7.8 26 Fold:SH3-like barrel Superfamily:C-terminal domain of transcriptional repressors Family:Transcriptional repressor protein KorB 33 d2gr8a1 not modelled 7.8 29 Fold:Pili subunits Superfamily:Pili subunits Family:YadA C-terminal domain-like 34 d1txna_ not modelled 7.0 29 Fold:Coproporphyrinogen III oxidase Superfamily:Coproporphyrinogen III oxidase Family:Coproporphyrinogen III oxidase 35 d1lrwb_ not modelled 6.9 50 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:Methanol dehydrogenase subunit Family:Methanol dehydrogenase subunit 36 c3hdfA_ not modelled 6.6 18 PDB header:hydrolase Chain: A: PDB Molecule:lysozyme; PDBTitle: crystal structure of truncated endolysin r21 from phage 21 37 c2c1lA_ not modelled 6.3 21 PDB header:hydrolase Chain: A: PDB Molecule:restriction endonuclease; PDBTitle: structure of the bfii restriction endonuclease 38 d1qjpa_ not modelled 6.2 25 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 39 c2inyA_ not modelled 6.0 26 PDB header:viral protein Chain: A: PDB Molecule:hexon protein; PDBTitle: nanoporous crystals of chicken embryo lethal orphan (celo) adenovirus2 major coat protein, hexon 40 c3c5yD_ not modelled 5.9 43 PDB header:isomerase Chain: D: PDB Molecule:ribose/galactose isomerase; PDBTitle: crystal structure of a putative ribose 5-phosphate isomerase2 (saro_3514) from novosphingobium aromaticivorans dsm at 1.81 a3 resolution 41 c2ppwA_ not modelled 5.9 43 PDB header:isomerase Chain: A: PDB Molecule:conserved domain protein; PDBTitle: the crystal structure of uncharacterized ribose 5-phosphate isomerase2 rpib from streptococcus pneumoniae 42 d1aa7a_ not modelled 5.8 20 Fold:Influenza virus matrix protein M1 Superfamily:Influenza virus matrix protein M1 Family:Influenza virus matrix protein M1 43 c3l4cB_ not modelled 5.7 28 PDB header:cell adhesion, cell invasion, apoptosis Chain: B: PDB Molecule:dedicator of cytokinesis protein 1; PDBTitle: structural basis of membrane-targeting by dock180 44 d1qj8a_ not modelled 5.7 20 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 45 d1t23a_ not modelled 5.7 46 Fold:Chromosomal protein MC1 Superfamily:Chromosomal protein MC1 Family:Chromosomal protein MC1 46 c2bviK_ not modelled 5.6 26 PDB header:virus Chain: K: PDB Molecule:hexon protein; PDBTitle: the quasi-atomic model of human adenovirus type 52 capsid (part 2) 47 d1xmeb2 not modelled 5.6 50 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 48 d1y60a_ not modelled 5.6 33 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:Formaldehyde-activating enzyme, FAE 49 c3onoA_ not modelled 5.5 57 PDB header:isomerase Chain: A: PDB Molecule:ribose/galactose isomerase; PDBTitle: crystal structure of ribose-5-phosphate isomerase lacab_rpib from2 vibrio parahaemolyticus 50 c3rpjA_ not modelled 5.5 25 PDB header:transcription regulator Chain: A: PDB Molecule:curlin genes transcriptional regulator; PDBTitle: structure of a curlin genes transcriptional regulator protein from2 proteus mirabilis hi4320. 51 d2hepa1 not modelled 5.4 29 Fold:Long alpha-hairpin Superfamily:YnzC-like Family:YznC-like 52 c2hepA_ not modelled 5.4 29 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: solution nmr structure of the upf0291 protein ynzc from2 bacillus subtilis. northeast structural genomics target3 sr384. 53 d1ncqa_ not modelled 5.1 13 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Picornaviridae-like VP (VP1, VP2, VP3 and VP4) 54 c2kebA_ not modelled 5.1 29 PDB header:dna binding protein Chain: A: PDB Molecule:dna polymerase subunit alpha b; PDBTitle: nmr solution structure of the n-terminal domain of the dna polymerase2 alpha p68 subunit

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