Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		G	S	A	T	I	A	L	N	K	R	A	R	H	E	Y	F	I	E	E	E	F	E	A	G	L	A	L	Q	G	W	E	V	K	S	L	R	A	G	K	A	N	I	S	D	S	Y	V	L	L	R	D	G	E	A	F	L	F	G	A	N
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																														?	?	?				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	T	P	M	A	V	A	S	T	H	V	V	C	D	P	T	R	T	R	K	L	L	L	N	Q	R	E	L	D	S	L	Y	G	R	V	N	R	E	G	Y	T	V	V	A	L	S	L	Y	W	K	N	A	W	C	K	V	K	I	G	V
Secondary structure
SS confidence
Disorder						?	?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.
Sequence		A	K	G	K	K	Q	H	D	K	R	S	D	I	K	E	R	E	W	Q	V	D	K	A	R	I	M	K	N	A	H	R
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 1p6v chain A Region: 1 - 126 Aligned: 122 Modelled: 126 Confidence: 100.0% Identity: 50% Fold: Small protein B (SmpB) Superfamily: Small protein B (SmpB) Family: Small protein B (SmpB) Phyre2 PDB 1p6v chain C Region: 1 - 126 Aligned: 122 Modelled: 126 Confidence: 100.0% Identity: 50% PDB header:rna binding protein/rna Chain: C: PDB Molecule:ssra-binding protein; PDBTitle: crystal structure of the trna domain of transfer-messenger2 rna in complex with smpb Phyre2 PDB 1j1h chain A Region: 3 - 124 Aligned: 121 Modelled: 122 Confidence: 100.0% Identity: 46% PDB header:rna binding protein Chain: A: PDB Molecule:small protein b; PDBTitle: solution structure of a tmrna-binding protein, smpb, from2 thermus thermophilus Phyre2 PDB 1wjx chain A Region: 5 - 124 Aligned: 111 Modelled: 120 Confidence: 100.0% Identity: 51% Fold: Small protein B (SmpB) Superfamily: Small protein B (SmpB) Family: Small protein B (SmpB) Phyre2 PDB 2ipq chain X domain 1 Region: 18 - 57 Aligned: 40 Modelled: 40 Confidence: 34.1% Identity: 28% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: STY4665 C-terminal domain-like Phyre2 PDB 2qnk chain A Region: 11 - 80 Aligned: 66 Modelled: 70 Confidence: 32.5% Identity: 33% PDB header:oxidoreductase Chain: A: PDB Molecule:3-hydroxyanthranilate 3,4-dioxygenase; PDBTitle: crystal structure of human 3-hydroxyanthranilate 3,4-dioxygenase Phyre2 PDB 2aga chain A Region: 51 - 106 Aligned: 56 Modelled: 56 Confidence: 23.3% Identity: 14% PDB header:transcription Chain: A: PDB Molecule:machado-joseph disease protein 1; PDBTitle: de-ubiquitinating function of ataxin-3: insights from the2 solution structure of the josephin domain Phyre2 PDB 1yfu chain A domain 1 Region: 11 - 66 Aligned: 53 Modelled: 56 Confidence: 18.0% Identity: 19% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: 3-hydroxyanthranilic acid dioxygenase-like Phyre2 PDB 1sdw chain A domain 2 Region: 21 - 59 Aligned: 39 Modelled: 39 Confidence: 17.0% Identity: 15% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: PHM/PNGase F Family: Peptidylglycine alpha-hydroxylating monooxygenase, PHM Phyre2 PDB 1wqs chain A Region: 22 - 69 Aligned: 48 Modelled: 48 Confidence: 16.5% Identity: 21% PDB header:hydrolase Chain: A: PDB Molecule:3c-like protease; PDBTitle: crystal structure of norovirus 3c-like protease Phyre2 PDB 1g31 chain A Region: 10 - 34 Aligned: 22 Modelled: 25 Confidence: 14.1% Identity: 36% Fold: GroES-like Superfamily: GroES-like Family: GroES Phyre2 PDB 3jsb chain A Region: 88 - 105 Aligned: 18 Modelled: 18 Confidence: 11.9% Identity: 22% PDB header:rna binding protein Chain: A: PDB Molecule:rna-directed rna polymerase; PDBTitle: crystal structure of the n-terminal domain of the lymphocytic2 choriomeningitis virus l protein Phyre2 PDB 1hf9 chain B Region: 84 - 97 Aligned: 14 Modelled: 14 Confidence: 11.5% Identity: 21% PDB header:atpase inhibitor Chain: B: PDB Molecule:atpase inhibitor (mitochondrial); PDBTitle: c-terminal coiled-coil domain from bovine if1 Phyre2 PDB 2qfa chain A domain 1 Region: 10 - 31 Aligned: 22 Modelled: 22 Confidence: 11.4% Identity: 27% Fold: Inhibitor of apoptosis (IAP) repeat Superfamily: Inhibitor of apoptosis (IAP) repeat Family: Inhibitor of apoptosis (IAP) repeat Phyre2 PDB 1zvf chain A domain 1 Region: 4 - 62 Aligned: 59 Modelled: 59 Confidence: 10.0% Identity: 15% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: 3-hydroxyanthranilic acid dioxygenase-like Phyre2 PDB 2quo chain A Region: 102 - 127 Aligned: 26 Modelled: 26 Confidence: 10.0% Identity: 27% PDB header:toxin Chain: A: PDB Molecule:heat-labile enterotoxin b chain; PDBTitle: crystal structure of c terminal fragment of clostridium2 perfringens enterotoxin Phyre2 PDB 2w3z chain A Region: 81 - 106 Aligned: 26 Modelled: 26 Confidence: 8.9% Identity: 23% PDB header:hydrolase Chain: A: PDB Molecule:putative deacetylase; PDBTitle: structure of a streptococcus mutans ce4 esterase Phyre2 PDB 2oa9 chain B Region: 27 - 47 Aligned: 21 Modelled: 21 Confidence: 8.7% Identity: 10% PDB header:hydrolase Chain: B: PDB Molecule:r.mvai; PDBTitle: restriction endonuclease mvai in the absence of dna Phyre2 PDB 2rax chain A domain 1 Region: 10 - 31 Aligned: 22 Modelled: 22 Confidence: 8.3% Identity: 27% Fold: Inhibitor of apoptosis (IAP) repeat Superfamily: Inhibitor of apoptosis (IAP) repeat Family: Inhibitor of apoptosis (IAP) repeat Phyre2 PDB 2nly chain A domain 1 Region: 81 - 106 Aligned: 26 Modelled: 26 Confidence: 7.8% Identity: 19% Fold: 7-stranded beta/alpha barrel Superfamily: Glycoside hydrolase/deacetylase Family: Divergent polysaccharide deacetylase Phyre2 1 d1p6va_ 2 c1p6vC_ 3 c1j1hA_ 4 d1wjxa_ 5 d2ipqx1 6 c2qnkA_ 7 c2agaA_ 8 d1yfua1 9 d1sdwa2 10 c1wqsA_ 11 d1g31a_ 12 c3jsbA_ 13 c1hf9B_ 14 d2qfaa1 15 d1zvfa1 16 c2quoA_ 17 c2w3zA_ 18 c2oa9B_ 19 d2raxa1 20 d2nlya1 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42

Detailed template information

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

1 d1p6va_ 100.0 50 Fold:Small protein B (SmpB) Superfamily:Small protein B (SmpB) Family:Small protein B (SmpB) 2 c1p6vC_ 100.0 50 PDB header:rna binding protein/rna Chain: C: PDB Molecule:ssra-binding protein; PDBTitle: crystal structure of the trna domain of transfer-messenger2 rna in complex with smpb 3 c1j1hA_ 100.0 46 PDB header:rna binding protein Chain: A: PDB Molecule:small protein b; PDBTitle: solution structure of a tmrna-binding protein, smpb, from2 thermus thermophilus 4 d1wjxa_ 100.0 51 Fold:Small protein B (SmpB) Superfamily:Small protein B (SmpB) Family:Small protein B (SmpB) 5 d2ipqx1 34.1 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:STY4665 C-terminal domain-like 6 c2qnkA_ 32.5 33 PDB header:oxidoreductase Chain: A: PDB Molecule:3-hydroxyanthranilate 3,4-dioxygenase; PDBTitle: crystal structure of human 3-hydroxyanthranilate 3,4-dioxygenase 7 c2agaA_ 23.3 14 PDB header:transcription Chain: A: PDB Molecule:machado-joseph disease protein 1; PDBTitle: de-ubiquitinating function of ataxin-3: insights from the2 solution structure of the josephin domain 8 d1yfua1 18.0 19 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:3-hydroxyanthranilic acid dioxygenase-like 9 d1sdwa2 17.0 15 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:PHM/PNGase F Family:Peptidylglycine alpha-hydroxylating monooxygenase, PHM 10 c1wqsA_ 16.5 21 PDB header:hydrolase Chain: A: PDB Molecule:3c-like protease; PDBTitle: crystal structure of norovirus 3c-like protease 11 d1g31a_ 14.1 36 Fold:GroES-like Superfamily:GroES-like Family:GroES 12 c3jsbA_ 11.9 22 PDB header:rna binding protein Chain: A: PDB Molecule:rna-directed rna polymerase; PDBTitle: crystal structure of the n-terminal domain of the lymphocytic2 choriomeningitis virus l protein 13 c1hf9B_ 11.5 21 PDB header:atpase inhibitor Chain: B: PDB Molecule:atpase inhibitor (mitochondrial); PDBTitle: c-terminal coiled-coil domain from bovine if1 14 d2qfaa1 11.4 27 Fold:Inhibitor of apoptosis (IAP) repeat Superfamily:Inhibitor of apoptosis (IAP) repeat Family:Inhibitor of apoptosis (IAP) repeat 15 d1zvfa1 10.0 15 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:3-hydroxyanthranilic acid dioxygenase-like 16 c2quoA_ 10.0 27 PDB header:toxin Chain: A: PDB Molecule:heat-labile enterotoxin b chain; PDBTitle: crystal structure of c terminal fragment of clostridium2 perfringens enterotoxin 17 c2w3zA_ 8.9 23 PDB header:hydrolase Chain: A: PDB Molecule:putative deacetylase; PDBTitle: structure of a streptococcus mutans ce4 esterase 18 c2oa9B_ 8.7 10 PDB header:hydrolase Chain: B: PDB Molecule:r.mvai; PDBTitle: restriction endonuclease mvai in the absence of dna 19 d2raxa1 8.3 27 Fold:Inhibitor of apoptosis (IAP) repeat Superfamily:Inhibitor of apoptosis (IAP) repeat Family:Inhibitor of apoptosis (IAP) repeat 20 d2nlya1 7.8 19 Fold:7-stranded beta/alpha barrel Superfamily:Glycoside hydrolase/deacetylase Family:Divergent polysaccharide deacetylase 21 d2c1ia1 not modelled 7.7 24 Fold:7-stranded beta/alpha barrel Superfamily:Glycoside hydrolase/deacetylase Family:NodB-like polysaccharide deacetylase 22 d1m4ma_ not modelled 7.7 27 Fold:Inhibitor of apoptosis (IAP) repeat Superfamily:Inhibitor of apoptosis (IAP) repeat Family:Inhibitor of apoptosis (IAP) repeat 23 d2qqra1 not modelled 7.6 31 Fold:SH3-like barrel Superfamily:Tudor/PWWP/MBT Family:Tudor domain 24 d1d1na_ not modelled 7.4 20 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:Elongation factors 25 d2cc0a1 not modelled 7.4 15 Fold:7-stranded beta/alpha barrel Superfamily:Glycoside hydrolase/deacetylase Family:NodB-like polysaccharide deacetylase 26 c3mjdA_ not modelled 6.9 22 PDB header:transferase Chain: A: PDB Molecule:orotate phosphoribosyltransferase; PDBTitle: 1.9 angstrom crystal structure of orotate2 phosphoribosyltransferase (pyre) francisella tularensis. 27 c2ylaA_ not modelled 6.4 15 PDB header:hydrolase Chain: A: PDB Molecule:beta-n-acetylhexosaminidase; PDBTitle: inhibition of the pneumococcal virulence factor strh and2 molecular insights into n-glycan recognition and3 hydrolysis 28 d1im3d_ not modelled 6.3 28 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Cytomegalovirus protein US2 29 d8ohma2 not modelled 6.2 24 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:RNA helicase 30 d1kk1a1 not modelled 6.1 36 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:Elongation factors 31 c2z59A_ not modelled 6.0 29 PDB header:protein transport Chain: A: PDB Molecule:protein adrm1; PDBTitle: complex structures of mouse rpn13 (22-130aa) and ubiquitin 32 c2r2yA_ not modelled 6.0 29 PDB header:protein binding Chain: A: PDB Molecule:protein adrm1; PDBTitle: crystal structure of the proteasomal rpn13 pru-domain 33 d1jd5a_ not modelled 5.9 26 Fold:Inhibitor of apoptosis (IAP) repeat Superfamily:Inhibitor of apoptosis (IAP) repeat Family:Inhibitor of apoptosis (IAP) repeat 34 d2ieca1 not modelled 5.7 71 Fold:MK0786-like Superfamily:MK0786-like Family:MK0786-like 35 c2crvA_ not modelled 5.5 29 PDB header:translation Chain: A: PDB Molecule:translation initiation factor if-2; PDBTitle: solution structure of c-terminal domain of mitochondrial2 translational initiationfactor 2 36 d2gjxa1 not modelled 5.4 15 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:beta-N-acetylhexosaminidase catalytic domain 37 d2i52a1 not modelled 5.4 71 Fold:MK0786-like Superfamily:MK0786-like Family:MK0786-like 38 d1jaka1 not modelled 5.4 15 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:beta-N-acetylhexosaminidase catalytic domain 39 d1yhta1 not modelled 5.3 20 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:beta-N-acetylhexosaminidase catalytic domain 40 d1mkya3 not modelled 5.2 9 Fold:Alpha-lytic protease prodomain-like Superfamily:Probable GTPase Der, C-terminal domain Family:Probable GTPase Der, C-terminal domain 41 c2elvA_ not modelled 5.2 21 PDB header:transcription Chain: A: PDB Molecule:zinc finger protein 406; PDBTitle: solution structure of the 6th c2h2 zinc finger of human2 zinc finger protein 406 42 c2ogfD_ not modelled 5.1 57 PDB header:structural genomics, unknown function Chain: D: PDB Molecule:hypothetical protein mj0408; PDBTitle: crystal structure of protein mj0408 from methanococcus jannaschii,2 pfam duf372

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