Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	T	N	R	S	L	V	V	I	V	S	L	I	T	A	T	L	L	L	T	A	C	A	Q	P	E	Q	S	S	L	A	G	D	W	L	L	T	P	K	D	K	T	R	G	L	T	G	S	I	A	V	N	I	A	P	F	R	C	K
Secondary structure
SS confidence
Disorder		?	?	?	?	?																					?	?	?	?	?	?	?	?								?	?	?		?	?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	N	C	R	G	D	N	L	P	D	N	T	R	R	W	Q	L	S	G	G	N	E	K	E	L	T	Y	L	H	N	M	S	A	Q	E	K	V	G	L	N	P	G	W	Q	C	Y	T	S	F	F	M	R	V	C	Q	G	K	P	G	T
Secondary structure
SS confidence
Disorder					?	?	?	?	?	?	?	?						?	?		?														?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.
Sequence		R	P	I	V	N	E	D	Y	V	S	E	S	G	F	F	G	S	M	M	H	V	G	I	I	E	L	R	R	C	Q	S	E	N	C	Q	Q	E	L	K	A	I	N	T	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 1jiw chain I Region: 26 - 80 Aligned: 55 Modelled: 55 Confidence: 54.9% Identity: 25% Fold: Streptavidin-like Superfamily: beta-Barrel protease inhibitors Family: Metalloprotease inhibitor Phyre2 PDB 3ko7 chain E Region: 69 - 144 Aligned: 68 Modelled: 76 Confidence: 51.6% Identity: 15% PDB header:hydrolase Chain: E: PDB Molecule:d-tyrosyl-trna(tyr) deacylase; PDBTitle: dtd from plasmodium falciparum in complex with d-lysine Phyre2 PDB 2f2a chain B domain 2 Region: 113 - 145 Aligned: 33 Modelled: 33 Confidence: 38.0% Identity: 21% Fold: Glutamine synthetase/guanido kinase Superfamily: Glutamine synthetase/guanido kinase Family: GatB/GatE catalytic domain-like Phyre2 PDB 3h0m chain E Region: 113 - 143 Aligned: 31 Modelled: 31 Confidence: 36.8% Identity: 32% PDB header:ligase Chain: E: PDB Molecule:aspartyl/glutamyl-trna(asn/gln) amidotransferase PDBTitle: structure of trna-dependent amidotransferase gatcab from2 aquifex aeolicus Phyre2 PDB 2g5i chain B Region: 113 - 145 Aligned: 33 Modelled: 33 Confidence: 36.3% Identity: 21% PDB header:ligase Chain: B: PDB Molecule:aspartyl/glutamyl-trna(asn/gln) amidotransferase PDBTitle: structure of trna-dependent amidotransferase gatcab2 complexed with adp-alf4 Phyre2 PDB 1j7g chain A Region: 106 - 144 Aligned: 28 Modelled: 39 Confidence: 31.3% Identity: 29% Fold: DTD-like Superfamily: DTD-like Family: DTD-like Phyre2 PDB 3al0 chain B Region: 113 - 143 Aligned: 31 Modelled: 31 Confidence: 27.5% Identity: 29% PDB header:ligase/rna Chain: B: PDB Molecule:aspartyl/glutamyl-trna(asn/gln) amidotransferase subunit b; PDBTitle: crystal structure of the glutamine transamidosome from thermotoga2 maritima in the glutamylation state. Phyre2 PDB 2xuv chain B Region: 90 - 111 Aligned: 21 Modelled: 22 Confidence: 27.5% Identity: 33% PDB header:unknown function Chain: B: PDB Molecule:hdeb; PDBTitle: the structure of hdeb Phyre2 PDB 2xi1 chain A Region: 90 - 121 Aligned: 24 Modelled: 32 Confidence: 23.5% Identity: 42% PDB header:viral protein Chain: A: PDB Molecule:nef; PDBTitle: crystal structure of the hiv-1 nef sequenced from a patient's sample Phyre2 PDB 3rbb chain A Region: 90 - 164 Aligned: 61 Modelled: 75 Confidence: 21.1% Identity: 23% PDB header:viral protein, protein binding Chain: A: PDB Molecule:protein nef; PDBTitle: hiv-1 nef protein in complex with engineered hck sh3 domain Phyre2 PDB 2nef chain A Region: 90 - 121 Aligned: 24 Modelled: 32 Confidence: 20.5% Identity: 38% Fold: Regulatory factor Nef Superfamily: Regulatory factor Nef Family: Regulatory factor Nef Phyre2 PDB 1jke chain A Region: 131 - 144 Aligned: 14 Modelled: 14 Confidence: 16.3% Identity: 29% Fold: DTD-like Superfamily: DTD-like Family: DTD-like Phyre2 PDB 2okv chain C Region: 131 - 144 Aligned: 14 Modelled: 14 Confidence: 13.8% Identity: 43% PDB header:hydrolase Chain: C: PDB Molecule:probable d-tyrosyl-trna(tyr) deacylase 1; PDBTitle: c-myc dna unwinding element binding protein Phyre2 PDB 2dbo chain A Region: 131 - 144 Aligned: 14 Modelled: 14 Confidence: 13.7% Identity: 57% PDB header:hydrolase Chain: A: PDB Molecule:d-tyrosyl-trna(tyr) deacylase; PDBTitle: crystal structure of d-tyr-trna(tyr) deacylase from aquifex aeolicus Phyre2 PDB 1f3v chain A Region: 143 - 160 Aligned: 18 Modelled: 18 Confidence: 13.2% Identity: 39% Fold: Ferredoxin-like Superfamily: TRADD, N-terminal domain Family: TRADD, N-terminal domain Phyre2 PDB 2pif chain A domain 1 Region: 106 - 133 Aligned: 25 Modelled: 28 Confidence: 12.1% Identity: 32% Fold: PSTPO5379-like Superfamily: PSTPO5379-like Family: PSTPO5379-like Phyre2 PDB 2yrc chain A Region: 48 - 76 Aligned: 29 Modelled: 29 Confidence: 11.4% Identity: 31% PDB header:protein transport Chain: A: PDB Molecule:protein transport protein sec23a; PDBTitle: solution structure of the zf-sec23_sec24 from human sec23a Phyre2 PDB 1w0n chain A Region: 125 - 153 Aligned: 27 Modelled: 29 Confidence: 10.5% Identity: 41% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: Family 36 carbohydrate binding module, CBM36 Phyre2 PDB 3nym chain A Region: 110 - 146 Aligned: 31 Modelled: 37 Confidence: 9.4% Identity: 23% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: the crystal structure of functionally unknown protein from neisseria2 meningitidis mc58 Phyre2 PDB 1yod chain B Region: 148 - 161 Aligned: 13 Modelled: 14 Confidence: 8.7% Identity: 77% PDB header:de novo protein Chain: B: PDB Molecule:water-solublized phospholamban; PDBTitle: crystal structure of a water soluble analog of phospholamban Phyre2 1 d1jiwi_ 2 c3ko7E_ 3 d2f2ab2 4 c3h0mE_ 5 c2g5iB_ 6 d1j7ga_ 7 c3al0B_ 8 c2xuvB_ 9 c2xi1A_ 10 c3rbbA_ 11 d2nefa_ 12 d1jkea_ 13 c2okvC_ 14 c2dboA_ 15 d1f3va_ 16 d2pifa1 17 c2yrcA_ 18 d1w0na_ 19 c3nymA_ 20 c1yodB_ 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

Detailed template information

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

1 d1jiwi_ 54.9 25 Fold:Streptavidin-like Superfamily:beta-Barrel protease inhibitors Family:Metalloprotease inhibitor 2 c3ko7E_ 51.6 15 PDB header:hydrolase Chain: E: PDB Molecule:d-tyrosyl-trna(tyr) deacylase; PDBTitle: dtd from plasmodium falciparum in complex with d-lysine 3 d2f2ab2 38.0 21 Fold:Glutamine synthetase/guanido kinase Superfamily:Glutamine synthetase/guanido kinase Family:GatB/GatE catalytic domain-like 4 c3h0mE_ 36.8 32 PDB header:ligase Chain: E: PDB Molecule:aspartyl/glutamyl-trna(asn/gln) amidotransferase PDBTitle: structure of trna-dependent amidotransferase gatcab from2 aquifex aeolicus 5 c2g5iB_ 36.3 21 PDB header:ligase Chain: B: PDB Molecule:aspartyl/glutamyl-trna(asn/gln) amidotransferase PDBTitle: structure of trna-dependent amidotransferase gatcab2 complexed with adp-alf4 6 d1j7ga_ 31.3 29 Fold:DTD-like Superfamily:DTD-like Family:DTD-like 7 c3al0B_ 27.5 29 PDB header:ligase/rna Chain: B: PDB Molecule:aspartyl/glutamyl-trna(asn/gln) amidotransferase subunit b; PDBTitle: crystal structure of the glutamine transamidosome from thermotoga2 maritima in the glutamylation state. 8 c2xuvB_ 27.5 33 PDB header:unknown function Chain: B: PDB Molecule:hdeb; PDBTitle: the structure of hdeb 9 c2xi1A_ 23.5 42 PDB header:viral protein Chain: A: PDB Molecule:nef; PDBTitle: crystal structure of the hiv-1 nef sequenced from a patient's sample 10 c3rbbA_ 21.1 23 PDB header:viral protein, protein binding Chain: A: PDB Molecule:protein nef; PDBTitle: hiv-1 nef protein in complex with engineered hck sh3 domain 11 d2nefa_ 20.5 38 Fold:Regulatory factor Nef Superfamily:Regulatory factor Nef Family:Regulatory factor Nef 12 d1jkea_ 16.3 29 Fold:DTD-like Superfamily:DTD-like Family:DTD-like 13 c2okvC_ 13.8 43 PDB header:hydrolase Chain: C: PDB Molecule:probable d-tyrosyl-trna(tyr) deacylase 1; PDBTitle: c-myc dna unwinding element binding protein 14 c2dboA_ 13.7 57 PDB header:hydrolase Chain: A: PDB Molecule:d-tyrosyl-trna(tyr) deacylase; PDBTitle: crystal structure of d-tyr-trna(tyr) deacylase from aquifex aeolicus 15 d1f3va_ 13.2 39 Fold:Ferredoxin-like Superfamily:TRADD, N-terminal domain Family:TRADD, N-terminal domain 16 d2pifa1 12.1 32 Fold:PSTPO5379-like Superfamily:PSTPO5379-like Family:PSTPO5379-like 17 c2yrcA_ 11.4 31 PDB header:protein transport Chain: A: PDB Molecule:protein transport protein sec23a; PDBTitle: solution structure of the zf-sec23_sec24 from human sec23a 18 d1w0na_ 10.5 41 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:Family 36 carbohydrate binding module, CBM36 19 c3nymA_ 9.4 23 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: the crystal structure of functionally unknown protein from neisseria2 meningitidis mc58 20 c1yodB_ 8.7 77 PDB header:de novo protein Chain: B: PDB Molecule:water-solublized phospholamban; PDBTitle: crystal structure of a water soluble analog of phospholamban 21 d1tc5a_ not modelled 8.6 22 Fold:DTD-like Superfamily:DTD-like Family:DTD-like 22 c3ho6B_ not modelled 8.6 16 PDB header:toxin Chain: B: PDB Molecule:toxin a; PDBTitle: structure-function analysis of inositol hexakisphosphate-2 induced autoprocessing in clostridium difficile toxin a 23 c2p22D_ not modelled 8.1 38 PDB header:transport protein Chain: D: PDB Molecule:hypothetical 12.0 kda protein in ade3-ser2 PDBTitle: structure of the yeast escrt-i heterotetramer core 24 d1zxqa2 not modelled 7.9 27 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:I set domains 25 d1efnb_ not modelled 7.9 32 Fold:Regulatory factor Nef Superfamily:Regulatory factor Nef Family:Regulatory factor Nef 26 c1yodA_ not modelled 7.8 77 PDB header:de novo protein Chain: A: PDB Molecule:water-solublized phospholamban; PDBTitle: crystal structure of a water soluble analog of phospholamban 27 c3ik5A_ not modelled 6.8 37 PDB header:viral protein/signaling protein Chain: A: PDB Molecule:protein nef; PDBTitle: sivmac239 nef in complex with tcr zeta itam 1 polypeptide2 (a63-r80) 28 d2qtva5 not modelled 6.6 16 Fold:Rubredoxin-like Superfamily:Zn-finger domain of Sec23/24 Family:Zn-finger domain of Sec23/24 29 d1a8oa_ not modelled 6.5 43 Fold:Acyl carrier protein-like Superfamily:Retrovirus capsid dimerization domain-like Family:Retrovirus capsid protein C-terminal domain 30 d1ny722 not modelled 6.4 29 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Comoviridae-like VP 31 d1smpi_ not modelled 6.3 19 Fold:Streptavidin-like Superfamily:beta-Barrel protease inhibitors Family:Metalloprotease inhibitor 32 c2bfuL_ not modelled 6.2 29 PDB header:virus Chain: L: PDB Molecule:cowpea mosaic virus, large (l) subunit; PDBTitle: x-ray structure of cpmv top component 33 d1pgl22 not modelled 6.2 35 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Comoviridae-like VP 34 d2ysca1 not modelled 6.1 83 Fold:WW domain-like Superfamily:WW domain Family:WW domain 35 d1jmxa5 not modelled 5.9 33 Fold:Streptavidin-like Superfamily:Quinohemoprotein amine dehydrogenase A chain, domain 3 Family:Quinohemoprotein amine dehydrogenase A chain, domain 3 36 d2oa4a1 not modelled 5.8 60 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:SPO1678-like 37 c2opkC_ not modelled 5.5 56 PDB header:isomerase Chain: C: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of a putative mannose-6-phosphate isomerase2 (reut_a1446) from ralstonia eutropha jmp134 at 2.10 a resolution 38 c3r47I_ not modelled 5.4 100 PDB header:de novo protein Chain: I: PDB Molecule:coiled coil helix l24h; PDBTitle: crystal structure of a 6-helix coiled coil cc-hex-h24 39 c3r47J_ not modelled 5.4 100 PDB header:de novo protein Chain: J: PDB Molecule:coiled coil helix l24h; PDBTitle: crystal structure of a 6-helix coiled coil cc-hex-h24 40 c3r47B_ not modelled 5.4 100 PDB header:de novo protein Chain: B: PDB Molecule:coiled coil helix l24h; PDBTitle: crystal structure of a 6-helix coiled coil cc-hex-h24 41 c3fzyA_ not modelled 5.3 50 PDB header:toxin Chain: A: PDB Molecule:rtx toxin rtxa; PDBTitle: crystal structure of pre-cleavage form of cysteine protease domain2 from vibrio cholerae rtxa toxin 42 c3eebB_ not modelled 5.2 50 PDB header:toxin Chain: B: PDB Molecule:rtx toxin rtxa; PDBTitle: structure of the v. cholerae rtx cysteine protease domain 43 c2re3A_ not modelled 5.2 58 PDB header:unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a duf1285 family protein (spo_0140) from2 silicibacter pomeroyi dss-3 at 2.50 a resolution 44 c1bmv2_ not modelled 5.1 35 PDB header:virus/rna Chain: 2: PDB Molecule:protein (icosahedral virus - b and c domain); PDBTitle: protein-rna interactions in an icosahedral virus at 3.02 angstroms resolution 45 c2xxzA_ not modelled 5.1 28 PDB header:oxidoreductase Chain: A: PDB Molecule:lysine-specific demethylase 6b; PDBTitle: crystal structure of the human jmjd3 jumonji domain 46 c3r47L_ not modelled 5.1 100 PDB header:de novo protein Chain: L: PDB Molecule:coiled coil helix l24h; PDBTitle: crystal structure of a 6-helix coiled coil cc-hex-h24 47 c3r47M_ not modelled 5.1 100 PDB header:de novo protein Chain: M: PDB Molecule:coiled coil helix l24h; PDBTitle: crystal structure of a 6-helix coiled coil cc-hex-h24 48 c3r47F_ not modelled 5.1 100 PDB header:de novo protein Chain: F: PDB Molecule:coiled coil helix l24h; PDBTitle: crystal structure of a 6-helix coiled coil cc-hex-h24

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