Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	Q	L	L	A	S	P	S	L	Q	L	V	T	Y	P	A	S	A	T	A	Q	S	A	E	F	A	S	A	D	C	V	T	G	L	N	E	I	G	Q	I	S	V	S	N	I	S	G	D	P	Q	D	V	E	R	I	V	A	L	K
Secondary structure
SS confidence
Disorder		?	?	?	?									?	?	?	?	?	?	?	?	?	?	?	?	?							?	?		?									?		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.
Sequence		A	D	E	Q	G	A	S	W	Y	R	I	I	T	M	Y	E	D	Q	Q	P	D	N	W	R	V	Q	A	I	L	Y	A
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 2jna chain A domain 1 Region: 1 - 90 Aligned: 86 Modelled: 90 Confidence: 100.0% Identity: 33% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 2noc chain A domain 1 Region: 1 - 90 Aligned: 84 Modelled: 87 Confidence: 99.9% Identity: 24% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 2k4q chain A Region: 29 - 72 Aligned: 43 Modelled: 44 Confidence: 41.8% Identity: 19% PDB header:viral protein Chain: A: PDB Molecule:major tail protein v; PDBTitle: the solution structure of gpv, the major tail protein from2 bacteriophage lambda Phyre2 PDB 3b9n chain B Region: 48 - 72 Aligned: 25 Modelled: 25 Confidence: 30.4% Identity: 20% PDB header:oxidoreductase Chain: B: PDB Molecule:alkane monoxygenase; PDBTitle: crystal structure of long-chain alkane monooxygenase (lada) Phyre2 PDB 3qkb chain B Region: 51 - 89 Aligned: 39 Modelled: 39 Confidence: 27.7% Identity: 15% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a protein with unknown function which belongs to2 pfam duf74 family (pepe_0654) from pediococcus pentosaceus atcc 257453 at 2.73 a resolution Phyre2 PDB 3sdo chain B Region: 46 - 71 Aligned: 26 Modelled: 26 Confidence: 23.1% Identity: 23% PDB header:oxidoreductase Chain: B: PDB Molecule:nitrilotriacetate monooxygenase; PDBTitle: structure of a nitrilotriacetate monooxygenase from burkholderia2 pseudomallei Phyre2 PDB 1hl8 chain B Region: 55 - 78 Aligned: 24 Modelled: 24 Confidence: 21.3% Identity: 21% PDB header:hydrolase Chain: B: PDB Molecule:putative alpha-l-fucosidase; PDBTitle: crystal structure of thermotoga maritima alpha-fucosidase Phyre2 PDB 1luc chain A Region: 46 - 71 Aligned: 26 Modelled: 26 Confidence: 21.0% Identity: 19% Fold: TIM beta/alpha-barrel Superfamily: Bacterial luciferase-like Family: Bacterial luciferase (alkanal monooxygenase) Phyre2 PDB 3eyp chain B Region: 55 - 78 Aligned: 24 Modelled: 24 Confidence: 17.3% Identity: 13% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative alpha-l-fucosidase; PDBTitle: crystal structure of putative alpha-l-fucosidase from bacteroides2 thetaiotaomicron Phyre2 PDB 2hqs chain A domain 2 Region: 13 - 90 Aligned: 77 Modelled: 78 Confidence: 16.3% Identity: 16% Fold: Anticodon-binding domain-like Superfamily: TolB, N-terminal domain Family: TolB, N-terminal domain Phyre2 PDB 3mo4 chain B Region: 55 - 78 Aligned: 24 Modelled: 24 Confidence: 15.9% Identity: 8% PDB header:hydrolase Chain: B: PDB Molecule:alpha-1,3/4-fucosidase; PDBTitle: the crystal structure of an alpha-(1-3,4)-fucosidase from2 bifidobacterium longum subsp. infantis atcc 15697 Phyre2 PDB 1luc chain B Region: 48 - 71 Aligned: 24 Modelled: 24 Confidence: 14.4% Identity: 13% Fold: TIM beta/alpha-barrel Superfamily: Bacterial luciferase-like Family: Bacterial luciferase (alkanal monooxygenase) Phyre2 PDB 3etj chain A domain 1 Region: 36 - 68 Aligned: 31 Modelled: 33 Confidence: 14.3% Identity: 6% Fold: Barrel-sandwich hybrid Superfamily: Rudiment single hybrid motif Family: BC C-terminal domain-like Phyre2 PDB 1z69 chain D Region: 48 - 71 Aligned: 23 Modelled: 24 Confidence: 12.3% Identity: 17% PDB header:oxidoreductase Chain: D: PDB Molecule:coenzyme f420-dependent n(5),n(10)- PDBTitle: crystal structure of methylenetetrahydromethanopterin2 reductase (mer) in complex with coenzyme f420 Phyre2 PDB 1hl9 chain A domain 2 Region: 55 - 78 Aligned: 24 Modelled: 24 Confidence: 11.2% Identity: 21% Fold: TIM beta/alpha-barrel Superfamily: (Trans)glycosidases Family: Putative alpha-L-fucosidase, catalytic domain Phyre2 PDB 1tqx chain A Region: 35 - 71 Aligned: 34 Modelled: 37 Confidence: 10.5% Identity: 21% Fold: TIM beta/alpha-barrel Superfamily: Ribulose-phoshate binding barrel Family: D-ribulose-5-phosphate 3-epimerase Phyre2 PDB 1kqf chain B Region: 47 - 86 Aligned: 40 Modelled: 40 Confidence: 10.4% Identity: 10% PDB header:oxidoreductase Chain: B: PDB Molecule:formate dehydrogenase, nitrate-inducible, iron-sulfur PDBTitle: formate dehydrogenase n from e. coli Phyre2 PDB 2wvs chain D Region: 55 - 78 Aligned: 24 Modelled: 24 Confidence: 10.0% Identity: 25% PDB header:hydrolase Chain: D: PDB Molecule:alpha-l-fucosidase; PDBTitle: crystal structure of an alpha-l-fucosidase gh29 trapped2 covalent intermediate from bacteroides thetaiotaomicron in3 complex with 2-fluoro-fucosyl fluoride using an e288q4 mutant Phyre2 PDB 1tvl chain A Region: 46 - 71 Aligned: 26 Modelled: 26 Confidence: 9.7% Identity: 15% Fold: TIM beta/alpha-barrel Superfamily: Bacterial luciferase-like Family: Ssud-like monoxygenases Phyre2 PDB 1tvl chain A Region: 46 - 71 Aligned: 26 Modelled: 26 Confidence: 9.7% Identity: 15% PDB header:oxidoreductase Chain: A: PDB Molecule:protein ytnj; PDBTitle: structure of ytnj from bacillus subtilis Phyre2 1 d2jnaa1 2 d2noca1 3 c2k4qA_ 4 c3b9nB_ 5 c3qkbB_ 6 c3sdoB_ 7 c1hl8B_ 8 d1luca_ 9 c3eypB_ 10 d2hqsa2 11 c3mo4B_ 12 d1lucb_ 13 d3etja1 14 c1z69D_ 15 d1hl9a2 16 d1tqxa_ 17 c1kqfB_ 18 c2wvsD_ 19 d1tvla_ 20 c1tvlA_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36

Detailed template information

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

1 d2jnaa1 100.0 33 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 2 d2noca1 99.9 24 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 3 c2k4qA_ 41.8 19 PDB header:viral protein Chain: A: PDB Molecule:major tail protein v; PDBTitle: the solution structure of gpv, the major tail protein from2 bacteriophage lambda 4 c3b9nB_ 30.4 20 PDB header:oxidoreductase Chain: B: PDB Molecule:alkane monoxygenase; PDBTitle: crystal structure of long-chain alkane monooxygenase (lada) 5 c3qkbB_ 27.7 15 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a protein with unknown function which belongs to2 pfam duf74 family (pepe_0654) from pediococcus pentosaceus atcc 257453 at 2.73 a resolution 6 c3sdoB_ 23.1 23 PDB header:oxidoreductase Chain: B: PDB Molecule:nitrilotriacetate monooxygenase; PDBTitle: structure of a nitrilotriacetate monooxygenase from burkholderia2 pseudomallei 7 c1hl8B_ 21.3 21 PDB header:hydrolase Chain: B: PDB Molecule:putative alpha-l-fucosidase; PDBTitle: crystal structure of thermotoga maritima alpha-fucosidase 8 d1luca_ 21.0 19 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:Bacterial luciferase (alkanal monooxygenase) 9 c3eypB_ 17.3 13 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative alpha-l-fucosidase; PDBTitle: crystal structure of putative alpha-l-fucosidase from bacteroides2 thetaiotaomicron 10 d2hqsa2 16.3 16 Fold:Anticodon-binding domain-like Superfamily:TolB, N-terminal domain Family:TolB, N-terminal domain 11 c3mo4B_ 15.9 8 PDB header:hydrolase Chain: B: PDB Molecule:alpha-1,3/4-fucosidase; PDBTitle: the crystal structure of an alpha-(1-3,4)-fucosidase from2 bifidobacterium longum subsp. infantis atcc 15697 12 d1lucb_ 14.4 13 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:Bacterial luciferase (alkanal monooxygenase) 13 d3etja1 14.3 6 Fold:Barrel-sandwich hybrid Superfamily:Rudiment single hybrid motif Family:BC C-terminal domain-like 14 c1z69D_ 12.3 17 PDB header:oxidoreductase Chain: D: PDB Molecule:coenzyme f420-dependent n(5),n(10)- PDBTitle: crystal structure of methylenetetrahydromethanopterin2 reductase (mer) in complex with coenzyme f420 15 d1hl9a2 11.2 21 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Putative alpha-L-fucosidase, catalytic domain 16 d1tqxa_ 10.5 21 Fold:TIM beta/alpha-barrel Superfamily:Ribulose-phoshate binding barrel Family:D-ribulose-5-phosphate 3-epimerase 17 c1kqfB_ 10.4 10 PDB header:oxidoreductase Chain: B: PDB Molecule:formate dehydrogenase, nitrate-inducible, iron-sulfur PDBTitle: formate dehydrogenase n from e. coli 18 c2wvsD_ 10.0 25 PDB header:hydrolase Chain: D: PDB Molecule:alpha-l-fucosidase; PDBTitle: crystal structure of an alpha-l-fucosidase gh29 trapped2 covalent intermediate from bacteroides thetaiotaomicron in3 complex with 2-fluoro-fucosyl fluoride using an e288q4 mutant 19 d1tvla_ 9.7 15 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:Ssud-like monoxygenases 20 c1tvlA_ 9.7 15 PDB header:oxidoreductase Chain: A: PDB Molecule:protein ytnj; PDBTitle: structure of ytnj from bacillus subtilis 21 c2i7gA_ not modelled 8.5 13 PDB header:oxidoreductase Chain: A: PDB Molecule:monooxygenase; PDBTitle: crystal structure of monooxygenase from agrobacterium tumefaciens 22 d1wu7a1 not modelled 8.0 22 Fold:Anticodon-binding domain-like Superfamily:Class II aaRS ABD-related Family:Anticodon-binding domain of Class II aaRS 23 d1nqka_ not modelled 7.8 22 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:Ssud-like monoxygenases 24 c2k38A_ not modelled 7.7 44 PDB header:antimicrobial protein Chain: A: PDB Molecule:cupiennin-1a; PDBTitle: cupiennin 1a, nmr, minimized average structure 25 c3ne8A_ not modelled 7.5 16 PDB header:hydrolase Chain: A: PDB Molecule:n-acetylmuramoyl-l-alanine amidase; PDBTitle: the crystal structure of a domain from n-acetylmuramoyl-l-alanine2 amidase of bartonella henselae str. houston-1 26 d2fiqa1 not modelled 7.4 31 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:GatZ-like 27 c3ir9A_ not modelled 7.0 19 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:peptide chain release factor subunit 1; PDBTitle: c-terminal domain of peptide chain release factor from2 methanosarcina mazei. 28 d2g39a1 not modelled 6.8 26 Fold:NagB/RpiA/CoA transferase-like Superfamily:NagB/RpiA/CoA transferase-like Family:CoA transferase alpha subunit-like 29 c3gzaB_ not modelled 6.5 13 PDB header:hydrolase Chain: B: PDB Molecule:putative alpha-l-fucosidase; PDBTitle: crystal structure of putative alpha-l-fucosidase (np_812709.1) from2 bacteroides thetaiotaomicron vpi-5482 at 1.60 a resolution 30 d1f07a_ not modelled 6.3 13 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:F420 dependent oxidoreductases 31 d1kjqa1 not modelled 6.3 12 Fold:Barrel-sandwich hybrid Superfamily:Rudiment single hybrid motif Family:BC C-terminal domain-like 32 c3raoB_ not modelled 6.2 12 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative luciferase-like monooxygenase; PDBTitle: crystal structure of the luciferase-like monooxygenase from bacillus2 cereus atcc 10987. 33 c2cokA_ not modelled 6.2 12 PDB header:transferase Chain: A: PDB Molecule:poly [adp-ribose] polymerase-1; PDBTitle: solution structure of brct domain of poly(adp-ribose)2 polymerase-1 34 c3no4A_ not modelled 6.0 21 PDB header:hydrolase Chain: A: PDB Molecule:creatinine amidohydrolase; PDBTitle: crystal structure of a creatinine amidohydrolase (npun_f1913) from2 nostoc punctiforme pcc 73102 at 2.00 a resolution 35 c2jz7A_ not modelled 5.7 17 PDB header:selenium-binding protein Chain: A: PDB Molecule:selenium binding protein; PDBTitle: solution nmr structure of selenium-binding protein from2 methanococcus vannielii 36 d1rhca_ not modelled 5.4 9 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:F420 dependent oxidoreductases

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