Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	A	F	N	K	L	F	S	L	V	V	A	S	V	L	V	F	S	L	A	G	C	G	D	K	E	E	S	K	K	F	S	A	N	L	N	G	T	E	I	A	I	T	Y	V	Y	K	G	D	K	V	L	K	Q	S	S	E	T	K
Secondary structure
SS confidence
Disorder		?	?																			?	?	?	?	?		?		?						?	?	?	?																			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	Q	F	A	S	I	G	A	T	T	K	E	D	A	A	K	T	L	E	P	L	S	A	K	Y	K	N	I	A	G	V	E	E	K	L	T	Y	T	D	T	Y	A	Q	E	N	V	T	I	D	M	E	K	V	D	F	K	A	L	Q	G
Secondary structure
SS confidence
Disorder							?		?	?	?															?	?			?																															?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.
Sequence		I	S	G	I	N	V	S	A	E	D	A	K	K	G	I	T	M	A	Q	M	E	L	V	M	K	A	A	G	F	K	E	V	K
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 2joe chain A domain 1 Region: 24 - 153 Aligned: 130 Modelled: 130 Confidence: 100.0% Identity: 100% Fold: YehR-like Superfamily: YehR-like Family: YehR-like Phyre2 PDB 2duy chain A domain 1 Region: 108 - 125 Aligned: 18 Modelled: 18 Confidence: 19.2% Identity: 17% Fold: SAM domain-like Superfamily: RuvA domain 2-like Family: ComEA-like Phyre2 PDB 1jb0 chain J Region: 1 - 24 Aligned: 24 Modelled: 24 Confidence: 18.9% Identity: 21% Fold: Single transmembrane helix Superfamily: Subunit IX of photosystem I reaction centre, PsaJ Family: Subunit IX of photosystem I reaction centre, PsaJ Phyre2 PDB 2axt chain U domain 1 Region: 108 - 125 Aligned: 18 Modelled: 18 Confidence: 15.4% Identity: 22% Fold: SAM domain-like Superfamily: PsbU/PolX domain-like Family: PsbU-like Phyre2 PDB 1s5l chain U Region: 108 - 125 Aligned: 18 Modelled: 18 Confidence: 12.6% Identity: 22% PDB header:photosynthesis Chain: U: PDB Molecule:photosystem ii 12 kda extrinsic protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 2fi0 chain A domain 1 Region: 133 - 150 Aligned: 18 Modelled: 18 Confidence: 12.0% Identity: 22% Fold: SP0561-like Superfamily: SP0561-like Family: SP0561-like Phyre2 PDB 1lfo chain A Region: 32 - 109 Aligned: 47 Modelled: 47 Confidence: 10.5% Identity: 13% Fold: Lipocalins Superfamily: Lipocalins Family: Fatty acid binding protein-like Phyre2 PDB 1wmh chain A Region: 40 - 100 Aligned: 49 Modelled: 50 Confidence: 10.4% Identity: 10% Fold: beta-Grasp (ubiquitin-like) Superfamily: CAD & PB1 domains Family: PB1 domain Phyre2 PDB 1p6p chain A Region: 36 - 109 Aligned: 42 Modelled: 42 Confidence: 9.9% Identity: 24% Fold: Lipocalins Superfamily: Lipocalins Family: Fatty acid binding protein-like Phyre2 PDB 1zoq chain A Region: 40 - 59 Aligned: 20 Modelled: 20 Confidence: 8.9% Identity: 30% PDB header:transcription/transferase Chain: A: PDB Molecule:interferon regulatory factor 3; PDBTitle: irf3-cbp complex Phyre2 PDB 3dsh chain A Region: 40 - 59 Aligned: 20 Modelled: 20 Confidence: 8.4% Identity: 15% PDB header:dna binding protein Chain: A: PDB Molecule:interferon regulatory factor 5; PDBTitle: crystal structure of dimeric interferon regulatory factor 5 (irf-5)2 transactivation domain Phyre2 PDB 3pn1 chain A Region: 88 - 107 Aligned: 20 Modelled: 20 Confidence: 8.4% Identity: 15% PDB header:ligase/ligase inhibitor Chain: A: PDB Molecule:dna ligase; PDBTitle: novel bacterial nad+-dependent dna ligase inhibitors with broad2 spectrum potency and antibacterial efficacy in vivo Phyre2 PDB 2dzl chain A Region: 13 - 30 Aligned: 18 Modelled: 18 Confidence: 8.0% Identity: 22% PDB header:structural genomics unknown function Chain: A: PDB Molecule:protein fam100b; PDBTitle: solution structure of the uba domain in human protein2 fam100b Phyre2 PDB 3em0 chain A Region: 37 - 109 Aligned: 41 Modelled: 41 Confidence: 8.0% Identity: 15% PDB header:lipid binding protein Chain: A: PDB Molecule:ileal bile acid-binding protein; PDBTitle: crystal structure of zebrafish ileal bile acid-bindin protein2 complexed with cholic acid (crystal form b). Phyre2 PDB 1im8 chain A Region: 135 - 153 Aligned: 19 Modelled: 19 Confidence: 7.1% Identity: 21% Fold: S-adenosyl-L-methionine-dependent methyltransferases Superfamily: S-adenosyl-L-methionine-dependent methyltransferases Family: Hypothetical protein HI0319 (YecO) Phyre2 PDB 1qwt chain A Region: 40 - 59 Aligned: 20 Modelled: 20 Confidence: 6.2% Identity: 30% Fold: SMAD/FHA domain Superfamily: SMAD/FHA domain Family: Interferon regulatory factor 3 (IRF3), transactivation domain Phyre2 PDB 3hkz chain Y Region: 67 - 85 Aligned: 19 Modelled: 19 Confidence: 6.2% Identity: 37% PDB header:transferase Chain: Y: PDB Molecule:dna-directed rna polymerase subunit 13; PDBTitle: the x-ray crystal structure of rna polymerase from archaea Phyre2 PDB 3kz5 chain E Region: 44 - 53 Aligned: 10 Modelled: 10 Confidence: 5.9% Identity: 60% PDB header:dna binding protein Chain: E: PDB Molecule:protein sopb; PDBTitle: structure of cdomain Phyre2 PDB 2ftb chain A domain 1 Region: 33 - 109 Aligned: 45 Modelled: 45 Confidence: 5.8% Identity: 18% Fold: Lipocalins Superfamily: Lipocalins Family: Fatty acid binding protein-like Phyre2 PDB 1fe0 chain A Region: 79 - 109 Aligned: 31 Modelled: 31 Confidence: 5.7% Identity: 13% Fold: Ferredoxin-like Superfamily: HMA, heavy metal-associated domain Family: HMA, heavy metal-associated domain Phyre2 1 d2joea1 2 d2duya1 3 d1jb0j_ 4 d2axtu1 5 c1s5lu_ 6 d2fi0a1 7 d1lfoa_ 8 d1wmha_ 9 d1p6pa_ 10 c1zoqA_ 11 c3dshA_ 12 c3pn1A_ 13 c2dzlA_ 14 c3em0A_ 15 d1im8a_ 16 d1qwta_ 17 c3hkzY_ 18 c3kz5E_ 19 d2ftba1 20 d1fe0a_ 21 22

Detailed template information

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

1 d2joea1 100.0 100 Fold:YehR-like Superfamily:YehR-like Family:YehR-like 2 d2duya1 19.2 17 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:ComEA-like 3 d1jb0j_ 18.9 21 Fold:Single transmembrane helix Superfamily:Subunit IX of photosystem I reaction centre, PsaJ Family:Subunit IX of photosystem I reaction centre, PsaJ 4 d2axtu1 15.4 22 Fold:SAM domain-like Superfamily:PsbU/PolX domain-like Family:PsbU-like 5 c1s5lu_ 12.6 22 PDB header:photosynthesis Chain: U: PDB Molecule:photosystem ii 12 kda extrinsic protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 6 d2fi0a1 12.0 22 Fold:SP0561-like Superfamily:SP0561-like Family:SP0561-like 7 d1lfoa_ 10.5 13 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 8 d1wmha_ 10.4 10 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 9 d1p6pa_ 9.9 24 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 10 c1zoqA_ 8.9 30 PDB header:transcription/transferase Chain: A: PDB Molecule:interferon regulatory factor 3; PDBTitle: irf3-cbp complex 11 c3dshA_ 8.4 15 PDB header:dna binding protein Chain: A: PDB Molecule:interferon regulatory factor 5; PDBTitle: crystal structure of dimeric interferon regulatory factor 5 (irf-5)2 transactivation domain 12 c3pn1A_ 8.4 15 PDB header:ligase/ligase inhibitor Chain: A: PDB Molecule:dna ligase; PDBTitle: novel bacterial nad+-dependent dna ligase inhibitors with broad2 spectrum potency and antibacterial efficacy in vivo 13 c2dzlA_ 8.0 22 PDB header:structural genomics unknown function Chain: A: PDB Molecule:protein fam100b; PDBTitle: solution structure of the uba domain in human protein2 fam100b 14 c3em0A_ 8.0 15 PDB header:lipid binding protein Chain: A: PDB Molecule:ileal bile acid-binding protein; PDBTitle: crystal structure of zebrafish ileal bile acid-bindin protein2 complexed with cholic acid (crystal form b). 15 d1im8a_ 7.1 21 Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:Hypothetical protein HI0319 (YecO) 16 d1qwta_ 6.2 30 Fold:SMAD/FHA domain Superfamily:SMAD/FHA domain Family:Interferon regulatory factor 3 (IRF3), transactivation domain 17 c3hkzY_ 6.2 37 PDB header:transferase Chain: Y: PDB Molecule:dna-directed rna polymerase subunit 13; PDBTitle: the x-ray crystal structure of rna polymerase from archaea 18 c3kz5E_ 5.9 60 PDB header:dna binding protein Chain: E: PDB Molecule:protein sopb; PDBTitle: structure of cdomain 19 d2ftba1 5.8 18 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 20 d1fe0a_ 5.7 13 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 21 d3bzka1 not modelled 5.7 33 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Tex HhH-containing domain-like 22 c2o01J_ not modelled 5.7 17 PDB header:photosynthesis Chain: J: PDB Molecule:photosystem i reaction center subunit ix; PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution

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