Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	M	K	K	S	I	L	A	F	L	L	L	T	S	S	A	A	A	L	A	A	P	Q	V	I	T	V	S	R	F	E	V	G	K	D	K	W	A	F	N	R	E	E	V	M	L	T	C	R	P	G	N	A	L	Y	V	I	N	P	S
Secondary structure
SS confidence
Disorder		?	?														?	?	?	?	?	?	?	?	?		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.
Sequence		T	L	V	Q	Y	P	L	N	D	I	A	Q	K	E	V	A	S	G	K	T	N	A	Q	P	I	S	V	I	Q	I	D	D	P	N	N	P	G	E	K	M	S	L	A	P	F	I	E	R	A	E	K	L	C
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 1d8j chain A Region: 29 - 43 Aligned: 14 Modelled: 15 Confidence: 28.7% Identity: 29% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: The central core domain of TFIIE beta Phyre2 PDB 1z1b chain A domain 1 Region: 46 - 67 Aligned: 22 Modelled: 22 Confidence: 20.7% Identity: 23% Fold: DNA-binding domain Superfamily: DNA-binding domain Family: lambda integrase N-terminal domain Phyre2 PDB 1kjk chain A Region: 46 - 67 Aligned: 22 Modelled: 22 Confidence: 20.7% Identity: 23% PDB header:viral protein Chain: A: PDB Molecule:integrase; PDBTitle: solution structure of the lambda integrase amino-terminal2 domain Phyre2 PDB 2jna chain A domain 1 Region: 2 - 31 Aligned: 27 Modelled: 30 Confidence: 16.8% Identity: 56% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 3ctz chain A Region: 70 - 109 Aligned: 40 Modelled: 40 Confidence: 15.8% Identity: 10% PDB header:hydrolase Chain: A: PDB Molecule:xaa-pro aminopeptidase 1; PDBTitle: structure of human cytosolic x-prolyl aminopeptidase Phyre2 PDB 2axt chain I domain 1 Region: 6 - 30 Aligned: 25 Modelled: 25 Confidence: 8.9% Identity: 16% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein I, PsbI Family: PsbI-like Phyre2 PDB 1lm7 chain A Region: 55 - 110 Aligned: 55 Modelled: 56 Confidence: 8.8% Identity: 16% Fold: beta-hairpin-alpha-hairpin repeat Superfamily: Plakin repeat Family: Plakin repeat Phyre2 PDB 1icc chain C Region: 39 - 73 Aligned: 32 Modelled: 35 Confidence: 7.9% Identity: 22% Fold: Cytochrome b5-like heme/steroid binding domain Superfamily: Cytochrome b5-like heme/steroid binding domain Family: Cytochrome b5 Phyre2 PDB 1vjq chain B Region: 52 - 102 Aligned: 43 Modelled: 51 Confidence: 6.6% Identity: 19% PDB header:structural genomics, de novo protein Chain: B: PDB Molecule:designed protein; PDBTitle: designed protein based on backbone conformation of2 procarboxypeptidase-a (1aye) with sidechains chosen for maximal3 predicted stability. Phyre2 PDB 1s21 chain A Region: 94 - 109 Aligned: 16 Modelled: 15 Confidence: 6.3% Identity: 19% Fold: ADP-ribosylation Superfamily: ADP-ribosylation Family: AvrPphF ORF2, a type III effector Phyre2 PDB 1s21 chain A Region: 94 - 109 Aligned: 16 Modelled: 15 Confidence: 6.3% Identity: 19% PDB header:chaperone Chain: A: PDB Molecule:orf2; PDBTitle: crystal structure of avrpphf orf2, a type iii effector from2 p. syringae Phyre2 PDB 2rm4 chain A Region: 22 - 62 Aligned: 41 Modelled: 41 Confidence: 6.0% Identity: 22% PDB header:protein binding Chain: A: PDB Molecule:cg6311-pb; PDBTitle: solution structure of the lsm domain of dm edc3 (enhancer2 of decapping 3) Phyre2 PDB 1st6 chain A domain 4 Region: 89 - 112 Aligned: 24 Modelled: 24 Confidence: 5.9% Identity: 25% Fold: Four-helical up-and-down bundle Superfamily: alpha-catenin/vinculin-like Family: alpha-catenin/vinculin Phyre2 PDB 2vc8 chain A Region: 38 - 64 Aligned: 27 Modelled: 27 Confidence: 5.8% Identity: 15% PDB header:protein-binding Chain: A: PDB Molecule:enhancer of mrna-decapping protein 3; PDBTitle: crystal structure of the lsm domain of human edc3 (enhancer2 of decapping 3) Phyre2 1 d1d8ja_ 2 d1z1ba1 3 c1kjkA_ 4 d2jnaa1 5 c3ctzA_ 6 d2axti1 7 d1lm7a_ 8 d1iccc_ 9 c1vjqB_ 10 d1s21a_ 11 c1s21A_ 12 c2rm4A_ 13 d1st6a4 14 c2vc8A_

Detailed template information

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

1 d1d8ja_ 28.7 29 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:The central core domain of TFIIE beta 2 d1z1ba1 20.7 23 Fold:DNA-binding domain Superfamily:DNA-binding domain Family:lambda integrase N-terminal domain 3 c1kjkA_ 20.7 23 PDB header:viral protein Chain: A: PDB Molecule:integrase; PDBTitle: solution structure of the lambda integrase amino-terminal2 domain 4 d2jnaa1 16.8 56 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 5 c3ctzA_ 15.8 10 PDB header:hydrolase Chain: A: PDB Molecule:xaa-pro aminopeptidase 1; PDBTitle: structure of human cytosolic x-prolyl aminopeptidase 6 d2axti1 8.9 16 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein I, PsbI Family:PsbI-like 7 d1lm7a_ 8.8 16 Fold:beta-hairpin-alpha-hairpin repeat Superfamily:Plakin repeat Family:Plakin repeat 8 d1iccc_ 7.9 22 Fold:Cytochrome b5-like heme/steroid binding domain Superfamily:Cytochrome b5-like heme/steroid binding domain Family:Cytochrome b5 9 c1vjqB_ 6.6 19 PDB header:structural genomics, de novo protein Chain: B: PDB Molecule:designed protein; PDBTitle: designed protein based on backbone conformation of2 procarboxypeptidase-a (1aye) with sidechains chosen for maximal3 predicted stability. 10 d1s21a_ 6.3 19 Fold:ADP-ribosylation Superfamily:ADP-ribosylation Family:AvrPphF ORF2, a type III effector 11 c1s21A_ 6.3 19 PDB header:chaperone Chain: A: PDB Molecule:orf2; PDBTitle: crystal structure of avrpphf orf2, a type iii effector from2 p. syringae 12 c2rm4A_ 6.0 22 PDB header:protein binding Chain: A: PDB Molecule:cg6311-pb; PDBTitle: solution structure of the lsm domain of dm edc3 (enhancer2 of decapping 3) 13 d1st6a4 5.9 25 Fold:Four-helical up-and-down bundle Superfamily:alpha-catenin/vinculin-like Family:alpha-catenin/vinculin 14 c2vc8A_ 5.8 15 PDB header:protein-binding Chain: A: PDB Molecule:enhancer of mrna-decapping protein 3; PDBTitle: crystal structure of the lsm domain of human edc3 (enhancer2 of decapping 3)

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