Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	K	V	L	G	V	I	L	G	G	L	L	L	L	P	V	V	S	N	A	A	D	A	Q	K	A	A	D	N	K	K	P	V	N	S	W	T	C	E	D	F	L	A	V	D	E	S	F	Q	P	T	A	V	G	F	A	E	A	L
Secondary structure
SS confidence
Disorder		?	?	?															?	?	?	?	?	?	?					?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110
Sequence		N	N	K	D	K	P	E	D	A	V	L	D	V	Q	G	I	A	T	V	T	P	A	I	V	Q	A	C	T	Q	D	K	Q	A	N	F	K	D	K	V	K	G	E	W	D	K	I	K	K	D	M
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 1dj8 chain A Region: 30 - 108 Aligned: 79 Modelled: 79 Confidence: 100.0% Identity: 100% Fold: Protein HNS-dependent expression A; HdeA Superfamily: Protein HNS-dependent expression A; HdeA Family: Protein HNS-dependent expression A; HdeA Phyre2 PDB 2xuv chain B Region: 37 - 92 Aligned: 50 Modelled: 56 Confidence: 91.1% Identity: 18% PDB header:unknown function Chain: B: PDB Molecule:hdeb; PDBTitle: the structure of hdeb Phyre2 PDB 3bs7 chain A Region: 32 - 64 Aligned: 33 Modelled: 33 Confidence: 37.8% Identity: 21% PDB header:signaling protein Chain: A: PDB Molecule:protein aveugle; PDBTitle: crystal structure of the sterile alpha motif (sam) domain2 of hyphen/aveugle Phyre2 PDB 3bq7 chain A Region: 32 - 44 Aligned: 13 Modelled: 13 Confidence: 31.4% Identity: 38% PDB header:transferase Chain: A: PDB Molecule:diacylglycerol kinase delta; PDBTitle: sam domain of diacylglycerol kinase delta1 (e35g) Phyre2 PDB 1kw4 chain A Region: 30 - 44 Aligned: 15 Modelled: 15 Confidence: 29.4% Identity: 27% Fold: SAM domain-like Superfamily: SAM/Pointed domain Family: SAM (sterile alpha motif) domain Phyre2 PDB 1v85 chain A Region: 18 - 65 Aligned: 48 Modelled: 48 Confidence: 23.4% Identity: 19% PDB header:apoptosis Chain: A: PDB Molecule:similar to ring finger protein 36; PDBTitle: sterile alpha motif (sam) domain of mouse bifunctional2 apoptosis regulator Phyre2 PDB 1pk1 chain C domain 1 Region: 33 - 41 Aligned: 9 Modelled: 9 Confidence: 18.9% Identity: 44% Fold: SAM domain-like Superfamily: SAM/Pointed domain Family: SAM (sterile alpha motif) domain Phyre2 PDB 1eq8 chain B Region: 1 - 19 Aligned: 19 Modelled: 19 Confidence: 18.5% Identity: 26% PDB header:signaling protein Chain: B: PDB Molecule:acetylcholine receptor protein; PDBTitle: three-dimensional structure of the pentameric helical2 bundle of the acetylcholine receptor m2 transmembrane3 segment Phyre2 PDB 1eq8 chain D Region: 1 - 19 Aligned: 19 Modelled: 19 Confidence: 18.5% Identity: 26% PDB header:signaling protein Chain: D: PDB Molecule:acetylcholine receptor protein; PDBTitle: three-dimensional structure of the pentameric helical2 bundle of the acetylcholine receptor m2 transmembrane3 segment Phyre2 PDB 1eq8 chain C Region: 1 - 19 Aligned: 19 Modelled: 19 Confidence: 18.5% Identity: 26% PDB header:signaling protein Chain: C: PDB Molecule:acetylcholine receptor protein; PDBTitle: three-dimensional structure of the pentameric helical2 bundle of the acetylcholine receptor m2 transmembrane3 segment Phyre2 PDB 1eq8 chain E Region: 1 - 19 Aligned: 19 Modelled: 19 Confidence: 18.5% Identity: 26% PDB header:signaling protein Chain: E: PDB Molecule:acetylcholine receptor protein; PDBTitle: three-dimensional structure of the pentameric helical2 bundle of the acetylcholine receptor m2 transmembrane3 segment Phyre2 PDB 1eq8 chain A Region: 1 - 19 Aligned: 19 Modelled: 19 Confidence: 18.5% Identity: 26% PDB header:signaling protein Chain: A: PDB Molecule:acetylcholine receptor protein; PDBTitle: three-dimensional structure of the pentameric helical2 bundle of the acetylcholine receptor m2 transmembrane3 segment Phyre2 PDB 1a11 chain A Region: 1 - 19 Aligned: 19 Modelled: 19 Confidence: 18.5% Identity: 26% PDB header:acetylcholine receptor Chain: A: PDB Molecule:acetylcholine receptor m2; PDBTitle: nmr structure of membrane spanning segment 2 of the2 acetylcholine receptor in dpc micelles, 10 structures Phyre2 PDB 1wwv chain A domain 1 Region: 32 - 41 Aligned: 10 Modelled: 10 Confidence: 16.4% Identity: 40% Fold: SAM domain-like Superfamily: SAM/Pointed domain Family: SAM (sterile alpha motif) domain Phyre2 PDB 3bs5 chain A Region: 32 - 64 Aligned: 33 Modelled: 33 Confidence: 14.0% Identity: 21% PDB header:signaling protein/membrane protein Chain: A: PDB Molecule:protein aveugle; PDBTitle: crystal structure of hcnk2-sam/dhyp-sam complex Phyre2 PDB 1usd chain A Region: 92 - 109 Aligned: 18 Modelled: 18 Confidence: 8.7% Identity: 28% PDB header:signaling protein Chain: A: PDB Molecule:vasodilator-stimulated phosphoprotein; PDBTitle: human vasp tetramerisation domain l352m Phyre2 PDB 2fj6 chain A domain 1 Region: 40 - 62 Aligned: 23 Modelled: 23 Confidence: 6.8% Identity: 22% Fold: SAM domain-like Superfamily: YozE-like Family: YozE-like Phyre2 PDB 2o6k chain A domain 1 Region: 40 - 62 Aligned: 23 Modelled: 23 Confidence: 6.6% Identity: 13% Fold: SAM domain-like Superfamily: YozE-like Family: YozE-like Phyre2 PDB 2ean chain A Region: 30 - 44 Aligned: 15 Modelled: 15 Confidence: 6.4% Identity: 13% PDB header:signaling protein Chain: A: PDB Molecule:connector enhancer of kinase suppressor of ras 2; PDBTitle: solution structure of the n-terminal sam-domain of human2 kiaa0902 protein (connector enhancer of kinase suppressor3 of ras 2) Phyre2 PDB 2f93 chain B domain 1 Region: 4 - 35 Aligned: 32 Modelled: 32 Confidence: 6.3% Identity: 28% Fold: Transmembrane helix hairpin Superfamily: Htr2 transmembrane domain-like Family: Htr2 transmembrane domain-like Phyre2 1 d1dj8a_ 2 c2xuvB_ 3 c3bs7A_ 4 c3bq7A_ 5 d1kw4a_ 6 c1v85A_ 7 d1pk1c1 8 c1eq8B_ 9 c1eq8D_ 10 c1eq8C_ 11 c1eq8E_ 12 c1eq8A_ 13 c1a11A_ 14 d1wwva1 15 c3bs5A_ 16 c1usdA_ 17 d2fj6a1 18 d2o6ka1 19 c2eanA_ 20 d2f93b1 21 22

Detailed template information

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

1 d1dj8a_ 100.0 100 Fold:Protein HNS-dependent expression A; HdeA Superfamily:Protein HNS-dependent expression A; HdeA Family:Protein HNS-dependent expression A; HdeA 2 c2xuvB_ 91.1 18 PDB header:unknown function Chain: B: PDB Molecule:hdeb; PDBTitle: the structure of hdeb 3 c3bs7A_ 37.8 21 PDB header:signaling protein Chain: A: PDB Molecule:protein aveugle; PDBTitle: crystal structure of the sterile alpha motif (sam) domain2 of hyphen/aveugle 4 c3bq7A_ 31.4 38 PDB header:transferase Chain: A: PDB Molecule:diacylglycerol kinase delta; PDBTitle: sam domain of diacylglycerol kinase delta1 (e35g) 5 d1kw4a_ 29.4 27 Fold:SAM domain-like Superfamily:SAM/Pointed domain Family:SAM (sterile alpha motif) domain 6 c1v85A_ 23.4 19 PDB header:apoptosis Chain: A: PDB Molecule:similar to ring finger protein 36; PDBTitle: sterile alpha motif (sam) domain of mouse bifunctional2 apoptosis regulator 7 d1pk1c1 18.9 44 Fold:SAM domain-like Superfamily:SAM/Pointed domain Family:SAM (sterile alpha motif) domain 8 c1eq8B_ 18.5 26 PDB header:signaling protein Chain: B: PDB Molecule:acetylcholine receptor protein; PDBTitle: three-dimensional structure of the pentameric helical2 bundle of the acetylcholine receptor m2 transmembrane3 segment 9 c1eq8D_ 18.5 26 PDB header:signaling protein Chain: D: PDB Molecule:acetylcholine receptor protein; PDBTitle: three-dimensional structure of the pentameric helical2 bundle of the acetylcholine receptor m2 transmembrane3 segment 10 c1eq8C_ 18.5 26 PDB header:signaling protein Chain: C: PDB Molecule:acetylcholine receptor protein; PDBTitle: three-dimensional structure of the pentameric helical2 bundle of the acetylcholine receptor m2 transmembrane3 segment 11 c1eq8E_ 18.5 26 PDB header:signaling protein Chain: E: PDB Molecule:acetylcholine receptor protein; PDBTitle: three-dimensional structure of the pentameric helical2 bundle of the acetylcholine receptor m2 transmembrane3 segment 12 c1eq8A_ 18.5 26 PDB header:signaling protein Chain: A: PDB Molecule:acetylcholine receptor protein; PDBTitle: three-dimensional structure of the pentameric helical2 bundle of the acetylcholine receptor m2 transmembrane3 segment 13 c1a11A_ 18.5 26 PDB header:acetylcholine receptor Chain: A: PDB Molecule:acetylcholine receptor m2; PDBTitle: nmr structure of membrane spanning segment 2 of the2 acetylcholine receptor in dpc micelles, 10 structures 14 d1wwva1 16.4 40 Fold:SAM domain-like Superfamily:SAM/Pointed domain Family:SAM (sterile alpha motif) domain 15 c3bs5A_ 14.0 21 PDB header:signaling protein/membrane protein Chain: A: PDB Molecule:protein aveugle; PDBTitle: crystal structure of hcnk2-sam/dhyp-sam complex 16 c1usdA_ 8.7 28 PDB header:signaling protein Chain: A: PDB Molecule:vasodilator-stimulated phosphoprotein; PDBTitle: human vasp tetramerisation domain l352m 17 d2fj6a1 6.8 22 Fold:SAM domain-like Superfamily:YozE-like Family:YozE-like 18 d2o6ka1 6.6 13 Fold:SAM domain-like Superfamily:YozE-like Family:YozE-like 19 c2eanA_ 6.4 13 PDB header:signaling protein Chain: A: PDB Molecule:connector enhancer of kinase suppressor of ras 2; PDBTitle: solution structure of the n-terminal sam-domain of human2 kiaa0902 protein (connector enhancer of kinase suppressor3 of ras 2) 20 d2f93b1 6.3 28 Fold:Transmembrane helix hairpin Superfamily:Htr2 transmembrane domain-like Family:Htr2 transmembrane domain-like 21 c2f93B_ not modelled 6.3 28 PDB header:membrane protein Chain: B: PDB Molecule:sensory rhodopsin ii transducer; PDBTitle: k intermediate structure of sensory rhodopsin ii/transducer complex in2 combination with the ground state structure 22 c2f95B_ not modelled 6.0 28 PDB header:membrane protein Chain: B: PDB Molecule:sensory rhodopsin ii transducer; PDBTitle: m intermediate structure of sensory rhodopsin ii/transducer complex in2 combination with the ground state structure

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