Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	N	Q	F	G	D	T	R	I	D	D	D	L	T	L	L	S	E	T	L	E	E	V	L	R	S	S	G	D	P	A	D	Q	K	Y	V	E	L	K	A	R	A	E	K	A	L	D	D	V	K	K	R	V	S	Q	A	S	D	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																							?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.
Sequence		Y	Y	Y	R	A	K	Q	A	V	Y	R	A	D	D	Y	V	H	E	K	P	W	Q	G	I	G	V	G	A	A	V	G	L	V	L	G	L	L	L	A	R	R
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 1nfo chain A Region: 9 - 76 Aligned: 68 Modelled: 68 Confidence: 90.9% Identity: 12% PDB header:lipid transport Chain: A: PDB Molecule:apolipoprotein e2; PDBTitle: apolipoprotein e2 (apoe2, d154a mutation) Phyre2 PDB 1gs9 chain A Region: 7 - 76 Aligned: 70 Modelled: 70 Confidence: 86.5% Identity: 11% Fold: Four-helical up-and-down bundle Superfamily: Apolipoprotein Family: Apolipoprotein Phyre2 PDB 3kdp chain H Region: 74 - 101 Aligned: 26 Modelled: 28 Confidence: 73.7% Identity: 27% PDB header:hydrolase Chain: H: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump Phyre2 PDB 3kdp chain G Region: 74 - 101 Aligned: 26 Modelled: 28 Confidence: 73.7% Identity: 27% PDB header:hydrolase Chain: G: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump Phyre2 PDB 2x43 chain S Region: 3 - 54 Aligned: 52 Modelled: 52 Confidence: 65.8% Identity: 10% PDB header:membrane protein Chain: S: PDB Molecule:sherp; PDBTitle: structural basis of molecular recognition by sherp at membrane2 surfaces Phyre2 PDB 3r2p chain A Region: 7 - 79 Aligned: 73 Modelled: 73 Confidence: 52.3% Identity: 8% PDB header:lipid transport Chain: A: PDB Molecule:apolipoprotein a-i; PDBTitle: 2.2 angstrom crystal structure of c terminal truncated human2 apolipoprotein a-i reveals the assembly of hdl by dimerization. Phyre2 PDB 2vs0 chain B Region: 7 - 70 Aligned: 64 Modelled: 64 Confidence: 42.6% Identity: 11% PDB header:cell invasion Chain: B: PDB Molecule:virulence factor esxa; PDBTitle: structural analysis of homodimeric staphylococcal aureus2 virulence factor esxa Phyre2 PDB 1wa8 chain B domain 1 Region: 8 - 66 Aligned: 59 Modelled: 59 Confidence: 40.8% Identity: 10% Fold: Ferritin-like Superfamily: EsxAB dimer-like Family: ESAT-6 like Phyre2 PDB 2a01 chain B Region: 7 - 78 Aligned: 72 Modelled: 72 Confidence: 39.6% Identity: 18% PDB header:lipid transport Chain: B: PDB Molecule:apolipoprotein a-i; PDBTitle: crystal structure of lipid-free human apolipoprotein a-i Phyre2 PDB 3gvm chain A Region: 7 - 71 Aligned: 65 Modelled: 65 Confidence: 39.2% Identity: 6% PDB header:viral protein Chain: A: PDB Molecule:putative uncharacterized protein sag1039; PDBTitle: structure of the homodimeric wxg-100 family protein from streptococcus2 agalactiae Phyre2 PDB 1eq1 chain A Region: 6 - 78 Aligned: 73 Modelled: 73 Confidence: 29.7% Identity: 14% Fold: Apolipophorin-III Superfamily: Apolipophorin-III Family: Apolipophorin-III Phyre2 PDB 1wa8 chain A domain 1 Region: 7 - 63 Aligned: 57 Modelled: 57 Confidence: 25.2% Identity: 11% Fold: Ferritin-like Superfamily: EsxAB dimer-like Family: ESAT-6 like Phyre2 PDB 2jwa chain A Region: 80 - 101 Aligned: 22 Modelled: 22 Confidence: 21.9% Identity: 36% PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure Phyre2 PDB 3onj chain A Region: 11 - 63 Aligned: 53 Modelled: 53 Confidence: 21.8% Identity: 11% PDB header:protein transport Chain: A: PDB Molecule:t-snare vti1; PDBTitle: crystal structure of yeast vti1p_habc domain Phyre2 PDB 1av1 chain B Region: 7 - 78 Aligned: 72 Modelled: 72 Confidence: 21.8% Identity: 7% PDB header:lipid transport Chain: B: PDB Molecule:apolipoprotein a-i; PDBTitle: crystal structure of human apolipoprotein a-i Phyre2 PDB 1p58 chain F Region: 62 - 95 Aligned: 33 Modelled: 34 Confidence: 21.4% Identity: 18% PDB header:virus Chain: F: PDB Molecule:envelope protein m; PDBTitle: complex organization of dengue virus membrane proteins as revealed by2 9.5 angstrom cryo-em reconstruction Phyre2 PDB 1f16 chain A Region: 63 - 101 Aligned: 39 Modelled: 39 Confidence: 21.3% Identity: 21% Fold: Toxins' membrane translocation domains Superfamily: Bcl-2 inhibitors of programmed cell death Family: Bcl-2 inhibitors of programmed cell death Phyre2 PDB 3lw5 chain K Region: 81 - 96 Aligned: 16 Modelled: 16 Confidence: 20.0% Identity: 44% PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit x psak; PDBTitle: improved model of plant photosystem i Phyre2 PDB 3e0s chain A Region: 12 - 101 Aligned: 80 Modelled: 90 Confidence: 18.5% Identity: 15% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of an uncharacterized protein from2 chlorobium tepidum Phyre2 PDB 2l5b chain A Region: 81 - 101 Aligned: 21 Modelled: 21 Confidence: 16.5% Identity: 33% PDB header:apoptosis Chain: A: PDB Molecule:activator of apoptosis harakiri; PDBTitle: solution structure of the transmembrane domain of bcl-2 member2 harakiri in micelles Phyre2 1 c1nfoA_ 2 d1gs9a_ 3 c3kdpH_ 4 c3kdpG_ 5 c2x43S_ 6 c3r2pA_ 7 c2vs0B_ 8 d1wa8b1 9 c2a01B_ 10 c3gvmA_ 11 d1eq1a_ 12 d1wa8a1 13 c2jwaA_ 14 c3onjA_ 15 c1av1B_ 16 c1p58F_ 17 d1f16a_ 18 c3lw5K_ 19 c3e0sA_ 20 c2l5bA_ 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 49 50 51 52 53 54 55 56 57 58 59

Detailed template information

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

1 c1nfoA_ 90.9 12 PDB header:lipid transport Chain: A: PDB Molecule:apolipoprotein e2; PDBTitle: apolipoprotein e2 (apoe2, d154a mutation) 2 d1gs9a_ 86.5 11 Fold:Four-helical up-and-down bundle Superfamily:Apolipoprotein Family:Apolipoprotein 3 c3kdpH_ 73.7 27 PDB header:hydrolase Chain: H: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump 4 c3kdpG_ 73.7 27 PDB header:hydrolase Chain: G: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump 5 c2x43S_ 65.8 10 PDB header:membrane protein Chain: S: PDB Molecule:sherp; PDBTitle: structural basis of molecular recognition by sherp at membrane2 surfaces 6 c3r2pA_ 52.3 8 PDB header:lipid transport Chain: A: PDB Molecule:apolipoprotein a-i; PDBTitle: 2.2 angstrom crystal structure of c terminal truncated human2 apolipoprotein a-i reveals the assembly of hdl by dimerization. 7 c2vs0B_ 42.6 11 PDB header:cell invasion Chain: B: PDB Molecule:virulence factor esxa; PDBTitle: structural analysis of homodimeric staphylococcal aureus2 virulence factor esxa 8 d1wa8b1 40.8 10 Fold:Ferritin-like Superfamily:EsxAB dimer-like Family:ESAT-6 like 9 c2a01B_ 39.6 18 PDB header:lipid transport Chain: B: PDB Molecule:apolipoprotein a-i; PDBTitle: crystal structure of lipid-free human apolipoprotein a-i 10 c3gvmA_ 39.2 6 PDB header:viral protein Chain: A: PDB Molecule:putative uncharacterized protein sag1039; PDBTitle: structure of the homodimeric wxg-100 family protein from streptococcus2 agalactiae 11 d1eq1a_ 29.7 14 Fold:Apolipophorin-III Superfamily:Apolipophorin-III Family:Apolipophorin-III 12 d1wa8a1 25.2 11 Fold:Ferritin-like Superfamily:EsxAB dimer-like Family:ESAT-6 like 13 c2jwaA_ 21.9 36 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 14 c3onjA_ 21.8 11 PDB header:protein transport Chain: A: PDB Molecule:t-snare vti1; PDBTitle: crystal structure of yeast vti1p_habc domain 15 c1av1B_ 21.8 7 PDB header:lipid transport Chain: B: PDB Molecule:apolipoprotein a-i; PDBTitle: crystal structure of human apolipoprotein a-i 16 c1p58F_ 21.4 18 PDB header:virus Chain: F: PDB Molecule:envelope protein m; PDBTitle: complex organization of dengue virus membrane proteins as revealed by2 9.5 angstrom cryo-em reconstruction 17 d1f16a_ 21.3 21 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 18 c3lw5K_ 20.0 44 PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit x psak; PDBTitle: improved model of plant photosystem i 19 c3e0sA_ 18.5 15 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of an uncharacterized protein from2 chlorobium tepidum 20 c2l5bA_ 16.5 33 PDB header:apoptosis Chain: A: PDB Molecule:activator of apoptosis harakiri; PDBTitle: solution structure of the transmembrane domain of bcl-2 member2 harakiri in micelles 21 d1nekd_ not modelled 16.2 15 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 22 d1l2pa_ not modelled 15.5 16 Fold:Single transmembrane helix Superfamily:F1F0 ATP synthase subunit B, membrane domain Family:F1F0 ATP synthase subunit B, membrane domain 23 d1vcsa1 not modelled 13.9 7 Fold:STAT-like Superfamily:t-snare proteins Family:t-snare proteins 24 d1i6la_ not modelled 13.8 4 Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Nucleotidylyl transferase Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain 25 c2v8sV_ not modelled 12.3 10 PDB header:protein transport Chain: V: PDB Molecule:vesicle transport through interaction with PDBTitle: vti1b habc domain - epsinr enth domain complex 26 c2kncB_ not modelled 12.3 15 PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 27 c2p2uA_ not modelled 12.2 24 PDB header:dna binding protein Chain: A: PDB Molecule:host-nuclease inhibitor protein gam, putative; PDBTitle: crystal structure of putative host-nuclease inhibitor2 protein gam from desulfovibrio vulgaris 28 c3m91B_ not modelled 10.7 17 PDB header:hydrolase regulator Chain: B: PDB Molecule:prokaryotic ubiquitin-like protein pup; PDBTitle: crystal structure of the prokaryotic ubiquitin-like protein (pup)2 complexed with the amino terminal coiled coil of the mycobacterium3 tuberculosis proteasomal atpase mpa 29 d1fioa_ not modelled 10.2 14 Fold:STAT-like Superfamily:t-snare proteins Family:t-snare proteins 30 d1ryka_ not modelled 10.1 9 Fold:SAM domain-like Superfamily:Hypothetical protein YjbJ Family:Hypothetical protein YjbJ 31 c2ww9B_ not modelled 8.9 14 PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sss1; PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome 32 d1s35a1 not modelled 8.8 9 Fold:Spectrin repeat-like Superfamily:Spectrin repeat Family:Spectrin repeat 33 c2j5dA_ not modelled 8.4 16 PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: nmr structure of bnip3 transmembrane domain in lipid2 bicelles 34 d1eiya1 not modelled 8.3 21 Fold:Long alpha-hairpin Superfamily:tRNA-binding arm Family:Phenylalanyl-tRNA synthetase (PheRS) 35 d1c99a_ not modelled 7.4 28 Fold:Transmembrane helix hairpin Superfamily:F1F0 ATP synthase subunit C Family:F1F0 ATP synthase subunit C 36 d1q2ha_ not modelled 7.1 10 Fold:Dimerisation interlock Superfamily:Phenylalanine zipper Family:Adapter protein APS, dimerisation domain 37 c2kp6A_ not modelled 6.9 8 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of protein cv0237 from2 chromobacterium violaceum. northeast structural genomics3 consortium (nesg) target cvt1 38 c1n54A_ not modelled 6.7 9 PDB header:rna binding protein Chain: A: PDB Molecule:80 kda nuclear cap binding protein; PDBTitle: cap binding complex m7gpppg free 39 c3a0hX_ not modelled 6.7 44 PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of i-substituted photosystem ii complex 40 c3a0bX_ not modelled 6.7 44 PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of br-substituted photosystem ii complex 41 c3a0hx_ not modelled 6.7 44 PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of i-substituted photosystem ii complex 42 c3a0bx_ not modelled 6.7 44 PDB header:electron transport Chain: X: PDB Molecule:photosystem ii reaction center protein x; PDBTitle: crystal structure of br-substituted photosystem ii complex 43 c3ipdB_ not modelled 6.5 11 PDB header:exocytosis Chain: B: PDB Molecule:syntaxin-1a; PDBTitle: helical extension of the neuronal snare complex into the2 membrane, spacegroup i 21 21 21 44 c3prhB_ not modelled 6.5 9 PDB header:ligase Chain: B: PDB Molecule:tryptophanyl-trna synthetase; PDBTitle: tryptophanyl-trna synthetase val144pro mutant from b. subtilis 45 c2kbvA_ not modelled 6.4 20 PDB header:membrane protein Chain: A: PDB Molecule:sodium/hydrogen exchanger 1; PDBTitle: structural and functional analysis of tm xi of the nhe12 isoform of the na+/h+ exchanger 46 d1lvfa_ not modelled 6.3 8 Fold:STAT-like Superfamily:t-snare proteins Family:t-snare proteins 47 c3sz3A_ not modelled 6.1 12 PDB header:ligase Chain: A: PDB Molecule:tryptophanyl-trna synthetase; PDBTitle: crystal structure of tryptophanyl-trna synthetase from vibrio cholerae2 with an endogenous tryptophan 48 c2ka1B_ not modelled 6.1 16 PDB header:membrane protein Chain: B: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles 49 c2ka2A_ not modelled 6.1 16 PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles with his173-ser172 intermonomer3 hydrogen bond restraints 50 c1s5lx_ not modelled 6.0 44 PDB header:photosynthesis Chain: X: PDB Molecule:photosystem ii psbx protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 51 d1dqna_ not modelled 5.8 16 Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases) 52 c2ka1A_ not modelled 5.7 13 PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles 53 c2ka2B_ not modelled 5.7 13 PDB header:membrane protein Chain: B: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles with his173-ser172 intermonomer3 hydrogen bond restraints 54 d1rhzb_ not modelled 5.7 21 Fold:Single transmembrane helix Superfamily:Preprotein translocase SecE subunit Family:Preprotein translocase SecE subunit 55 c1q90L_ not modelled 5.6 33 PDB header:photosynthesis Chain: L: PDB Molecule:cytochrome b6f complex subunit petl; PDBTitle: structure of the cytochrome b6f (plastohydroquinone : plastocyanin2 oxidoreductase) from chlamydomonas reinhardtii 56 d1q90l_ not modelled 5.6 33 Fold:Single transmembrane helix Superfamily:PetL subunit of the cytochrome b6f complex Family:PetL subunit of the cytochrome b6f complex 57 c3hd7A_ not modelled 5.4 15 PDB header:exocytosis Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1 58 d1t72a_ not modelled 5.4 13 Fold:Spectrin repeat-like Superfamily:PhoU-like Family:PhoU-like 59 c3py7A_ not modelled 5.4 18 PDB header:viral protein Chain: A: PDB Molecule:maltose-binding periplasmic protein,paxillin ld1,protein e6 PDBTitle: crystal structure of full-length bovine papillomavirus oncoprotein e62 in complex with ld1 motif of paxillin at 2.3a 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

Transmembrane helix prediction

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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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