Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	K	E	H	T	T	E	H	L	R	A	E	L	K	S	L	S	D	T	L	E	E	V	L	S	S	S	G	E	K	S	K	E	E	L	S	K	I	R	S	K	A	E	Q	A	L	K	Q	S	R	Y	R	L	G	E	T	G	D	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?																										?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.
Sequence		I	A	K	Q	T	R	V	A	A	A	R	A	D	E	Y	V	R	E	N	P	W	T	G	V	G	I	G	A	A	I	G	V	V	L	G	V	L	L	S	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: 10 - 76 Aligned: 67 Modelled: 67 Confidence: 91.4% Identity: 15% PDB header:lipid transport Chain: A: PDB Molecule:apolipoprotein e2; PDBTitle: apolipoprotein e2 (apoe2, d154a mutation) Phyre2 PDB 1gs9 chain A Region: 4 - 76 Aligned: 73 Modelled: 73 Confidence: 88.3% Identity: 16% Fold: Four-helical up-and-down bundle Superfamily: Apolipoprotein Family: Apolipoprotein Phyre2 PDB 2x43 chain S Region: 4 - 55 Aligned: 52 Modelled: 52 Confidence: 80.0% Identity: 8% PDB header:membrane protein Chain: S: PDB Molecule:sherp; PDBTitle: structural basis of molecular recognition by sherp at membrane2 surfaces Phyre2 PDB 3kdp chain G Region: 74 - 101 Aligned: 26 Modelled: 28 Confidence: 72.3% Identity: 31% 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 3kdp chain H Region: 74 - 101 Aligned: 26 Modelled: 28 Confidence: 72.3% Identity: 31% 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 3r2p chain A Region: 4 - 79 Aligned: 76 Modelled: 76 Confidence: 60.9% Identity: 13% 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 1av1 chain B Region: 5 - 78 Aligned: 74 Modelled: 74 Confidence: 58.8% Identity: 12% PDB header:lipid transport Chain: B: PDB Molecule:apolipoprotein a-i; PDBTitle: crystal structure of human apolipoprotein a-i Phyre2 PDB 1eq1 chain A Region: 4 - 78 Aligned: 75 Modelled: 75 Confidence: 41.8% Identity: 19% Fold: Apolipophorin-III Superfamily: Apolipophorin-III Family: Apolipophorin-III Phyre2 PDB 2a01 chain B Region: 3 - 78 Aligned: 76 Modelled: 76 Confidence: 39.4% Identity: 21% 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: 4 - 76 Aligned: 72 Modelled: 73 Confidence: 35.3% Identity: 7% 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 2jwa chain A Region: 81 - 101 Aligned: 21 Modelled: 21 Confidence: 31.4% Identity: 38% PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure Phyre2 PDB 1wa8 chain B domain 1 Region: 4 - 66 Aligned: 63 Modelled: 63 Confidence: 25.6% Identity: 11% Fold: Ferritin-like Superfamily: EsxAB dimer-like Family: ESAT-6 like Phyre2 PDB 1ryk chain A Region: 1 - 64 Aligned: 64 Modelled: 64 Confidence: 24.7% Identity: 5% Fold: SAM domain-like Superfamily: Hypothetical protein YjbJ Family: Hypothetical protein YjbJ Phyre2 PDB 2vs0 chain B Region: 4 - 75 Aligned: 72 Modelled: 72 Confidence: 23.6% 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 1i6l chain A Region: 4 - 78 Aligned: 71 Modelled: 68 Confidence: 23.4% Identity: 14% Fold: Adenine nucleotide alpha hydrolase-like Superfamily: Nucleotidylyl transferase Family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain Phyre2 PDB 3prh chain B Region: 4 - 78 Aligned: 71 Modelled: 75 Confidence: 22.7% Identity: 18% PDB header:ligase Chain: B: PDB Molecule:tryptophanyl-trna synthetase; PDBTitle: tryptophanyl-trna synthetase val144pro mutant from b. subtilis Phyre2 PDB 2ooc chain A domain 1 Region: 4 - 84 Aligned: 73 Modelled: 81 Confidence: 21.5% Identity: 14% Fold: Four-helical up-and-down bundle Superfamily: Histidine-containing phosphotransfer domain, HPT domain Family: SphA-like Phyre2 PDB 1p58 chain F Region: 62 - 95 Aligned: 33 Modelled: 34 Confidence: 21.4% Identity: 15% 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 3e0s chain A Region: 12 - 101 Aligned: 80 Modelled: 90 Confidence: 21.4% Identity: 23% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of an uncharacterized protein from2 chlorobium tepidum Phyre2 PDB 3lw5 chain K Region: 81 - 96 Aligned: 16 Modelled: 16 Confidence: 20.1% Identity: 44% PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit x psak; PDBTitle: improved model of plant photosystem i Phyre2 1 c1nfoA_ 2 d1gs9a_ 3 c2x43S_ 4 c3kdpG_ 5 c3kdpH_ 6 c3r2pA_ 7 c1av1B_ 8 d1eq1a_ 9 c2a01B_ 10 c3gvmA_ 11 c2jwaA_ 12 d1wa8b1 13 d1ryka_ 14 c2vs0B_ 15 d1i6la_ 16 c3prhB_ 17 d2ooca1 18 c1p58F_ 19 c3e0sA_ 20 c3lw5K_ 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 60 61 62 63 64 65 66 67

Detailed template information

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

1 c1nfoA_ 91.4 15 PDB header:lipid transport Chain: A: PDB Molecule:apolipoprotein e2; PDBTitle: apolipoprotein e2 (apoe2, d154a mutation) 2 d1gs9a_ 88.3 16 Fold:Four-helical up-and-down bundle Superfamily:Apolipoprotein Family:Apolipoprotein 3 c2x43S_ 80.0 8 PDB header:membrane protein Chain: S: PDB Molecule:sherp; PDBTitle: structural basis of molecular recognition by sherp at membrane2 surfaces 4 c3kdpG_ 72.3 31 PDB header:hydrolase Chain: G: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump 5 c3kdpH_ 72.3 31 PDB header:hydrolase Chain: H: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump 6 c3r2pA_ 60.9 13 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 c1av1B_ 58.8 12 PDB header:lipid transport Chain: B: PDB Molecule:apolipoprotein a-i; PDBTitle: crystal structure of human apolipoprotein a-i 8 d1eq1a_ 41.8 19 Fold:Apolipophorin-III Superfamily:Apolipophorin-III Family:Apolipophorin-III 9 c2a01B_ 39.4 21 PDB header:lipid transport Chain: B: PDB Molecule:apolipoprotein a-i; PDBTitle: crystal structure of lipid-free human apolipoprotein a-i 10 c3gvmA_ 35.3 7 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 c2jwaA_ 31.4 38 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 12 d1wa8b1 25.6 11 Fold:Ferritin-like Superfamily:EsxAB dimer-like Family:ESAT-6 like 13 d1ryka_ 24.7 5 Fold:SAM domain-like Superfamily:Hypothetical protein YjbJ Family:Hypothetical protein YjbJ 14 c2vs0B_ 23.6 11 PDB header:cell invasion Chain: B: PDB Molecule:virulence factor esxa; PDBTitle: structural analysis of homodimeric staphylococcal aureus2 virulence factor esxa 15 d1i6la_ 23.4 14 Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Nucleotidylyl transferase Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain 16 c3prhB_ 22.7 18 PDB header:ligase Chain: B: PDB Molecule:tryptophanyl-trna synthetase; PDBTitle: tryptophanyl-trna synthetase val144pro mutant from b. subtilis 17 d2ooca1 21.5 14 Fold:Four-helical up-and-down bundle Superfamily:Histidine-containing phosphotransfer domain, HPT domain Family:SphA-like 18 c1p58F_ 21.4 15 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 19 c3e0sA_ 21.4 23 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of an uncharacterized protein from2 chlorobium tepidum 20 c3lw5K_ 20.1 44 PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit x psak; PDBTitle: improved model of plant photosystem i 21 c2l5bA_ not modelled 19.4 29 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 22 d2gtsa1 not modelled 17.1 16 Fold:Ferritin-like Superfamily:HP0062-like Family:HP0062-like 23 d1wa8a1 not modelled 16.7 12 Fold:Ferritin-like Superfamily:EsxAB dimer-like Family:ESAT-6 like 24 d1nekd_ not modelled 16.5 7 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) 25 c3onjA_ not modelled 12.0 9 PDB header:protein transport Chain: A: PDB Molecule:t-snare vti1; PDBTitle: crystal structure of yeast vti1p_habc domain 26 d1vcsa1 not modelled 11.8 11 Fold:STAT-like Superfamily:t-snare proteins Family:t-snare proteins 27 d1s35a1 not modelled 11.7 12 Fold:Spectrin repeat-like Superfamily:Spectrin repeat Family:Spectrin repeat 28 d1c99a_ not modelled 10.0 28 Fold:Transmembrane helix hairpin Superfamily:F1F0 ATP synthase subunit C Family:F1F0 ATP synthase subunit C 29 c2kncB_ not modelled 9.7 5 PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 30 d1eiya1 not modelled 9.5 23 Fold:Long alpha-hairpin Superfamily:tRNA-binding arm Family:Phenylalanyl-tRNA synthetase (PheRS) 31 d1k75a_ not modelled 9.3 10 Fold:ALDH-like Superfamily:ALDH-like Family:L-histidinol dehydrogenase HisD 32 d1f16a_ not modelled 8.9 21 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 33 c2g36A_ not modelled 8.3 16 PDB header:ligase Chain: A: PDB Molecule:tryptophanyl-trna synthetase; PDBTitle: crystal structure of tryptophanyl-trna synthetase (ec 6.1.1.2)2 (tryptophan-trna ligase)(trprs) (tm0492) from thermotoga maritima at3 2.50 a resolution 34 c3py7A_ not modelled 7.9 14 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 35 c1n54A_ not modelled 7.8 19 PDB header:rna binding protein Chain: A: PDB Molecule:80 kda nuclear cap binding protein; PDBTitle: cap binding complex m7gpppg free 36 c2kbvA_ not modelled 7.8 30 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 37 c2j5dA_ not modelled 7.6 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 38 d1q2ha_ not modelled 7.6 20 Fold:Dimerisation interlock Superfamily:Phenylalanine zipper Family:Adapter protein APS, dimerisation domain 39 c2v8sV_ not modelled 7.2 15 PDB header:protein transport Chain: V: PDB Molecule:vesicle transport through interaction with PDBTitle: vti1b habc domain - epsinr enth domain complex 40 c2ww9B_ not modelled 7.1 21 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 41 c1yi8C_ not modelled 7.1 13 PDB header:ligase Chain: C: PDB Molecule:tryptophanyl-trna synthetase; PDBTitle: crystal structure of tryptophanyl trrna synthetase ii from deinococcus2 radiodurans in complex with l-trp 42 c1q90L_ not modelled 7.1 27 PDB header:photosynthesis Chain: L: PDB Molecule:cytochrome b6f complex subunit petl; PDBTitle: structure of the cytochrome b6f (plastohydroquinone : plastocyanin2 oxidoreductase) from chlamydomonas reinhardtii 43 d1q90l_ not modelled 7.1 27 Fold:Single transmembrane helix Superfamily:PetL subunit of the cytochrome b6f complex Family:PetL subunit of the cytochrome b6f complex 44 c1ywwA_ not modelled 6.9 6 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein pa4738; PDBTitle: nmr structure of p. aeruginosa protein pa4738: northeast2 structural genomics consortium target pap2 45 c1xq8A_ not modelled 6.8 18 PDB header:lipid binding protein Chain: A: PDB Molecule:alpha-synuclein; PDBTitle: human micelle-bound alpha-synuclein 46 c3hd7A_ not modelled 6.7 14 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 47 c2p2uA_ not modelled 6.6 10 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 48 d1l2pa_ not modelled 6.5 13 Fold:Single transmembrane helix Superfamily:F1F0 ATP synthase subunit B, membrane domain Family:F1F0 ATP synthase subunit B, membrane domain 49 c3m5wB_ not modelled 6.3 17 PDB header:ligase Chain: B: PDB Molecule:tryptophanyl-trna synthetase; PDBTitle: crystal structure of tryptophanyl-trna synthetase from2 campylobacter jejuni 50 c3b9yA_ not modelled 6.3 21 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 51 d1szia_ not modelled 6.1 22 Fold:Four-helical up-and-down bundle Superfamily:Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain Family:Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain 52 d1tqga_ not modelled 6.0 10 Fold:Four-helical up-and-down bundle Superfamily:Histidine-containing phosphotransfer domain, HPT domain Family:Chemotaxis protein CheA P1 domain 53 c3kb8A_ not modelled 5.9 14 PDB header:transferase Chain: A: PDB Molecule:hypoxanthine phosphoribosyltransferase; PDBTitle: 2.09 angstrom resolution structure of a hypoxanthine-guanine2 phosphoribosyltransferase (hpt-1) from bacillus anthracis str. 'ames3 ancestor' in complex with gmp 54 d2o97b1 not modelled 5.6 16 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 55 c2ka2A_ not modelled 5.6 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 56 c2ka1B_ not modelled 5.6 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 57 c2ks1B_ not modelled 5.5 14 PDB header:transferase Chain: B: PDB Molecule:epidermal growth factor receptor; PDBTitle: heterodimeric association of transmembrane domains of erbb1 and erbb22 receptors enabling kinase activation 58 c2k1lB_ not modelled 5.5 31 PDB header:signaling protein Chain: B: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 6.3 59 c2k1lA_ not modelled 5.5 31 PDB header:signaling protein Chain: A: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 6.3 60 c2k1kA_ not modelled 5.5 31 PDB header:signaling protein Chain: A: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 4.3 61 c2k1kB_ not modelled 5.5 31 PDB header:signaling protein Chain: B: PDB Molecule:ephrin type-a receptor 1; PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 4.3 62 d1dqna_ not modelled 5.5 19 Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases) 63 d1g9sa_ not modelled 5.5 14 Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases) 64 c2el7A_ not modelled 5.3 25 PDB header:ligase Chain: A: PDB Molecule:tryptophanyl-trna synthetase; PDBTitle: crystal structure of tryptophanyl-trna synthetase from thermus2 thermophilus 65 c2hroA_ not modelled 5.3 15 PDB header:transferase Chain: A: PDB Molecule:phosphoenolpyruvate-protein phosphotransferase; PDBTitle: structure of the full-lenght enzyme i of the pts system from2 staphylococcus carnosus 66 c2ka2B_ not modelled 5.2 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 67 c2ka1A_ not modelled 5.2 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

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