Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	V	K	H	A	V	V	L	L	M	L	I	S	P	L	S	W	A	G	T	M	T	F	Q	F	R	N	P	N	F	G	G	N	P	N	N	G	A	F	L	L	N	S	A	Q	A	Q	N	S	Y	K	D	P	S	Y	N	D	D	F
Secondary structure
SS confidence
Disorder		?	?	?											?	?																												?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	I	E	T	P	S	A	L	D	N	F	T	Q	A	I	Q	S	Q	I	L	G	G	L	L	S	N	I	N	T	G	K	P	G	R	M	V	T	N	D	Y	I	V	D	I	A	N	R	D	G	Q	L	Q	L	N	V	T	D	R	K	T
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																				?	?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.
Sequence		G	Q	T	S	T	I	Q	V	S	G	L	Q	N	N	S	T	D	F
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 2hc5 chain A domain 1 Region: 99 - 123 Aligned: 25 Modelled: 25 Confidence: 45.5% Identity: 8% Fold: FlaG-like Superfamily: FlaG-like Family: FlaG-like Phyre2 PDB 3sd2 chain A Region: 100 - 123 Aligned: 24 Modelled: 24 Confidence: 44.1% Identity: 21% PDB header:unknown function Chain: A: PDB Molecule:putative member of duf3244 protein family; PDBTitle: crystal structure of a putative member of duf3244 protein family2 (bt_3571) from bacteroides thetaiotaomicron vpi-5482 at 1.40 a3 resolution Phyre2 PDB 2hzs chain H Region: 21 - 40 Aligned: 19 Modelled: 20 Confidence: 41.6% Identity: 16% PDB header:transcription Chain: H: PDB Molecule:rna polymerase ii mediator complex subunit 18; PDBTitle: structure of the mediator head submodule med8c/18/20 Phyre2 PDB 1dkz chain A domain 2 Region: 99 - 129 Aligned: 31 Modelled: 31 Confidence: 28.3% Identity: 23% Fold: Heat shock protein 70kD (HSP70), peptide-binding domain Superfamily: Heat shock protein 70kD (HSP70), peptide-binding domain Family: Heat shock protein 70kD (HSP70), peptide-binding domain Phyre2 PDB 1u00 chain A domain 2 Region: 99 - 128 Aligned: 30 Modelled: 30 Confidence: 24.6% Identity: 30% Fold: Heat shock protein 70kD (HSP70), peptide-binding domain Superfamily: Heat shock protein 70kD (HSP70), peptide-binding domain Family: Heat shock protein 70kD (HSP70), peptide-binding domain Phyre2 PDB 3dqg chain C Region: 100 - 128 Aligned: 29 Modelled: 29 Confidence: 20.5% Identity: 24% PDB header:chaperone Chain: C: PDB Molecule:heat shock 70 kda protein f; PDBTitle: peptide-binding domain of heat shock 70 kda protein f, mitochondrial2 precursor, from caenorhabditis elegans. Phyre2 PDB 1m8o chain B Region: 25 - 33 Aligned: 9 Modelled: 9 Confidence: 16.6% Identity: 33% PDB header:membrane protein Chain: B: PDB Molecule:platele integrin beta3 subunit: cytoplasmic PDBTitle: platelet integrin alfaiib-beta3 cytoplasmic domain Phyre2 PDB 3iei chain D Region: 8 - 32 Aligned: 25 Modelled: 25 Confidence: 15.5% Identity: 20% PDB header:transferase Chain: D: PDB Molecule:leucine carboxyl methyltransferase 1; PDBTitle: crystal structure of human leucine carboxylmethyltransferase-1 in2 complex with s-adenosyl homocysteine Phyre2 PDB 3fcg chain B Region: 92 - 129 Aligned: 29 Modelled: 38 Confidence: 13.4% Identity: 14% PDB header:membrane protein, protein transport Chain: B: PDB Molecule:f1 capsule-anchoring protein; PDBTitle: crystal structure analysis of the middle domain of the2 caf1a usher Phyre2 PDB 1s4x chain A Region: 25 - 33 Aligned: 9 Modelled: 9 Confidence: 12.4% Identity: 33% PDB header:cell adhesion Chain: A: PDB Molecule:integrin beta-3; PDBTitle: nmr structure of the integrin b3 cytoplasmic domain in dpc2 micelles Phyre2 PDB 2jpi chain A Region: 77 - 116 Aligned: 40 Modelled: 40 Confidence: 12.0% Identity: 10% PDB header:structural genomics Chain: A: PDB Molecule:hypothetical protein; PDBTitle: chemical shift assignments of pa4090 from pseudomonas2 aeruginosa Phyre2 PDB 1hzn chain A Region: 44 - 66 Aligned: 23 Modelled: 23 Confidence: 11.7% Identity: 26% PDB header:hormone/growth factor Chain: A: PDB Molecule:cholecystokinin type a receptor; PDBTitle: nmr solution structure of the third extracellular loop of2 the cholecystokinin a receptor Phyre2 PDB 2knc chain B Region: 25 - 33 Aligned: 9 Modelled: 9 Confidence: 11.5% Identity: 33% PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 1u00 chain A Region: 100 - 128 Aligned: 29 Modelled: 29 Confidence: 10.7% Identity: 31% PDB header:chaperone Chain: A: PDB Molecule:chaperone protein hsca; PDBTitle: hsca substrate binding domain complexed with the iscu2 recognition peptide elppvkihc Phyre2 PDB 2oq0 chain A domain 1 Region: 85 - 133 Aligned: 49 Modelled: 49 Confidence: 10.6% Identity: 8% Fold: OB-fold Superfamily: HIN-2000 domain-like Family: HIN-200/IF120x domain Phyre2 PDB 3d33 chain B Region: 100 - 123 Aligned: 24 Modelled: 24 Confidence: 10.6% Identity: 21% PDB header:unknown function Chain: B: PDB Molecule:domain of unknown function with an immunoglobulin-like PDBTitle: crystal structure of a duf3244 family protein with an immunoglobulin-2 like beta-sandwich fold (bvu_0276) from bacteroides vulgatus atcc3 8482 at 1.70 a resolution Phyre2 PDB 3dpq chain E Region: 99 - 128 Aligned: 30 Modelled: 30 Confidence: 10.5% Identity: 23% PDB header:chaperone, peptide binding protein Chain: E: PDB Molecule:chaperone protein dnak; PDBTitle: crystal structure of the substrate binding domain of e.2 coli dnak in complex with a long pyrrhocoricin-derived3 inhibitor peptide (form b) Phyre2 PDB 1ddw chain A Region: 21 - 79 Aligned: 42 Modelled: 40 Confidence: 10.4% Identity: 29% Fold: PH domain-like barrel Superfamily: PH domain-like Family: Enabled/VASP homology 1 domain (EVH1 domain) Phyre2 PDB 3rj1 chain S Region: 22 - 32 Aligned: 10 Modelled: 11 Confidence: 9.7% Identity: 20% PDB header:transcription Chain: S: PDB Molecule:mediator of rna polymerase ii transcription subunit 18; PDBTitle: architecture of the mediator head module Phyre2 PDB 5csm chain A Region: 8 - 41 Aligned: 33 Modelled: 34 Confidence: 9.6% Identity: 18% Fold: Chorismate mutase II Superfamily: Chorismate mutase II Family: Allosteric chorismate mutase Phyre2 1 d2hc5a1 2 c3sd2A_ 3 c2hzsH_ 4 d1dkza2 5 d1u00a2 6 c3dqgC_ 7 c1m8oB_ 8 c3ieiD_ 9 c3fcgB_ 10 c1s4xA_ 11 c2jpiA_ 12 c1hznA_ 13 c2kncB_ 14 c1u00A_ 15 d2oq0a1 16 c3d33B_ 17 c3dpqE_ 18 d1ddwa_ 19 c3rj1S_ 20 d5csma_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43

Detailed template information

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

1 d2hc5a1 45.5 8 Fold:FlaG-like Superfamily:FlaG-like Family:FlaG-like 2 c3sd2A_ 44.1 21 PDB header:unknown function Chain: A: PDB Molecule:putative member of duf3244 protein family; PDBTitle: crystal structure of a putative member of duf3244 protein family2 (bt_3571) from bacteroides thetaiotaomicron vpi-5482 at 1.40 a3 resolution 3 c2hzsH_ 41.6 16 PDB header:transcription Chain: H: PDB Molecule:rna polymerase ii mediator complex subunit 18; PDBTitle: structure of the mediator head submodule med8c/18/20 4 d1dkza2 28.3 23 Fold:Heat shock protein 70kD (HSP70), peptide-binding domain Superfamily:Heat shock protein 70kD (HSP70), peptide-binding domain Family:Heat shock protein 70kD (HSP70), peptide-binding domain 5 d1u00a2 24.6 30 Fold:Heat shock protein 70kD (HSP70), peptide-binding domain Superfamily:Heat shock protein 70kD (HSP70), peptide-binding domain Family:Heat shock protein 70kD (HSP70), peptide-binding domain 6 c3dqgC_ 20.5 24 PDB header:chaperone Chain: C: PDB Molecule:heat shock 70 kda protein f; PDBTitle: peptide-binding domain of heat shock 70 kda protein f, mitochondrial2 precursor, from caenorhabditis elegans. 7 c1m8oB_ 16.6 33 PDB header:membrane protein Chain: B: PDB Molecule:platele integrin beta3 subunit: cytoplasmic PDBTitle: platelet integrin alfaiib-beta3 cytoplasmic domain 8 c3ieiD_ 15.5 20 PDB header:transferase Chain: D: PDB Molecule:leucine carboxyl methyltransferase 1; PDBTitle: crystal structure of human leucine carboxylmethyltransferase-1 in2 complex with s-adenosyl homocysteine 9 c3fcgB_ 13.4 14 PDB header:membrane protein, protein transport Chain: B: PDB Molecule:f1 capsule-anchoring protein; PDBTitle: crystal structure analysis of the middle domain of the2 caf1a usher 10 c1s4xA_ 12.4 33 PDB header:cell adhesion Chain: A: PDB Molecule:integrin beta-3; PDBTitle: nmr structure of the integrin b3 cytoplasmic domain in dpc2 micelles 11 c2jpiA_ 12.0 10 PDB header:structural genomics Chain: A: PDB Molecule:hypothetical protein; PDBTitle: chemical shift assignments of pa4090 from pseudomonas2 aeruginosa 12 c1hznA_ 11.7 26 PDB header:hormone/growth factor Chain: A: PDB Molecule:cholecystokinin type a receptor; PDBTitle: nmr solution structure of the third extracellular loop of2 the cholecystokinin a receptor 13 c2kncB_ 11.5 33 PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 14 c1u00A_ 10.7 31 PDB header:chaperone Chain: A: PDB Molecule:chaperone protein hsca; PDBTitle: hsca substrate binding domain complexed with the iscu2 recognition peptide elppvkihc 15 d2oq0a1 10.6 8 Fold:OB-fold Superfamily:HIN-2000 domain-like Family:HIN-200/IF120x domain 16 c3d33B_ 10.6 21 PDB header:unknown function Chain: B: PDB Molecule:domain of unknown function with an immunoglobulin-like PDBTitle: crystal structure of a duf3244 family protein with an immunoglobulin-2 like beta-sandwich fold (bvu_0276) from bacteroides vulgatus atcc3 8482 at 1.70 a resolution 17 c3dpqE_ 10.5 23 PDB header:chaperone, peptide binding protein Chain: E: PDB Molecule:chaperone protein dnak; PDBTitle: crystal structure of the substrate binding domain of e.2 coli dnak in complex with a long pyrrhocoricin-derived3 inhibitor peptide (form b) 18 d1ddwa_ 10.4 29 Fold:PH domain-like barrel Superfamily:PH domain-like Family:Enabled/VASP homology 1 domain (EVH1 domain) 19 c3rj1S_ 9.7 20 PDB header:transcription Chain: S: PDB Molecule:mediator of rna polymerase ii transcription subunit 18; PDBTitle: architecture of the mediator head module 20 d5csma_ 9.6 18 Fold:Chorismate mutase II Superfamily:Chorismate mutase II Family:Allosteric chorismate mutase 21 d2fwua1 not modelled 9.2 9 Fold:Immunoglobulin-like beta-sandwich Superfamily:CalX-like Family:CalX-beta domain 22 d1y71a1 not modelled 8.0 26 Fold:SH3-like barrel Superfamily:Kinase-associated protein B-like Family:Kinase-associated protein B-like 23 c3hftA_ not modelled 7.9 44 PDB header:hydrolase Chain: A: PDB Molecule:wbms, polysaccharide deacetylase involved in o-antigen PDBTitle: crystal structure of a putative polysaccharide deacetylase involved in2 o-antigen biosynthesis (wbms, bb0128) from bordetella bronchiseptica3 at 1.90 a resolution 24 c3l9fD_ not modelled 7.2 13 PDB header:transcription regulator Chain: D: PDB Molecule:putative uncharacterized protein smu.1604c; PDBTitle: the crystal structure of smu.1604c from streptococcus mutans ua159 25 d1gcya1 not modelled 6.7 21 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 26 d1egxa_ not modelled 6.3 27 Fold:PH domain-like barrel Superfamily:PH domain-like Family:Enabled/VASP homology 1 domain (EVH1 domain) 27 c2op6A_ not modelled 5.9 19 PDB header:peptide binding protein Chain: A: PDB Molecule:heat shock 70 kda protein d; PDBTitle: peptide-binding domain of heat shock 70 kda protein d precursor from2 c.elegans 28 c2q6fB_ not modelled 5.9 42 PDB header:hydrolase Chain: B: PDB Molecule:infectious bronchitis virus (ibv) main protease; PDBTitle: crystal structure of infectious bronchitis virus (ibv) main2 protease in complex with a michael acceptor inhibitor n3 29 c3e9uA_ not modelled 5.9 26 PDB header:membrane protein Chain: A: PDB Molecule:na/ca exchange protein; PDBTitle: crystal structure of calx cbd2 domain 30 d1j7na2 not modelled 5.8 25 Fold:Zincin-like Superfamily:Metalloproteases ("zincins"), catalytic domain Family:Anthrax toxin lethal factor, N- and C-terminal domains 31 d1lvoa_ not modelled 5.8 42 Fold:Trypsin-like serine proteases Superfamily:Trypsin-like serine proteases Family:Viral cysteine protease of trypsin fold 32 d1jb0d_ not modelled 5.8 40 Fold:Photosystem I subunit PsaD Superfamily:Photosystem I subunit PsaD Family:Photosystem I subunit PsaD 33 c3nztA_ not modelled 5.8 5 PDB header:ligase Chain: A: PDB Molecule:glutamate--cysteine ligase; PDBTitle: 2.0 angstrom crystal structure of glutamate--cysteine ligase (gsha)2 ftom francisella tularensis in complex with amp 34 c3d23A_ not modelled 5.7 33 PDB header:hydrolase Chain: A: PDB Molecule:3c-like proteinase; PDBTitle: main protease of hcov-hku1 35 c3cu2A_ not modelled 5.7 19 PDB header:isomerase Chain: A: PDB Molecule:ribulose-5-phosphate 3-epimerase; PDBTitle: crystal structure of ribulose-5-phosphate 3-epimerase (yp_718263.1)2 from haemophilus somnus 129pt at 1.91 a resolution 36 c2j3mA_ not modelled 5.5 12 PDB header:ligase Chain: A: PDB Molecule:prolyl-trna synthetase; PDBTitle: prolyl-trna synthetase from enterococcus faecalis complexed2 with atp, manganese and prolinol 37 d1qc6a_ not modelled 5.5 12 Fold:PH domain-like barrel Superfamily:PH domain-like Family:Enabled/VASP homology 1 domain (EVH1 domain) 38 d2duca1 not modelled 5.4 33 Fold:Trypsin-like serine proteases Superfamily:Trypsin-like serine proteases Family:Viral cysteine protease of trypsin fold 39 c2oq0D_ not modelled 5.4 8 PDB header:protein binding Chain: D: PDB Molecule:gamma-interferon-inducible protein ifi-16; PDBTitle: crystal structure of the first hin-200 domain of interferon-inducible2 protein 16 40 c3n8eA_ not modelled 5.3 20 PDB header:chaperone Chain: A: PDB Molecule:stress-70 protein, mitochondrial; PDBTitle: substrate binding domain of the human heat shock 70kda protein 92 (mortalin) 41 c3fyfA_ not modelled 5.2 55 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein bvu-3222; PDBTitle: crystal structure of uncharacterized protein bvu_3222 from2 bacteroides vulgatus 42 d1g5ga1 not modelled 5.2 22 Fold:Head and neck region of the ectodomain of NDV fusion glycoprotein Superfamily:Head and neck region of the ectodomain of NDV fusion glycoprotein Family:Head and neck region of the ectodomain of NDV fusion glycoprotein 43 c2cblA_ not modelled 5.1 23 PDB header:complex (proto-oncogene/peptide) Chain: A: PDB Molecule:proto-oncogene cbl; PDBTitle: n-terminal domain of cbl in complex with its binding site2 on zap-70

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