Secondary structure and disorder prediction

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Sequence		M	K	Q	A	N	Q	D	R	G	T	L	L	L	A	L	V	A	G	L	S	I	N	G	T	F	A	A	L	F	S	S	I	V	P	F	S	V	F	P	I	I	S	L	V	L	T	V	Y	C	L	H	Q	R	Y	L	N	R	T	M	P
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																						?	?																												?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.
Sequence		V	G	L	P	G	L	A	A	A	C	F	I	L	G	V	L	L	Y	S	T	V	V	R	A	E	Y	P	D	I	G	S	N	F	F	P	A	V	L	S	V	I	M	V	F	W	I	G	A	K	M	R	N	R	K	Q	E	V	A	E
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 3gia chain A Region: 2 - 114 Aligned: 113 Modelled: 113 Confidence: 34.4% Identity: 8% PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter Phyre2 PDB 3fo8 chain D Region: 85 - 92 Aligned: 8 Modelled: 8 Confidence: 34.1% Identity: 75% PDB header:viral protein Chain: D: PDB Molecule:tail sheath protein gp18; PDBTitle: crystal structure of the bacteriophage t4 tail sheath2 protein, protease resistant fragment gp18pr Phyre2 PDB 2nr9 chain A domain 1 Region: 2 - 116 Aligned: 112 Modelled: 115 Confidence: 32.1% Identity: 13% Fold: Rhomboid-like Superfamily: Rhomboid-like Family: Rhomboid-like Phyre2 PDB 2h3o chain A Region: 72 - 117 Aligned: 37 Modelled: 46 Confidence: 26.4% Identity: 30% PDB header:membrane protein Chain: A: PDB Molecule:merf; PDBTitle: structure of merft, a membrane protein with two trans-2 membrane helices Phyre2 PDB 2j5d chain A Region: 91 - 110 Aligned: 20 Modelled: 20 Confidence: 23.8% Identity: 20% 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 Phyre2 PDB 1y5i chain C domain 1 Region: 35 - 119 Aligned: 85 Modelled: 85 Confidence: 21.1% Identity: 15% Fold: Heme-binding four-helical bundle Superfamily: Respiratory nitrate reductase 1 gamma chain Family: Respiratory nitrate reductase 1 gamma chain Phyre2 PDB 3blh chain B domain 2 Region: 44 - 74 Aligned: 31 Modelled: 31 Confidence: 19.9% Identity: 19% Fold: Cyclin-like Superfamily: Cyclin-like Family: Cyclin Phyre2 PDB 2ka2 chain A Region: 91 - 110 Aligned: 20 Modelled: 20 Confidence: 18.3% Identity: 20% 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 Phyre2 PDB 2ka2 chain B Region: 91 - 110 Aligned: 20 Modelled: 20 Confidence: 18.3% Identity: 20% 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 Phyre2 PDB 2ka1 chain A Region: 91 - 110 Aligned: 20 Modelled: 20 Confidence: 18.3% Identity: 20% 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 Phyre2 PDB 2ka1 chain B Region: 91 - 110 Aligned: 20 Modelled: 20 Confidence: 18.3% Identity: 20% 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 Phyre2 PDB 1jkw chain A domain 1 Region: 39 - 74 Aligned: 36 Modelled: 36 Confidence: 15.9% Identity: 19% Fold: Cyclin-like Superfamily: Cyclin-like Family: Cyclin Phyre2 PDB 1ppr chain M domain 2 Region: 78 - 95 Aligned: 18 Modelled: 18 Confidence: 15.6% Identity: 22% Fold: Peridinin-chlorophyll protein Superfamily: Peridinin-chlorophyll protein Family: Peridinin-chlorophyll protein Phyre2 PDB 1zp2 chain A Region: 44 - 74 Aligned: 31 Modelled: 31 Confidence: 13.3% Identity: 29% PDB header:transcription/cell cycle Chain: A: PDB Molecule:rna polymerase ii holoenzyme cyclin-like subunit; PDBTitle: structure of the mediator subunit cyclin c Phyre2 PDB 2jpl chain A Region: 102 - 116 Aligned: 15 Modelled: 15 Confidence: 12.4% Identity: 40% PDB header:antimicrobial protein Chain: A: PDB Molecule:bacteriocin lactococcin-g subunit alpha; PDBTitle: lactococcin g-a in tfe Phyre2 PDB 1ehk chain B domain 2 Region: 7 - 15 Aligned: 9 Modelled: 9 Confidence: 10.9% Identity: 33% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 1hfe chain T Region: 46 - 60 Aligned: 15 Modelled: 15 Confidence: 9.7% Identity: 27% PDB header:hydrogenase Chain: T: PDB Molecule:protein (fe-only hydrogenase (e.c.1.18.99.1) PDBTitle: 1.6 a resolution structure of the fe-only hydrogenase from2 desulfovibrio desulfuricans Phyre2 PDB 1hfe chain S Region: 46 - 60 Aligned: 15 Modelled: 15 Confidence: 9.7% Identity: 27% Fold: Non-globular all-alpha subunits of globular proteins Superfamily: Fe-only hydrogenase smaller subunit Family: Fe-only hydrogenase smaller subunit Phyre2 PDB 2pb9 chain A domain 1 Region: 87 - 93 Aligned: 7 Modelled: 7 Confidence: 8.9% Identity: 57% Fold: AraD/HMP-PK domain-like Superfamily: AraD/HMP-PK domain-like Family: Phosphomethylpyrimidine kinase C-terminal domain-like Phyre2 PDB 2i53 chain A Region: 38 - 74 Aligned: 37 Modelled: 37 Confidence: 7.7% Identity: 16% PDB header:cell cycle Chain: A: PDB Molecule:cyclin k; PDBTitle: crystal structure of cyclin k Phyre2 1 c3giaA_ 2 c3fo8D_ 3 d2nr9a1 4 c2h3oA_ 5 c2j5dA_ 6 d1y5ic1 7 d3blhb2 8 c2ka2A_ 9 c2ka2B_ 10 c2ka1A_ 11 c2ka1B_ 12 d1jkwa1 13 d1pprm2 14 c1zp2A_ 15 c2jplA_ 16 d1ehkb2 17 c1hfeT_ 18 d1hfes_ 19 d2pb9a1 20 c2i53A_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37

Detailed template information

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

1 c3giaA_ 34.4 8 PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter 2 c3fo8D_ 34.1 75 PDB header:viral protein Chain: D: PDB Molecule:tail sheath protein gp18; PDBTitle: crystal structure of the bacteriophage t4 tail sheath2 protein, protease resistant fragment gp18pr 3 d2nr9a1 32.1 13 Fold:Rhomboid-like Superfamily:Rhomboid-like Family:Rhomboid-like 4 c2h3oA_ 26.4 30 PDB header:membrane protein Chain: A: PDB Molecule:merf; PDBTitle: structure of merft, a membrane protein with two trans-2 membrane helices 5 c2j5dA_ 23.8 20 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 6 d1y5ic1 21.1 15 Fold:Heme-binding four-helical bundle Superfamily:Respiratory nitrate reductase 1 gamma chain Family:Respiratory nitrate reductase 1 gamma chain 7 d3blhb2 19.9 19 Fold:Cyclin-like Superfamily:Cyclin-like Family:Cyclin 8 c2ka2A_ 18.3 20 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 9 c2ka2B_ 18.3 20 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 10 c2ka1A_ 18.3 20 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 11 c2ka1B_ 18.3 20 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 12 d1jkwa1 15.9 19 Fold:Cyclin-like Superfamily:Cyclin-like Family:Cyclin 13 d1pprm2 15.6 22 Fold:Peridinin-chlorophyll protein Superfamily:Peridinin-chlorophyll protein Family:Peridinin-chlorophyll protein 14 c1zp2A_ 13.3 29 PDB header:transcription/cell cycle Chain: A: PDB Molecule:rna polymerase ii holoenzyme cyclin-like subunit; PDBTitle: structure of the mediator subunit cyclin c 15 c2jplA_ 12.4 40 PDB header:antimicrobial protein Chain: A: PDB Molecule:bacteriocin lactococcin-g subunit alpha; PDBTitle: lactococcin g-a in tfe 16 d1ehkb2 10.9 33 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 17 c1hfeT_ 9.7 27 PDB header:hydrogenase Chain: T: PDB Molecule:protein (fe-only hydrogenase (e.c.1.18.99.1) PDBTitle: 1.6 a resolution structure of the fe-only hydrogenase from2 desulfovibrio desulfuricans 18 d1hfes_ 9.7 27 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:Fe-only hydrogenase smaller subunit Family:Fe-only hydrogenase smaller subunit 19 d2pb9a1 8.9 57 Fold:AraD/HMP-PK domain-like Superfamily:AraD/HMP-PK domain-like Family:Phosphomethylpyrimidine kinase C-terminal domain-like 20 c2i53A_ 7.7 16 PDB header:cell cycle Chain: A: PDB Molecule:cyclin k; PDBTitle: crystal structure of cyclin k 21 c1wazA_ not modelled 7.6 33 PDB header:transport protein Chain: A: PDB Molecule:merf; PDBTitle: nmr structure determination of the bacterial mercury2 transporter, merf, in micelles 22 c2cjqA_ not modelled 7.1 22 PDB header:transferase Chain: A: PDB Molecule:rna-directed rna polymerase; PDBTitle: bovine viral diarrhea virus cp7-r12 rna-dependent rna2 polymerase 23 c2v1nA_ not modelled 7.0 6 PDB header:nuclear protein Chain: A: PDB Molecule:protein kin homolog; PDBTitle: solution structure of the region 51-160 of human kin172 reveals a winged helix fold 24 c3nd0A_ not modelled 6.4 9 PDB header:transport protein Chain: A: PDB Molecule:sll0855 protein; PDBTitle: x-ray crystal structure of a slow cyanobacterial cl-/h+ antiporter 25 d1xmeb2 not modelled 6.3 33 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 26 c1kxuA_ not modelled 6.3 19 PDB header:regulatory protein Chain: A: PDB Molecule:cyclin h; PDBTitle: cyclin h, a positive regulatory subunit of cdk activating kinase 27 c1vk5A_ not modelled 6.2 29 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:expressed protein; PDBTitle: x-ray structure of gene product from arabidopsis thaliana at3g22680 28 d1vk5a_ not modelled 6.2 29 Fold:Hypothetical protein At3g22680 Superfamily:Hypothetical protein At3g22680 Family:Hypothetical protein At3g22680 29 d2phpa1 not modelled 6.1 57 Fold:AraD/HMP-PK domain-like Superfamily:AraD/HMP-PK domain-like Family:Phosphomethylpyrimidine kinase C-terminal domain-like 30 d2ivxa1 not modelled 6.0 8 Fold:Cyclin-like Superfamily:Cyclin-like Family:Cyclin 31 d2i53a1 not modelled 5.8 17 Fold:Cyclin-like Superfamily:Cyclin-like Family:Cyclin 32 c2joxA_ not modelled 5.7 50 PDB header:transcription Chain: A: PDB Molecule:churchill protein; PDBTitle: embryonic neural inducing factor churchill is not a dna-2 binding zinc finger protein: solution structure reveals a3 solvent-exposed beta-sheet and zinc binuclear cluster 33 d1m0da_ not modelled 5.7 22 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:Endonuclease I (Holliday junction resolvase) 34 c3hzqA_ not modelled 5.7 17 PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: structure of a tetrameric mscl in an expanded intermediate2 state 35 c2nysA_ not modelled 5.6 20 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:agr_c_3712p; PDBTitle: x-ray crystal structure of protein agr_c_3712 from2 agrobacterium tumefaciens. northeast structural genomics3 consortium target atr88. 36 d2nysa1 not modelled 5.6 20 Fold:SspB-like Superfamily:SspB-like Family:AGR C 3712p-like 37 c2qasA_ not modelled 5.2 30 PDB header:hydrolase activator Chain: A: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of caulobacter crescentus sspb ortholog

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