Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	G	K	A	T	Y	T	V	T	V	T	N	N	S	N	G	V	S	V	D	Y	E	T	E	T	P	M	T	L	L	V	P	E	V	A	A	E	V	I	K	D	L	V	N	T	V	R	S	Y	D	T	E	N	E	H	D	V	C	G	W
Secondary structure
SS confidence
Disorder		?	?	?	?	?																				?				?	?	?	?	?																					?	?	?	?	?	?	?
Disorder confidence
Sequence
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 1nei chain A Region: 1 - 60 Aligned: 60 Modelled: 60 Confidence: 100.0% Identity: 100% Fold: Hypothetical protein YoaG Superfamily: Hypothetical protein YoaG Family: Hypothetical protein YoaG Phyre2 PDB 1e2w chain A domain 2 Region: 3 - 33 Aligned: 30 Modelled: 31 Confidence: 36.2% Identity: 27% Fold: Barrel-sandwich hybrid Superfamily: Rudiment single hybrid motif Family: Cytochrome f, small domain Phyre2 PDB 1czp chain A Region: 4 - 31 Aligned: 28 Modelled: 28 Confidence: 20.8% Identity: 29% Fold: beta-Grasp (ubiquitin-like) Superfamily: 2Fe-2S ferredoxin-like Family: 2Fe-2S ferredoxin-related Phyre2 PDB 1ci3 chain M domain 2 Region: 3 - 33 Aligned: 30 Modelled: 31 Confidence: 16.1% Identity: 17% Fold: Barrel-sandwich hybrid Superfamily: Rudiment single hybrid motif Family: Cytochrome f, small domain Phyre2 PDB 2ww1 chain B Region: 26 - 47 Aligned: 22 Modelled: 22 Confidence: 15.7% Identity: 32% PDB header:hydrolase Chain: B: PDB Molecule:putative alpha-1,2-mannosidase; PDBTitle: structure of the family gh92 inverting mannosidase bt39902 from bacteroides thetaiotaomicron vpi-5482 in complex with3 thiomannobioside Phyre2 PDB 1hcz chain A domain 2 Region: 3 - 33 Aligned: 31 Modelled: 31 Confidence: 12.9% Identity: 32% Fold: Barrel-sandwich hybrid Superfamily: Rudiment single hybrid motif Family: Cytochrome f, small domain Phyre2 PDB 1pfd chain A Region: 4 - 20 Aligned: 17 Modelled: 17 Confidence: 11.3% Identity: 29% Fold: beta-Grasp (ubiquitin-like) Superfamily: 2Fe-2S ferredoxin-like Family: 2Fe-2S ferredoxin-related Phyre2 PDB 1off chain A Region: 4 - 20 Aligned: 17 Modelled: 17 Confidence: 11.2% Identity: 29% Fold: beta-Grasp (ubiquitin-like) Superfamily: 2Fe-2S ferredoxin-like Family: 2Fe-2S ferredoxin-related Phyre2 PDB 1wcu chain A Region: 46 - 57 Aligned: 12 Modelled: 12 Confidence: 10.3% Identity: 42% PDB header:carbohydrate binding Chain: A: PDB Molecule:non-catalytic protein 1; PDBTitle: cbm29_1, a family 29 carbohydrate binding module from2 piromyces equi Phyre2 PDB 1j8y chain F domain 1 Region: 24 - 47 Aligned: 24 Modelled: 24 Confidence: 10.0% Identity: 21% Fold: Four-helical up-and-down bundle Superfamily: Domain of the SRP/SRP receptor G-proteins Family: Domain of the SRP/SRP receptor G-proteins Phyre2 PDB 1rj9 chain B domain 1 Region: 24 - 47 Aligned: 24 Modelled: 24 Confidence: 9.5% Identity: 38% Fold: Four-helical up-and-down bundle Superfamily: Domain of the SRP/SRP receptor G-proteins Family: Domain of the SRP/SRP receptor G-proteins Phyre2 PDB 1gaq chain B Region: 4 - 20 Aligned: 17 Modelled: 17 Confidence: 9.3% Identity: 29% Fold: beta-Grasp (ubiquitin-like) Superfamily: 2Fe-2S ferredoxin-like Family: 2Fe-2S ferredoxin-related Phyre2 PDB 2wvy chain A Region: 26 - 47 Aligned: 22 Modelled: 22 Confidence: 9.0% Identity: 36% PDB header:hydrolase Chain: A: PDB Molecule:alpha-1,2-mannosidase; PDBTitle: structure of the family gh92 inverting mannosidase bt21992 from bacteroides thetaiotaomicron vpi-5482 Phyre2 PDB 1ls1 chain A domain 1 Region: 24 - 47 Aligned: 24 Modelled: 24 Confidence: 8.7% Identity: 38% Fold: Four-helical up-and-down bundle Superfamily: Domain of the SRP/SRP receptor G-proteins Family: Domain of the SRP/SRP receptor G-proteins Phyre2 PDB 1gwm chain A Region: 46 - 57 Aligned: 12 Modelled: 12 Confidence: 8.6% Identity: 17% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: Family 29 carbohydrate binding module, CBM29 Phyre2 PDB 1wgw chain A Region: 24 - 47 Aligned: 24 Modelled: 24 Confidence: 8.6% Identity: 29% Fold: Four-helical up-and-down bundle Superfamily: Domain of the SRP/SRP receptor G-proteins Family: Domain of the SRP/SRP receptor G-proteins Phyre2 PDB 4fxc chain A Region: 4 - 31 Aligned: 28 Modelled: 28 Confidence: 8.6% Identity: 29% Fold: beta-Grasp (ubiquitin-like) Superfamily: 2Fe-2S ferredoxin-like Family: 2Fe-2S ferredoxin-related Phyre2 PDB 2wuk chain D Region: 47 - 53 Aligned: 7 Modelled: 7 Confidence: 7.2% Identity: 43% PDB header:cell cycle Chain: D: PDB Molecule:septum site-determining protein diviva; PDBTitle: diviva n-terminal domain, f17a mutant Phyre2 PDB 3ku7 chain B Region: 37 - 49 Aligned: 13 Modelled: 13 Confidence: 7.0% Identity: 23% PDB header:cell cycle Chain: B: PDB Molecule:cell division topological specificity factor; PDBTitle: crystal structure of helicobacter pylori mine, a cell division2 topological specificity factor Phyre2 PDB 3emi chain A Region: 5 - 22 Aligned: 18 Modelled: 18 Confidence: 6.8% Identity: 44% PDB header:cell adhesion Chain: A: PDB Molecule:hia (adhesin); PDBTitle: crystal structure of hia 307-422 non-adhesive domain Phyre2 1 d1neia_ 2 d1e2wa2 3 d1czpa_ 4 d1ci3m2 5 c2ww1B_ 6 d1hcza2 7 d1pfda_ 8 d1offa_ 9 c1wcuA_ 10 d1j8yf1 11 d1rj9b1 12 d1gaqb_ 13 c2wvyA_ 14 d1ls1a1 15 d1gwma_ 16 d1wgwa_ 17 d4fxca_ 18 c2wukD_ 19 c3ku7B_ 20 c3emiA_ 21 22

Detailed template information

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

1 d1neia_ 100.0 100 Fold:Hypothetical protein YoaG Superfamily:Hypothetical protein YoaG Family:Hypothetical protein YoaG 2 d1e2wa2 36.2 27 Fold:Barrel-sandwich hybrid Superfamily:Rudiment single hybrid motif Family:Cytochrome f, small domain 3 d1czpa_ 20.8 29 Fold:beta-Grasp (ubiquitin-like) Superfamily:2Fe-2S ferredoxin-like Family:2Fe-2S ferredoxin-related 4 d1ci3m2 16.1 17 Fold:Barrel-sandwich hybrid Superfamily:Rudiment single hybrid motif Family:Cytochrome f, small domain 5 c2ww1B_ 15.7 32 PDB header:hydrolase Chain: B: PDB Molecule:putative alpha-1,2-mannosidase; PDBTitle: structure of the family gh92 inverting mannosidase bt39902 from bacteroides thetaiotaomicron vpi-5482 in complex with3 thiomannobioside 6 d1hcza2 12.9 32 Fold:Barrel-sandwich hybrid Superfamily:Rudiment single hybrid motif Family:Cytochrome f, small domain 7 d1pfda_ 11.3 29 Fold:beta-Grasp (ubiquitin-like) Superfamily:2Fe-2S ferredoxin-like Family:2Fe-2S ferredoxin-related 8 d1offa_ 11.2 29 Fold:beta-Grasp (ubiquitin-like) Superfamily:2Fe-2S ferredoxin-like Family:2Fe-2S ferredoxin-related 9 c1wcuA_ 10.3 42 PDB header:carbohydrate binding Chain: A: PDB Molecule:non-catalytic protein 1; PDBTitle: cbm29_1, a family 29 carbohydrate binding module from2 piromyces equi 10 d1j8yf1 10.0 21 Fold:Four-helical up-and-down bundle Superfamily:Domain of the SRP/SRP receptor G-proteins Family:Domain of the SRP/SRP receptor G-proteins 11 d1rj9b1 9.5 38 Fold:Four-helical up-and-down bundle Superfamily:Domain of the SRP/SRP receptor G-proteins Family:Domain of the SRP/SRP receptor G-proteins 12 d1gaqb_ 9.3 29 Fold:beta-Grasp (ubiquitin-like) Superfamily:2Fe-2S ferredoxin-like Family:2Fe-2S ferredoxin-related 13 c2wvyA_ 9.0 36 PDB header:hydrolase Chain: A: PDB Molecule:alpha-1,2-mannosidase; PDBTitle: structure of the family gh92 inverting mannosidase bt21992 from bacteroides thetaiotaomicron vpi-5482 14 d1ls1a1 8.7 38 Fold:Four-helical up-and-down bundle Superfamily:Domain of the SRP/SRP receptor G-proteins Family:Domain of the SRP/SRP receptor G-proteins 15 d1gwma_ 8.6 17 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:Family 29 carbohydrate binding module, CBM29 16 d1wgwa_ 8.6 29 Fold:Four-helical up-and-down bundle Superfamily:Domain of the SRP/SRP receptor G-proteins Family:Domain of the SRP/SRP receptor G-proteins 17 d4fxca_ 8.6 29 Fold:beta-Grasp (ubiquitin-like) Superfamily:2Fe-2S ferredoxin-like Family:2Fe-2S ferredoxin-related 18 c2wukD_ 7.2 43 PDB header:cell cycle Chain: D: PDB Molecule:septum site-determining protein diviva; PDBTitle: diviva n-terminal domain, f17a mutant 19 c3ku7B_ 7.0 23 PDB header:cell cycle Chain: B: PDB Molecule:cell division topological specificity factor; PDBTitle: crystal structure of helicobacter pylori mine, a cell division2 topological specificity factor 20 c3emiA_ 6.8 44 PDB header:cell adhesion Chain: A: PDB Molecule:hia (adhesin); PDBTitle: crystal structure of hia 307-422 non-adhesive domain 21 d1a70a_ not modelled 6.0 29 Fold:beta-Grasp (ubiquitin-like) Superfamily:2Fe-2S ferredoxin-like Family:2Fe-2S ferredoxin-related 22 d1qzxa1 not modelled 6.0 13 Fold:Four-helical up-and-down bundle Superfamily:Domain of the SRP/SRP receptor G-proteins Family:Domain of the SRP/SRP receptor G-proteins

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