Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	L	A	V	V	T	G	Q	I	V	C	T	V	R	H	H	G	L	A	H	D	K	L	L	M	V	E	M	I	D	P	Q	G	N	P	D	G	Q	C	A	V	A	I	D	N	I	G	A	G	T	G	E	W	V	L	L	V	S	G
Secondary structure
SS confidence
Disorder		?																														?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.
Sequence		S	S	A	R	Q	A	H	K	S	E	T	S	P	V	D	L	C	V	I	G	I	V	D	E	V	V	S	G	G	Q	V	I	F	H	K
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 2qw7 chain A domain 1 Region: 1 - 95 Aligned: 95 Modelled: 95 Confidence: 100.0% Identity: 39% Fold: OB-fold Superfamily: EutN/CcmL-like Family: EutN/CcmL-like Phyre2 PDB 2hd3 chain A domain 1 Region: 1 - 95 Aligned: 95 Modelled: 94 Confidence: 100.0% Identity: 97% Fold: OB-fold Superfamily: EutN/CcmL-like Family: EutN/CcmL-like Phyre2 PDB 2rcf chain A domain 1 Region: 1 - 86 Aligned: 81 Modelled: 86 Confidence: 100.0% Identity: 41% Fold: OB-fold Superfamily: EutN/CcmL-like Family: EutN/CcmL-like Phyre2 PDB 1jjc chain B domain 3 Region: 6 - 61 Aligned: 48 Modelled: 56 Confidence: 36.5% Identity: 17% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Myf domain Phyre2 PDB 2akw chain B Region: 6 - 61 Aligned: 48 Modelled: 56 Confidence: 29.7% Identity: 17% PDB header:ligase Chain: B: PDB Molecule:phenylalanyl-trna synthetase beta chain; PDBTitle: crystal structure of t.thermophilus phenylalanyl-trna synthetase2 complexed with p-cl-phenylalanine Phyre2 PDB 2z1c chain A domain 1 Region: 49 - 62 Aligned: 14 Modelled: 14 Confidence: 20.5% Identity: 29% Fold: OB-fold Superfamily: HupF/HypC-like Family: HupF/HypC-like Phyre2 PDB 3bbn chain Q Region: 5 - 60 Aligned: 56 Modelled: 56 Confidence: 19.4% Identity: 16% PDB header:ribosome Chain: Q: PDB Molecule:ribosomal protein s17; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. Phyre2 PDB 3bu2 chain B Region: 6 - 61 Aligned: 50 Modelled: 56 Confidence: 17.0% Identity: 18% PDB header:rna binding protein Chain: B: PDB Molecule:putative trna-binding protein; PDBTitle: crystal structure of a trna-binding protein from2 staphylococcus saprophyticus subsp. saprophyticus.3 northeast structural genomics consortium target syr77 Phyre2 PDB 2ot2 chain A domain 1 Region: 49 - 62 Aligned: 14 Modelled: 14 Confidence: 16.7% Identity: 36% Fold: OB-fold Superfamily: HupF/HypC-like Family: HupF/HypC-like Phyre2 PDB 2gy9 chain Q domain 1 Region: 5 - 60 Aligned: 56 Modelled: 56 Confidence: 15.8% Identity: 14% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 2z1e chain A domain 2 Region: 48 - 63 Aligned: 16 Modelled: 16 Confidence: 15.5% Identity: 38% Fold: PurM C-terminal domain-like Superfamily: PurM C-terminal domain-like Family: PurM C-terminal domain-like Phyre2 PDB 3d3r chain A Region: 49 - 62 Aligned: 14 Modelled: 14 Confidence: 13.8% Identity: 29% PDB header:chaperone Chain: A: PDB Molecule:hydrogenase assembly chaperone hypc/hupf; PDBTitle: crystal structure of the hydrogenase assembly chaperone hypc/hupf2 family protein from shewanella oneidensis mr-1 Phyre2 PDB 1rfo chain C Region: 32 - 59 Aligned: 22 Modelled: 28 Confidence: 13.8% Identity: 55% PDB header:viral protein Chain: C: PDB Molecule:whisker antigen control protein; PDBTitle: trimeric foldon of the t4 phagehead fibritin Phyre2 PDB 2id1 chain A domain 1 Region: 37 - 66 Aligned: 30 Modelled: 30 Confidence: 13.1% Identity: 20% Fold: Nucleotidyltransferase Superfamily: Nucleotidyltransferase Family: Iojap/YbeB-like Phyre2 PDB 3d3r chain A domain 1 Region: 39 - 62 Aligned: 24 Modelled: 24 Confidence: 12.9% Identity: 21% Fold: OB-fold Superfamily: HupF/HypC-like Family: HupF/HypC-like Phyre2 PDB 2zod chain A domain 2 Region: 48 - 63 Aligned: 16 Modelled: 16 Confidence: 11.2% Identity: 31% Fold: PurM C-terminal domain-like Superfamily: PurM C-terminal domain-like Family: PurM C-terminal domain-like Phyre2 PDB 3bal chain B Region: 49 - 94 Aligned: 46 Modelled: 46 Confidence: 10.9% Identity: 17% PDB header:oxidoreductase Chain: B: PDB Molecule:acetylacetone-cleaving enzyme; PDBTitle: crystal structure of an acetylacetone dioxygenase from2 acinetobacter johnsonii Phyre2 PDB 1e8c chain A domain 2 Region: 49 - 75 Aligned: 27 Modelled: 27 Confidence: 10.7% Identity: 19% Fold: MurD-like peptide ligases, peptide-binding domain Superfamily: MurD-like peptide ligases, peptide-binding domain Family: MurCDEF C-terminal domain Phyre2 PDB 2jfg chain A domain 2 Region: 49 - 69 Aligned: 21 Modelled: 21 Confidence: 10.2% Identity: 24% Fold: MurD-like peptide ligases, peptide-binding domain Superfamily: MurD-like peptide ligases, peptide-binding domain Family: MurCDEF C-terminal domain Phyre2 PDB 1g29 chain 1 domain 4 Region: 71 - 93 Aligned: 23 Modelled: 23 Confidence: 9.4% Identity: 22% Fold: OB-fold Superfamily: MOP-like Family: ABC-transporter additional domain Phyre2 1 d2qw7a1 2 d2hd3a1 3 d2rcfa1 4 d1jjcb3 5 c2akwB_ 6 d2z1ca1 7 c3bbnQ_ 8 c3bu2B_ 9 d2ot2a1 10 d2gy9q1 11 d2z1ea2 12 c3d3rA_ 13 c1rfoC_ 14 d2id1a1 15 d3d3ra1 16 d2zoda2 17 c3balB_ 18 d1e8ca2 19 d2jfga2 20 d1g2914 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 d2qw7a1 100.0 39 Fold:OB-fold Superfamily:EutN/CcmL-like Family:EutN/CcmL-like 2 d2hd3a1 100.0 97 Fold:OB-fold Superfamily:EutN/CcmL-like Family:EutN/CcmL-like 3 d2rcfa1 100.0 41 Fold:OB-fold Superfamily:EutN/CcmL-like Family:EutN/CcmL-like 4 d1jjcb3 36.5 17 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Myf domain 5 c2akwB_ 29.7 17 PDB header:ligase Chain: B: PDB Molecule:phenylalanyl-trna synthetase beta chain; PDBTitle: crystal structure of t.thermophilus phenylalanyl-trna synthetase2 complexed with p-cl-phenylalanine 6 d2z1ca1 20.5 29 Fold:OB-fold Superfamily:HupF/HypC-like Family:HupF/HypC-like 7 c3bbnQ_ 19.4 16 PDB header:ribosome Chain: Q: PDB Molecule:ribosomal protein s17; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. 8 c3bu2B_ 17.0 18 PDB header:rna binding protein Chain: B: PDB Molecule:putative trna-binding protein; PDBTitle: crystal structure of a trna-binding protein from2 staphylococcus saprophyticus subsp. saprophyticus.3 northeast structural genomics consortium target syr77 9 d2ot2a1 16.7 36 Fold:OB-fold Superfamily:HupF/HypC-like Family:HupF/HypC-like 10 d2gy9q1 15.8 14 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 11 d2z1ea2 15.5 38 Fold:PurM C-terminal domain-like Superfamily:PurM C-terminal domain-like Family:PurM C-terminal domain-like 12 c3d3rA_ 13.8 29 PDB header:chaperone Chain: A: PDB Molecule:hydrogenase assembly chaperone hypc/hupf; PDBTitle: crystal structure of the hydrogenase assembly chaperone hypc/hupf2 family protein from shewanella oneidensis mr-1 13 c1rfoC_ 13.8 55 PDB header:viral protein Chain: C: PDB Molecule:whisker antigen control protein; PDBTitle: trimeric foldon of the t4 phagehead fibritin 14 d2id1a1 13.1 20 Fold:Nucleotidyltransferase Superfamily:Nucleotidyltransferase Family:Iojap/YbeB-like 15 d3d3ra1 12.9 21 Fold:OB-fold Superfamily:HupF/HypC-like Family:HupF/HypC-like 16 d2zoda2 11.2 31 Fold:PurM C-terminal domain-like Superfamily:PurM C-terminal domain-like Family:PurM C-terminal domain-like 17 c3balB_ 10.9 17 PDB header:oxidoreductase Chain: B: PDB Molecule:acetylacetone-cleaving enzyme; PDBTitle: crystal structure of an acetylacetone dioxygenase from2 acinetobacter johnsonii 18 d1e8ca2 10.7 19 Fold:MurD-like peptide ligases, peptide-binding domain Superfamily:MurD-like peptide ligases, peptide-binding domain Family:MurCDEF C-terminal domain 19 d2jfga2 10.2 24 Fold:MurD-like peptide ligases, peptide-binding domain Superfamily:MurD-like peptide ligases, peptide-binding domain Family:MurCDEF C-terminal domain 20 d1g2914 9.4 22 Fold:OB-fold Superfamily:MOP-like Family:ABC-transporter additional domain 21 c1avyA_ not modelled 7.7 55 PDB header:coiled coil Chain: A: PDB Molecule:fibritin; PDBTitle: fibritin deletion mutant m (bacteriophage t4) 22 c1ox3A_ not modelled 7.5 55 PDB header:chaperone Chain: A: PDB Molecule:fibritin; PDBTitle: crystal structure of mini-fibritin 23 d1wpga1 not modelled 7.3 28 Fold:Double-stranded beta-helix Superfamily:Calcium ATPase, transduction domain A Family:Calcium ATPase, transduction domain A 24 d3c9ua2 not modelled 7.2 38 Fold:PurM C-terminal domain-like Superfamily:PurM C-terminal domain-like Family:PurM C-terminal domain-like 25 c3mvnA_ not modelled 7.2 31 PDB header:ligase Chain: A: PDB Molecule:udp-n-acetylmuramate:l-alanyl-gamma-d-glutamayl-medo- PDBTitle: crystal structure of a domain from a putative udp-n-acetylmuramate:l-2 alanyl-gamma-d-glutamayl-medo-diaminopimelate ligase from haemophilus3 ducreyi 35000hp 26 d1c0aa2 not modelled 7.1 15 Fold:DCoH-like Superfamily:GAD domain-like Family:GAD domain 27 c1e8cB_ not modelled 7.0 19 PDB header:ligase Chain: B: PDB Molecule:udp-n-acetylmuramoylalanyl-d-glutamate--2,6- PDBTitle: structure of mure the udp-n-acetylmuramyl tripeptide2 synthetase from e. coli 28 c3b8eC_ not modelled 6.9 31 PDB header:hydrolase/transport protein Chain: C: PDB Molecule:sodium/potassium-transporting atpase subunit PDBTitle: crystal structure of the sodium-potassium pump 29 d1vk3a3 not modelled 6.8 17 Fold:PurM C-terminal domain-like Superfamily:PurM C-terminal domain-like Family:PurM C-terminal domain-like 30 c3upsA_ not modelled 6.6 23 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:iojap-like protein; PDBTitle: crystal structure of iojap-like protein from zymomonas mobilis 31 d1ylqa1 not modelled 6.5 20 Fold:Nucleotidyltransferase Superfamily:Nucleotidyltransferase Family:Catalytic subunit of bi-partite nucleotidyltransferase 32 d2atza1 not modelled 6.3 25 Fold:Prim-pol domain Superfamily:Prim-pol domain Family:HP0184-like 33 c2opkC_ not modelled 6.1 70 PDB header:isomerase Chain: C: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of a putative mannose-6-phosphate isomerase2 (reut_a1446) from ralstonia eutropha jmp134 at 2.10 a resolution 34 d2c42a3 not modelled 6.0 35 Fold:TK C-terminal domain-like Superfamily:TK C-terminal domain-like Family:Pyruvate-ferredoxin oxidoreductase, PFOR, domain II 35 c1s1hQ_ not modelled 5.9 13 PDB header:ribosome Chain: Q: PDB Molecule:40s ribosomal protein s11; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1h,4 contains 40s subunit. the 60s ribosomal subunit is in file5 1s1i. 36 c3b9bA_ not modelled 5.9 28 PDB header:hydrolase Chain: A: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: structure of the e2 beryllium fluoride complex of the serca2 ca2+-atpase 37 c3fq6A_ not modelled 5.6 40 PDB header:transferase Chain: A: PDB Molecule:methyltransferase; PDBTitle: the crystal structure of a methyltransferase domain from bacteroides2 thetaiotaomicron vpi 38 c3ixzA_ not modelled 5.6 28 PDB header:hydrolase Chain: A: PDB Molecule:potassium-transporting atpase alpha; PDBTitle: pig gastric h+/k+-atpase complexed with aluminium fluoride 39 c3p9zA_ not modelled 5.2 12 PDB header:ligase Chain: A: PDB Molecule:uroporphyrinogen iii cosynthase (hemd); PDBTitle: crystal structure of uroporphyrinogen-iii synthetase from helicobacter2 pylori 26695 40 c3ajvA_ not modelled 5.2 29 PDB header:hydrolase Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: splicing endonuclease from aeropyrum pernix 41 c1v1hB_ not modelled 5.1 50 PDB header:adenovirus Chain: B: PDB Molecule:fibritin, fiber protein; PDBTitle: adenovirus fibre shaft sequence n-terminally fused to the2 bacteriophage t4 fibritin foldon trimerisation motif with3 a short linker 42 c2gq1A_ not modelled 5.1 20 PDB header:hydrolase Chain: A: PDB Molecule:fructose-1,6-bisphosphatase; PDBTitle: crystal structure of recombinant type i fructose-1,6-bisphosphatase2 from escherichia coli complexed with sulfate ions 43 d2o5aa1 not modelled 5.1 24 Fold:Nucleotidyltransferase Superfamily:Nucleotidyltransferase Family:Iojap/YbeB-like

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