Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	K	F	L	F	A	A	A	L	I	V	S	G	L	L	V	G	C	N	Q	L	T	Q	Y	T	I	T	E	Q	E	I	N	Q	S	L	A	K	H	N	N	F	S	K	D	I	G	L	P	G	V	A	D	A	H	I	V	L	T	N
Secondary structure
SS confidence
Disorder		?	?	?	?													?		?	?	?	?																?		?		?	?	?	?	?			?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	T	S	Q	I	G	R	E	E	P	N	K	V	T	L	T	G	D	A	N	L	D	M	N	S	L	F	G	S	Q	K	A	T	M	K	L	K	L	K	A	L	P	V	F	D	K	E	K	G	A	I	F	L	K	E	M	E	V	V	D
Secondary structure
SS confidence
Disorder		?	?			?			?		?														?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	T	V	Q	P	E	K	M	Q	T	V	M	Q	T	L	L	P	Y	L	N	Q	A	L	R	N	Y	F	N	Q	Q	P	A	Y	V	L	R	E	D	G	S	Q	G	E	A	M	A	K	K	L	A	K	G	I	E	V	K	P	G	E	I
Secondary structure
SS confidence
Disorder					?																																		?		?								?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.
Sequence		V	I	P	F	T	D
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 3eyr chain A Region: 19 - 185 Aligned: 167 Modelled: 166 Confidence: 100.0% Identity: 96% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized lipoprotein yceb; PDBTitle: crystal structure of the uncharacterized lipoprotein yceb2 from e. coli at the resolution 2.0a. northeast structural3 genomics consortium target er542 Phyre2 PDB 3d85 chain D domain 2 Region: 89 - 116 Aligned: 28 Modelled: 28 Confidence: 26.7% Identity: 7% Fold: Immunoglobulin-like beta-sandwich Superfamily: Fibronectin type III Family: Fibronectin type III Phyre2 PDB 1t11 chain A domain 2 Region: 18 - 50 Aligned: 33 Modelled: 33 Confidence: 22.6% Identity: 21% Fold: Ribosome binding domain-like Superfamily: Trigger factor ribosome-binding domain Family: Trigger factor ribosome-binding domain Phyre2 PDB 1w26 chain A domain 2 Region: 16 - 50 Aligned: 35 Modelled: 35 Confidence: 22.2% Identity: 20% Fold: Ribosome binding domain-like Superfamily: Trigger factor ribosome-binding domain Family: Trigger factor ribosome-binding domain Phyre2 PDB 3bz6 chain A domain 1 Region: 12 - 38 Aligned: 27 Modelled: 27 Confidence: 21.8% Identity: 33% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: PSPTO2686-like Phyre2 PDB 1p9y chain A Region: 18 - 50 Aligned: 33 Modelled: 33 Confidence: 21.0% Identity: 21% Fold: Ribosome binding domain-like Superfamily: Trigger factor ribosome-binding domain Family: Trigger factor ribosome-binding domain Phyre2 PDB 1w26 chain B Region: 16 - 50 Aligned: 35 Modelled: 35 Confidence: 20.7% Identity: 20% PDB header:chaperone Chain: B: PDB Molecule:trigger factor; PDBTitle: trigger factor in complex with the ribosome forms a2 molecular cradle for nascent proteins Phyre2 PDB 1t11 chain A Region: 16 - 50 Aligned: 35 Modelled: 35 Confidence: 20.6% Identity: 23% PDB header:chaperone Chain: A: PDB Molecule:trigger factor; PDBTitle: trigger factor Phyre2 PDB 3bz6 chain A Region: 12 - 38 Aligned: 27 Modelled: 27 Confidence: 18.7% Identity: 33% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0502 protein pspto_2686; PDBTitle: crystal structure of a conserved protein of unknown function from2 pseudomonas syringae pv. tomato str. dc3000 Phyre2 PDB 2im5 chain C Region: 22 - 77 Aligned: 55 Modelled: 56 Confidence: 15.6% Identity: 13% PDB header:transferase Chain: C: PDB Molecule:nicotinate phosphoribosyltransferase; PDBTitle: crystal structure of nicotinate phosphoribosyltransferase2 from porphyromonas gingivalis Phyre2 PDB 1vq0 chain A domain 2 Region: 19 - 40 Aligned: 20 Modelled: 22 Confidence: 15.6% Identity: 35% Fold: HSP33 redox switch-like Superfamily: HSP33 redox switch-like Family: HSP33 redox switch-like Phyre2 PDB 2nsc chain A Region: 24 - 50 Aligned: 27 Modelled: 27 Confidence: 11.4% Identity: 26% PDB header:chaperone Chain: A: PDB Molecule:trigger factor; PDBTitle: structures of and interactions between domains of trigger factor from2 themotoga maritima Phyre2 PDB 1p32 chain A Region: 28 - 152 Aligned: 125 Modelled: 125 Confidence: 9.4% Identity: 13% Fold: Mitochondrial glycoprotein MAM33-like Superfamily: Mitochondrial glycoprotein MAM33-like Family: Mitochondrial glycoprotein MAM33-like Phyre2 PDB 1wd6 chain B Region: 28 - 67 Aligned: 40 Modelled: 40 Confidence: 9.1% Identity: 25% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:protein ydhr; PDBTitle: crystal structure of jw1657 from escherichia coli Phyre2 PDB 1vzy chain A domain 2 Region: 19 - 38 Aligned: 18 Modelled: 20 Confidence: 9.1% Identity: 28% Fold: HSP33 redox switch-like Superfamily: HSP33 redox switch-like Family: HSP33 redox switch-like Phyre2 PDB 3gty chain X Region: 18 - 50 Aligned: 33 Modelled: 33 Confidence: 8.1% Identity: 21% PDB header:chaperone/ribosomal protein Chain: X: PDB Molecule:trigger factor; PDBTitle: promiscuous substrate recognition in folding and assembly activities2 of the trigger factor chaperone Phyre2 PDB 1ex2 chain A Region: 26 - 52 Aligned: 27 Modelled: 27 Confidence: 7.4% Identity: 22% Fold: Anticodon-binding domain-like Superfamily: ITPase-like Family: Maf-like Phyre2 PDB 3alz chain B Region: 100 - 118 Aligned: 19 Modelled: 19 Confidence: 7.3% Identity: 16% PDB header:viral protein/membrane protein Chain: B: PDB Molecule:cdw150; PDBTitle: crystal structure of the measles virus hemagglutinin bound to its2 cellular receptor slam (form i) Phyre2 PDB 2d3o chain 1 Region: 24 - 50 Aligned: 27 Modelled: 27 Confidence: 7.2% Identity: 19% PDB header:ribosome Chain: 1: PDB Molecule:trigger factor; PDBTitle: structure of ribosome binding domain of the trigger factor2 on the 50s ribosomal subunit from d. radiodurans Phyre2 PDB 2k78 chain A Region: 152 - 185 Aligned: 33 Modelled: 34 Confidence: 6.9% Identity: 24% PDB header:heme-binding protein Chain: A: PDB Molecule:iron-regulated surface determinant protein c; PDBTitle: solution structure of the isdc neat domain bound to zinc2 protoporphyrin Phyre2 1 c3eyrA_ 2 d3d85d2 3 d1t11a2 4 d1w26a2 5 d3bz6a1 6 d1p9ya_ 7 c1w26B_ 8 c1t11A_ 9 c3bz6A_ 10 c2im5C_ 11 d1vq0a2 12 c2nscA_ 13 d1p32a_ 14 c1wd6B_ 15 d1vzya2 16 c3gtyX_ 17 d1ex2a_ 18 c3alzB_ 19 c2d3o1_ 20 c2k78A_ 21 22 23 24 25 26

Detailed template information

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

1 c3eyrA_ 100.0 96 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized lipoprotein yceb; PDBTitle: crystal structure of the uncharacterized lipoprotein yceb2 from e. coli at the resolution 2.0a. northeast structural3 genomics consortium target er542 2 d3d85d2 26.7 7 Fold:Immunoglobulin-like beta-sandwich Superfamily:Fibronectin type III Family:Fibronectin type III 3 d1t11a2 22.6 21 Fold:Ribosome binding domain-like Superfamily:Trigger factor ribosome-binding domain Family:Trigger factor ribosome-binding domain 4 d1w26a2 22.2 20 Fold:Ribosome binding domain-like Superfamily:Trigger factor ribosome-binding domain Family:Trigger factor ribosome-binding domain 5 d3bz6a1 21.8 33 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PSPTO2686-like 6 d1p9ya_ 21.0 21 Fold:Ribosome binding domain-like Superfamily:Trigger factor ribosome-binding domain Family:Trigger factor ribosome-binding domain 7 c1w26B_ 20.7 20 PDB header:chaperone Chain: B: PDB Molecule:trigger factor; PDBTitle: trigger factor in complex with the ribosome forms a2 molecular cradle for nascent proteins 8 c1t11A_ 20.6 23 PDB header:chaperone Chain: A: PDB Molecule:trigger factor; PDBTitle: trigger factor 9 c3bz6A_ 18.7 33 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0502 protein pspto_2686; PDBTitle: crystal structure of a conserved protein of unknown function from2 pseudomonas syringae pv. tomato str. dc3000 10 c2im5C_ 15.6 13 PDB header:transferase Chain: C: PDB Molecule:nicotinate phosphoribosyltransferase; PDBTitle: crystal structure of nicotinate phosphoribosyltransferase2 from porphyromonas gingivalis 11 d1vq0a2 15.6 35 Fold:HSP33 redox switch-like Superfamily:HSP33 redox switch-like Family:HSP33 redox switch-like 12 c2nscA_ 11.4 26 PDB header:chaperone Chain: A: PDB Molecule:trigger factor; PDBTitle: structures of and interactions between domains of trigger factor from2 themotoga maritima 13 d1p32a_ 9.4 13 Fold:Mitochondrial glycoprotein MAM33-like Superfamily:Mitochondrial glycoprotein MAM33-like Family:Mitochondrial glycoprotein MAM33-like 14 c1wd6B_ 9.1 25 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:protein ydhr; PDBTitle: crystal structure of jw1657 from escherichia coli 15 d1vzya2 9.1 28 Fold:HSP33 redox switch-like Superfamily:HSP33 redox switch-like Family:HSP33 redox switch-like 16 c3gtyX_ 8.1 21 PDB header:chaperone/ribosomal protein Chain: X: PDB Molecule:trigger factor; PDBTitle: promiscuous substrate recognition in folding and assembly activities2 of the trigger factor chaperone 17 d1ex2a_ 7.4 22 Fold:Anticodon-binding domain-like Superfamily:ITPase-like Family:Maf-like 18 c3alzB_ 7.3 16 PDB header:viral protein/membrane protein Chain: B: PDB Molecule:cdw150; PDBTitle: crystal structure of the measles virus hemagglutinin bound to its2 cellular receptor slam (form i) 19 c2d3o1_ 7.2 19 PDB header:ribosome Chain: 1: PDB Molecule:trigger factor; PDBTitle: structure of ribosome binding domain of the trigger factor2 on the 50s ribosomal subunit from d. radiodurans 20 c2k78A_ 6.9 24 PDB header:heme-binding protein Chain: A: PDB Molecule:iron-regulated surface determinant protein c; PDBTitle: solution structure of the isdc neat domain bound to zinc2 protoporphyrin 21 d2cpja1 not modelled 6.6 18 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 22 c3evyB_ not modelled 6.5 32 PDB header:hydrolase Chain: B: PDB Molecule:putative type i restriction enzyme r protein; PDBTitle: crystal structure of a fragment of a putative type i2 restriction enzyme r protein from bacteroides fragilis 23 d1rgya_ not modelled 6.0 30 Fold:beta-lactamase/transpeptidase-like Superfamily:beta-lactamase/transpeptidase-like Family:beta-Lactamase/D-ala carboxypeptidase 24 d2o6pa1 not modelled 5.8 24 Fold:Immunoglobulin-like beta-sandwich Superfamily:NEAT domain-like Family:NEAT domain 25 c3n3fB_ not modelled 5.8 6 PDB header:protein binding Chain: B: PDB Molecule:collagen alpha-1(xv) chain; PDBTitle: crystal structure of the human collagen xv trimerization domain: a2 potent trimerizing unit common to multiplexin collagens 26 c2o6pA_ not modelled 5.6 24 PDB header:transport protein Chain: A: PDB Molecule:iron-regulated surface determinant protein c; PDBTitle: crystal structure of the heme-isdc complex

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

---

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