Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	M	F	F	D	W	W	F	A	T	S	P	R	L	R	Q	L	C	W	A	F	W	L	L	M	L	V	T	L	I	F	L	S	S	T	H	H	E	E	R	D	A	L	I	R	L	R	A	S	H	H	Q	Q	W	A	A	L	Y	R
Secondary structure
SS confidence
Disorder		?	?	?	?																												?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	V	D	T	A	P	F	S	E	E	K	T	L	P	F	S	P	L	D	F	Q	L	S	G	A	Q	L	V	S	W	H	P	S	A	Q	G	G	E	L	A	L	K	T	L	W	E	A	V	P	S	A	F	T	R	L	A	E	R	N	V
Secondary structure
SS confidence
Disorder			?	?	?	?	?	?	?	?	?	?	?									?	?											?		?	?	?	?																			?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.
Sequence		S	V	S	R	F	S	L	S	V	E	G	D	D	L	L	F	T	L	Q	L	E	T	P	H	E	G
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 1uv7 chain A Region: 84 - 142 Aligned: 56 Modelled: 59 Confidence: 89.6% Identity: 20% PDB header:transport Chain: A: PDB Molecule:general secretion pathway protein m; PDBTitle: periplasmic domain of epsm from vibrio cholerae Phyre2 PDB 1uv7 chain A Region: 84 - 142 Aligned: 56 Modelled: 59 Confidence: 89.6% Identity: 20% Fold: RRF/tRNA synthetase additional domain-like Superfamily: General secretion pathway protein M, EpsM Family: General secretion pathway protein M, EpsM Phyre2 PDB 2rjz chain A Region: 39 - 140 Aligned: 101 Modelled: 102 Confidence: 70.3% Identity: 10% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:pilo protein; PDBTitle: crystal structure of the type 4 fimbrial biogenesis protein pilo from2 pseudomonas aeruginosa Phyre2 PDB 2e26 chain A Region: 77 - 98 Aligned: 22 Modelled: 22 Confidence: 16.2% Identity: 23% PDB header:signaling protein Chain: A: PDB Molecule:reelin; PDBTitle: crystal structure of two repeat fragment of reelin Phyre2 PDB 1ikp chain A domain 2 Region: 92 - 124 Aligned: 25 Modelled: 33 Confidence: 13.8% Identity: 44% Fold: ADP-ribosylation Superfamily: ADP-ribosylation Family: ADP-ribosylating toxins Phyre2 PDB 2htb chain B Region: 80 - 142 Aligned: 63 Modelled: 63 Confidence: 13.5% Identity: 24% PDB header:isomerase Chain: B: PDB Molecule:putative enzyme related to aldose 1-epimerase; PDBTitle: crystal structure of a putative mutarotase (yead) from2 salmonella typhimurium in monoclinic form Phyre2 PDB 3sbt chain B Region: 71 - 97 Aligned: 27 Modelled: 27 Confidence: 12.4% Identity: 11% PDB header:splicing Chain: B: PDB Molecule:a1 cistron-splicing factor aar2; PDBTitle: crystal structure of a aar2-prp8 complex Phyre2 PDB 2et1 chain A domain 1 Region: 78 - 95 Aligned: 18 Modelled: 18 Confidence: 11.7% Identity: 33% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: Germin/Seed storage 7S protein Phyre2 PDB 2css chain A domain 1 Region: 88 - 99 Aligned: 12 Modelled: 12 Confidence: 9.6% Identity: 50% Fold: PDZ domain-like Superfamily: PDZ domain-like Family: PDZ domain Phyre2 PDB 1fxz chain A domain 2 Region: 78 - 95 Aligned: 18 Modelled: 18 Confidence: 8.8% Identity: 6% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: Germin/Seed storage 7S protein Phyre2 PDB 1r89 chain A domain 3 Region: 110 - 142 Aligned: 33 Modelled: 33 Confidence: 8.6% Identity: 12% Fold: Ferredoxin-like Superfamily: PAP/Archaeal CCA-adding enzyme, C-terminal domain Family: Archaeal tRNA CCA-adding enzyme Phyre2 PDB 1lc0 chain A domain 2 Region: 119 - 146 Aligned: 28 Modelled: 28 Confidence: 8.4% Identity: 32% Fold: FwdE/GAPDH domain-like Superfamily: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family: Biliverdin reductase Phyre2 PDB 1od5 chain A domain 2 Region: 78 - 95 Aligned: 18 Modelled: 18 Confidence: 8.3% Identity: 17% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: Germin/Seed storage 7S protein Phyre2 PDB 1lsh chain B Region: 99 - 144 Aligned: 46 Modelled: 46 Confidence: 8.0% Identity: 20% PDB header:lipid binding protein Chain: B: PDB Molecule:lipovitellin (lv-2); PDBTitle: lipid-protein interactions in lipovitellin Phyre2 PDB 1lsh chain B Region: 99 - 144 Aligned: 46 Modelled: 46 Confidence: 8.0% Identity: 20% Fold: Lipovitellin-phosvitin complex; beta-sheet shell regions Superfamily: Lipovitellin-phosvitin complex; beta-sheet shell regions Family: Lipovitellin-phosvitin complex; beta-sheet shell regions Phyre2 PDB 2xte chain H Region: 111 - 132 Aligned: 22 Modelled: 22 Confidence: 7.1% Identity: 27% PDB header:transcription Chain: H: PDB Molecule:f-box-like/wd repeat-containing protein tbl1x; PDBTitle: structure of the tbl1 tetramerisation domain Phyre2 PDB 2xtd chain B Region: 111 - 132 Aligned: 22 Modelled: 22 Confidence: 7.0% Identity: 27% PDB header:transcription Chain: B: PDB Molecule:tbl1 f-box-like/wd repeat-containing protein tbl1x; PDBTitle: structure of the tbl1 tetramerisation domain Phyre2 PDB 2p5k chain A domain 1 Region: 111 - 130 Aligned: 20 Modelled: 20 Confidence: 5.9% Identity: 15% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Arginine repressor (ArgR), N-terminal DNA-binding domain Phyre2 PDB 2csp chain A domain 1 Region: 70 - 92 Aligned: 23 Modelled: 23 Confidence: 5.7% Identity: 35% Fold: Immunoglobulin-like beta-sandwich Superfamily: Fibronectin type III Family: Fibronectin type III Phyre2 PDB 3ktb chain D Region: 108 - 130 Aligned: 23 Modelled: 23 Confidence: 5.4% Identity: 22% PDB header:transcription regulator Chain: D: PDB Molecule:arsenical resistance operon trans-acting repressor; PDBTitle: crystal structure of arsenical resistance operon trans-acting2 repressor from bacteroides vulgatus atcc 8482 Phyre2 1 c1uv7A_ 2 d1uv7a_ 3 c2rjzA_ 4 c2e26A_ 5 d1ikpa2 6 c2htbB_ 7 c3sbtB_ 8 d2et1a1 9 d2cssa1 10 d1fxza2 11 d1r89a3 12 d1lc0a2 13 d1od5a2 14 c1lshB_ 15 d1lshb_ 16 c2xteH_ 17 c2xtdB_ 18 d2p5ka1 19 d2cspa1 20 c3ktbD_

Detailed template information

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

1 c1uv7A_ 89.6 20 PDB header:transport Chain: A: PDB Molecule:general secretion pathway protein m; PDBTitle: periplasmic domain of epsm from vibrio cholerae 2 d1uv7a_ 89.6 20 Fold:RRF/tRNA synthetase additional domain-like Superfamily:General secretion pathway protein M, EpsM Family:General secretion pathway protein M, EpsM 3 c2rjzA_ 70.3 10 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:pilo protein; PDBTitle: crystal structure of the type 4 fimbrial biogenesis protein pilo from2 pseudomonas aeruginosa 4 c2e26A_ 16.2 23 PDB header:signaling protein Chain: A: PDB Molecule:reelin; PDBTitle: crystal structure of two repeat fragment of reelin 5 d1ikpa2 13.8 44 Fold:ADP-ribosylation Superfamily:ADP-ribosylation Family:ADP-ribosylating toxins 6 c2htbB_ 13.5 24 PDB header:isomerase Chain: B: PDB Molecule:putative enzyme related to aldose 1-epimerase; PDBTitle: crystal structure of a putative mutarotase (yead) from2 salmonella typhimurium in monoclinic form 7 c3sbtB_ 12.4 11 PDB header:splicing Chain: B: PDB Molecule:a1 cistron-splicing factor aar2; PDBTitle: crystal structure of a aar2-prp8 complex 8 d2et1a1 11.7 33 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 9 d2cssa1 9.6 50 Fold:PDZ domain-like Superfamily:PDZ domain-like Family:PDZ domain 10 d1fxza2 8.8 6 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 11 d1r89a3 8.6 12 Fold:Ferredoxin-like Superfamily:PAP/Archaeal CCA-adding enzyme, C-terminal domain Family:Archaeal tRNA CCA-adding enzyme 12 d1lc0a2 8.4 32 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:Biliverdin reductase 13 d1od5a2 8.3 17 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 14 c1lshB_ 8.0 20 PDB header:lipid binding protein Chain: B: PDB Molecule:lipovitellin (lv-2); PDBTitle: lipid-protein interactions in lipovitellin 15 d1lshb_ 8.0 20 Fold:Lipovitellin-phosvitin complex; beta-sheet shell regions Superfamily:Lipovitellin-phosvitin complex; beta-sheet shell regions Family:Lipovitellin-phosvitin complex; beta-sheet shell regions 16 c2xteH_ 7.1 27 PDB header:transcription Chain: H: PDB Molecule:f-box-like/wd repeat-containing protein tbl1x; PDBTitle: structure of the tbl1 tetramerisation domain 17 c2xtdB_ 7.0 27 PDB header:transcription Chain: B: PDB Molecule:tbl1 f-box-like/wd repeat-containing protein tbl1x; PDBTitle: structure of the tbl1 tetramerisation domain 18 d2p5ka1 5.9 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain 19 d2cspa1 5.7 35 Fold:Immunoglobulin-like beta-sandwich Superfamily:Fibronectin type III Family:Fibronectin type III 20 c3ktbD_ 5.4 22 PDB header:transcription regulator Chain: D: PDB Molecule:arsenical resistance operon trans-acting repressor; PDBTitle: crystal structure of arsenical resistance operon trans-acting2 repressor from bacteroides vulgatus atcc 8482

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