Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	K	Q	K	I	K	T	I	F	E	A	L	L	Y	I	M	L	T	Y	W	L	I	D	S	F	F	A	F	N	K	Y	D	W	M	L	E	S	G	G	N	I	C	S	I	P	S	V	S	G	E	D	R	I	L	Q	A	M	I	A
Secondary structure
SS confidence
Disorder		?	?	?	?																																														?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110
Sequence		A	F	F	L	L	T	P	L	I	I	L	I	L	R	K	L	F	M	R	E	M	F	E	F	W	V	Y	V	F	S	L	G	I	C	L	V	C	G	W	W	L	F	W	G	R	F	I	F	C	Y
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 1nl1 chain A domain 2 Region: 102 - 109 Aligned: 8 Modelled: 8 Confidence: 23.6% Identity: 38% Fold: GLA-domain Superfamily: GLA-domain Family: GLA-domain Phyre2 PDB 2pf1 chain A domain 2 Region: 102 - 109 Aligned: 8 Modelled: 8 Confidence: 20.0% Identity: 38% Fold: GLA-domain Superfamily: GLA-domain Family: GLA-domain Phyre2 PDB 3imo chain C Region: 40 - 64 Aligned: 25 Modelled: 25 Confidence: 12.3% Identity: 16% PDB header:unknown function Chain: C: PDB Molecule:integron cassette protein; PDBTitle: structure from the mobile metagenome of vibrio cholerae.2 integron cassette protein vch_cass14 Phyre2 PDB 5rub chain A domain 1 Region: 28 - 68 Aligned: 40 Modelled: 41 Confidence: 10.5% Identity: 23% Fold: TIM beta/alpha-barrel Superfamily: RuBisCo, C-terminal domain Family: RuBisCo, large subunit, C-terminal domain Phyre2 PDB 3mpb chain A Region: 36 - 46 Aligned: 11 Modelled: 11 Confidence: 9.6% Identity: 45% PDB header:isomerase Chain: A: PDB Molecule:sugar isomerase; PDBTitle: z5688 from e. coli o157:h7 bound to fructose Phyre2 PDB 2y0o chain A Region: 36 - 46 Aligned: 11 Modelled: 11 Confidence: 9.3% Identity: 45% PDB header:isomerase Chain: A: PDB Molecule:probable d-lyxose ketol-isomerase; PDBTitle: the structure of a d-lyxose isomerase from the sigmab2 regulon of bacillus subtilis Phyre2 PDB 1tel chain A Region: 28 - 68 Aligned: 40 Modelled: 41 Confidence: 8.6% Identity: 20% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ribulose bisphosphate carboxylase, large subunit; PDBTitle: crystal structure of a rubisco-like protein from chlorobium2 tepidum Phyre2 PDB 1rld chain B Region: 28 - 72 Aligned: 44 Modelled: 45 Confidence: 8.4% Identity: 23% PDB header:lyase(carbon-carbon) Chain: B: PDB Molecule:ribulose 1,5 bisphosphate carboxylase/oxygenase (large PDBTitle: solid-state phase transition in the crystal structure of ribulose 1,5-2 biphosphate carboxylase(slash)oxygenase Phyre2 PDB 2qyg chain C Region: 28 - 68 Aligned: 40 Modelled: 41 Confidence: 8.2% Identity: 23% PDB header:unknown function Chain: C: PDB Molecule:ribulose bisphosphate carboxylase-like protein 2; PDBTitle: crystal structure of a rubisco-like protein rlp2 from rhodopseudomonas2 palustris Phyre2 PDB 3lyn chain A Region: 71 - 86 Aligned: 16 Modelled: 16 Confidence: 7.8% Identity: 25% Fold: Fertilization protein Superfamily: Fertilization protein Family: Fertilization protein Phyre2 PDB 1ykw chain A domain 1 Region: 28 - 68 Aligned: 40 Modelled: 41 Confidence: 7.8% Identity: 20% Fold: TIM beta/alpha-barrel Superfamily: RuBisCo, C-terminal domain Family: RuBisCo, large subunit, C-terminal domain Phyre2 PDB 1yro chain A domain 1 Region: 26 - 61 Aligned: 36 Modelled: 36 Confidence: 7.3% Identity: 28% Fold: Lysozyme-like Superfamily: Lysozyme-like Family: C-type lysozyme Phyre2 PDB 1r7m chain A domain 2 Region: 18 - 65 Aligned: 40 Modelled: 48 Confidence: 7.2% Identity: 23% Fold: Homing endonuclease-like Superfamily: Homing endonucleases Family: Group I mobile intron endonuclease Phyre2 PDB 1bwv chain A Region: 28 - 72 Aligned: 43 Modelled: 45 Confidence: 7.0% Identity: 23% PDB header:lyase Chain: A: PDB Molecule:protein (ribulose bisphosphate carboxylase); PDBTitle: activated ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco)2 complexed with the reaction intermediate analogue 2-carboxyarabinitol3 1,5-bisphosphate Phyre2 PDB 1c8s chain A Region: 6 - 98 Aligned: 75 Modelled: 75 Confidence: 6.7% Identity: 24% Fold: Family A G protein-coupled receptor-like Superfamily: Family A G protein-coupled receptor-like Family: Bacteriorhodopsin-like Phyre2 PDB 3nwr chain A Region: 33 - 68 Aligned: 35 Modelled: 36 Confidence: 6.6% Identity: 37% PDB header:lyase Chain: A: PDB Molecule:a rubisco-like protein; PDBTitle: crystal structure of a rubisco-like protein from burkholderia fungorum Phyre2 PDB 1shp chain A Region: 41 - 50 Aligned: 10 Modelled: 10 Confidence: 6.2% Identity: 50% Fold: BPTI-like Superfamily: BPTI-like Family: Small Kunitz-type inhibitors & BPTI-like toxins Phyre2 PDB 2qyv chain B Region: 42 - 63 Aligned: 22 Modelled: 22 Confidence: 6.1% Identity: 32% PDB header:hydrolase Chain: B: PDB Molecule:xaa-his dipeptidase; PDBTitle: crystal structure of putative xaa-his dipeptidase (yp_718209.1) from2 haemophilus somnus 129pt at 2.11 a resolution Phyre2 PDB 1al0 chain B Region: 29 - 40 Aligned: 12 Modelled: 12 Confidence: 6.1% Identity: 33% PDB header:virus Chain: B: PDB Molecule:scaffolding protein gpb; PDBTitle: procapsid of bacteriophage phix174 Phyre2 PDB 1ysj chain B Region: 42 - 63 Aligned: 22 Modelled: 22 Confidence: 5.9% Identity: 14% PDB header:hydrolase Chain: B: PDB Molecule:protein yxep; PDBTitle: crystal structure of bacillus subtilis yxep protein (apc1829), a2 dinuclear metal binding peptidase from m20 family Phyre2 1 d1nl1a2 2 d2pf1a2 3 c3imoC_ 4 d5ruba1 5 c3mpbA_ 6 c2y0oA_ 7 c1telA_ 8 c1rldB_ 9 c2qygC_ 10 d3lyna_ 11 d1ykwa1 12 d1yroa1 13 d1r7ma2 14 c1bwvA_ 15 d1c8sa_ 16 c3nwrA_ 17 d1shpa_ 18 c2qyvB_ 19 c1al0B_ 20 c1ysjB_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

Detailed template information

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

1 d1nl1a2 23.6 38 Fold:GLA-domain Superfamily:GLA-domain Family:GLA-domain 2 d2pf1a2 20.0 38 Fold:GLA-domain Superfamily:GLA-domain Family:GLA-domain 3 c3imoC_ 12.3 16 PDB header:unknown function Chain: C: PDB Molecule:integron cassette protein; PDBTitle: structure from the mobile metagenome of vibrio cholerae.2 integron cassette protein vch_cass14 4 d5ruba1 10.5 23 Fold:TIM beta/alpha-barrel Superfamily:RuBisCo, C-terminal domain Family:RuBisCo, large subunit, C-terminal domain 5 c3mpbA_ 9.6 45 PDB header:isomerase Chain: A: PDB Molecule:sugar isomerase; PDBTitle: z5688 from e. coli o157:h7 bound to fructose 6 c2y0oA_ 9.3 45 PDB header:isomerase Chain: A: PDB Molecule:probable d-lyxose ketol-isomerase; PDBTitle: the structure of a d-lyxose isomerase from the sigmab2 regulon of bacillus subtilis 7 c1telA_ 8.6 20 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ribulose bisphosphate carboxylase, large subunit; PDBTitle: crystal structure of a rubisco-like protein from chlorobium2 tepidum 8 c1rldB_ 8.4 23 PDB header:lyase(carbon-carbon) Chain: B: PDB Molecule:ribulose 1,5 bisphosphate carboxylase/oxygenase (large PDBTitle: solid-state phase transition in the crystal structure of ribulose 1,5-2 biphosphate carboxylase(slash)oxygenase 9 c2qygC_ 8.2 23 PDB header:unknown function Chain: C: PDB Molecule:ribulose bisphosphate carboxylase-like protein 2; PDBTitle: crystal structure of a rubisco-like protein rlp2 from rhodopseudomonas2 palustris 10 d3lyna_ 7.8 25 Fold:Fertilization protein Superfamily:Fertilization protein Family:Fertilization protein 11 d1ykwa1 7.8 20 Fold:TIM beta/alpha-barrel Superfamily:RuBisCo, C-terminal domain Family:RuBisCo, large subunit, C-terminal domain 12 d1yroa1 7.3 28 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:C-type lysozyme 13 d1r7ma2 7.2 23 Fold:Homing endonuclease-like Superfamily:Homing endonucleases Family:Group I mobile intron endonuclease 14 c1bwvA_ 7.0 23 PDB header:lyase Chain: A: PDB Molecule:protein (ribulose bisphosphate carboxylase); PDBTitle: activated ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco)2 complexed with the reaction intermediate analogue 2-carboxyarabinitol3 1,5-bisphosphate 15 d1c8sa_ 6.7 24 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 16 c3nwrA_ 6.6 37 PDB header:lyase Chain: A: PDB Molecule:a rubisco-like protein; PDBTitle: crystal structure of a rubisco-like protein from burkholderia fungorum 17 d1shpa_ 6.2 50 Fold:BPTI-like Superfamily:BPTI-like Family:Small Kunitz-type inhibitors & BPTI-like toxins 18 c2qyvB_ 6.1 32 PDB header:hydrolase Chain: B: PDB Molecule:xaa-his dipeptidase; PDBTitle: crystal structure of putative xaa-his dipeptidase (yp_718209.1) from2 haemophilus somnus 129pt at 2.11 a resolution 19 c1al0B_ 6.1 33 PDB header:virus Chain: B: PDB Molecule:scaffolding protein gpb; PDBTitle: procapsid of bacteriophage phix174 20 c1ysjB_ 5.9 14 PDB header:hydrolase Chain: B: PDB Molecule:protein yxep; PDBTitle: crystal structure of bacillus subtilis yxep protein (apc1829), a2 dinuclear metal binding peptidase from m20 family 21 d1bxna1 not modelled 5.9 23 Fold:TIM beta/alpha-barrel Superfamily:RuBisCo, C-terminal domain Family:RuBisCo, large subunit, C-terminal domain 22 d1smpi_ not modelled 5.9 25 Fold:Streptavidin-like Superfamily:beta-Barrel protease inhibitors Family:Metalloprotease inhibitor 23 c9rubB_ not modelled 5.7 23 PDB header:lyase(carbon-carbon) Chain: B: PDB Molecule:ribulose-1,5-bisphosphate carboxylase; PDBTitle: crystal structure of activated ribulose-1,5-bisphosphate2 carboxylase complexed with its substrate, ribulose-1,5-3 bisphosphate 24 c1rcxH_ not modelled 5.6 27 PDB header:lyase (carbon-carbon) Chain: H: PDB Molecule:ribulose bisphosphate carboxylase/oxygenase; PDBTitle: non-activated spinach rubisco in complex with its substrate2 ribulose-1,5-bisphosphate 25 c3fk4A_ not modelled 5.6 29 PDB header:isomerase Chain: A: PDB Molecule:rubisco-like protein; PDBTitle: crystal structure of rubisco-like protein from bacillus2 cereus atcc 14579 26 c3i5pA_ not modelled 5.5 30 PDB header:protein transport Chain: A: PDB Molecule:nucleoporin nup170; PDBTitle: nup170(aa979-1502), s.cerevisiae 27 c3oakC_ not modelled 5.5 71 PDB header:transcription Chain: C: PDB Molecule:transcription elongation factor spt6; PDBTitle: crystal structure of a spn1 (iws1)-spt6 complex 28 c3jrzA_ not modelled 5.4 8 PDB header:toxin Chain: A: PDB Molecule:ccdb; PDBTitle: ccdbvfi-formii-ph5.6 29 c2fbdB_ not modelled 5.4 28 PDB header:hydrolase Chain: B: PDB Molecule:lysozyme 1; PDBTitle: the crystallographic structure of the digestive lysozyme 1 from musca2 domestica at 1.90 ang. 30 d2nwdx1 not modelled 5.4 25 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:C-type lysozyme 31 d1wdda1 not modelled 5.3 23 Fold:TIM beta/alpha-barrel Superfamily:RuBisCo, C-terminal domain Family:RuBisCo, large subunit, C-terminal domain 32 d1gd6a_ not modelled 5.3 28 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:C-type lysozyme 33 c2d69B_ not modelled 5.2 26 PDB header:lyase Chain: B: PDB Molecule:ribulose bisphosphate carboxylase; PDBTitle: crystal structure of the complex of sulfate ion and octameric2 ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) from3 pyrococcus horikoshii ot3 (form-2 crystal) 34 d2io8a2 not modelled 5.2 31 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:CHAP domain 35 d1alca_ not modelled 5.2 24 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:C-type lysozyme

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