Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	Q	E	Q	T	M	L	N	V	A	D	N	S	G	A	R	R	V	M	C	I	K	V	L	G	G	S	H	R	R	Y	A	G	V	G	D	I	I	K	I	T	I	K	E	A	I	P	R	G	K	V	K	K	G	D	V	L	K	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																							?	?		?	?												?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		V	V	V	R	T	K	K	G	V	R	R	P	D	G	S	V	I	R	F	D	G	N	A	C	V	L	L	N	N	N	S	E	Q	P	I	G	T	R	I	F	G	P	V	T	R	E	L	R	S	E	K	F	M	K	I	I	S	L	A	P
Secondary structure
SS confidence
Disorder										?			?																				?																									?	?	?	?
Disorder confidence
		.	.	.
Sequence		E	V	L
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 1whi chain A Region: 1 - 123 Aligned: 122 Modelled: 123 Confidence: 100.0% Identity: 69% Fold: Ribosomal protein L14 Superfamily: Ribosomal protein L14 Family: Ribosomal protein L14 Phyre2 PDB 2j01 chain O domain 1 Region: 1 - 123 Aligned: 122 Modelled: 123 Confidence: 100.0% Identity: 69% Fold: Ribosomal protein L14 Superfamily: Ribosomal protein L14 Family: Ribosomal protein L14 Phyre2 PDB 2zjr chain H domain 1 Region: 1 - 123 Aligned: 122 Modelled: 123 Confidence: 100.0% Identity: 66% Fold: Ribosomal protein L14 Superfamily: Ribosomal protein L14 Family: Ribosomal protein L14 Phyre2 PDB 2gyc chain I domain 1 Region: 2 - 122 Aligned: 121 Modelled: 121 Confidence: 100.0% Identity: 100% Fold: Ribosomal protein L14 Superfamily: Ribosomal protein L14 Family: Ribosomal protein L14 Phyre2 PDB 3bbo chain M Region: 1 - 123 Aligned: 121 Modelled: 123 Confidence: 100.0% Identity: 59% PDB header:ribosome Chain: M: PDB Molecule:ribosomal protein l14; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome Phyre2 PDB 2zkr chain K Region: 2 - 122 Aligned: 116 Modelled: 121 Confidence: 100.0% Identity: 38% PDB header:ribosomal protein/rna Chain: K: PDB Molecule:rna expansion segment es19; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map Phyre2 PDB 1vqo chain K domain 1 Region: 2 - 123 Aligned: 117 Modelled: 122 Confidence: 100.0% Identity: 39% Fold: Ribosomal protein L14 Superfamily: Ribosomal protein L14 Family: Ribosomal protein L14 Phyre2 PDB 1zv9 chain A domain 1 Region: 30 - 44 Aligned: 15 Modelled: 15 Confidence: 21.2% Identity: 33% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Carbohydrate-binding domain Family: Cellulose-binding domain family III Phyre2 PDB 1wyh chain A domain 1 Region: 92 - 102 Aligned: 11 Modelled: 11 Confidence: 20.3% Identity: 64% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: LIM domain Phyre2 PDB 1tyj chain A domain 1 Region: 30 - 44 Aligned: 15 Modelled: 15 Confidence: 19.0% Identity: 33% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Carbohydrate-binding domain Family: Cellulose-binding domain family III Phyre2 PDB 3ghp chain A Region: 30 - 44 Aligned: 15 Modelled: 15 Confidence: 17.9% Identity: 53% PDB header:structural protein Chain: A: PDB Molecule:cellulosomal scaffoldin adaptor protein b; PDBTitle: structure of the second type ii cohesin module from the2 adaptor scaa scaffoldin of acetivibrio cellulolyticus3 (including long c-terminal linker) Phyre2 PDB 2bm3 chain A domain 1 Region: 30 - 44 Aligned: 15 Modelled: 15 Confidence: 17.2% Identity: 40% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Carbohydrate-binding domain Family: Cellulose-binding domain family III Phyre2 PDB 2b59 chain A Region: 30 - 44 Aligned: 15 Modelled: 15 Confidence: 17.1% Identity: 40% PDB header:hydrolase/structural protein Chain: A: PDB Molecule:cog1196: chromosome segregation atpases; PDBTitle: the type ii cohesin dockerin complex Phyre2 PDB 1oj5 chain A Region: 67 - 98 Aligned: 31 Modelled: 32 Confidence: 16.5% Identity: 10% Fold: Profilin-like Superfamily: PYP-like sensor domain (PAS domain) Family: PAS domain of steroid receptor coactivator 1A, NCo-A1 Phyre2 PDB 3fnk chain A Region: 30 - 44 Aligned: 15 Modelled: 15 Confidence: 16.3% Identity: 53% PDB header:structural protein Chain: A: PDB Molecule:cellulosomal scaffoldin adaptor protein b; PDBTitle: crystal structure of the second type ii cohesin module from2 the cellulosomal adaptor scaa scaffoldin of acetivibrio3 cellulolyticus Phyre2 PDB 1gd7 chain A Region: 2 - 100 Aligned: 84 Modelled: 87 Confidence: 13.5% Identity: 23% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Myf domain Phyre2 PDB 2e5q chain A Region: 55 - 96 Aligned: 39 Modelled: 42 Confidence: 9.6% Identity: 15% PDB header:transcription Chain: A: PDB Molecule:phd finger protein 19; PDBTitle: solution structure of the tudor domain of phd finger2 protein 19, isoform b [homo sapiens] Phyre2 PDB 2xk0 chain A Region: 55 - 83 Aligned: 24 Modelled: 29 Confidence: 9.2% Identity: 25% PDB header:transcription Chain: A: PDB Molecule:polycomb protein pcl; PDBTitle: solution structure of the tudor domain from drosophila2 polycomblike (pcl) Phyre2 PDB 3icy chain B Region: 63 - 96 Aligned: 33 Modelled: 34 Confidence: 9.2% Identity: 9% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:sensor protein; PDBTitle: the crystal structure of sensory box histidine2 kinase/response regulator domain from chlorobium tepidum3 tls Phyre2 PDB 3ewk chain A Region: 61 - 96 Aligned: 35 Modelled: 36 Confidence: 9.1% Identity: 11% PDB header:flavoprotein Chain: A: PDB Molecule:sensor protein; PDBTitle: structure of the redox sensor domain of methylococcus capsulatus2 (bath) mmos Phyre2 1 d1whia_ 2 d2j01o1 3 d2zjrh1 4 d2gyci1 5 c3bboM_ 6 c2zkrk_ 7 d1vqok1 8 d1zv9a1 9 d1wyha1 10 d1tyja1 11 c3ghpA_ 12 d2bm3a1 13 c2b59A_ 14 d1oj5a_ 15 c3fnkA_ 16 d1gd7a_ 17 c2e5qA_ 18 c2xk0A_ 19 c3icyB_ 20 c3ewkA_ 21 22 23 24 25 26 27 28 29 30 31 32

Detailed template information

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

1 d1whia_ 100.0 69 Fold:Ribosomal protein L14 Superfamily:Ribosomal protein L14 Family:Ribosomal protein L14 2 d2j01o1 100.0 69 Fold:Ribosomal protein L14 Superfamily:Ribosomal protein L14 Family:Ribosomal protein L14 3 d2zjrh1 100.0 66 Fold:Ribosomal protein L14 Superfamily:Ribosomal protein L14 Family:Ribosomal protein L14 4 d2gyci1 100.0 100 Fold:Ribosomal protein L14 Superfamily:Ribosomal protein L14 Family:Ribosomal protein L14 5 c3bboM_ 100.0 59 PDB header:ribosome Chain: M: PDB Molecule:ribosomal protein l14; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome 6 c2zkrk_ 100.0 38 PDB header:ribosomal protein/rna Chain: K: PDB Molecule:rna expansion segment es19; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 7 d1vqok1 100.0 39 Fold:Ribosomal protein L14 Superfamily:Ribosomal protein L14 Family:Ribosomal protein L14 8 d1zv9a1 21.2 33 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Carbohydrate-binding domain Family:Cellulose-binding domain family III 9 d1wyha1 20.3 64 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 10 d1tyja1 19.0 33 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Carbohydrate-binding domain Family:Cellulose-binding domain family III 11 c3ghpA_ 17.9 53 PDB header:structural protein Chain: A: PDB Molecule:cellulosomal scaffoldin adaptor protein b; PDBTitle: structure of the second type ii cohesin module from the2 adaptor scaa scaffoldin of acetivibrio cellulolyticus3 (including long c-terminal linker) 12 d2bm3a1 17.2 40 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Carbohydrate-binding domain Family:Cellulose-binding domain family III 13 c2b59A_ 17.1 40 PDB header:hydrolase/structural protein Chain: A: PDB Molecule:cog1196: chromosome segregation atpases; PDBTitle: the type ii cohesin dockerin complex 14 d1oj5a_ 16.5 10 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:PAS domain of steroid receptor coactivator 1A, NCo-A1 15 c3fnkA_ 16.3 53 PDB header:structural protein Chain: A: PDB Molecule:cellulosomal scaffoldin adaptor protein b; PDBTitle: crystal structure of the second type ii cohesin module from2 the cellulosomal adaptor scaa scaffoldin of acetivibrio3 cellulolyticus 16 d1gd7a_ 13.5 23 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Myf domain 17 c2e5qA_ 9.6 15 PDB header:transcription Chain: A: PDB Molecule:phd finger protein 19; PDBTitle: solution structure of the tudor domain of phd finger2 protein 19, isoform b [homo sapiens] 18 c2xk0A_ 9.2 25 PDB header:transcription Chain: A: PDB Molecule:polycomb protein pcl; PDBTitle: solution structure of the tudor domain from drosophila2 polycomblike (pcl) 19 c3icyB_ 9.2 9 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:sensor protein; PDBTitle: the crystal structure of sensory box histidine2 kinase/response regulator domain from chlorobium tepidum3 tls 20 c3ewkA_ 9.1 11 PDB header:flavoprotein Chain: A: PDB Molecule:sensor protein; PDBTitle: structure of the redox sensor domain of methylococcus capsulatus2 (bath) mmos 21 d1b12a_ not modelled 9.0 13 Fold:LexA/Signal peptidase Superfamily:LexA/Signal peptidase Family:Type 1 signal peptidase 22 c2q2iA_ not modelled 7.6 18 PDB header:chaperone Chain: A: PDB Molecule:secretion chaperone; PDBTitle: crystal structure of the protein secretion chaperone csaa from2 agrobacterium tumefaciens. 23 d1ijdb_ not modelled 7.3 44 Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits 24 c3s6xA_ not modelled 6.3 21 PDB header:viral protein Chain: A: PDB Molecule:outer capsid protein sigma-1; PDBTitle: structure of reovirus attachment protein sigma1 in complex with alpha-2 2,3-sialyllactose 25 d2do3a1 not modelled 6.3 24 Fold:SH3-like barrel Superfamily:Translation proteins SH3-like domain Family:SPT5 KOW domain-like 26 d1k8ke_ not modelled 6.1 25 Fold:Arp2/3 complex 21 kDa subunit ARPC3 Superfamily:Arp2/3 complex 21 kDa subunit ARPC3 Family:Arp2/3 complex 21 kDa subunit ARPC3 27 d2zjrm1 not modelled 5.7 19 Fold:SH3-like barrel Superfamily:Translation proteins SH3-like domain Family:Ribosomal protein L19 28 c2eqjA_ not modelled 5.7 13 PDB header:transcription Chain: A: PDB Molecule:metal-response element-binding transcription PDBTitle: solution structure of the tudor domain of metal-response2 element-binding transcription factor 2 29 c2dyoB_ not modelled 5.1 100 PDB header:protein turnover/protein turnover Chain: B: PDB Molecule:autophagy protein 16; PDBTitle: the crystal structure of saccharomyces cerevisiae atg5-2 atg16(1-57) complex 30 d1mb4a1 not modelled 5.1 13 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain 31 d1x4ka1 not modelled 5.1 50 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 32 d1t3ta4 not modelled 5.1 33 Fold:Bacillus chorismate mutase-like Superfamily:PurM N-terminal domain-like Family:PurM N-terminal domain-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