Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	H	Y	E	I	V	F	M	V	H	P	D	Q	S	E	Q	V	P	G	M	I	E	R	Y	T	A	A	I	T	G	A	E	G	K	I	H	R	L	E	D	W	G	R	R	Q	L	A	Y	P	I	N	K	L	H	K	A	H	Y	V
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	M	N	V	E	A	P	Q	E	V	I	D	E	L	E	T	T	F	R	F	N	D	A	V	I	R	S	M	V	M	R	T	K	H	A	V	T	E	A	S	P	M	V	K	A	K	D	E	R	R	E	R	R	D	D	F	A	N	E	T
Secondary structure
SS confidence
Disorder																																			?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.
Sequence		A	D	D	A	E	A	G	D	S	E	E	E	E	E	E
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 2qal chain F domain 1 Region: 1 - 100 Aligned: 100 Modelled: 100 Confidence: 100.0% Identity: 100% Fold: Ferredoxin-like Superfamily: Ribosomal protein S6 Family: Ribosomal protein S6 Phyre2 PDB 2qbb chain F Region: 1 - 100 Aligned: 100 Modelled: 100 Confidence: 100.0% Identity: 100% PDB header:ribosome Chain: F: PDB Molecule:30s ribosomal protein s6; PDBTitle: crystal structure of the bacterial ribosome from2 escherichia coli in complex with gentamicin. this file3 contains the 30s subunit of the second 70s ribosome, with4 gentamicin bound. the entire crystal structure contains5 two 70s ribosomes and is described in remark 400. Phyre2 PDB 1lou chain A Region: 1 - 96 Aligned: 96 Modelled: 96 Confidence: 100.0% Identity: 28% Fold: Ferredoxin-like Superfamily: Ribosomal protein S6 Family: Ribosomal protein S6 Phyre2 PDB 2j5a chain A domain 1 Region: 1 - 100 Aligned: 100 Modelled: 100 Confidence: 100.0% Identity: 34% Fold: Ferredoxin-like Superfamily: Ribosomal protein S6 Family: Ribosomal protein S6 Phyre2 PDB 1qjh chain A Region: 1 - 91 Aligned: 91 Modelled: 91 Confidence: 100.0% Identity: 27% Fold: Ferredoxin-like Superfamily: Ribosomal protein S6 Family: Ribosomal protein S6 Phyre2 PDB 3bbn chain F Region: 1 - 95 Aligned: 95 Modelled: 95 Confidence: 100.0% Identity: 25% PDB header:ribosome Chain: F: PDB Molecule:ribosomal protein s6; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. Phyre2 PDB 1vmb chain A Region: 1 - 94 Aligned: 94 Modelled: 94 Confidence: 100.0% Identity: 29% PDB header:translation Chain: A: PDB Molecule:30s ribosomal protein s6; PDBTitle: crystal structure of 30s ribosomal protein s6 (tm0603) from thermotoga2 maritima at 1.70 a resolution Phyre2 PDB 1vmb chain A Region: 1 - 94 Aligned: 94 Modelled: 94 Confidence: 100.0% Identity: 29% Fold: Ferredoxin-like Superfamily: Ribosomal protein S6 Family: Ribosomal protein S6 Phyre2 PDB 3r3t chain A Region: 2 - 93 Aligned: 92 Modelled: 92 Confidence: 100.0% Identity: 32% PDB header:rna binding protein Chain: A: PDB Molecule:30s ribosomal protein s6; PDBTitle: crystal structure of 30s ribosomal protein s from bacillus anthracis Phyre2 PDB 2kjw chain A Region: 1 - 53 Aligned: 53 Modelled: 53 Confidence: 99.7% Identity: 28% PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s6; PDBTitle: solution structure and backbone dynamics of the permutant2 p54-55 Phyre2 PDB 1gtd chain A Region: 44 - 95 Aligned: 51 Modelled: 51 Confidence: 35.6% Identity: 10% Fold: PurS-like Superfamily: PurS-like Family: PurS subunit of FGAM synthetase Phyre2 PDB 1sc6 chain A domain 3 Region: 20 - 90 Aligned: 61 Modelled: 71 Confidence: 32.9% Identity: 16% Fold: Ferredoxin-like Superfamily: ACT-like Family: Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain Phyre2 PDB 3o1l chain B Region: 1 - 78 Aligned: 64 Modelled: 62 Confidence: 28.2% Identity: 16% PDB header:hydrolase Chain: B: PDB Molecule:formyltetrahydrofolate deformylase; PDBTitle: crystal structure of a formyltetrahydrofolate deformylase (pspto_4314)2 from pseudomonas syringae pv. tomato str. dc3000 at 2.20 a resolution Phyre2 PDB 1phz chain A domain 1 Region: 20 - 85 Aligned: 59 Modelled: 59 Confidence: 24.2% Identity: 10% Fold: Ferredoxin-like Superfamily: ACT-like Family: Phenylalanine metabolism regulatory domain Phyre2 PDB 1uzh chain C domain 1 Region: 2 - 79 Aligned: 65 Modelled: 78 Confidence: 18.9% Identity: 11% Fold: RuBisCO, small subunit Superfamily: RuBisCO, small subunit Family: RuBisCO, small subunit Phyre2 PDB 2yy8 chain B Region: 19 - 85 Aligned: 63 Modelled: 67 Confidence: 18.1% Identity: 13% PDB header:transferase Chain: B: PDB Molecule:upf0106 protein ph0461; PDBTitle: crystal structure of archaeal trna-methylase for position2 56 (atrm56) from pyrococcus horikoshii, complexed with s-3 adenosyl-l-methionine Phyre2 PDB 2zw2 chain B Region: 1 - 94 Aligned: 75 Modelled: 75 Confidence: 15.1% Identity: 13% PDB header:ligase Chain: B: PDB Molecule:putative uncharacterized protein sts178; PDBTitle: crystal structure of formylglycinamide ribonucleotide amidotransferase2 iii from sulfolobus tokodaii (stpurs) Phyre2 PDB 1t4a chain A Region: 44 - 94 Aligned: 50 Modelled: 51 Confidence: 14.2% Identity: 14% Fold: PurS-like Superfamily: PurS-like Family: PurS subunit of FGAM synthetase Phyre2 PDB 1jjc chain B domain 4 Region: 11 - 40 Aligned: 30 Modelled: 30 Confidence: 13.0% Identity: 17% Fold: Ferredoxin-like Superfamily: Anticodon-binding domain of PheRS Family: Anticodon-binding domain of PheRS Phyre2 PDB 3b5h chain A domain 2 Region: 33 - 68 Aligned: 35 Modelled: 36 Confidence: 10.7% Identity: 6% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: I set domains Phyre2 1 d2qalf1 2 c2qbbF_ 3 d1loua_ 4 d2j5aa1 5 d1qjha_ 6 c3bbnF_ 7 c1vmbA_ 8 d1vmba_ 9 c3r3tA_ 10 c2kjwA_ 11 d1gtda_ 12 d1sc6a3 13 c3o1lB_ 14 d1phza1 15 d1uzhc1 16 c2yy8B_ 17 c2zw2B_ 18 d1t4aa_ 19 d1jjcb4 20 d3b5ha2 21 22 23 24 25 26 27 28 29 30 31

Detailed template information

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

1 d2qalf1 100.0 100 Fold:Ferredoxin-like Superfamily:Ribosomal protein S6 Family:Ribosomal protein S6 2 c2qbbF_ 100.0 100 PDB header:ribosome Chain: F: PDB Molecule:30s ribosomal protein s6; PDBTitle: crystal structure of the bacterial ribosome from2 escherichia coli in complex with gentamicin. this file3 contains the 30s subunit of the second 70s ribosome, with4 gentamicin bound. the entire crystal structure contains5 two 70s ribosomes and is described in remark 400. 3 d1loua_ 100.0 28 Fold:Ferredoxin-like Superfamily:Ribosomal protein S6 Family:Ribosomal protein S6 4 d2j5aa1 100.0 34 Fold:Ferredoxin-like Superfamily:Ribosomal protein S6 Family:Ribosomal protein S6 5 d1qjha_ 100.0 27 Fold:Ferredoxin-like Superfamily:Ribosomal protein S6 Family:Ribosomal protein S6 6 c3bbnF_ 100.0 25 PDB header:ribosome Chain: F: PDB Molecule:ribosomal protein s6; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. 7 c1vmbA_ 100.0 29 PDB header:translation Chain: A: PDB Molecule:30s ribosomal protein s6; PDBTitle: crystal structure of 30s ribosomal protein s6 (tm0603) from thermotoga2 maritima at 1.70 a resolution 8 d1vmba_ 100.0 29 Fold:Ferredoxin-like Superfamily:Ribosomal protein S6 Family:Ribosomal protein S6 9 c3r3tA_ 100.0 32 PDB header:rna binding protein Chain: A: PDB Molecule:30s ribosomal protein s6; PDBTitle: crystal structure of 30s ribosomal protein s from bacillus anthracis 10 c2kjwA_ 99.7 28 PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s6; PDBTitle: solution structure and backbone dynamics of the permutant2 p54-55 11 d1gtda_ 35.6 10 Fold:PurS-like Superfamily:PurS-like Family:PurS subunit of FGAM synthetase 12 d1sc6a3 32.9 16 Fold:Ferredoxin-like Superfamily:ACT-like Family:Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain 13 c3o1lB_ 28.2 16 PDB header:hydrolase Chain: B: PDB Molecule:formyltetrahydrofolate deformylase; PDBTitle: crystal structure of a formyltetrahydrofolate deformylase (pspto_4314)2 from pseudomonas syringae pv. tomato str. dc3000 at 2.20 a resolution 14 d1phza1 24.2 10 Fold:Ferredoxin-like Superfamily:ACT-like Family:Phenylalanine metabolism regulatory domain 15 d1uzhc1 18.9 11 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 16 c2yy8B_ 18.1 13 PDB header:transferase Chain: B: PDB Molecule:upf0106 protein ph0461; PDBTitle: crystal structure of archaeal trna-methylase for position2 56 (atrm56) from pyrococcus horikoshii, complexed with s-3 adenosyl-l-methionine 17 c2zw2B_ 15.1 13 PDB header:ligase Chain: B: PDB Molecule:putative uncharacterized protein sts178; PDBTitle: crystal structure of formylglycinamide ribonucleotide amidotransferase2 iii from sulfolobus tokodaii (stpurs) 18 d1t4aa_ 14.2 14 Fold:PurS-like Superfamily:PurS-like Family:PurS subunit of FGAM synthetase 19 d1jjcb4 13.0 17 Fold:Ferredoxin-like Superfamily:Anticodon-binding domain of PheRS Family:Anticodon-binding domain of PheRS 20 d3b5ha2 10.7 6 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:I set domains 21 c2dgbA_ not modelled 9.7 13 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein purs; PDBTitle: structure of thermus thermophilus purs in the p21 form 22 d1xhja_ not modelled 8.1 23 Fold:Alpha-lytic protease prodomain-like Superfamily:Fe-S cluster assembly (FSCA) domain-like Family:NifU C-terminal domain-like 23 d1rbli_ not modelled 7.3 20 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 24 c1kcfB_ not modelled 6.8 13 PDB header:hydrolase Chain: B: PDB Molecule:hypothetical 30.2 kd protein c25g10.02 in PDBTitle: crystal structure of the yeast mitochondrial holliday2 junction resolvase, ydc2 25 c3a6mB_ not modelled 6.3 18 PDB header:chaperone Chain: B: PDB Molecule:protein grpe; PDBTitle: crystal structure of grpe from thermus thermophilus hb8 26 c3nrbD_ not modelled 6.3 14 PDB header:hydrolase Chain: D: PDB Molecule:formyltetrahydrofolate deformylase; PDBTitle: crystal structure of a formyltetrahydrofolate deformylase (puru,2 pp_1943) from pseudomonas putida kt2440 at 2.05 a resolution 27 c2l42A_ not modelled 6.1 12 PDB header:protein binding Chain: A: PDB Molecule:dna-binding protein rap1; PDBTitle: the solution structure of rap1 brct domain from saccharomyces2 cerevisiae 28 d1wdds_ not modelled 6.1 9 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 29 d3bpda1 not modelled 6.0 28 Fold:Ferredoxin-like Superfamily:MTH889-like Family:MTH889-like 30 d2raqa1 not modelled 5.8 33 Fold:Ferredoxin-like Superfamily:MTH889-like Family:MTH889-like 31 d1nkga3 not modelled 5.5 15 Fold:Supersandwich Superfamily:Galactose mutarotase-like Family:Rhamnogalacturonase B, RhgB, N-terminal domain

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