Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	D	D	T	S	R	D	P	A	I	T	E	D	E	I	R	A	L	Q	F	S	A	G	D	V	A	E	I	E	Q	T	I	L	S	F	V	D	A	C	H	T	R	K	V	A	M	V	V	G	S	T	I	N	T	L	K	D	R	D	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?			?																																											?	?		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.
Sequence		K	R	W	G	N	L	P	D	I	Y	C	A	Y	L	I	R	C	L	V	F	R	G	E	L	V	G	Y	G	D	L	F	R	M	R	Y	S	E	I	K	R	P	V	T	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 1kut chain A Region: 2 - 52 Aligned: 49 Modelled: 51 Confidence: 69.7% Identity: 14% Fold: SAICAR synthase-like Superfamily: SAICAR synthase-like Family: SAICAR synthase Phyre2 PDB 2ywv chain B Region: 2 - 52 Aligned: 49 Modelled: 51 Confidence: 65.5% Identity: 29% PDB header:ligase Chain: B: PDB Molecule:phosphoribosylaminoimidazole succinocarboxamide synthetase; PDBTitle: crystal structure of saicar synthetase from geobacillus kaustophilus Phyre2 PDB 3kre chain A Region: 2 - 52 Aligned: 49 Modelled: 51 Confidence: 64.2% Identity: 20% PDB header:ligase Chain: A: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide synthase; PDBTitle: crystal structure of phosphoribosylaminoimidazole-succinocarboxamide2 synthase from ehrlichia chaffeensis at 1.8a resolution Phyre2 PDB 2h31 chain A Region: 2 - 52 Aligned: 49 Modelled: 51 Confidence: 63.0% Identity: 22% PDB header:ligase, lyase Chain: A: PDB Molecule:multifunctional protein ade2; PDBTitle: crystal structure of human paics, a bifunctional carboxylase and2 synthetase in purine biosynthesis Phyre2 PDB 2gqs chain A Region: 2 - 52 Aligned: 49 Modelled: 51 Confidence: 60.7% Identity: 18% PDB header:ligase Chain: A: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide PDBTitle: saicar synthetase complexed with cair-mg2+ and adp Phyre2 PDB 2z02 chain A Region: 2 - 52 Aligned: 49 Modelled: 51 Confidence: 43.1% Identity: 22% PDB header:ligase Chain: A: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide PDBTitle: crystal structure of2 phosphoribosylaminoimidazolesuccinocarboxamide synthase3 wit atp from methanocaldococcus jannaschii Phyre2 PDB 3nua chain B Region: 2 - 40 Aligned: 39 Modelled: 39 Confidence: 37.1% Identity: 15% PDB header:ligase Chain: B: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide synthase; PDBTitle: crystal structure of phosphoribosylaminoimidazole-succinocarboxamide2 synthase from clostridium perfringens Phyre2 PDB 3duk chain D Region: 17 - 47 Aligned: 31 Modelled: 30 Confidence: 26.9% Identity: 13% PDB header:unknown function Chain: D: PDB Molecule:ntf2-like protein of unknown function; PDBTitle: crystal structure of a ntf2-like protein of unknown function2 (mfla_0564) from methylobacillus flagellatus kt at 2.200 a resolution Phyre2 PDB 3noy chain A Region: 20 - 76 Aligned: 56 Modelled: 57 Confidence: 18.6% Identity: 18% PDB header:oxidoreductase Chain: A: PDB Molecule:4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; PDBTitle: crystal structure of ispg (gcpe) Phyre2 PDB 2rgq chain A domain 1 Region: 20 - 50 Aligned: 31 Modelled: 31 Confidence: 18.2% Identity: 19% Fold: Cystatin-like Superfamily: NTF2-like Family: Rv3472-like Phyre2 PDB 1whr chain A Region: 15 - 37 Aligned: 23 Modelled: 23 Confidence: 16.5% Identity: 30% Fold: IF3-like Superfamily: R3H domain Family: R3H domain Phyre2 PDB 3fka chain D Region: 21 - 45 Aligned: 25 Modelled: 25 Confidence: 14.7% Identity: 12% PDB header:unknown function Chain: D: PDB Molecule:uncharacterized ntf-2 like protein; PDBTitle: crystal structure of a ntf-2 like protein of unknown function2 (spo1084) from silicibacter pomeroyi dss-3 at 1.69 a resolution Phyre2 PDB 1x4t chain A domain 1 Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 12.5% Identity: 29% Fold: Long alpha-hairpin Superfamily: ISY1 domain-like Family: ISY1 N-terminal domain-like Phyre2 PDB 1h8b chain A Region: 8 - 25 Aligned: 17 Modelled: 18 Confidence: 12.3% Identity: 24% Fold: EF Hand-like Superfamily: EF-hand Family: EF-hand modules in multidomain proteins Phyre2 PDB 2ply chain B Region: 21 - 101 Aligned: 77 Modelled: 81 Confidence: 11.2% Identity: 14% PDB header:translation/rna Chain: B: PDB Molecule:selenocysteine-specific elongation factor; PDBTitle: structure of the mrna binding fragment of elongation factor2 selb in complex with secis rna. Phyre2 PDB 1zk8 chain A domain 2 Region: 12 - 37 Aligned: 26 Modelled: 26 Confidence: 8.6% Identity: 4% Fold: Tetracyclin repressor-like, C-terminal domain Superfamily: Tetracyclin repressor-like, C-terminal domain Family: Tetracyclin repressor-like, C-terminal domain Phyre2 PDB 1k9v chain F Region: 9 - 42 Aligned: 34 Modelled: 34 Confidence: 7.4% Identity: 21% Fold: Flavodoxin-like Superfamily: Class I glutamine amidotransferase-like Family: Class I glutamine amidotransferases (GAT) Phyre2 PDB 1ofc chain X domain 1 Region: 83 - 99 Aligned: 17 Modelled: 17 Confidence: 6.6% Identity: 29% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Myb/SANT domain Phyre2 PDB 1xly chain A Region: 56 - 78 Aligned: 23 Modelled: 23 Confidence: 6.5% Identity: 4% Fold: RNA-binding protein She2p Superfamily: RNA-binding protein She2p Family: RNA-binding protein She2p Phyre2 PDB 1ogy chain B Region: 39 - 67 Aligned: 29 Modelled: 29 Confidence: 6.5% Identity: 28% Fold: Multiheme cytochromes Superfamily: Multiheme cytochromes Family: Di-heme elbow motif Phyre2 1 d1kuta_ 2 c2ywvB_ 3 c3kreA_ 4 c2h31A_ 5 c2gqsA_ 6 c2z02A_ 7 c3nuaB_ 8 c3dukD_ 9 c3noyA_ 10 d2rgqa1 11 d1whra_ 12 c3fkaD_ 13 d1x4ta1 14 d1h8ba_ 15 c2plyB_ 16 d1zk8a2 17 d1k9vf_ 18 d1ofcx1 19 d1xlya_ 20 d1ogyb_ 21 22 23 24

Detailed template information

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

1 d1kuta_ 69.7 14 Fold:SAICAR synthase-like Superfamily:SAICAR synthase-like Family:SAICAR synthase 2 c2ywvB_ 65.5 29 PDB header:ligase Chain: B: PDB Molecule:phosphoribosylaminoimidazole succinocarboxamide synthetase; PDBTitle: crystal structure of saicar synthetase from geobacillus kaustophilus 3 c3kreA_ 64.2 20 PDB header:ligase Chain: A: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide synthase; PDBTitle: crystal structure of phosphoribosylaminoimidazole-succinocarboxamide2 synthase from ehrlichia chaffeensis at 1.8a resolution 4 c2h31A_ 63.0 22 PDB header:ligase, lyase Chain: A: PDB Molecule:multifunctional protein ade2; PDBTitle: crystal structure of human paics, a bifunctional carboxylase and2 synthetase in purine biosynthesis 5 c2gqsA_ 60.7 18 PDB header:ligase Chain: A: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide PDBTitle: saicar synthetase complexed with cair-mg2+ and adp 6 c2z02A_ 43.1 22 PDB header:ligase Chain: A: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide PDBTitle: crystal structure of2 phosphoribosylaminoimidazolesuccinocarboxamide synthase3 wit atp from methanocaldococcus jannaschii 7 c3nuaB_ 37.1 15 PDB header:ligase Chain: B: PDB Molecule:phosphoribosylaminoimidazole-succinocarboxamide synthase; PDBTitle: crystal structure of phosphoribosylaminoimidazole-succinocarboxamide2 synthase from clostridium perfringens 8 c3dukD_ 26.9 13 PDB header:unknown function Chain: D: PDB Molecule:ntf2-like protein of unknown function; PDBTitle: crystal structure of a ntf2-like protein of unknown function2 (mfla_0564) from methylobacillus flagellatus kt at 2.200 a resolution 9 c3noyA_ 18.6 18 PDB header:oxidoreductase Chain: A: PDB Molecule:4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; PDBTitle: crystal structure of ispg (gcpe) 10 d2rgqa1 18.2 19 Fold:Cystatin-like Superfamily:NTF2-like Family:Rv3472-like 11 d1whra_ 16.5 30 Fold:IF3-like Superfamily:R3H domain Family:R3H domain 12 c3fkaD_ 14.7 12 PDB header:unknown function Chain: D: PDB Molecule:uncharacterized ntf-2 like protein; PDBTitle: crystal structure of a ntf-2 like protein of unknown function2 (spo1084) from silicibacter pomeroyi dss-3 at 1.69 a resolution 13 d1x4ta1 12.5 29 Fold:Long alpha-hairpin Superfamily:ISY1 domain-like Family:ISY1 N-terminal domain-like 14 d1h8ba_ 12.3 24 Fold:EF Hand-like Superfamily:EF-hand Family:EF-hand modules in multidomain proteins 15 c2plyB_ 11.2 14 PDB header:translation/rna Chain: B: PDB Molecule:selenocysteine-specific elongation factor; PDBTitle: structure of the mrna binding fragment of elongation factor2 selb in complex with secis rna. 16 d1zk8a2 8.6 4 Fold:Tetracyclin repressor-like, C-terminal domain Superfamily:Tetracyclin repressor-like, C-terminal domain Family:Tetracyclin repressor-like, C-terminal domain 17 d1k9vf_ 7.4 21 Fold:Flavodoxin-like Superfamily:Class I glutamine amidotransferase-like Family:Class I glutamine amidotransferases (GAT) 18 d1ofcx1 6.6 29 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain 19 d1xlya_ 6.5 4 Fold:RNA-binding protein She2p Superfamily:RNA-binding protein She2p Family:RNA-binding protein She2p 20 d1ogyb_ 6.5 28 Fold:Multiheme cytochromes Superfamily:Multiheme cytochromes Family:Di-heme elbow motif 21 c2jpmA_ not modelled 6.0 19 PDB header:antimicrobial protein Chain: A: PDB Molecule:bacteriocin lactococcin-g subunit beta; PDBTitle: lactococcin g-b in tfe 22 c1y32A_ not modelled 5.8 71 PDB header:unknown function Chain: A: PDB Molecule:humanin; PDBTitle: nmr structure of humanin in 30% tfe solution 23 d1o98a1 not modelled 5.6 20 Fold:2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain Superfamily:2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain Family:2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain 24 d1ycya1 not modelled 5.6 47 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:PF1955-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