Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	D	E	Y	S	P	K	R	H	D	I	A	Q	L	K	F	L	C	E	T	L	Y	H	D	C	L	A	N	L	E	E	S	N	H	G	W	V	N	D	P	T	S	A	I	N	L	Q	L	N	E	L	I	E	H	I	A	T	F	A	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																										?										?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		N	Y	K	I	K	Y	N	E	D	N	K	L	I	E	Q	I	D	E	Y	L	D	D	T	F	M	L	F	S	S	Y	G	I	N	M	Q	D	L	Q	K	W	R	K	S	G	N	R	L	F	R	C	F	V	N	A	T	K	E	N	P	A
Secondary structure
SS confidence
Disorder																																												?													?	?	?	?	?
Disorder confidence
		.	.	.	.
Sequence		S	L	S	C
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 1aug chain A Region: 16 - 60 Aligned: 45 Modelled: 45 Confidence: 31.6% Identity: 18% Fold: Phosphorylase/hydrolase-like Superfamily: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) Family: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) Phyre2 PDB 3giu chain A Region: 16 - 63 Aligned: 48 Modelled: 48 Confidence: 29.4% Identity: 13% PDB header:hydrolase Chain: A: PDB Molecule:pyrrolidone-carboxylate peptidase; PDBTitle: 1.25 angstrom crystal structure of pyrrolidone-carboxylate peptidase2 (pcp) from staphylococcus aureus Phyre2 PDB 1iu8 chain A Region: 16 - 60 Aligned: 45 Modelled: 45 Confidence: 21.4% Identity: 16% Fold: Phosphorylase/hydrolase-like Superfamily: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) Family: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) Phyre2 PDB 2ve8 chain A domain 1 Region: 61 - 78 Aligned: 18 Modelled: 18 Confidence: 21.4% Identity: 33% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: FtsK C-terminal domain-like Phyre2 PDB 2j5p chain A domain 1 Region: 61 - 78 Aligned: 18 Modelled: 18 Confidence: 19.0% Identity: 33% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: FtsK C-terminal domain-like Phyre2 PDB 2btv chain A Region: 78 - 106 Aligned: 29 Modelled: 29 Confidence: 14.4% Identity: 24% Fold: Reovirus inner layer core protein p3 Superfamily: Reovirus inner layer core protein p3 Family: Orbivirus core Phyre2 PDB 2btv chain B Region: 78 - 106 Aligned: 29 Modelled: 29 Confidence: 13.9% Identity: 24% PDB header:virus Chain: B: PDB Molecule:protein (vp3 core protein); PDBTitle: atomic model for bluetongue virus (btv) core Phyre2 PDB 1pwk chain A Region: 50 - 84 Aligned: 35 Modelled: 35 Confidence: 10.9% Identity: 17% Fold: DLC Superfamily: DLC Family: DLC Phyre2 PDB 1a2z chain A Region: 16 - 59 Aligned: 44 Modelled: 44 Confidence: 9.9% Identity: 18% Fold: Phosphorylase/hydrolase-like Superfamily: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) Family: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) Phyre2 PDB 1n3k chain A Region: 10 - 18 Aligned: 9 Modelled: 9 Confidence: 9.8% Identity: 56% Fold: DEATH domain Superfamily: DEATH domain Family: DEATH effector domain, DED Phyre2 PDB 1cmi chain A Region: 50 - 84 Aligned: 35 Modelled: 35 Confidence: 9.2% Identity: 20% Fold: DLC Superfamily: DLC Family: DLC Phyre2 PDB 2bbr chain A Region: 10 - 18 Aligned: 9 Modelled: 9 Confidence: 8.2% Identity: 44% PDB header:viral protein Chain: A: PDB Molecule:viral casp8 and fadd-like apoptosis regulator; PDBTitle: crystal structure of mc159 reveals molecular mechanism of2 disc assembly and vflip inhibition Phyre2 PDB 2ebj chain B Region: 16 - 59 Aligned: 44 Modelled: 44 Confidence: 8.1% Identity: 18% PDB header:hydrolase Chain: B: PDB Molecule:pyrrolidone carboxyl peptidase; PDBTitle: crystal structure of pyrrolidone carboxyl peptidase from thermus2 thermophilus Phyre2 PDB 1k0m chain A domain 2 Region: 74 - 84 Aligned: 11 Modelled: 11 Confidence: 7.4% Identity: 27% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: Glutathione S-transferase (GST), N-terminal domain Phyre2 PDB 3e2b chain A domain 1 Region: 50 - 84 Aligned: 35 Modelled: 35 Confidence: 7.4% Identity: 20% Fold: DLC Superfamily: DLC Family: DLC Phyre2 PDB 1iof chain A Region: 16 - 59 Aligned: 44 Modelled: 44 Confidence: 7.3% Identity: 20% Fold: Phosphorylase/hydrolase-like Superfamily: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) Family: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) Phyre2 PDB 3t5q chain A Region: 47 - 75 Aligned: 29 Modelled: 29 Confidence: 6.1% Identity: 24% PDB header:viral protein/rna Chain: A: PDB Molecule:nucleoprotein; PDBTitle: 3a structure of lassa virus nucleoprotein in complex with ssrna Phyre2 PDB 1ogl chain A Region: 11 - 81 Aligned: 66 Modelled: 71 Confidence: 6.1% Identity: 18% Fold: all-alpha NTP pyrophosphatases Superfamily: all-alpha NTP pyrophosphatases Family: Type II deoxyuridine triphosphatase Phyre2 PDB 1pi1 chain A Region: 105 - 114 Aligned: 10 Modelled: 10 Confidence: 6.0% Identity: 40% Fold: Bromodomain-like Superfamily: Mob1/phocein Family: Mob1/phocein Phyre2 PDB 1uyp chain A domain 2 Region: 31 - 44 Aligned: 14 Modelled: 14 Confidence: 5.9% Identity: 43% Fold: 5-bladed beta-propeller Superfamily: Arabinanase/levansucrase/invertase Family: Glycosyl hydrolases family 32 N-terminal domain Phyre2 1 d1auga_ 2 c3giuA_ 3 d1iu8a_ 4 d2ve8a1 5 d2j5pa1 6 d2btva_ 7 c2btvB_ 8 d1pwka_ 9 d1a2za_ 10 d1n3ka_ 11 d1cmia_ 12 c2bbrA_ 13 c2ebjB_ 14 d1k0ma2 15 d3e2ba1 16 d1iofa_ 17 c3t5qA_ 18 d1ogla_ 19 d1pi1a_ 20 d1uypa2 21 22 23 24 25 26 27 28 29 30

Detailed template information

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

1 d1auga_ 31.6 18 Fold:Phosphorylase/hydrolase-like Superfamily:Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) Family:Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) 2 c3giuA_ 29.4 13 PDB header:hydrolase Chain: A: PDB Molecule:pyrrolidone-carboxylate peptidase; PDBTitle: 1.25 angstrom crystal structure of pyrrolidone-carboxylate peptidase2 (pcp) from staphylococcus aureus 3 d1iu8a_ 21.4 16 Fold:Phosphorylase/hydrolase-like Superfamily:Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) Family:Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) 4 d2ve8a1 21.4 33 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:FtsK C-terminal domain-like 5 d2j5pa1 19.0 33 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:FtsK C-terminal domain-like 6 d2btva_ 14.4 24 Fold:Reovirus inner layer core protein p3 Superfamily:Reovirus inner layer core protein p3 Family:Orbivirus core 7 c2btvB_ 13.9 24 PDB header:virus Chain: B: PDB Molecule:protein (vp3 core protein); PDBTitle: atomic model for bluetongue virus (btv) core 8 d1pwka_ 10.9 17 Fold:DLC Superfamily:DLC Family:DLC 9 d1a2za_ 9.9 18 Fold:Phosphorylase/hydrolase-like Superfamily:Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) Family:Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) 10 d1n3ka_ 9.8 56 Fold:DEATH domain Superfamily:DEATH domain Family:DEATH effector domain, DED 11 d1cmia_ 9.2 20 Fold:DLC Superfamily:DLC Family:DLC 12 c2bbrA_ 8.2 44 PDB header:viral protein Chain: A: PDB Molecule:viral casp8 and fadd-like apoptosis regulator; PDBTitle: crystal structure of mc159 reveals molecular mechanism of2 disc assembly and vflip inhibition 13 c2ebjB_ 8.1 18 PDB header:hydrolase Chain: B: PDB Molecule:pyrrolidone carboxyl peptidase; PDBTitle: crystal structure of pyrrolidone carboxyl peptidase from thermus2 thermophilus 14 d1k0ma2 7.4 27 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione S-transferase (GST), N-terminal domain 15 d3e2ba1 7.4 20 Fold:DLC Superfamily:DLC Family:DLC 16 d1iofa_ 7.3 20 Fold:Phosphorylase/hydrolase-like Superfamily:Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) Family:Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) 17 c3t5qA_ 6.1 24 PDB header:viral protein/rna Chain: A: PDB Molecule:nucleoprotein; PDBTitle: 3a structure of lassa virus nucleoprotein in complex with ssrna 18 d1ogla_ 6.1 18 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:Type II deoxyuridine triphosphatase 19 d1pi1a_ 6.0 40 Fold:Bromodomain-like Superfamily:Mob1/phocein Family:Mob1/phocein 20 d1uypa2 5.9 43 Fold:5-bladed beta-propeller Superfamily:Arabinanase/levansucrase/invertase Family:Glycosyl hydrolases family 32 N-terminal domain 21 d1qf8a_ not modelled 5.9 33 Fold:Rubredoxin-like Superfamily:Casein kinase II beta subunit Family:Casein kinase II beta subunit 22 c3oakC_ not modelled 5.9 13 PDB header:transcription Chain: C: PDB Molecule:transcription elongation factor spt6; PDBTitle: crystal structure of a spn1 (iws1)-spt6 complex 23 d1bg4a_ not modelled 5.8 23 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:beta-glycanases 24 d2gf5a2 not modelled 5.8 44 Fold:DEATH domain Superfamily:DEATH domain Family:DEATH effector domain, DED 25 c2bbzC_ not modelled 5.7 44 PDB header:viral protein Chain: C: PDB Molecule:viral casp8 and fadd-like apoptosis regulator; PDBTitle: crystal structure of mc159 reveals molecular mechanism of2 disc assembly and vflip inhibition 26 c3mx2A_ not modelled 5.5 22 PDB header:nuclear protein Chain: A: PDB Molecule:nucleoprotein; PDBTitle: lassa fever virus nucleoprotein complexed with dttp 27 c2xi1A_ not modelled 5.4 36 PDB header:viral protein Chain: A: PDB Molecule:nef; PDBTitle: crystal structure of the hiv-1 nef sequenced from a patient's sample 28 c3kf5A_ not modelled 5.4 71 PDB header:hydrolase Chain: A: PDB Molecule:invertase; PDBTitle: structure of invertase from schwanniomyces occidentalis 29 d1efnb_ not modelled 5.3 45 Fold:Regulatory factor Nef Superfamily:Regulatory factor Nef Family:Regulatory factor Nef 30 c3ik5A_ not modelled 5.2 45 PDB header:viral protein/signaling protein Chain: A: PDB Molecule:protein nef; PDBTitle: sivmac239 nef in complex with tcr zeta itam 1 polypeptide2 (a63-r80)

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