Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	K	I	A	L	I	L	A	M	L	L	I	P	C	V	S	F	A	G	L	L	G	S	S	S	S	T	T	P	V	S	K	E	Y	K	Q	Q	L	M	G	S	P	V	Y	I	Q	I	F	K	E	E	R	T	L	D	L	Y	V	K
Secondary structure
SS confidence
Disorder		?	?	?																?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		M	G	E	Q	Y	Q	L	L	D	S	Y	K	I	C	K	Y	S	G	G	L	G	P	K	Q	R	Q	G	D	F	K	S	P	E	G	F	Y	S	V	Q	R	N	Q	L	K	P	D	S	R	Y	Y	K	A	I	N	I	G	F	P	N	A
Secondary structure
SS confidence
Disorder																								?	?	?	?															?				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		Y	D	R	A	H	G	Y	E	G	K	Y	L	M	I	H	G	D	C	V	S	I	G	C	Y	A	M	T	N	Q	G	I	D	E	I	F	Q	F	V	T	G	A	L	V	F	G	Q	P	S	V	Q	V	S	I	Y	P	F	R	M	T	D
Secondary structure
SS confidence
Disorder							?		?	?																																		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		A	N	M	K	R	H	K	Y	S	N	F	K	D	F	W	E	Q	L	K	P	G	Y	D	Y	F	E	Q	T	R	K	P	P	T	V	S	V	V	N	G	R	Y	V	V	S	K	P	L	S	H	E	V	V	Q	P	Q	L	A	S	N	Y
Secondary structure
SS confidence
Disorder				?	?	?	?		?																																					?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.
Sequence		T	L	P	E	A	K
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 1zat chain A domain 1 Region: 45 - 174 Aligned: 108 Modelled: 130 Confidence: 99.6% Identity: 19% Fold: L,D-transpeptidase catalytic domain-like Superfamily: L,D-transpeptidase catalytic domain-like Family: L,D-transpeptidase catalytic domain-like Phyre2 PDB 1y7m chain A domain 1 Region: 43 - 158 Aligned: 91 Modelled: 107 Confidence: 99.5% Identity: 23% Fold: L,D-transpeptidase catalytic domain-like Superfamily: L,D-transpeptidase catalytic domain-like Family: L,D-transpeptidase catalytic domain-like Phyre2 PDB 1y7m chain B Region: 42 - 158 Aligned: 92 Modelled: 108 Confidence: 99.4% Identity: 25% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein bsu14040; PDBTitle: crystal structure of the b. subtilis ykud protein at 2 a2 resolution Phyre2 PDB 2hkl chain B Region: 45 - 158 Aligned: 99 Modelled: 114 Confidence: 99.3% Identity: 18% PDB header:transferase Chain: B: PDB Molecule:l,d-transpeptidase; PDBTitle: crystal structure of enterococcus faecium l,d-2 transpeptidase c442s mutant Phyre2 PDB 2q3l chain A domain 1 Region: 146 - 215 Aligned: 62 Modelled: 70 Confidence: 51.6% Identity: 15% Fold: SpoIIaa-like Superfamily: SpoIIaa-like Family: Sfri0576-like Phyre2 PDB 2khf chain A Region: 191 - 202 Aligned: 12 Modelled: 12 Confidence: 37.9% Identity: 42% PDB header:antimicrobial protein Chain: A: PDB Molecule:plnj; PDBTitle: plantaricin j in dpc-micelles Phyre2 PDB 3qi7 chain A Region: 155 - 189 Aligned: 35 Modelled: 34 Confidence: 32.1% Identity: 9% PDB header:transcription Chain: A: PDB Molecule:putative transcriptional regulator; PDBTitle: crystal structure of a putative transcriptional regulator2 (yp_001089212.1) from clostridium difficile 630 at 1.86 a resolution Phyre2 PDB 1z8g chain A domain 2 Region: 46 - 68 Aligned: 23 Modelled: 23 Confidence: 29.7% Identity: 22% Fold: SRCR-like Superfamily: SRCR-like Family: Hepsin, N-terminal domain Phyre2 PDB 2khg chain A Region: 191 - 209 Aligned: 19 Modelled: 19 Confidence: 29.5% Identity: 37% PDB header:antimicrobial protein Chain: A: PDB Molecule:plnj; PDBTitle: plantaricin j in tfe Phyre2 PDB 3p3d chain A Region: 113 - 154 Aligned: 40 Modelled: 40 Confidence: 26.7% Identity: 15% PDB header:nuclear protein Chain: A: PDB Molecule:nucleoporin 53; PDBTitle: crystal structure of the nup53 rrm domain from pichia guilliermondii Phyre2 PDB 1q5m chain A Region: 142 - 170 Aligned: 29 Modelled: 29 Confidence: 22.6% Identity: 17% Fold: TIM beta/alpha-barrel Superfamily: NAD(P)-linked oxidoreductase Family: Aldo-keto reductases (NADP) Phyre2 PDB 1j96 chain A Region: 142 - 170 Aligned: 29 Modelled: 29 Confidence: 19.8% Identity: 21% Fold: TIM beta/alpha-barrel Superfamily: NAD(P)-linked oxidoreductase Family: Aldo-keto reductases (NADP) Phyre2 PDB 2ook chain A domain 1 Region: 146 - 215 Aligned: 62 Modelled: 70 Confidence: 15.4% Identity: 19% Fold: SpoIIaa-like Superfamily: SpoIIaa-like Family: Sfri0576-like Phyre2 PDB 1s1p chain A Region: 142 - 170 Aligned: 29 Modelled: 29 Confidence: 14.9% Identity: 17% Fold: TIM beta/alpha-barrel Superfamily: NAD(P)-linked oxidoreductase Family: Aldo-keto reductases (NADP) Phyre2 PDB 3l5a chain A Region: 143 - 173 Aligned: 31 Modelled: 31 Confidence: 13.8% Identity: 32% PDB header:oxidoreductase Chain: A: PDB Molecule:nadh/flavin oxidoreductase/nadh oxidase; PDBTitle: crystal structure of a probable nadh-dependent flavin oxidoreductase2 from staphylococcus aureus Phyre2 PDB 1vyr chain A Region: 143 - 173 Aligned: 31 Modelled: 31 Confidence: 13.7% Identity: 26% Fold: TIM beta/alpha-barrel Superfamily: FMN-linked oxidoreductases Family: FMN-linked oxidoreductases Phyre2 PDB 2l4d chain A Region: 146 - 175 Aligned: 30 Modelled: 30 Confidence: 13.6% Identity: 10% PDB header:electron transport Chain: A: PDB Molecule:sco1/senc family protein/cytochrome c; PDBTitle: cytochrome c domain of pp3183 protein from pseudomonas putida Phyre2 PDB 1hng chain A domain 1 Region: 39 - 99 Aligned: 57 Modelled: 61 Confidence: 13.2% Identity: 12% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 PDB 1d8j chain A Region: 206 - 226 Aligned: 21 Modelled: 21 Confidence: 11.2% Identity: 24% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: The central core domain of TFIIE beta Phyre2 PDB 3o12 chain A Region: 38 - 78 Aligned: 41 Modelled: 41 Confidence: 10.8% Identity: 7% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yjl217w; PDBTitle: the crystal structure of a functionally unknown protein from2 saccharomyces cerevisiae. Phyre2 1 d1zata1 2 d1y7ma1 3 c1y7mB_ 4 c2hklB_ 5 d2q3la1 6 c2khfA_ 7 c3qi7A_ 8 d1z8ga2 9 c2khgA_ 10 c3p3dA_ 11 d1q5ma_ 12 d1j96a_ 13 d2ooka1 14 d1s1pa_ 15 c3l5aA_ 16 d1vyra_ 17 c2l4dA_ 18 d1hnga1 19 d1d8ja_ 20 c3o12A_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58

Detailed template information

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

1 d1zata1 99.6 19 Fold:L,D-transpeptidase catalytic domain-like Superfamily:L,D-transpeptidase catalytic domain-like Family:L,D-transpeptidase catalytic domain-like 2 d1y7ma1 99.5 23 Fold:L,D-transpeptidase catalytic domain-like Superfamily:L,D-transpeptidase catalytic domain-like Family:L,D-transpeptidase catalytic domain-like 3 c1y7mB_ 99.4 25 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein bsu14040; PDBTitle: crystal structure of the b. subtilis ykud protein at 2 a2 resolution 4 c2hklB_ 99.3 18 PDB header:transferase Chain: B: PDB Molecule:l,d-transpeptidase; PDBTitle: crystal structure of enterococcus faecium l,d-2 transpeptidase c442s mutant 5 d2q3la1 51.6 15 Fold:SpoIIaa-like Superfamily:SpoIIaa-like Family:Sfri0576-like 6 c2khfA_ 37.9 42 PDB header:antimicrobial protein Chain: A: PDB Molecule:plnj; PDBTitle: plantaricin j in dpc-micelles 7 c3qi7A_ 32.1 9 PDB header:transcription Chain: A: PDB Molecule:putative transcriptional regulator; PDBTitle: crystal structure of a putative transcriptional regulator2 (yp_001089212.1) from clostridium difficile 630 at 1.86 a resolution 8 d1z8ga2 29.7 22 Fold:SRCR-like Superfamily:SRCR-like Family:Hepsin, N-terminal domain 9 c2khgA_ 29.5 37 PDB header:antimicrobial protein Chain: A: PDB Molecule:plnj; PDBTitle: plantaricin j in tfe 10 c3p3dA_ 26.7 15 PDB header:nuclear protein Chain: A: PDB Molecule:nucleoporin 53; PDBTitle: crystal structure of the nup53 rrm domain from pichia guilliermondii 11 d1q5ma_ 22.6 17 Fold:TIM beta/alpha-barrel Superfamily:NAD(P)-linked oxidoreductase Family:Aldo-keto reductases (NADP) 12 d1j96a_ 19.8 21 Fold:TIM beta/alpha-barrel Superfamily:NAD(P)-linked oxidoreductase Family:Aldo-keto reductases (NADP) 13 d2ooka1 15.4 19 Fold:SpoIIaa-like Superfamily:SpoIIaa-like Family:Sfri0576-like 14 d1s1pa_ 14.9 17 Fold:TIM beta/alpha-barrel Superfamily:NAD(P)-linked oxidoreductase Family:Aldo-keto reductases (NADP) 15 c3l5aA_ 13.8 32 PDB header:oxidoreductase Chain: A: PDB Molecule:nadh/flavin oxidoreductase/nadh oxidase; PDBTitle: crystal structure of a probable nadh-dependent flavin oxidoreductase2 from staphylococcus aureus 16 d1vyra_ 13.7 26 Fold:TIM beta/alpha-barrel Superfamily:FMN-linked oxidoreductases Family:FMN-linked oxidoreductases 17 c2l4dA_ 13.6 10 PDB header:electron transport Chain: A: PDB Molecule:sco1/senc family protein/cytochrome c; PDBTitle: cytochrome c domain of pp3183 protein from pseudomonas putida 18 d1hnga1 13.2 12 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 19 d1d8ja_ 11.2 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:The central core domain of TFIIE beta 20 c3o12A_ 10.8 7 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yjl217w; PDBTitle: the crystal structure of a functionally unknown protein from2 saccharomyces cerevisiae. 21 c2zkr6_ not modelled 10.3 15 PDB header:ribosomal protein/rna Chain: 6: PDB Molecule:60s ribosomal protein l30e; 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 22 d2vzsa5 not modelled 10.0 20 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:beta-glycanases 23 c3euhF_ not modelled 10.0 33 PDB header:cell cycle Chain: F: PDB Molecule:muke; PDBTitle: crystal structure of the muke-mukf complex 24 c1ta9A_ not modelled 9.8 9 PDB header:oxidoreductase Chain: A: PDB Molecule:glycerol dehydrogenase; PDBTitle: crystal structure of glycerol dehydrogenase from schizosaccharomyces2 pombe 25 d1afsa_ not modelled 9.5 17 Fold:TIM beta/alpha-barrel Superfamily:NAD(P)-linked oxidoreductase Family:Aldo-keto reductases (NADP) 26 c2vd9A_ not modelled 9.2 13 PDB header:isomerase Chain: A: PDB Molecule:alanine racemase; PDBTitle: the crystal structure of alanine racemase from bacillus2 anthracis (ba0252) with bound l-ala-p 27 c3cpqB_ not modelled 9.1 16 PDB header:ribosomal protein Chain: B: PDB Molecule:50s ribosomal protein l30e; PDBTitle: crystal structure of l30e a ribosomal protein from2 methanocaldococcus jannaschii dsm2661 (mj1044) 28 c3canA_ not modelled 9.1 8 PDB header:lyase activator Chain: A: PDB Molecule:pyruvate-formate lyase-activating enzyme; PDBTitle: crystal structure of a domain of pyruvate-formate lyase-activating2 enzyme from bacteroides vulgatus atcc 8482 29 d1q2ya_ not modelled 8.2 17 Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:N-acetyl transferase, NAT 30 c1vliA_ not modelled 8.0 11 PDB header:biosynthetic protein Chain: A: PDB Molecule:spore coat polysaccharide biosynthesis protein spse; PDBTitle: crystal structure of spore coat polysaccharide biosynthesis protein2 spse (bsu37870) from bacillus subtilis at 2.38 a resolution 31 c3l7xA_ not modelled 7.6 26 PDB header:cell cycle Chain: A: PDB Molecule:putative hit-like protein involved in cell-cycle PDBTitle: the crystal structure of smu.412c from streptococcus mutans ua159 32 c2bgsA_ not modelled 7.4 19 PDB header:oxidoreductase Chain: A: PDB Molecule:aldose reductase; PDBTitle: holo aldose reductase from barley 33 d1vaza_ not modelled 7.4 18 Fold:NSFL1 (p97 ATPase) cofactor p47, SEP domain Superfamily:NSFL1 (p97 ATPase) cofactor p47, SEP domain Family:NSFL1 (p97 ATPase) cofactor p47, SEP domain 34 d1f61a_ not modelled 7.2 44 Fold:TIM beta/alpha-barrel Superfamily:Phosphoenolpyruvate/pyruvate domain Family:Phosphoenolpyruvate mutase/Isocitrate lyase-like 35 d1uera1 not modelled 7.2 38 Fold:Long alpha-hairpin Superfamily:Fe,Mn superoxide dismutase (SOD), N-terminal domain Family:Fe,Mn superoxide dismutase (SOD), N-terminal domain 36 d1dqua_ not modelled 7.0 36 Fold:TIM beta/alpha-barrel Superfamily:Phosphoenolpyruvate/pyruvate domain Family:Phosphoenolpyruvate mutase/Isocitrate lyase-like 37 c3up8B_ not modelled 6.8 26 PDB header:oxidoreductase Chain: B: PDB Molecule:putative 2,5-diketo-d-gluconic acid reductase b; PDBTitle: crystal structure of a putative 2,5-diketo-d-gluconic acid reductase b 38 c1x4rA_ not modelled 6.6 17 PDB header:apoptosis Chain: A: PDB Molecule:parp14 protein; PDBTitle: solution structure of wwe domain in parp14 protein 39 c1zr6A_ not modelled 6.6 14 PDB header:oxidoreductase Chain: A: PDB Molecule:glucooligosaccharide oxidase; PDBTitle: the crystal structure of an acremonium strictum glucooligosaccharide2 oxidase reveals a novel flavinylation 40 d1frba_ not modelled 6.5 15 Fold:TIM beta/alpha-barrel Superfamily:NAD(P)-linked oxidoreductase Family:Aldo-keto reductases (NADP) 41 d1igwa_ not modelled 6.5 27 Fold:TIM beta/alpha-barrel Superfamily:Phosphoenolpyruvate/pyruvate domain Family:Phosphoenolpyruvate mutase/Isocitrate lyase-like 42 c2gq8A_ not modelled 6.4 23 PDB header:oxidoreductase Chain: A: PDB Molecule:oxidoreductase, fmn-binding; PDBTitle: structure of sye1, an oye homologue from s. ondeidensis, in complex2 with p-hydroxyacetophenone 43 c1ynpA_ not modelled 6.4 16 PDB header:oxidoreductase Chain: A: PDB Molecule:oxidoreductase; PDBTitle: aldo-keto reductase akr11c1 from bacillus halodurans (apo form) 44 c1wveB_ not modelled 6.2 5 PDB header:oxidoreductase Chain: B: PDB Molecule:4-cresol dehydrogenase [hydroxylating] PDBTitle: p-cresol methylhydroxylase: alteration of the structure of2 the flavoprotein subunit upon its binding to the3 cytochrome subunit 45 c3f7jB_ not modelled 6.1 29 PDB header:oxidoreductase Chain: B: PDB Molecule:yvgn protein; PDBTitle: b.subtilis yvgn 46 c3b3dA_ not modelled 6.0 30 PDB header:oxidoreductase Chain: A: PDB Molecule:putative morphine dehydrogenase; PDBTitle: b.subtilis ytbe 47 c2vxdA_ not modelled 5.8 35 PDB header:nuclear protein Chain: A: PDB Molecule:nucleophosmin; PDBTitle: the structure of the c-terminal domain of nucleophosmin 48 d2cb5a_ not modelled 5.8 23 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Papain-like 49 c3e5bB_ not modelled 5.7 56 PDB header:lyase Chain: B: PDB Molecule:isocitrate lyase; PDBTitle: 2.4 a crystal structure of isocitrate lyase from brucella2 melitensis 50 c3h7uA_ not modelled 5.6 15 PDB header:oxidoreductase Chain: A: PDB Molecule:aldo-keto reductase; PDBTitle: crystal structure of the plant stress-response enzyme akr4c9 51 d2gdqa1 not modelled 5.6 26 Fold:TIM beta/alpha-barrel Superfamily:Enolase C-terminal domain-like Family:D-glucarate dehydratase-like 52 d1qnra_ not modelled 5.5 15 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:beta-glycanases 53 c3o0kB_ not modelled 5.4 31 PDB header:oxidoreductase Chain: B: PDB Molecule:aldo/keto reductase; PDBTitle: crystal structure of aldo/keto reductase from brucella melitensis 54 c1o98A_ not modelled 5.3 9 PDB header:isomerase Chain: A: PDB Molecule:2,3-bisphosphoglycerate-independent PDBTitle: 1.4a crystal structure of phosphoglycerate mutase from2 bacillus stearothermophilus complexed with3 2-phosphoglycerate 55 c2dsjA_ not modelled 5.3 17 PDB header:transferase Chain: A: PDB Molecule:pyrimidine-nucleoside (thymidine) phosphorylase; PDBTitle: crystal structure of project id tt0128 from thermus thermophilus hb8 56 c2vldA_ not modelled 5.2 17 PDB header:hydrolase Chain: A: PDB Molecule:upf0286 protein pyrab01260; PDBTitle: crystal structure of a repair endonuclease from pyrococcus2 abyssi 57 d1cbya_ not modelled 5.1 23 Fold:CytB endotoxin-like Superfamily:CytB endotoxin-like Family:CytB endotoxin-like 58 c1cbyA_ not modelled 5.1 23 PDB header:toxin Chain: A: PDB Molecule:delta-endotoxin cytb; PDBTitle: delta-endotoxin

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

---

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