Secondary structure and disorder prediction

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Sequence		M	R	T	I	S	Y	S	E	A	R	Q	N	L	S	A	T	M	M	K	A	V	E	D	H	A	P	I	L	I	T	R	Q	N	G	E	A	C	V	L	M	S	L	E	E	Y	N	S	L	E	E	T	A	Y	L	L	R	S	P	A	N
Secondary structure
SS confidence
Disorder		?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.
Sequence		A	R	R	L	M	D	S	I	D	S	L	K	S	G	K	G	T	E	K	D	I	I	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 2a6q chain A domain 1 Region: 1 - 83 Aligned: 83 Modelled: 83 Confidence: 100.0% Identity: 100% Fold: YefM-like Superfamily: YefM-like Family: YefM-like Phyre2 PDB 3g5o chain A Region: 1 - 82 Aligned: 82 Modelled: 82 Confidence: 99.9% Identity: 27% PDB header:toxin/antitoxin Chain: A: PDB Molecule:uncharacterized protein rv2865; PDBTitle: the crystal structure of the toxin-antitoxin complex relbe2 (rv2865-2 2866) from mycobacterium tuberculosis Phyre2 PDB 2a6q chain B domain 1 Region: 1 - 55 Aligned: 55 Modelled: 55 Confidence: 99.8% Identity: 100% Fold: YefM-like Superfamily: YefM-like Family: YefM-like Phyre2 PDB 3hs2 chain H Region: 1 - 53 Aligned: 52 Modelled: 53 Confidence: 99.6% Identity: 29% PDB header:antitoxin Chain: H: PDB Molecule:prevent host death protein; PDBTitle: crystal structure of phd truncated to residue 57 in an orthorhombic2 space group Phyre2 PDB 3hry chain A Region: 1 - 50 Aligned: 49 Modelled: 50 Confidence: 99.5% Identity: 27% PDB header:antitoxin Chain: A: PDB Molecule:prevent host death protein; PDBTitle: crystal structure of phd in a trigonal space group and partially2 disordered Phyre2 PDB 2odk chain D Region: 1 - 51 Aligned: 50 Modelled: 50 Confidence: 99.2% Identity: 18% PDB header:structural genomics, unknown function Chain: D: PDB Molecule:hypothetical protein; PDBTitle: putative prevent-host-death protein from nitrosomonas europaea Phyre2 PDB 2odk chain A domain 1 Region: 1 - 51 Aligned: 50 Modelled: 50 Confidence: 99.1% Identity: 18% Fold: YefM-like Superfamily: YefM-like Family: YefM-like Phyre2 PDB 3k6q chain B Region: 1 - 51 Aligned: 49 Modelled: 50 Confidence: 95.4% Identity: 27% PDB header:ligand binding protein Chain: B: PDB Molecule:putative ligand binding protein; PDBTitle: crystal structure of an antitoxin part of a putative toxin/antitoxin2 system (swol_0700) from syntrophomonas wolfei subsp. wolfei at 1.80 a3 resolution Phyre2 PDB 1grj chain A domain 1 Region: 38 - 70 Aligned: 33 Modelled: 33 Confidence: 35.3% Identity: 21% Fold: Long alpha-hairpin Superfamily: GreA transcript cleavage protein, N-terminal domain Family: GreA transcript cleavage protein, N-terminal domain Phyre2 PDB 2iyf chain A Region: 34 - 79 Aligned: 46 Modelled: 46 Confidence: 30.5% Identity: 30% PDB header:transferase Chain: A: PDB Molecule:oleandomycin glycosyltransferase; PDBTitle: the crystal structure of macrolide glycosyltransferases: a2 blueprint for antibiotic engineering Phyre2 PDB 1n0e chain A Region: 7 - 52 Aligned: 36 Modelled: 46 Confidence: 27.2% Identity: 14% Fold: Double-split beta-barrel Superfamily: AbrB/MazE/MraZ-like Family: Hypothetical protein MraZ Phyre2 PDB 1ez4 chain A domain 2 Region: 26 - 73 Aligned: 45 Modelled: 48 Confidence: 27.0% Identity: 16% Fold: LDH C-terminal domain-like Superfamily: LDH C-terminal domain-like Family: Lactate & malate dehydrogenases, C-terminal domain Phyre2 PDB 1n0f chain F Region: 7 - 53 Aligned: 37 Modelled: 47 Confidence: 21.8% Identity: 14% PDB header:biosynthetic protein Chain: F: PDB Molecule:protein mraz; PDBTitle: crystal structure of a cell division and cell wall2 biosynthesis protein upf0040 from mycoplasma pneumoniae:3 indication of a novel fold with a possible new conserved4 sequence motif Phyre2 PDB 1pzg chain A domain 2 Region: 26 - 73 Aligned: 44 Modelled: 48 Confidence: 20.0% Identity: 23% Fold: LDH C-terminal domain-like Superfamily: LDH C-terminal domain-like Family: Lactate & malate dehydrogenases, C-terminal domain Phyre2 PDB 2p6p chain B Region: 26 - 76 Aligned: 51 Modelled: 51 Confidence: 18.5% Identity: 18% PDB header:transferase Chain: B: PDB Molecule:glycosyl transferase; PDBTitle: x-ray crystal structure of c-c bond-forming dtdp-d-olivose-transferase2 urdgt2 Phyre2 PDB 2iya chain B Region: 34 - 79 Aligned: 46 Modelled: 46 Confidence: 16.8% Identity: 15% PDB header:transferase Chain: B: PDB Molecule:oleandomycin glycosyltransferase; PDBTitle: the crystal structure of macrolide glycosyltransferases: a2 blueprint for antibiotic engineering Phyre2 PDB 1y0n chain A Region: 40 - 77 Aligned: 37 Modelled: 38 Confidence: 16.6% Identity: 19% Fold: YehU-like Superfamily: YehU-like Family: YehU-like Phyre2 PDB 3oth chain B Region: 14 - 79 Aligned: 65 Modelled: 66 Confidence: 15.2% Identity: 15% PDB header:transferase/antibiotic Chain: B: PDB Molecule:calg1; PDBTitle: crystal structure of calg1, calicheamicin glycostyltransferase, tdp2 and calicheamicin alpha3i bound form Phyre2 PDB 3ia7 chain A Region: 34 - 76 Aligned: 43 Modelled: 43 Confidence: 15.1% Identity: 16% PDB header:transferase Chain: A: PDB Molecule:calg4; PDBTitle: crystal structure of calg4, the calicheamicin glycosyltransferase Phyre2 PDB 2qzs chain A Region: 26 - 77 Aligned: 52 Modelled: 52 Confidence: 14.3% Identity: 12% PDB header:transferase Chain: A: PDB Molecule:glycogen synthase; PDBTitle: crystal structure of wild-type e.coli gs in complex with adp2 and glucose(wtgsb) Phyre2 1 d2a6qa1 2 c3g5oA_ 3 d2a6qb1 4 c3hs2H_ 5 c3hryA_ 6 c2odkD_ 7 d2odka1 8 c3k6qB_ 9 d1grja1 10 c2iyfA_ 11 d1n0ea_ 12 d1ez4a2 13 c1n0fF_ 14 d1pzga2 15 c2p6pB_ 16 c2iyaB_ 17 d1y0na_ 18 c3othB_ 19 c3ia7A_ 20 c2qzsA_ 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

Detailed template information

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

1 d2a6qa1 100.0 100 Fold:YefM-like Superfamily:YefM-like Family:YefM-like 2 c3g5oA_ 99.9 27 PDB header:toxin/antitoxin Chain: A: PDB Molecule:uncharacterized protein rv2865; PDBTitle: the crystal structure of the toxin-antitoxin complex relbe2 (rv2865-2 2866) from mycobacterium tuberculosis 3 d2a6qb1 99.8 100 Fold:YefM-like Superfamily:YefM-like Family:YefM-like 4 c3hs2H_ 99.6 29 PDB header:antitoxin Chain: H: PDB Molecule:prevent host death protein; PDBTitle: crystal structure of phd truncated to residue 57 in an orthorhombic2 space group 5 c3hryA_ 99.5 27 PDB header:antitoxin Chain: A: PDB Molecule:prevent host death protein; PDBTitle: crystal structure of phd in a trigonal space group and partially2 disordered 6 c2odkD_ 99.2 18 PDB header:structural genomics, unknown function Chain: D: PDB Molecule:hypothetical protein; PDBTitle: putative prevent-host-death protein from nitrosomonas europaea 7 d2odka1 99.1 18 Fold:YefM-like Superfamily:YefM-like Family:YefM-like 8 c3k6qB_ 95.4 27 PDB header:ligand binding protein Chain: B: PDB Molecule:putative ligand binding protein; PDBTitle: crystal structure of an antitoxin part of a putative toxin/antitoxin2 system (swol_0700) from syntrophomonas wolfei subsp. wolfei at 1.80 a3 resolution 9 d1grja1 35.3 21 Fold:Long alpha-hairpin Superfamily:GreA transcript cleavage protein, N-terminal domain Family:GreA transcript cleavage protein, N-terminal domain 10 c2iyfA_ 30.5 30 PDB header:transferase Chain: A: PDB Molecule:oleandomycin glycosyltransferase; PDBTitle: the crystal structure of macrolide glycosyltransferases: a2 blueprint for antibiotic engineering 11 d1n0ea_ 27.2 14 Fold:Double-split beta-barrel Superfamily:AbrB/MazE/MraZ-like Family:Hypothetical protein MraZ 12 d1ez4a2 27.0 16 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 13 c1n0fF_ 21.8 14 PDB header:biosynthetic protein Chain: F: PDB Molecule:protein mraz; PDBTitle: crystal structure of a cell division and cell wall2 biosynthesis protein upf0040 from mycoplasma pneumoniae:3 indication of a novel fold with a possible new conserved4 sequence motif 14 d1pzga2 20.0 23 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 15 c2p6pB_ 18.5 18 PDB header:transferase Chain: B: PDB Molecule:glycosyl transferase; PDBTitle: x-ray crystal structure of c-c bond-forming dtdp-d-olivose-transferase2 urdgt2 16 c2iyaB_ 16.8 15 PDB header:transferase Chain: B: PDB Molecule:oleandomycin glycosyltransferase; PDBTitle: the crystal structure of macrolide glycosyltransferases: a2 blueprint for antibiotic engineering 17 d1y0na_ 16.6 19 Fold:YehU-like Superfamily:YehU-like Family:YehU-like 18 c3othB_ 15.2 15 PDB header:transferase/antibiotic Chain: B: PDB Molecule:calg1; PDBTitle: crystal structure of calg1, calicheamicin glycostyltransferase, tdp2 and calicheamicin alpha3i bound form 19 c3ia7A_ 15.1 16 PDB header:transferase Chain: A: PDB Molecule:calg4; PDBTitle: crystal structure of calg4, the calicheamicin glycosyltransferase 20 c2qzsA_ 14.3 12 PDB header:transferase Chain: A: PDB Molecule:glycogen synthase; PDBTitle: crystal structure of wild-type e.coli gs in complex with adp2 and glucose(wtgsb) 21 d2iw1a1 not modelled 12.7 15 Fold:UDP-Glycosyltransferase/glycogen phosphorylase Superfamily:UDP-Glycosyltransferase/glycogen phosphorylase Family:Glycosyl transferases group 1 22 c3dzcA_ not modelled 12.6 23 PDB header:isomerase Chain: A: PDB Molecule:udp-n-acetylglucosamine 2-epimerase; PDBTitle: 2.35 angstrom resolution structure of wecb (vc0917), a udp-n-2 acetylglucosamine 2-epimerase from vibrio cholerae. 23 d1f6da_ not modelled 11.9 21 Fold:UDP-Glycosyltransferase/glycogen phosphorylase Superfamily:UDP-Glycosyltransferase/glycogen phosphorylase Family:UDP-N-acetylglucosamine 2-epimerase 24 d1g8ma1 not modelled 11.9 8 Fold:Methylglyoxal synthase-like Superfamily:Methylglyoxal synthase-like Family:Inosicase 25 c2p4vA_ not modelled 11.8 18 PDB header:transcription Chain: A: PDB Molecule:transcription elongation factor greb; PDBTitle: crystal structure of the transcript cleavage factor, greb2 at 2.6a resolution 26 c2jjmH_ not modelled 11.7 20 PDB header:transferase Chain: H: PDB Molecule:glycosyl transferase, group 1 family protein; PDBTitle: crystal structure of a family gt4 glycosyltransferase from2 bacillus anthracis orf ba1558. 27 c1grjA_ not modelled 11.6 21 PDB header:transcription regulation Chain: A: PDB Molecule:grea protein; PDBTitle: grea transcript cleavage factor from escherichia coli 28 d2vgna2 not modelled 11.6 20 Fold:Ribonuclease H-like motif Superfamily:Translational machinery components Family:ERF1/Dom34 middle domain-like 29 c3iaaB_ not modelled 11.3 15 PDB header:transferase Chain: B: PDB Molecule:calg2; PDBTitle: crystal structure of calg2, calicheamicin glycosyltransferase, tdp2 bound form 30 c1ez4B_ not modelled 10.6 16 PDB header:oxidoreductase Chain: B: PDB Molecule:lactate dehydrogenase; PDBTitle: crystal structure of non-allosteric l-lactate dehydrogenase2 from lactobacillus pentosus at 2.3 angstrom resolution 31 c3s29C_ not modelled 10.2 14 PDB header:transferase Chain: C: PDB Molecule:sucrose synthase 1; PDBTitle: the crystal structure of sucrose synthase-1 from arabidopsis thaliana2 and its functional implications. 32 c2r60A_ not modelled 9.0 17 PDB header:transferase Chain: A: PDB Molecule:glycosyl transferase, group 1; PDBTitle: structure of apo sucrose phosphate synthase (sps) of2 halothermothrix orenii 33 c3zvkG_ not modelled 9.0 3 PDB header:antitoxin/toxin/dna Chain: G: PDB Molecule:antitoxin of toxin-antitoxin system vapb; PDBTitle: crystal structure of vapbc2 from rickettsia felis bound to2 a dna fragment from their promoter 34 d1a5za2 not modelled 8.5 21 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 35 c3ot5D_ not modelled 8.3 16 PDB header:isomerase Chain: D: PDB Molecule:udp-n-acetylglucosamine 2-epimerase; PDBTitle: 2.2 angstrom resolution crystal structure of putative udp-n-2 acetylglucosamine 2-epimerase from listeria monocytogenes 36 d1o6ca_ not modelled 7.7 18 Fold:UDP-Glycosyltransferase/glycogen phosphorylase Superfamily:UDP-Glycosyltransferase/glycogen phosphorylase Family:UDP-N-acetylglucosamine 2-epimerase 37 d1mlda2 not modelled 7.6 19 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 38 d2cmda2 not modelled 7.5 19 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 39 c2fy2A_ not modelled 6.7 16 PDB header:transferase Chain: A: PDB Molecule:choline o-acetyltransferase; PDBTitle: structures of ligand bound human choline acetyltransferase2 provide insight into regulation of acetylcholine synthesis 40 c1zrxA_ not modelled 6.7 17 PDB header:antimicrobial protein, antibiotic Chain: A: PDB Molecule:stomoxyn; PDBTitle: solution structure of stomoxyn in h20/tfe 50% 41 c1smkD_ not modelled 6.5 19 PDB header:oxidoreductase Chain: D: PDB Molecule:malate dehydrogenase, glyoxysomal; PDBTitle: mature and translocatable forms of glyoxysomal malate2 dehydrogenase have different activities and stabilities3 but similar crystal structures 42 c1sevA_ not modelled 6.5 19 PDB header:oxidoreductase Chain: A: PDB Molecule:malate dehydrogenase, glyoxysomal precursor; PDBTitle: mature and translocatable forms of glyoxysomal malate2 dehydrogenase have different activities and stabilities3 but similar crystal structures 43 d1uxja2 not modelled 6.4 23 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 44 d1ghca_ not modelled 5.8 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Linker histone H1/H5 45 c1vjqB_ not modelled 5.7 14 PDB header:structural genomics, de novo protein Chain: B: PDB Molecule:designed protein; PDBTitle: designed protein based on backbone conformation of2 procarboxypeptidase-a (1aye) with sidechains chosen for maximal3 predicted stability. 46 d1gv0a2 not modelled 5.5 18 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 47 c2zqeA_ not modelled 5.3 14 PDB header:dna binding protein Chain: A: PDB Molecule:muts2 protein; PDBTitle: crystal structure of the smr domain of thermus thermophilus muts2 48 d1pkxa1 not modelled 5.1 13 Fold:Methylglyoxal synthase-like Superfamily:Methylglyoxal synthase-like Family:Inosicase

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