Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	D	D	L	T	A	Q	A	L	K	D	F	T	A	R	Y	C	D	A	W	H	E	E	H	K	S	W	P	L	S	E	E	L	Y	G	V	P	S	P	C	I	I	S	T	T	E	D	A	V	Y	W	Q	P	Q	P	F	T	G	E	Q
Secondary structure
SS confidence
Disorder		?	?	?																																										?	?									?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		N	V	N	A	V	E	R	A	F	D	I	V	I	Q	P	T	I	H	T	F	Y	T	T	Q	F	A	G	D	M	H	A	Q	F	G	D	I	K	L	T	L	L	Q	T	W	S	E	D	D	F	R	R	V	Q	E	N	L	I	G	H	L
Secondary structure
SS confidence
Disorder		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	T	Q	K	R	L	K	L	P	P	T	L	F	I	A	T	L	E	E	E	L	E	V	I	S	V	C	N	L	S	G	E	V	C	K	E	T	L	G	T	R	K	R	T	H	L	A	S	N	L	A	E	F	L	N	Q	L	K	P	L
Secondary structure
SS confidence
Disorder																																																										?	?	?	?
Disorder confidence
		.
Sequence		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 3ffv chain A Region: 1 - 181 Aligned: 181 Modelled: 181 Confidence: 100.0% Identity: 100% PDB header:protein binding Chain: A: PDB Molecule:protein syd; PDBTitle: crystal structure analysis of syd Phyre2 PDB 3d5p chain B Region: 51 - 177 Aligned: 116 Modelled: 127 Confidence: 97.7% Identity: 13% PDB header:gene regulation Chain: B: PDB Molecule:putative glucan synthesis regulator of smi1/knr4 family; PDBTitle: crystal structure of a putative glucan synthesis regulator of2 smi1/knr4 family (bf1740) from bacteroides fragilis nctc 9343 at 1.453 a resolution Phyre2 PDB 2prv chain A domain 1 Region: 62 - 177 Aligned: 104 Modelled: 112 Confidence: 97.1% Identity: 10% Fold: SMI1/KNR4-like Superfamily: SMI1/KNR4-like Family: SMI1/KNR4-like Phyre2 PDB 2icg chain A domain 1 Region: 51 - 177 Aligned: 121 Modelled: 127 Confidence: 96.2% Identity: 11% Fold: SMI1/KNR4-like Superfamily: SMI1/KNR4-like Family: SMI1/KNR4-like Phyre2 PDB 2pag chain A domain 1 Region: 53 - 176 Aligned: 110 Modelled: 124 Confidence: 83.0% Identity: 15% Fold: SMI1/KNR4-like Superfamily: SMI1/KNR4-like Family: SMI1/KNR4-like Phyre2 PDB 1hf9 chain B Region: 108 - 130 Aligned: 23 Modelled: 23 Confidence: 32.2% Identity: 26% PDB header:atpase inhibitor Chain: B: PDB Molecule:atpase inhibitor (mitochondrial); PDBTitle: c-terminal coiled-coil domain from bovine if1 Phyre2 PDB 1z5s chain D Region: 124 - 142 Aligned: 19 Modelled: 19 Confidence: 30.0% Identity: 53% PDB header:ligase Chain: D: PDB Molecule:ran-binding protein 2; PDBTitle: crystal structure of a complex between ubc9, sumo-1,2 rangap1 and nup358/ranbp2 Phyre2 PDB 3o27 chain B Region: 135 - 155 Aligned: 21 Modelled: 21 Confidence: 28.5% Identity: 5% PDB header:dna binding protein Chain: B: PDB Molecule:putative uncharacterized protein; PDBTitle: the crystal structure of c68 from the hybrid virus-plasmid pssvx Phyre2 PDB 2bv3 chain A domain 4 Region: 130 - 159 Aligned: 30 Modelled: 30 Confidence: 23.6% Identity: 17% Fold: Ferredoxin-like Superfamily: EF-G C-terminal domain-like Family: EF-G/eEF-2 domains III and V Phyre2 PDB 2wry chain A Region: 130 - 152 Aligned: 23 Modelled: 23 Confidence: 20.1% Identity: 22% PDB header:immune system Chain: A: PDB Molecule:interleukin-1beta; PDBTitle: crystal structure of chicken cytokine interleukin 1 beta Phyre2 PDB 1e2w chain A domain 2 Region: 137 - 162 Aligned: 26 Modelled: 26 Confidence: 19.3% Identity: 15% Fold: Barrel-sandwich hybrid Superfamily: Rudiment single hybrid motif Family: Cytochrome f, small domain Phyre2 PDB 1ci3 chain M domain 2 Region: 134 - 162 Aligned: 29 Modelled: 29 Confidence: 17.2% Identity: 10% Fold: Barrel-sandwich hybrid Superfamily: Rudiment single hybrid motif Family: Cytochrome f, small domain Phyre2 PDB 3kep chain A Region: 97 - 152 Aligned: 47 Modelled: 56 Confidence: 16.4% Identity: 17% PDB header:protein transport, rna binding protein Chain: A: PDB Molecule:nucleoporin nup145; PDBTitle: crystal structure of the autoproteolytic domain from the2 nuclear pore complex component nup145 from saccharomyces3 cerevisiae Phyre2 PDB 1q2l chain A Region: 53 - 177 Aligned: 119 Modelled: 125 Confidence: 14.3% Identity: 13% PDB header:hydrolase Chain: A: PDB Molecule:protease iii; PDBTitle: crystal structure of pitrilysin Phyre2 PDB 2jbu chain B Region: 62 - 177 Aligned: 110 Modelled: 116 Confidence: 13.9% Identity: 12% PDB header:hydrolase Chain: B: PDB Molecule:insulin-degrading enzyme; PDBTitle: crystal structure of human insulin degrading enzyme2 complexed with co-purified peptides. Phyre2 PDB 3dx5 chain A Region: 151 - 175 Aligned: 25 Modelled: 25 Confidence: 12.2% Identity: 16% PDB header:lyase Chain: A: PDB Molecule:uncharacterized protein asbf; PDBTitle: crystal structure of the probable 3-dhs dehydratase asbf involved in2 the petrobactin synthesis from bacillus anthracis Phyre2 PDB 2wk3 chain A Region: 62 - 177 Aligned: 110 Modelled: 116 Confidence: 11.7% Identity: 12% PDB header:hydrolase Chain: A: PDB Molecule:insulin degrading enzyme; PDBTitle: crystal structure of human insulin-degrading enzyme in2 complex with amyloid-beta (1-42) Phyre2 PDB 1j83 chain A Region: 132 - 150 Aligned: 16 Modelled: 19 Confidence: 11.5% Identity: 31% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: Family 17 carbohydrate binding module, CBM17 Phyre2 PDB 3lge chain F Region: 31 - 39 Aligned: 9 Modelled: 9 Confidence: 11.4% Identity: 11% PDB header:lyase/protein binding Chain: F: PDB Molecule:sorting nexin-9; PDBTitle: crystal structure of rabbit muscle aldolase-snx9 lc4 complex Phyre2 PDB 3lge chain G Region: 31 - 39 Aligned: 9 Modelled: 9 Confidence: 11.4% Identity: 11% PDB header:lyase/protein binding Chain: G: PDB Molecule:sorting nexin-9; PDBTitle: crystal structure of rabbit muscle aldolase-snx9 lc4 complex Phyre2 1 c3ffvA_ 2 c3d5pB_ 3 d2prva1 4 d2icga1 5 d2paga1 6 c1hf9B_ 7 c1z5sD_ 8 c3o27B_ 9 d2bv3a4 10 c2wryA_ 11 d1e2wa2 12 d1ci3m2 13 c3kepA_ 14 c1q2lA_ 15 c2jbuB_ 16 c3dx5A_ 17 c2wk3A_ 18 d1j83a_ 19 c3lgeF_ 20 c3lgeG_ 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 59

Detailed template information

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

1 c3ffvA_ 100.0 100 PDB header:protein binding Chain: A: PDB Molecule:protein syd; PDBTitle: crystal structure analysis of syd 2 c3d5pB_ 97.7 13 PDB header:gene regulation Chain: B: PDB Molecule:putative glucan synthesis regulator of smi1/knr4 family; PDBTitle: crystal structure of a putative glucan synthesis regulator of2 smi1/knr4 family (bf1740) from bacteroides fragilis nctc 9343 at 1.453 a resolution 3 d2prva1 97.1 10 Fold:SMI1/KNR4-like Superfamily:SMI1/KNR4-like Family:SMI1/KNR4-like 4 d2icga1 96.2 11 Fold:SMI1/KNR4-like Superfamily:SMI1/KNR4-like Family:SMI1/KNR4-like 5 d2paga1 83.0 15 Fold:SMI1/KNR4-like Superfamily:SMI1/KNR4-like Family:SMI1/KNR4-like 6 c1hf9B_ 32.2 26 PDB header:atpase inhibitor Chain: B: PDB Molecule:atpase inhibitor (mitochondrial); PDBTitle: c-terminal coiled-coil domain from bovine if1 7 c1z5sD_ 30.0 53 PDB header:ligase Chain: D: PDB Molecule:ran-binding protein 2; PDBTitle: crystal structure of a complex between ubc9, sumo-1,2 rangap1 and nup358/ranbp2 8 c3o27B_ 28.5 5 PDB header:dna binding protein Chain: B: PDB Molecule:putative uncharacterized protein; PDBTitle: the crystal structure of c68 from the hybrid virus-plasmid pssvx 9 d2bv3a4 23.6 17 Fold:Ferredoxin-like Superfamily:EF-G C-terminal domain-like Family:EF-G/eEF-2 domains III and V 10 c2wryA_ 20.1 22 PDB header:immune system Chain: A: PDB Molecule:interleukin-1beta; PDBTitle: crystal structure of chicken cytokine interleukin 1 beta 11 d1e2wa2 19.3 15 Fold:Barrel-sandwich hybrid Superfamily:Rudiment single hybrid motif Family:Cytochrome f, small domain 12 d1ci3m2 17.2 10 Fold:Barrel-sandwich hybrid Superfamily:Rudiment single hybrid motif Family:Cytochrome f, small domain 13 c3kepA_ 16.4 17 PDB header:protein transport, rna binding protein Chain: A: PDB Molecule:nucleoporin nup145; PDBTitle: crystal structure of the autoproteolytic domain from the2 nuclear pore complex component nup145 from saccharomyces3 cerevisiae 14 c1q2lA_ 14.3 13 PDB header:hydrolase Chain: A: PDB Molecule:protease iii; PDBTitle: crystal structure of pitrilysin 15 c2jbuB_ 13.9 12 PDB header:hydrolase Chain: B: PDB Molecule:insulin-degrading enzyme; PDBTitle: crystal structure of human insulin degrading enzyme2 complexed with co-purified peptides. 16 c3dx5A_ 12.2 16 PDB header:lyase Chain: A: PDB Molecule:uncharacterized protein asbf; PDBTitle: crystal structure of the probable 3-dhs dehydratase asbf involved in2 the petrobactin synthesis from bacillus anthracis 17 c2wk3A_ 11.7 12 PDB header:hydrolase Chain: A: PDB Molecule:insulin degrading enzyme; PDBTitle: crystal structure of human insulin-degrading enzyme in2 complex with amyloid-beta (1-42) 18 d1j83a_ 11.5 31 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:Family 17 carbohydrate binding module, CBM17 19 c3lgeF_ 11.4 11 PDB header:lyase/protein binding Chain: F: PDB Molecule:sorting nexin-9; PDBTitle: crystal structure of rabbit muscle aldolase-snx9 lc4 complex 20 c3lgeG_ 11.4 11 PDB header:lyase/protein binding Chain: G: PDB Molecule:sorting nexin-9; PDBTitle: crystal structure of rabbit muscle aldolase-snx9 lc4 complex 21 c3d22A_ not modelled 11.2 25 PDB header:oxidoreductase Chain: A: PDB Molecule:thioredoxin h-type; PDBTitle: crystal structure of a poplar thioredoxin h mutant,2 pttrxh4c61s 22 d1ilr1_ not modelled 10.9 30 Fold:beta-Trefoil Superfamily:Cytokine Family:Interleukin-1 (IL-1) 23 c1m45B_ not modelled 10.6 25 PDB header:cell cycle protein Chain: B: PDB Molecule:iq2 motif from myo2p, a class v myosin; PDBTitle: crystal structure of mlc1p bound to iq2 of myo2p, a class v2 myosin 24 c2j57J_ not modelled 10.5 18 PDB header:oxidoreductase Chain: J: PDB Molecule:methylamine dehydrogenase heavy chain; PDBTitle: x-ray reduced paraccocus denitrificans methylamine2 dehydrogenase n-quinol in complex with amicyanin. 25 d2a6qb1 not modelled 10.5 14 Fold:YefM-like Superfamily:YefM-like Family:YefM-like 26 d1st9a_ not modelled 10.4 34 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione peroxidase-like 27 d8i1ba_ not modelled 10.1 30 Fold:beta-Trefoil Superfamily:Cytokine Family:Interleukin-1 (IL-1) 28 d2bg1a1 not modelled 10.1 17 Fold:beta-lactamase/transpeptidase-like Superfamily:beta-lactamase/transpeptidase-like Family:beta-Lactamase/D-ala carboxypeptidase 29 c2kllA_ not modelled 10.0 33 PDB header:cytokine Chain: A: PDB Molecule:interleukin-33; PDBTitle: solution structure of human interleukin-33 30 c2hlwA_ not modelled 9.2 15 PDB header:ligase, signaling protein Chain: A: PDB Molecule:ubiquitin-conjugating enzyme e2 variant 1; PDBTitle: solution structure of the human ubiquitin-conjugating2 enzyme variant uev1a 31 c2a7oA_ not modelled 8.9 16 PDB header:transcription Chain: A: PDB Molecule:huntingtin interacting protein b; PDBTitle: solution structure of the hset2/hypb sri domain 32 d1smya1 not modelled 8.8 24 Fold:DCoH-like Superfamily:RBP11-like subunits of RNA polymerase Family:RNA polymerase alpha subunit dimerisation domain 33 d1md6a_ not modelled 8.0 17 Fold:beta-Trefoil Superfamily:Cytokine Family:Interleukin-1 (IL-1) 34 d2v0ea1 not modelled 7.8 16 Fold:GYF/BRK domain-like Superfamily:BRK domain-like Family:BRK domain-like 35 c3psiA_ not modelled 7.6 11 PDB header:transcription Chain: A: PDB Molecule:transcription elongation factor spt6; PDBTitle: crystal structure of the spt6 core domain from saccharomyces2 cerevisiae, form spt6(239-1451) 36 d1tu2b2 not modelled 7.6 26 Fold:Barrel-sandwich hybrid Superfamily:Rudiment single hybrid motif Family:Cytochrome f, small domain 37 c2nogA_ not modelled 7.1 6 PDB header:dna binding protein Chain: A: PDB Molecule:iswi protein; PDBTitle: sant domain structure of xenopus remodeling factor iswi 38 c3kh7A_ not modelled 7.0 18 PDB header:oxidoreductase Chain: A: PDB Molecule:thiol:disulfide interchange protein dsbe; PDBTitle: crystal structure of the periplasmic soluble domain of reduced ccmg2 from pseudomonas aeruginosa 39 c3iu6A_ not modelled 6.8 9 PDB header:transcription Chain: A: PDB Molecule:protein polybromo-1; PDBTitle: crystal structure of the sixth bromodomain of human poly-bromodomain2 containing protein 1 (pb1) 40 c2jciA_ not modelled 6.8 17 PDB header:drug-binding protein Chain: A: PDB Molecule:penicillin-binding protein 1b; PDBTitle: structural insights into the catalytic mechanism and the2 role of streptococcus pneumoniae pbp1b 41 c2j04C_ not modelled 6.6 13 PDB header:transcription Chain: C: PDB Molecule:hypothetical protein ypl007c; PDBTitle: the tau60-tau91 subcomplex of yeast transcription factor2 iiic 42 d1qy9a1 not modelled 6.1 20 Fold:Diaminopimelate epimerase-like Superfamily:Diaminopimelate epimerase-like Family:PhzC/PhzF-like 43 d1ii2a2 not modelled 6.0 32 Fold:PEP carboxykinase N-terminal domain Superfamily:PEP carboxykinase N-terminal domain Family:PEP carboxykinase N-terminal domain 44 c3uinD_ not modelled 5.9 70 PDB header:ligase/isomerase/protein binding Chain: D: PDB Molecule:e3 sumo-protein ligase ranbp2; PDBTitle: complex between human rangap1-sumo2, ubc9 and the ir1 domain from2 ranbp2 45 d1wb9a3 not modelled 5.6 20 Fold:Ribonuclease H-like motif Superfamily:DNA repair protein MutS, domain II Family:DNA repair protein MutS, domain II 46 d1zyma2 not modelled 5.6 14 Fold:The "swivelling" beta/beta/alpha domain Superfamily:Phosphohistidine domain Family:N-terminal domain of enzyme I of the PEP:sugar phosphotransferase system 47 d1yrva1 not modelled 5.5 21 Fold:UBC-like Superfamily:UBC-like Family:UBC-related 48 c3b79A_ not modelled 5.5 20 PDB header:nucleotide binding protein Chain: A: PDB Molecule:toxin secretion atp-binding protein; PDBTitle: crystal structure of the n-terminal peptidase c39 like2 domain of the toxin secretion atp-binding protein from3 vibrio parahaemolyticus 49 c1n2dC_ not modelled 5.5 25 PDB header:cell cycle Chain: C: PDB Molecule:iq2 and iq3 motifs from myo2p, a class v myosin; PDBTitle: ternary complex of mlc1p bound to iq2 and iq3 of myo2p, a2 class v myosin 50 c2o3oD_ not modelled 5.5 23 PDB header:signaling protein Chain: D: PDB Molecule:yyci protein; PDBTitle: crystal structure of the sensor histidine kinase regulator yyci from2 bacillus subtitlis 51 d1tf5a1 not modelled 5.4 22 Fold:Pre-protein crosslinking domain of SecA Superfamily:Pre-protein crosslinking domain of SecA Family:Pre-protein crosslinking domain of SecA 52 c1mzwB_ not modelled 5.4 38 PDB header:isomerase Chain: B: PDB Molecule:u4/u6 snrnp 60kda protein; PDBTitle: crystal structure of a u4/u6 snrnp complex between human2 spliceosomal cyclophilin h and a u4/u6-60k peptide 53 c2wadB_ not modelled 5.3 17 PDB header:peptide binding protein Chain: B: PDB Molecule:penicillin-binding protein 2b; PDBTitle: penicillin-binding protein 2b (pbp-2b) from streptococcus2 pneumoniae (strain 5204) 54 d2olua2 not modelled 5.2 8 Fold:beta-lactamase/transpeptidase-like Superfamily:beta-lactamase/transpeptidase-like Family:beta-Lactamase/D-ala carboxypeptidase 55 c1ezaA_ not modelled 5.2 14 PDB header:phosphotransferase Chain: A: PDB Molecule:enzyme i; PDBTitle: amino terminal domain of enzyme i from escherichia coli nmr,2 restrained regularized mean structure 56 c1qy9B_ not modelled 5.1 19 PDB header:unknown function Chain: B: PDB Molecule:hypothetical protein ydde; PDBTitle: crystal structure of e. coli se-met protein ydde 57 d2gw6a1 not modelled 5.1 22 Fold:Restriction endonuclease-like Superfamily:tRNA-intron endonuclease catalytic domain-like Family:tRNA-intron endonuclease catalytic domain-like 58 d1s1qa_ not modelled 5.1 19 Fold:UBC-like Superfamily:UBC-like Family:UEV domain 59 c3udiA_ not modelled 5.1 17 PDB header:penicillin-binding protein/antibiotic Chain: A: PDB Molecule:penicillin-binding protein 1a; PDBTitle: crystal structure of acinetobacter baumannii pbp1a in complex with2 penicillin g

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