Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	M	K	L	K	T	L	F	A	A	A	F	A	V	V	G	F	C	S	T	A	S	A	V	T	Y	P	L	P	T	D	G	S	R	L	V	G	Q	N	Q	V	I	T	I	P	E	G	N	T	Q	P	L	E	Y	F	A	A	E	Y
Secondary structure
SS confidence
Disorder		?	?	?	?	?															?	?	?	?	?	?														?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Q	M	G	L	S	N	M	M	E	A	N	P	G	V	D	T	F	L	P	K	G	G	T	V	L	N	I	P	Q	Q	L	I	L	P	D	T	V	H	E	G	I	V	I	N	S	A	E	M	R	L	Y	Y	Y	P	K	G	T	N	T	V
Secondary structure
SS confidence
Disorder															?	?	?	?											?	?	?	?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		I	V	L	P	I	G	I	G	Q	L	G	K	D	T	P	I	N	W	T	T	K	V	E	R	K	K	A	G	P	T	W	T	P	T	A	K	M	H	A	E	Y	R	A	A	G	E	P	L	P	A	V	V	P	A	G	P	D	N	P	M
Secondary structure
SS confidence
Disorder																																					?	?	?		?		?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		G	L	Y	A	L	Y	I	G	R	L	Y	A	I	H	G	T	N	A	N	F	G	I	G	L	R	V	S	H	G	C	V	R	L	R	N	E	D	I	K	F	L	F	E	K	V	P	V	G	T	R	V	Q	F	I	D	E	P	V	K	A
Secondary structure
SS confidence
Disorder																																																													?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		T	T	E	P	D	G	S	R	Y	I	E	V	H	N	P	L	S	T	T	E	A	Q	F	E	G	Q	E	I	V	P	I	T	L	T	K	S	V	Q	T	V	T	G	Q	P	D	V	D	Q	V	V	L	D	E	A	I	K	N	R	S	G
Secondary structure
SS confidence
Disorder																?	?	?	?	?	?	?	?	?		?	?	?													?	?	?	?	?	?	?												?		?
Disorder confidence
		.	.	.	.	.	.
Sequence		M	P	V	R	L	N
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 1y7m chain B Region: 41 - 235 Aligned: 162 Modelled: 168 Confidence: 100.0% Identity: 28% 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 1y7m chain A domain 1 Region: 94 - 233 Aligned: 111 Modelled: 113 Confidence: 100.0% Identity: 32% Fold: L,D-transpeptidase catalytic domain-like Superfamily: L,D-transpeptidase catalytic domain-like Family: L,D-transpeptidase catalytic domain-like Phyre2 PDB 2hkl chain B Region: 94 - 233 Aligned: 120 Modelled: 122 Confidence: 100.0% Identity: 26% PDB header:transferase Chain: B: PDB Molecule:l,d-transpeptidase; PDBTitle: crystal structure of enterococcus faecium l,d-2 transpeptidase c442s mutant Phyre2 PDB 1zat chain A domain 1 Region: 97 - 233 Aligned: 117 Modelled: 119 Confidence: 100.0% Identity: 26% Fold: L,D-transpeptidase catalytic domain-like Superfamily: L,D-transpeptidase catalytic domain-like Family: L,D-transpeptidase catalytic domain-like Phyre2 PDB 2l9y chain A Region: 38 - 90 Aligned: 51 Modelled: 53 Confidence: 97.9% Identity: 22% PDB header:sugar binding protein Chain: A: PDB Molecule:cvnh-lysm lectin; PDBTitle: solution structure of the mocvnh-lysm module from the rice blast2 fungus magnaporthe oryzae protein (mgg_03307) Phyre2 PDB 1y7m chain A domain 2 Region: 42 - 89 Aligned: 45 Modelled: 48 Confidence: 97.4% Identity: 24% Fold: LysM domain Superfamily: LysM domain Family: LysM domain Phyre2 PDB 2djp chain A Region: 39 - 100 Aligned: 60 Modelled: 62 Confidence: 97.4% Identity: 20% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein sb145; PDBTitle: the solution structure of the lysm domain of human2 hypothetical protein sb145 Phyre2 PDB 1e0g chain A Region: 42 - 88 Aligned: 43 Modelled: 47 Confidence: 97.2% Identity: 16% Fold: LysM domain Superfamily: LysM domain Family: LysM domain Phyre2 PDB 2gu1 chain A Region: 42 - 121 Aligned: 77 Modelled: 80 Confidence: 90.4% Identity: 12% PDB header:hydrolase Chain: A: PDB Molecule:zinc peptidase; PDBTitle: crystal structure of a zinc containing peptidase from2 vibrio cholerae Phyre2 PDB 1h5n chain C Region: 128 - 236 Aligned: 96 Modelled: 109 Confidence: 70.6% Identity: 15% PDB header:oxidoreductase Chain: C: PDB Molecule:dmso reductase; PDBTitle: dmso reductase modified by the presence of dms and air Phyre2 PDB 3mca chain B Region: 209 - 232 Aligned: 24 Modelled: 24 Confidence: 57.5% Identity: 25% PDB header:translation regulation/hydrolase Chain: B: PDB Molecule:protein dom34; PDBTitle: structure of the dom34-hbs1 complex and implications for its role in2 no-go decay Phyre2 PDB 1wjj chain A Region: 209 - 252 Aligned: 39 Modelled: 42 Confidence: 41.6% Identity: 15% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Single strand DNA-binding domain, SSB Phyre2 PDB 2kke chain A Region: 211 - 229 Aligned: 19 Modelled: 19 Confidence: 25.7% Identity: 42% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of a dimeric protein of unknown2 function from methanobacterium thermoautotrophicum,3 northeast structural genomics consortium target tr5 Phyre2 PDB 2k50 chain A Region: 207 - 250 Aligned: 44 Modelled: 44 Confidence: 21.2% Identity: 14% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:replication factor a related protein; PDBTitle: solution nmr structure of the replication factor a related2 protein from methanobacterium thermoautotrophicum.3 northeast structural genomics target tr91a. Phyre2 PDB 1eu1 chain A Region: 131 - 236 Aligned: 93 Modelled: 106 Confidence: 20.5% Identity: 11% PDB header:oxidoreductase Chain: A: PDB Molecule:dimethyl sulfoxide reductase; PDBTitle: the crystal structure of rhodobacter sphaeroides dimethylsulfoxide2 reductase reveals two distinct molybdenum coordination environments. Phyre2 PDB 1y5i chain A Region: 128 - 235 Aligned: 104 Modelled: 108 Confidence: 18.2% Identity: 13% PDB header:oxidoreductase Chain: A: PDB Molecule:respiratory nitrate reductase 1 alpha chain; PDBTitle: the crystal structure of the narghi mutant nari-k86a Phyre2 PDB 1ogy chain A domain 1 Region: 208 - 236 Aligned: 27 Modelled: 29 Confidence: 17.6% Identity: 19% Fold: Double psi beta-barrel Superfamily: ADC-like Family: Formate dehydrogenase/DMSO reductase, C-terminal domain Phyre2 PDB 2ki8 chain A Region: 194 - 254 Aligned: 59 Modelled: 61 Confidence: 15.8% Identity: 20% PDB header:oxidoreductase Chain: A: PDB Molecule:tungsten formylmethanofuran dehydrogenase, PDBTitle: solution nmr structure of tungsten formylmethanofuran2 dehydrogenase subunit d from archaeoglobus fulgidus,3 northeast structural genomics consortium target att7 Phyre2 PDB 1y5i chain A domain 1 Region: 173 - 236 Aligned: 58 Modelled: 64 Confidence: 14.9% Identity: 21% Fold: Double psi beta-barrel Superfamily: ADC-like Family: Formate dehydrogenase/DMSO reductase, C-terminal domain Phyre2 PDB 1t3l chain A domain 1 Region: 177 - 220 Aligned: 44 Modelled: 44 Confidence: 13.3% Identity: 25% Fold: SH3-like barrel Superfamily: SH3-domain Family: SH3-domain Phyre2 1 c1y7mB_ 2 d1y7ma1 3 c2hklB_ 4 d1zata1 5 c2l9yA_ 6 d1y7ma2 7 c2djpA_ 8 d1e0ga_ 9 c2gu1A_ 10 c1h5nC_ 11 c3mcaB_ 12 d1wjja_ 13 c2kkeA_ 14 c2k50A_ 15 c1eu1A_ 16 c1y5iA_ 17 d1ogya1 18 c2ki8A_ 19 d1y5ia1 20 d1t3la1 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

Detailed template information

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

1 c1y7mB_ 100.0 28 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 2 d1y7ma1 100.0 32 Fold:L,D-transpeptidase catalytic domain-like Superfamily:L,D-transpeptidase catalytic domain-like Family:L,D-transpeptidase catalytic domain-like 3 c2hklB_ 100.0 26 PDB header:transferase Chain: B: PDB Molecule:l,d-transpeptidase; PDBTitle: crystal structure of enterococcus faecium l,d-2 transpeptidase c442s mutant 4 d1zata1 100.0 26 Fold:L,D-transpeptidase catalytic domain-like Superfamily:L,D-transpeptidase catalytic domain-like Family:L,D-transpeptidase catalytic domain-like 5 c2l9yA_ 97.9 22 PDB header:sugar binding protein Chain: A: PDB Molecule:cvnh-lysm lectin; PDBTitle: solution structure of the mocvnh-lysm module from the rice blast2 fungus magnaporthe oryzae protein (mgg_03307) 6 d1y7ma2 97.4 24 Fold:LysM domain Superfamily:LysM domain Family:LysM domain 7 c2djpA_ 97.4 20 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein sb145; PDBTitle: the solution structure of the lysm domain of human2 hypothetical protein sb145 8 d1e0ga_ 97.2 16 Fold:LysM domain Superfamily:LysM domain Family:LysM domain 9 c2gu1A_ 90.4 12 PDB header:hydrolase Chain: A: PDB Molecule:zinc peptidase; PDBTitle: crystal structure of a zinc containing peptidase from2 vibrio cholerae 10 c1h5nC_ 70.6 15 PDB header:oxidoreductase Chain: C: PDB Molecule:dmso reductase; PDBTitle: dmso reductase modified by the presence of dms and air 11 c3mcaB_ 57.5 25 PDB header:translation regulation/hydrolase Chain: B: PDB Molecule:protein dom34; PDBTitle: structure of the dom34-hbs1 complex and implications for its role in2 no-go decay 12 d1wjja_ 41.6 15 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Single strand DNA-binding domain, SSB 13 c2kkeA_ 25.7 42 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of a dimeric protein of unknown2 function from methanobacterium thermoautotrophicum,3 northeast structural genomics consortium target tr5 14 c2k50A_ 21.2 14 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:replication factor a related protein; PDBTitle: solution nmr structure of the replication factor a related2 protein from methanobacterium thermoautotrophicum.3 northeast structural genomics target tr91a. 15 c1eu1A_ 20.5 11 PDB header:oxidoreductase Chain: A: PDB Molecule:dimethyl sulfoxide reductase; PDBTitle: the crystal structure of rhodobacter sphaeroides dimethylsulfoxide2 reductase reveals two distinct molybdenum coordination environments. 16 c1y5iA_ 18.2 13 PDB header:oxidoreductase Chain: A: PDB Molecule:respiratory nitrate reductase 1 alpha chain; PDBTitle: the crystal structure of the narghi mutant nari-k86a 17 d1ogya1 17.6 19 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Formate dehydrogenase/DMSO reductase, C-terminal domain 18 c2ki8A_ 15.8 20 PDB header:oxidoreductase Chain: A: PDB Molecule:tungsten formylmethanofuran dehydrogenase, PDBTitle: solution nmr structure of tungsten formylmethanofuran2 dehydrogenase subunit d from archaeoglobus fulgidus,3 northeast structural genomics consortium target att7 19 d1y5ia1 14.9 21 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Formate dehydrogenase/DMSO reductase, C-terminal domain 20 d1t3la1 13.3 25 Fold:SH3-like barrel Superfamily:SH3-domain Family:SH3-domain 21 d2iv2x1 not modelled 11.3 17 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Formate dehydrogenase/DMSO reductase, C-terminal domain 22 d2vgna1 not modelled 10.9 19 Fold:Sm-like fold Superfamily:Dom34/Pelota N-terminal domain-like Family:Dom34/Pelota N-terminal domain-like 23 c1tmoA_ not modelled 10.6 13 PDB header:oxidoreductase Chain: A: PDB Molecule:trimethylamine n-oxide reductase; PDBTitle: trimethylamine n-oxide reductase from shewanella massilia 24 d1k78a1 not modelled 10.4 100 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 25 d2hthb1 not modelled 10.4 16 Fold:PH domain-like barrel Superfamily:PH domain-like Family:VPS36 N-terminal domain-like 26 d2jioa1 not modelled 9.2 15 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Formate dehydrogenase/DMSO reductase, C-terminal domain 27 d2qi2a1 not modelled 9.1 19 Fold:Sm-like fold Superfamily:Dom34/Pelota N-terminal domain-like Family:Dom34/Pelota N-terminal domain-like 28 c3rf1B_ not modelled 9.0 21 PDB header:ligase Chain: B: PDB Molecule:glycyl-trna synthetase alpha subunit; PDBTitle: the crystal structure of glycyl-trna synthetase subunit alpha from2 campylobacter jejuni subsp. jejuni nctc 11168 29 d1eu1a1 not modelled 9.0 12 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Formate dehydrogenase/DMSO reductase, C-terminal domain 30 d6paxa1 not modelled 8.8 71 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 31 c3d12A_ not modelled 8.6 25 PDB header:hydrolase/membrane protein Chain: A: PDB Molecule:hemagglutinin-neuraminidase; PDBTitle: crystal structures of nipah virus g attachment glycoprotein in complex2 with its receptor ephrin-b3 32 c2iheA_ not modelled 8.2 18 PDB header:dna binding protein Chain: A: PDB Molecule:single-stranded dna-binding protein; PDBTitle: crystal structure of wild-type single-stranded dna binding protein2 from thermus aquaticus 33 d2c42a3 not modelled 8.1 24 Fold:TK C-terminal domain-like Superfamily:TK C-terminal domain-like Family:Pyruvate-ferredoxin oxidoreductase, PFOR, domain II 34 c1r1gB_ not modelled 8.0 27 PDB header:toxin Chain: B: PDB Molecule:neurotoxin bmk37; PDBTitle: crystal structure of the scorpion toxin bmbkttx1 35 c1r1gA_ not modelled 8.0 27 PDB header:toxin Chain: A: PDB Molecule:neurotoxin bmk37; PDBTitle: crystal structure of the scorpion toxin bmbkttx1 36 d1r1ga_ not modelled 8.0 27 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Scorpion toxin-like Family:Short-chain scorpion toxins 37 d1h0ha1 not modelled 7.7 11 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Formate dehydrogenase/DMSO reductase, C-terminal domain 38 d2gp4a1 not modelled 7.3 29 Fold:The "swivelling" beta/beta/alpha domain Superfamily:LeuD/IlvD-like Family:IlvD/EDD C-terminal domain-like 39 c2vw9B_ not modelled 7.0 12 PDB header:dna-binding protein Chain: B: PDB Molecule:single-stranded dna binding protein; PDBTitle: single stranded dna binding protein complex from2 helicobacter pylori 40 d1cz5a1 not modelled 6.9 18 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Cdc48 N-terminal domain-like 41 c3bbnD_ not modelled 6.6 13 PDB header:ribosome Chain: D: PDB Molecule:ribosomal protein s4; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. 42 c1eqqD_ not modelled 6.5 15 PDB header:replication/rna Chain: D: PDB Molecule:single stranded dna binding protein; PDBTitle: single stranded dna binding protein and ssdna complex 43 c2k27A_ not modelled 6.4 88 PDB header:transcription regulator Chain: A: PDB Molecule:paired box protein pax-8; PDBTitle: solution structure of human pax8 paired box domain 44 d2hh8a1 not modelled 6.3 29 Fold:YdfO-like Superfamily:YdfO-like Family:YdfO-like 45 c2pjhB_ not modelled 6.0 19 PDB header:transport protein Chain: B: PDB Molecule:transitional endoplasmic reticulum atpase; PDBTitle: strctural model of the p97 n domain- npl4 ubd complex 46 d1usra_ not modelled 6.0 38 Fold:6-bladed beta-propeller Superfamily:Sialidases Family:Sialidases (neuraminidases) 47 c3nfgG_ not modelled 5.8 17 PDB header:transcription Chain: G: PDB Molecule:dna-directed rna polymerase i subunit rpa49; PDBTitle: crystal structure of dimerization module of rna polymerase i2 subcomplex a49/a34.5 48 c3agjB_ not modelled 5.3 31 PDB header:translation/hydrolase Chain: B: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of archaeal pelota and gtp-bound ef1 alpha complex 49 c3agjD_ not modelled 5.3 31 PDB header:translation/hydrolase Chain: D: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of archaeal pelota and gtp-bound ef1 alpha complex 50 c1z4xA_ not modelled 5.3 38 PDB header:hydrolase Chain: A: PDB Molecule:hemagglutinin-neuraminidase; PDBTitle: parainfluenza virus 5 (sv5) hemagglutinin-neuraminidase (hn) with2 ligand sialyllactose (soaked with sialyllactose, ph8.0) 51 c3obyB_ not modelled 5.3 20 PDB header:hydrolase Chain: B: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of archaeoglobus fulgidus pelota reveals inter-2 domain structural plasticity 52 c2yx0A_ not modelled 5.1 43 PDB header:metal binding protein Chain: A: PDB Molecule:radical sam enzyme; PDBTitle: crystal structure of p. horikoshii tyw1

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