Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	R	A	S	L	L	T	L	T	L	I	G	A	F	S	A	I	Q	A	A	W	A	V	D	Y	P	L	P	P	T	G	S	R	L	V	G	Q	N	Q	T	Y	T	V	Q	E	G	D	K	N	L	Q	A	I	A	R	R	F	D	T
Secondary structure
SS confidence
Disorder		?	?	?	?	?											?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	A	M	L	I	L	E	A	N	N	T	I	A	P	V	P	K	P	G	T	T	I	T	I	P	S	Q	L	L	L	P	D	A	P	R	Q	G	I	I	V	N	L	A	E	L	R	L	Y	Y	Y	P	P	G	E	N	I	V	Q	V	Y
Secondary structure
SS confidence
Disorder													?	?	?	?										?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		P	I	G	I	G	L	Q	G	L	E	T	P	V	M	E	T	R	V	G	Q	K	I	P	N	P	T	W	T	P	T	A	G	I	R	Q	R	S	L	E	R	G	I	K	L	P	P	V	V	P	A	G	P	N	N	P	L	G	R	Y	A
Secondary structure
SS confidence
Disorder								?																															?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	R	L	A	H	G	N	G	E	Y	L	I	H	G	T	S	A	P	D	S	V	G	L	R	V	S	S	G	C	I	R	M	N	A	P	D	I	K	A	L	F	S	S	V	R	T	G	T	P	V	K	V	I	N	E	P	V	K	Y	S
Secondary structure
SS confidence
Disorder																																																												?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		V	E	P	N	G	M	R	Y	V	E	V	H	R	P	L	S	A	E	E	Q	Q	N	V	Q	T	M	P	Y	T	L	P	A	G	F	T	Q	F	K	D	N	K	A	V	D	Q	K	L	V	D	K	A	L	Y	R	R	A	G	Y	P	V
Secondary structure
SS confidence
Disorder						?									?	?		?	?	?	?	?	?														?	?	?	?	?	?	?	?	?											?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.
Sequence		S	V	S	S	G	A	T	P	A	A	S	N	A	P	S	V	E	S	A	Q	N	G	E	P	E	Q	G	N	M	L	R	V	T	Q
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: 40 - 233 Aligned: 162 Modelled: 167 Confidence: 100.0% Identity: 38% 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: 91 - 232 Aligned: 112 Modelled: 115 Confidence: 100.0% Identity: 39% 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: 91 - 233 Aligned: 122 Modelled: 125 Confidence: 100.0% Identity: 29% 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: 95 - 232 Aligned: 117 Modelled: 120 Confidence: 100.0% Identity: 30% 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 2 Region: 41 - 86 Aligned: 45 Modelled: 46 Confidence: 98.1% Identity: 36% Fold: LysM domain Superfamily: LysM domain Family: LysM domain Phyre2 PDB 2l9y chain A Region: 37 - 86 Aligned: 49 Modelled: 50 Confidence: 98.0% Identity: 39% 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 1e0g chain A Region: 41 - 87 Aligned: 45 Modelled: 47 Confidence: 97.6% Identity: 31% Fold: LysM domain Superfamily: LysM domain Family: LysM domain Phyre2 PDB 2djp chain A Region: 38 - 85 Aligned: 47 Modelled: 48 Confidence: 97.6% Identity: 21% 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 2gu1 chain A Region: 41 - 85 Aligned: 44 Modelled: 45 Confidence: 91.3% Identity: 18% 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: 125 - 252 Aligned: 108 Modelled: 128 Confidence: 87.9% Identity: 19% PDB header:oxidoreductase Chain: C: PDB Molecule:dmso reductase; PDBTitle: dmso reductase modified by the presence of dms and air Phyre2 PDB 1y5i chain A Region: 125 - 251 Aligned: 108 Modelled: 127 Confidence: 86.3% Identity: 19% 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 1eu1 chain A Region: 128 - 239 Aligned: 100 Modelled: 112 Confidence: 49.9% Identity: 16% 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 3mca chain B Region: 208 - 231 Aligned: 24 Modelled: 24 Confidence: 44.8% Identity: 29% 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: 208 - 251 Aligned: 39 Modelled: 42 Confidence: 43.1% Identity: 23% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Single strand DNA-binding domain, SSB Phyre2 PDB 1y5i chain A domain 1 Region: 178 - 239 Aligned: 60 Modelled: 62 Confidence: 39.9% Identity: 18% Fold: Double psi beta-barrel Superfamily: ADC-like Family: Formate dehydrogenase/DMSO reductase, C-terminal domain Phyre2 PDB 1kqg chain A Region: 125 - 252 Aligned: 118 Modelled: 128 Confidence: 37.7% Identity: 14% PDB header:oxidoreductase Chain: A: PDB Molecule:formate dehydrogenase, nitrate-inducible, major subunit; PDBTitle: formate dehydrogenase n from e. coli Phyre2 PDB 2e7z chain A Region: 126 - 239 Aligned: 98 Modelled: 100 Confidence: 34.7% Identity: 15% PDB header:lyase Chain: A: PDB Molecule:acetylene hydratase ahy; PDBTitle: acetylene hydratase from pelobacter acetylenicus Phyre2 PDB 1tmo chain A Region: 129 - 239 Aligned: 99 Modelled: 111 Confidence: 31.9% Identity: 16% PDB header:oxidoreductase Chain: A: PDB Molecule:trimethylamine n-oxide reductase; PDBTitle: trimethylamine n-oxide reductase from shewanella massilia Phyre2 PDB 1eu1 chain A domain 1 Region: 174 - 239 Aligned: 64 Modelled: 66 Confidence: 27.0% Identity: 14% Fold: Double psi beta-barrel Superfamily: ADC-like Family: Formate dehydrogenase/DMSO reductase, C-terminal domain Phyre2 PDB 2iv2 chain X Region: 126 - 252 Aligned: 92 Modelled: 106 Confidence: 26.3% Identity: 22% PDB header:oxidoreductase Chain: X: PDB Molecule:formate dehydrogenase h; PDBTitle: reinterpretation of reduced form of formate dehydrogenase h2 from e. coli Phyre2 1 c1y7mB_ 2 d1y7ma1 3 c2hklB_ 4 d1zata1 5 d1y7ma2 6 c2l9yA_ 7 d1e0ga_ 8 c2djpA_ 9 c2gu1A_ 10 c1h5nC_ 11 c1y5iA_ 12 c1eu1A_ 13 c3mcaB_ 14 d1wjja_ 15 d1y5ia1 16 c1kqgA_ 17 c2e7zA_ 18 c1tmoA_ 19 d1eu1a1 20 c2iv2X_ 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

Detailed template information

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

1 c1y7mB_ 100.0 38 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 39 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 29 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 30 Fold:L,D-transpeptidase catalytic domain-like Superfamily:L,D-transpeptidase catalytic domain-like Family:L,D-transpeptidase catalytic domain-like 5 d1y7ma2 98.1 36 Fold:LysM domain Superfamily:LysM domain Family:LysM domain 6 c2l9yA_ 98.0 39 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) 7 d1e0ga_ 97.6 31 Fold:LysM domain Superfamily:LysM domain Family:LysM domain 8 c2djpA_ 97.6 21 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 9 c2gu1A_ 91.3 18 PDB header:hydrolase Chain: A: PDB Molecule:zinc peptidase; PDBTitle: crystal structure of a zinc containing peptidase from2 vibrio cholerae 10 c1h5nC_ 87.9 19 PDB header:oxidoreductase Chain: C: PDB Molecule:dmso reductase; PDBTitle: dmso reductase modified by the presence of dms and air 11 c1y5iA_ 86.3 19 PDB header:oxidoreductase Chain: A: PDB Molecule:respiratory nitrate reductase 1 alpha chain; PDBTitle: the crystal structure of the narghi mutant nari-k86a 12 c1eu1A_ 49.9 16 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. 13 c3mcaB_ 44.8 29 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 14 d1wjja_ 43.1 23 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Single strand DNA-binding domain, SSB 15 d1y5ia1 39.9 18 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Formate dehydrogenase/DMSO reductase, C-terminal domain 16 c1kqgA_ 37.7 14 PDB header:oxidoreductase Chain: A: PDB Molecule:formate dehydrogenase, nitrate-inducible, major subunit; PDBTitle: formate dehydrogenase n from e. coli 17 c2e7zA_ 34.7 15 PDB header:lyase Chain: A: PDB Molecule:acetylene hydratase ahy; PDBTitle: acetylene hydratase from pelobacter acetylenicus 18 c1tmoA_ 31.9 16 PDB header:oxidoreductase Chain: A: PDB Molecule:trimethylamine n-oxide reductase; PDBTitle: trimethylamine n-oxide reductase from shewanella massilia 19 d1eu1a1 27.0 14 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Formate dehydrogenase/DMSO reductase, C-terminal domain 20 c2iv2X_ 26.3 22 PDB header:oxidoreductase Chain: X: PDB Molecule:formate dehydrogenase h; PDBTitle: reinterpretation of reduced form of formate dehydrogenase h2 from e. coli 21 c1bmv2_ not modelled 20.8 17 PDB header:virus/rna Chain: 2: PDB Molecule:protein (icosahedral virus - b and c domain); PDBTitle: protein-rna interactions in an icosahedral virus at 3.02 angstroms resolution 22 c2kkeA_ not modelled 16.9 37 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 23 d1ogya1 not modelled 16.4 20 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Formate dehydrogenase/DMSO reductase, C-terminal domain 24 d2jioa1 not modelled 16.4 15 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Formate dehydrogenase/DMSO reductase, C-terminal domain 25 c1vlfQ_ not modelled 15.1 13 PDB header:oxidoreductase Chain: Q: PDB Molecule:pyrogallol hydroxytransferase large subunit; PDBTitle: crystal structure of pyrogallol-phloroglucinol2 transhydroxylase from pelobacter acidigallici complexed3 with inhibitor 1,2,4,5-tetrahydroxy-benzene 26 c2k50A_ not modelled 13.9 11 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. 27 d2hthb1 not modelled 13.0 16 Fold:PH domain-like barrel Superfamily:PH domain-like Family:VPS36 N-terminal domain-like 28 d1kqfa1 not modelled 13.0 12 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Formate dehydrogenase/DMSO reductase, C-terminal domain 29 c2ivfA_ not modelled 11.4 21 PDB header:oxidoreductase Chain: A: PDB Molecule:ethylbenzene dehydrogenase alpha-subunit; PDBTitle: ethylbenzene dehydrogenase from aromatoleum aromaticum 30 d2c42a3 not modelled 11.0 11 Fold:TK C-terminal domain-like Superfamily:TK C-terminal domain-like Family:Pyruvate-ferredoxin oxidoreductase, PFOR, domain II 31 d2vgna1 not modelled 10.3 12 Fold:Sm-like fold Superfamily:Dom34/Pelota N-terminal domain-like Family:Dom34/Pelota N-terminal domain-like 32 d1h0ha1 not modelled 10.3 11 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Formate dehydrogenase/DMSO reductase, C-terminal domain 33 d1g8ka1 not modelled 8.4 25 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Formate dehydrogenase/DMSO reductase, C-terminal domain 34 d1k78a1 not modelled 8.1 71 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 35 c3pjvD_ not modelled 7.9 12 PDB header:lyase Chain: D: PDB Molecule:cyclic dimeric gmp binding protein; PDBTitle: structure of pseudomonas fluorescence lapd periplasmic domain 36 d1vlfm1 not modelled 7.8 15 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Formate dehydrogenase/DMSO reductase, C-terminal domain 37 d2qi2a1 not modelled 7.5 16 Fold:Sm-like fold Superfamily:Dom34/Pelota N-terminal domain-like Family:Dom34/Pelota N-terminal domain-like 38 d6paxa1 not modelled 6.8 57 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 39 d1qvpa_ not modelled 6.7 21 Fold:SH3-like barrel Superfamily:C-terminal domain of transcriptional repressors Family:FeoA-like 40 d1qvca_ not modelled 6.7 13 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Single strand DNA-binding domain, SSB 41 d1t3la1 not modelled 6.1 17 Fold:SH3-like barrel Superfamily:SH3-domain Family:SH3-domain 42 c2vw9B_ not modelled 5.9 13 PDB header:dna-binding protein Chain: B: PDB Molecule:single-stranded dna binding protein; PDBTitle: single stranded dna binding protein complex from2 helicobacter pylori 43 c2iheA_ not modelled 5.4 13 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 44 c2bfuL_ not modelled 5.2 33 PDB header:virus Chain: L: PDB Molecule:cowpea mosaic virus, large (l) subunit; PDBTitle: x-ray structure of cpmv top component 45 c2inpE_ not modelled 5.2 9 PDB header:oxidoreductase Chain: E: PDB Molecule:phenol hydroxylase component pho; PDBTitle: structure of the phenol hydroxylase-regulatory protein2 complex 46 d1e0ta1 not modelled 5.2 36 Fold:PK beta-barrel domain-like Superfamily:PK beta-barrel domain-like Family:Pyruvate kinase beta-barrel domain 47 c3rf1B_ not modelled 5.1 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

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