Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	M	I	K	T	R	F	S	R	W	L	T	F	F	T	F	A	A	A	V	A	L	A	L	P	A	K	A	N	T	W	P	L	P	P	A	G	S	R	L	V	G	E	N	K	F	H	V	V	E	N	D	G	G	S	L	E	A	I	A
Secondary structure
SS confidence
Disorder		?	?	?																				?	?	?	?	?	?	?			?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		K	K	Y	N	V	G	F	L	A	L	L	Q	A	N	P	G	V	D	P	Y	V	P	R	A	G	S	V	L	T	I	P	L	Q	T	L	L	P	D	A	P	R	E	G	I	V	I	N	I	A	E	L	R	L	Y	Y	Y	P	P	G	K
Secondary structure
SS confidence
Disorder																?	?	?	?	?	?											?		?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		N	S	V	T	V	Y	P	I	G	I	G	Q	L	G	G	D	T	L	T	P	T	M	V	T	T	V	S	D	K	R	A	N	P	T	W	T	P	T	A	N	I	R	A	R	Y	K	A	Q	G	I	E	L	P	A	V	V	P	A	G	L
Secondary structure
SS confidence
Disorder																?																										?			?		?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		D	N	P	M	G	H	H	A	I	R	L	A	A	Y	G	G	V	Y	L	L	H	G	T	N	A	D	F	G	I	G	M	R	V	S	S	G	C	I	R	L	R	D	D	D	I	K	T	L	F	S	Q	V	T	P	G	T	K	V	N	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		I	N	T	P	I	K	V	S	A	E	P	N	G	A	R	L	V	E	V	H	Q	P	L	S	E	K	I	D	D	D	P	Q	L	L	P	I	T	L	N	S	A	M	Q	S	F	K	D	A	A	Q	T	D	A	E	V	M	Q	H	V	M
Secondary structure
SS confidence
Disorder								?															?	?	?	?	?	?	?	?	?	?	?												?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320
Sequence		D	V	R	S	G	M	P	V	D	V	R	R	H	Q	V	S	P	Q	T	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 1y7m chain B Region: 46 - 242 Aligned: 163 Modelled: 170 Confidence: 100.0% Identity: 33% 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: 97 - 240 Aligned: 112 Modelled: 117 Confidence: 100.0% Identity: 35% 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: 104 - 240 Aligned: 114 Modelled: 119 Confidence: 100.0% Identity: 25% 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: 101 - 240 Aligned: 117 Modelled: 122 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: 36 - 122 Aligned: 84 Modelled: 87 Confidence: 98.2% Identity: 15% 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 2djp chain A Region: 35 - 103 Aligned: 69 Modelled: 69 Confidence: 98.0% Identity: 25% 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 1y7m chain A domain 2 Region: 47 - 91 Aligned: 44 Modelled: 45 Confidence: 97.7% Identity: 34% Fold: LysM domain Superfamily: LysM domain Family: LysM domain Phyre2 PDB 1e0g chain A Region: 47 - 93 Aligned: 45 Modelled: 47 Confidence: 97.5% Identity: 24% Fold: LysM domain Superfamily: LysM domain Family: LysM domain Phyre2 PDB 2gu1 chain A Region: 45 - 91 Aligned: 47 Modelled: 47 Confidence: 93.0% Identity: 17% 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: 137 - 243 Aligned: 95 Modelled: 107 Confidence: 61.2% Identity: 20% 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: 216 - 239 Aligned: 24 Modelled: 24 Confidence: 59.7% Identity: 21% 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 1y5i chain A Region: 137 - 243 Aligned: 89 Modelled: 91 Confidence: 47.2% 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 2vda chain B Region: 1 - 28 Aligned: 28 Modelled: 28 Confidence: 26.9% Identity: 36% PDB header:protein transport Chain: B: PDB Molecule:maltoporin; PDBTitle: solution structure of the seca-signal peptide complex Phyre2 PDB 1y5i chain A domain 1 Region: 186 - 243 Aligned: 56 Modelled: 58 Confidence: 16.4% Identity: 13% Fold: Double psi beta-barrel Superfamily: ADC-like Family: Formate dehydrogenase/DMSO reductase, C-terminal domain Phyre2 PDB 2hth chain B domain 1 Region: 238 - 269 Aligned: 31 Modelled: 32 Confidence: 15.8% Identity: 19% Fold: PH domain-like barrel Superfamily: PH domain-like Family: VPS36 N-terminal domain-like Phyre2 PDB 2k50 chain A Region: 214 - 257 Aligned: 44 Modelled: 44 Confidence: 14.5% 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 1wjj chain A Region: 216 - 257 Aligned: 39 Modelled: 40 Confidence: 14.2% Identity: 23% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Single strand DNA-binding domain, SSB Phyre2 PDB 2kke chain A Region: 218 - 236 Aligned: 19 Modelled: 19 Confidence: 13.5% 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 1eu1 chain A Region: 137 - 243 Aligned: 95 Modelled: 107 Confidence: 13.4% Identity: 15% 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 1tmo chain A Region: 137 - 243 Aligned: 95 Modelled: 107 Confidence: 13.2% Identity: 16% PDB header:oxidoreductase Chain: A: PDB Molecule:trimethylamine n-oxide reductase; PDBTitle: trimethylamine n-oxide reductase from shewanella massilia Phyre2 1 c1y7mB_ 2 d1y7ma1 3 c2hklB_ 4 d1zata1 5 c2l9yA_ 6 c2djpA_ 7 d1y7ma2 8 d1e0ga_ 9 c2gu1A_ 10 c1h5nC_ 11 c3mcaB_ 12 c1y5iA_ 13 c2vdaB_ 14 d1y5ia1 15 d2hthb1 16 c2k50A_ 17 d1wjja_ 18 c2kkeA_ 19 c1eu1A_ 20 c1tmoA_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37

Detailed template information

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

1 c1y7mB_ 100.0 33 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 35 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 25 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_ 98.2 15 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 c2djpA_ 98.0 25 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 7 d1y7ma2 97.7 34 Fold:LysM domain Superfamily:LysM domain Family:LysM domain 8 d1e0ga_ 97.5 24 Fold:LysM domain Superfamily:LysM domain Family:LysM domain 9 c2gu1A_ 93.0 17 PDB header:hydrolase Chain: A: PDB Molecule:zinc peptidase; PDBTitle: crystal structure of a zinc containing peptidase from2 vibrio cholerae 10 c1h5nC_ 61.2 20 PDB header:oxidoreductase Chain: C: PDB Molecule:dmso reductase; PDBTitle: dmso reductase modified by the presence of dms and air 11 c3mcaB_ 59.7 21 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 c1y5iA_ 47.2 13 PDB header:oxidoreductase Chain: A: PDB Molecule:respiratory nitrate reductase 1 alpha chain; PDBTitle: the crystal structure of the narghi mutant nari-k86a 13 c2vdaB_ 26.9 36 PDB header:protein transport Chain: B: PDB Molecule:maltoporin; PDBTitle: solution structure of the seca-signal peptide complex 14 d1y5ia1 16.4 13 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Formate dehydrogenase/DMSO reductase, C-terminal domain 15 d2hthb1 15.8 19 Fold:PH domain-like barrel Superfamily:PH domain-like Family:VPS36 N-terminal domain-like 16 c2k50A_ 14.5 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. 17 d1wjja_ 14.2 23 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Single strand DNA-binding domain, SSB 18 c2kkeA_ 13.5 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 19 c1eu1A_ 13.4 15 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. 20 c1tmoA_ 13.2 16 PDB header:oxidoreductase Chain: A: PDB Molecule:trimethylamine n-oxide reductase; PDBTitle: trimethylamine n-oxide reductase from shewanella massilia 21 d2vgna1 not modelled 7.4 17 Fold:Sm-like fold Superfamily:Dom34/Pelota N-terminal domain-like Family:Dom34/Pelota N-terminal domain-like 22 d1k78a1 not modelled 7.2 71 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 23 d2qi2a1 not modelled 7.1 26 Fold:Sm-like fold Superfamily:Dom34/Pelota N-terminal domain-like Family:Dom34/Pelota N-terminal domain-like 24 c3d12A_ not modelled 6.9 38 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 25 d1ogya1 not modelled 6.9 15 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Formate dehydrogenase/DMSO reductase, C-terminal domain 26 c3obyB_ not modelled 6.8 21 PDB header:hydrolase Chain: B: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of archaeoglobus fulgidus pelota reveals inter-2 domain structural plasticity 27 d1t3la1 not modelled 6.7 30 Fold:SH3-like barrel Superfamily:SH3-domain Family:SH3-domain 28 d1eu1a1 not modelled 6.3 12 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Formate dehydrogenase/DMSO reductase, C-terminal domain 29 c3rf1B_ not modelled 6.1 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 30 d6paxa1 not modelled 6.1 57 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 31 c3nadB_ not modelled 5.8 14 PDB header:lyase Chain: B: PDB Molecule:ferulate decarboxylase; PDBTitle: crystal structure of phenolic acid decarboxylase from bacillus pumilus2 ui-670 32 c3agjD_ not modelled 5.6 28 PDB header:translation/hydrolase Chain: D: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of archaeal pelota and gtp-bound ef1 alpha complex 33 c3agjB_ not modelled 5.6 28 PDB header:translation/hydrolase Chain: B: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of archaeal pelota and gtp-bound ef1 alpha complex 34 d1r1ga_ not modelled 5.4 55 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Scorpion toxin-like Family:Short-chain scorpion toxins 35 c1r1gA_ not modelled 5.4 55 PDB header:toxin Chain: A: PDB Molecule:neurotoxin bmk37; PDBTitle: crystal structure of the scorpion toxin bmbkttx1 36 c1r1gB_ not modelled 5.4 55 PDB header:toxin Chain: B: PDB Molecule:neurotoxin bmk37; PDBTitle: crystal structure of the scorpion toxin bmbkttx1 37 c2bfuL_ not modelled 5.4 33 PDB header:virus Chain: L: PDB Molecule:cowpea mosaic virus, large (l) subunit; PDBTitle: x-ray structure of cpmv top component

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