Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	R	V	N	I	L	C	S	F	A	L	L	F	A	S	H	T	S	L	A	V	T	Y	P	L	P	P	E	G	S	R	L	V	G	Q	S	F	T	V	T	V	P	D	H	N	T	Q	P	L	E	T	F	A	A	Q	Y	G	Q	G
Secondary structure
SS confidence
Disorder		?	?	?	?											?	?	?	?	?	?	?	?	?	?	?			?	?	?	?	?	?	?	?	?	?	?	?	?	?	?		?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	S	N	M	L	E	A	N	P	G	A	D	V	F	L	P	K	S	G	S	Q	L	T	I	P	Q	Q	L	I	L	P	D	T	V	R	K	G	I	V	V	N	V	A	E	M	R	L	Y	Y	Y	P	P	D	S	N	T	V	E	V	F
Secondary structure
SS confidence
Disorder													?													?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		P	I	G	I	G	Q	A	G	R	E	T	P	R	N	W	V	T	T	V	E	R	K	Q	E	A	P	T	W	T	P	T	P	N	T	R	R	E	Y	A	K	R	G	E	S	L	P	A	F	V	P	A	G	P	D	N	P	M	G	L	Y
Secondary structure
SS confidence
Disorder								?																											?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		A	I	Y	I	G	R	L	Y	A	I	H	G	T	N	A	N	F	G	I	G	L	R	V	S	Q	G	C	I	R	L	R	N	D	D	I	K	Y	L	F	D	N	V	P	V	G	T	R	V	Q	I	I	D	Q	P	V	K	Y	T	T	E
Secondary structure
SS confidence
Disorder																																																										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		P	D	G	S	N	W	L	E	V	H	E	P	L	S	R	N	R	A	E	Y	E	S	D	R	K	V	P	L	P	V	T	P	S	L	R	A	F	I	N	G	Q	E	V	D	V	N	R	A	N	A	A	L	Q	R	R	S	G	M	P	V
Secondary structure
SS confidence
Disorder															?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?				?	?	?	?	?	?	?	?												?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310
Sequence		Q	I	S	S	G	S	R	Q	M	F
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: 38 - 231 Aligned: 161 Modelled: 167 Confidence: 100.0% Identity: 32% 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 - 230 Aligned: 111 Modelled: 113 Confidence: 100.0% Identity: 36% Fold: L,D-transpeptidase catalytic domain-like Superfamily: L,D-transpeptidase catalytic domain-like Family: L,D-transpeptidase catalytic domain-like Phyre2 PDB 1zat chain A domain 1 Region: 93 - 230 Aligned: 118 Modelled: 120 Confidence: 100.0% Identity: 29% 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 - 230 Aligned: 120 Modelled: 122 Confidence: 100.0% Identity: 28% PDB header:transferase Chain: B: PDB Molecule:l,d-transpeptidase; PDBTitle: crystal structure of enterococcus faecium l,d-2 transpeptidase c442s mutant Phyre2 PDB 2l9y chain A Region: 35 - 87 Aligned: 51 Modelled: 53 Confidence: 98.3% Identity: 24% 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: 39 - 86 Aligned: 45 Modelled: 48 Confidence: 98.0% Identity: 29% Fold: LysM domain Superfamily: LysM domain Family: LysM domain Phyre2 PDB 2djp chain A Region: 36 - 85 Aligned: 48 Modelled: 50 Confidence: 97.9% 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 1e0g chain A Region: 39 - 87 Aligned: 45 Modelled: 49 Confidence: 97.8% Identity: 20% Fold: LysM domain Superfamily: LysM domain Family: LysM domain Phyre2 PDB 2gu1 chain A Region: 39 - 118 Aligned: 77 Modelled: 80 Confidence: 95.0% Identity: 16% PDB header:hydrolase Chain: A: PDB Molecule:zinc peptidase; PDBTitle: crystal structure of a zinc containing peptidase from2 vibrio cholerae Phyre2 PDB 3mca chain B Region: 206 - 229 Aligned: 24 Modelled: 24 Confidence: 51.1% 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: 206 - 249 Aligned: 39 Modelled: 42 Confidence: 46.7% Identity: 23% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Single strand DNA-binding domain, SSB Phyre2 PDB 1h5n chain C Region: 125 - 233 Aligned: 96 Modelled: 109 Confidence: 41.6% Identity: 17% PDB header:oxidoreductase Chain: C: PDB Molecule:dmso reductase; PDBTitle: dmso reductase modified by the presence of dms and air Phyre2 PDB 2kke chain A Region: 208 - 226 Aligned: 19 Modelled: 19 Confidence: 26.0% 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 1y5i chain A Region: 125 - 233 Aligned: 98 Modelled: 109 Confidence: 17.0% Identity: 15% 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: 205 - 233 Aligned: 27 Modelled: 29 Confidence: 14.4% Identity: 15% Fold: Double psi beta-barrel Superfamily: ADC-like Family: Formate dehydrogenase/DMSO reductase, C-terminal domain Phyre2 PDB 2k50 chain A Region: 204 - 247 Aligned: 44 Modelled: 44 Confidence: 10.2% Identity: 16% 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 2ken chain A Region: 206 - 251 Aligned: 42 Modelled: 46 Confidence: 9.6% Identity: 12% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved protein; PDBTitle: solution nmr structure of the ob domain (residues 67-166)2 of mm0293 from methanosarcina mazei. northeast structural3 genomics consortium target mar214a. Phyre2 PDB 3rf1 chain B Region: 203 - 216 Aligned: 14 Modelled: 12 Confidence: 9.3% Identity: 29% 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 Phyre2 PDB 2vw9 chain B Region: 208 - 249 Aligned: 42 Modelled: 42 Confidence: 9.0% Identity: 14% PDB header:dna-binding protein Chain: B: PDB Molecule:single-stranded dna binding protein; PDBTitle: single stranded dna binding protein complex from2 helicobacter pylori Phyre2 PDB 2ihe chain A Region: 207 - 244 Aligned: 38 Modelled: 38 Confidence: 8.9% Identity: 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 Phyre2 1 c1y7mB_ 2 d1y7ma1 3 d1zata1 4 c2hklB_ 5 c2l9yA_ 6 d1y7ma2 7 c2djpA_ 8 d1e0ga_ 9 c2gu1A_ 10 c3mcaB_ 11 d1wjja_ 12 c1h5nC_ 13 c2kkeA_ 14 c1y5iA_ 15 d1ogya1 16 c2k50A_ 17 c2kenA_ 18 c3rf1B_ 19 c2vw9B_ 20 c2iheA_ 21 22 23 24 25 26 27 28 29

Detailed template information

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

1 c1y7mB_ 100.0 32 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 36 Fold:L,D-transpeptidase catalytic domain-like Superfamily:L,D-transpeptidase catalytic domain-like Family:L,D-transpeptidase catalytic domain-like 3 d1zata1 100.0 29 Fold:L,D-transpeptidase catalytic domain-like Superfamily:L,D-transpeptidase catalytic domain-like Family:L,D-transpeptidase catalytic domain-like 4 c2hklB_ 100.0 28 PDB header:transferase Chain: B: PDB Molecule:l,d-transpeptidase; PDBTitle: crystal structure of enterococcus faecium l,d-2 transpeptidase c442s mutant 5 c2l9yA_ 98.3 24 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 98.0 29 Fold:LysM domain Superfamily:LysM domain Family:LysM domain 7 c2djpA_ 97.9 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 8 d1e0ga_ 97.8 20 Fold:LysM domain Superfamily:LysM domain Family:LysM domain 9 c2gu1A_ 95.0 16 PDB header:hydrolase Chain: A: PDB Molecule:zinc peptidase; PDBTitle: crystal structure of a zinc containing peptidase from2 vibrio cholerae 10 c3mcaB_ 51.1 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 11 d1wjja_ 46.7 23 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Single strand DNA-binding domain, SSB 12 c1h5nC_ 41.6 17 PDB header:oxidoreductase Chain: C: PDB Molecule:dmso reductase; PDBTitle: dmso reductase modified by the presence of dms and air 13 c2kkeA_ 26.0 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 c1y5iA_ 17.0 15 PDB header:oxidoreductase Chain: A: PDB Molecule:respiratory nitrate reductase 1 alpha chain; PDBTitle: the crystal structure of the narghi mutant nari-k86a 15 d1ogya1 14.4 15 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Formate dehydrogenase/DMSO reductase, C-terminal domain 16 c2k50A_ 10.2 16 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 c2kenA_ 9.6 12 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved protein; PDBTitle: solution nmr structure of the ob domain (residues 67-166)2 of mm0293 from methanosarcina mazei. northeast structural3 genomics consortium target mar214a. 18 c3rf1B_ 9.3 29 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 19 c2vw9B_ 9.0 14 PDB header:dna-binding protein Chain: B: PDB Molecule:single-stranded dna binding protein; PDBTitle: single stranded dna binding protein complex from2 helicobacter pylori 20 c2iheA_ 8.9 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 21 d2hthb1 not modelled 7.3 27 Fold:PH domain-like barrel Superfamily:PH domain-like Family:VPS36 N-terminal domain-like 22 c1r1gA_ not modelled 7.2 36 PDB header:toxin Chain: A: PDB Molecule:neurotoxin bmk37; PDBTitle: crystal structure of the scorpion toxin bmbkttx1 23 d1r1ga_ not modelled 7.2 36 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Scorpion toxin-like Family:Short-chain scorpion toxins 24 c1eqqD_ not modelled 7.2 15 PDB header:replication/rna Chain: D: PDB Molecule:single stranded dna binding protein; PDBTitle: single stranded dna binding protein and ssdna complex 25 c1r1gB_ not modelled 6.9 36 PDB header:toxin Chain: B: PDB Molecule:neurotoxin bmk37; PDBTitle: crystal structure of the scorpion toxin bmbkttx1 26 d1y0pa3 not modelled 6.4 17 Fold:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Superfamily:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Family:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain 27 d2c42a3 not modelled 6.1 25 Fold:TK C-terminal domain-like Superfamily:TK C-terminal domain-like Family:Pyruvate-ferredoxin oxidoreductase, PFOR, domain II 28 d2hh8a1 not modelled 5.6 33 Fold:YdfO-like Superfamily:YdfO-like Family:YdfO-like 29 c1eu1A_ not modelled 5.5 13 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.

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

---

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