Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	G	Q	S	S	S	Q	A	A	T	P	I	Q	W	W	K	P	A	L	F	F	L	V	V	I	A	G	L	W	Y	V	K	W	E	P	Y	Y	G	K	A	F	T	A	A	E	T	H	S	I	G	K	S	I	L	A	Q	A	D	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?																																							?	?	?	?	?		?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		N	P	W	Q	A	A	L	D	Y	A	M	I	Y	F	L	A	V	W	K	A	A	V	L	G	V	I	L	G	S	L	I	Q	V	L	I	P	R	D	W	L	L	R	T	L	G	Q	S	R	F	R	G	T	L	L	G	T	L	F	S	L
Secondary structure
SS confidence
Disorder																																																	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		P	G	M	M	C	T	C	C	A	A	P	V	A	A	G	M	R	R	Q	Q	V	S	M	G	G	A	L	A	F	W	M	G	N	P	V	L	N	P	A	T	L	V	F	M	G	F	V	L	G	W	G	F	A	A	I	R	L	V	A	G
Secondary structure
SS confidence
Disorder																				?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	V	M	V	L	L	I	A	T	L	V	Q	K	W	V	R	E	T	P	Q	T	Q	A	P	V	E	I	D	I	P	E	A	Q	G	G	F	F	S	R	W	G	R	A	L	W	T	L	F	W	S	T	I	P	V	Y	I	L	A	V	L
Secondary structure
SS confidence
Disorder																																?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		V	L	G	A	A	R	V	W	L	F	P	H	A	D	G	A	V	D	N	S	L	M	W	V	V	A	M	A	V	A	G	C	L	F	V	I	P	T	A	A	E	I	P	I	V	Q	T	M	M	L	A	G	M	G	T	A	P	A	L	A
Secondary structure
SS confidence
Disorder																	?																								?	?										?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.
Sequence		L	L	M	T	L	P	A	V	S	L	P	S	L	I	M	L	R	K	A	F	P	A	K	A	L	W	L	T	G	A	M	V	A	V	S	G	V	I	V	G	G	L	A	L	L	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 3ldg chain A Region: 123 - 144 Aligned: 22 Modelled: 22 Confidence: 15.1% Identity: 14% PDB header:transferase Chain: A: PDB Molecule:putative uncharacterized protein smu.472; PDBTitle: crystal structure of smu.472, a putative methyltransferase complexed2 with sah Phyre2 PDB 2wpn chain B Region: 123 - 129 Aligned: 6 Modelled: 7 Confidence: 15.1% Identity: 17% PDB header:oxidoreductase Chain: B: PDB Molecule:periplasmic [nifese] hydrogenase, large subunit, PDBTitle: structure of the oxidised, as-isolated nifese hydrogenase2 from d. vulgaris hildenborough Phyre2 PDB 3k3g chain A Region: 59 - 317 Aligned: 242 Modelled: 242 Confidence: 13.7% Identity: 16% PDB header:transport protein Chain: A: PDB Molecule:urea transporter; PDBTitle: crystal structure of the urea transporter from desulfovibrio vulgaris2 bound to 1,3-dimethylurea Phyre2 PDB 1cc1 chain L Region: 123 - 129 Aligned: 6 Modelled: 7 Confidence: 11.5% Identity: 17% Fold: HydB/Nqo4-like Superfamily: HydB/Nqo4-like Family: Nickel-iron hydrogenase, large subunit Phyre2 PDB 2f2b chain A Region: 151 - 237 Aligned: 87 Modelled: 87 Confidence: 10.3% Identity: 11% PDB header:membrane protein Chain: A: PDB Molecule:aquaporin aqpm; PDBTitle: crystal structure of integral membrane protein aquaporin aqpm at 1.68a2 resolution Phyre2 PDB 2ciw chain A domain 2 Region: 7 - 21 Aligned: 15 Modelled: 15 Confidence: 9.7% Identity: 27% Fold: EF Hand-like Superfamily: Cloroperoxidase Family: Cloroperoxidase Phyre2 PDB 2haw chain A domain 1 Region: 123 - 156 Aligned: 33 Modelled: 34 Confidence: 8.8% Identity: 9% Fold: DHH phosphoesterases Superfamily: DHH phosphoesterases Family: Manganese-dependent inorganic pyrophosphatase (family II) Phyre2 PDB 1wui chain L domain 1 Region: 123 - 129 Aligned: 6 Modelled: 7 Confidence: 8.5% Identity: 17% Fold: HydB/Nqo4-like Superfamily: HydB/Nqo4-like Family: Nickel-iron hydrogenase, large subunit Phyre2 PDB 3k0b chain A Region: 123 - 144 Aligned: 22 Modelled: 22 Confidence: 8.2% Identity: 23% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:predicted n6-adenine-specific dna methylase; PDBTitle: crystal structure of a predicted n6-adenine-specific dna methylase2 from listeria monocytogenes str. 4b f2365 Phyre2 PDB 1hgv chain A Region: 63 - 75 Aligned: 13 Modelled: 13 Confidence: 7.9% Identity: 31% PDB header:virus Chain: A: PDB Molecule:ph75 inovirus major coat protein; PDBTitle: filamentous bacteriophage ph75 Phyre2 PDB 2fqc chain A Region: 104 - 127 Aligned: 24 Modelled: 24 Confidence: 7.7% Identity: 13% PDB header:toxin Chain: A: PDB Molecule:conotoxin pl14a; PDBTitle: solution structure of conotoxin pl14a Phyre2 PDB 2k7g chain A Region: 122 - 128 Aligned: 7 Modelled: 7 Confidence: 6.9% Identity: 29% PDB header:plant protein Chain: A: PDB Molecule:varv peptide f; PDBTitle: solution structure of varv f Phyre2 PDB 2lam chain A Region: 122 - 128 Aligned: 7 Modelled: 7 Confidence: 6.6% Identity: 29% PDB header:antiviral protein Chain: A: PDB Molecule:cyclotide cter m; PDBTitle: three-dimensional structure of the cyclotide cter m Phyre2 PDB 3e4h chain A Region: 122 - 128 Aligned: 7 Modelled: 7 Confidence: 6.5% Identity: 29% PDB header:plant protein Chain: A: PDB Molecule:varv peptide f; PDBTitle: crystal structure of the cyclotide varv f Phyre2 PDB 1wij chain A Region: 82 - 99 Aligned: 18 Modelled: 18 Confidence: 6.2% Identity: 39% Fold: LEM/SAP HeH motif Superfamily: DNA-binding domain of EIN3-like Family: DNA-binding domain of EIN3-like Phyre2 PDB 1pt4 chain A Region: 122 - 128 Aligned: 7 Modelled: 7 Confidence: 5.8% Identity: 29% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Cyclotides Family: Kalata B1 Phyre2 PDB 1n1u chain A Region: 122 - 128 Aligned: 7 Modelled: 7 Confidence: 5.7% Identity: 29% PDB header:antibiotic Chain: A: PDB Molecule:kalata b1; PDBTitle: nmr structure of [ala1,15]kalata b1 Phyre2 PDB 1n1u chain A Region: 122 - 128 Aligned: 7 Modelled: 7 Confidence: 5.7% Identity: 29% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Cyclotides Family: Kalata B1 Phyre2 PDB 2f2j chain A Region: 122 - 128 Aligned: 7 Modelled: 7 Confidence: 5.6% Identity: 43% PDB header:antimicrobial protein Chain: A: PDB Molecule:kalata-b1; PDBTitle: solution structure of [w19k, p20n, v21k]-kalata b1 Phyre2 PDB 1nb1 chain A Region: 122 - 128 Aligned: 7 Modelled: 7 Confidence: 5.6% Identity: 43% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Cyclotides Family: Kalata B1 Phyre2 1 c3ldgA_ 2 c2wpnB_ 3 c3k3gA_ 4 d1cc1l_ 5 c2f2bA_ 6 d2ciwa2 7 d2hawa1 8 d1wuil1 9 c3k0bA_ 10 c1hgvA_ 11 c2fqcA_ 12 c2k7gA_ 13 c2lamA_ 14 c3e4hA_ 15 d1wija_ 16 d1pt4a_ 17 c1n1uA_ 18 d1n1ua_ 19 c2f2jA_ 20 d1nb1a_ 21 22 23 24 25

Detailed template information

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

1 c3ldgA_ 15.1 14 PDB header:transferase Chain: A: PDB Molecule:putative uncharacterized protein smu.472; PDBTitle: crystal structure of smu.472, a putative methyltransferase complexed2 with sah 2 c2wpnB_ 15.1 17 PDB header:oxidoreductase Chain: B: PDB Molecule:periplasmic [nifese] hydrogenase, large subunit, PDBTitle: structure of the oxidised, as-isolated nifese hydrogenase2 from d. vulgaris hildenborough 3 c3k3gA_ 13.7 16 PDB header:transport protein Chain: A: PDB Molecule:urea transporter; PDBTitle: crystal structure of the urea transporter from desulfovibrio vulgaris2 bound to 1,3-dimethylurea 4 d1cc1l_ 11.5 17 Fold:HydB/Nqo4-like Superfamily:HydB/Nqo4-like Family:Nickel-iron hydrogenase, large subunit 5 c2f2bA_ 10.3 11 PDB header:membrane protein Chain: A: PDB Molecule:aquaporin aqpm; PDBTitle: crystal structure of integral membrane protein aquaporin aqpm at 1.68a2 resolution 6 d2ciwa2 9.7 27 Fold:EF Hand-like Superfamily:Cloroperoxidase Family:Cloroperoxidase 7 d2hawa1 8.8 9 Fold:DHH phosphoesterases Superfamily:DHH phosphoesterases Family:Manganese-dependent inorganic pyrophosphatase (family II) 8 d1wuil1 8.5 17 Fold:HydB/Nqo4-like Superfamily:HydB/Nqo4-like Family:Nickel-iron hydrogenase, large subunit 9 c3k0bA_ 8.2 23 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:predicted n6-adenine-specific dna methylase; PDBTitle: crystal structure of a predicted n6-adenine-specific dna methylase2 from listeria monocytogenes str. 4b f2365 10 c1hgvA_ 7.9 31 PDB header:virus Chain: A: PDB Molecule:ph75 inovirus major coat protein; PDBTitle: filamentous bacteriophage ph75 11 c2fqcA_ 7.7 13 PDB header:toxin Chain: A: PDB Molecule:conotoxin pl14a; PDBTitle: solution structure of conotoxin pl14a 12 c2k7gA_ 6.9 29 PDB header:plant protein Chain: A: PDB Molecule:varv peptide f; PDBTitle: solution structure of varv f 13 c2lamA_ 6.6 29 PDB header:antiviral protein Chain: A: PDB Molecule:cyclotide cter m; PDBTitle: three-dimensional structure of the cyclotide cter m 14 c3e4hA_ 6.5 29 PDB header:plant protein Chain: A: PDB Molecule:varv peptide f; PDBTitle: crystal structure of the cyclotide varv f 15 d1wija_ 6.2 39 Fold:LEM/SAP HeH motif Superfamily:DNA-binding domain of EIN3-like Family:DNA-binding domain of EIN3-like 16 d1pt4a_ 5.8 29 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Cyclotides Family:Kalata B1 17 c1n1uA_ 5.7 29 PDB header:antibiotic Chain: A: PDB Molecule:kalata b1; PDBTitle: nmr structure of [ala1,15]kalata b1 18 d1n1ua_ 5.7 29 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Cyclotides Family:Kalata B1 19 c2f2jA_ 5.6 43 PDB header:antimicrobial protein Chain: A: PDB Molecule:kalata-b1; PDBTitle: solution structure of [w19k, p20n, v21k]-kalata b1 20 d1nb1a_ 5.6 43 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Cyclotides Family:Kalata B1 21 c2f2iA_ not modelled 5.5 43 PDB header:antimicrobial protein Chain: A: PDB Molecule:kalata-b1; PDBTitle: solution structure of [p20d,v21k]-kalata b1 22 c2fqaA_ not modelled 5.5 29 PDB header:plant protein Chain: A: PDB Molecule:violacin 1; PDBTitle: violacin a 23 c2khbA_ not modelled 5.5 43 PDB header:antimicrobial protein Chain: A: PDB Molecule:kalata-b1; PDBTitle: solution structure of linear kalata b1 (loop 6) 24 c1motA_ not modelled 5.4 55 PDB header:membrane protein Chain: A: PDB Molecule:glycine receptor alpha-1 chain; PDBTitle: nmr structure of extended second transmembrane domain of2 glycine receptor alpha1 subunit in sds micelles 25 c2gj0A_ not modelled 5.2 27 PDB header:plant protein Chain: A: PDB Molecule:cycloviolacin o14; PDBTitle: cycloviolacin o14

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