Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	P	P	V	L	W	R	G	W	I	P	F	C	R	C	T	E	E	K	K	V	R	N	K	Q	V	V	L	L	I	A	G	I	S	G	I	V	T	G	I	I	V	S	L	N	I	P	F	I	R	Q	G	L	F	Y	P	A	S	P	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?												?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.
Sequence		E	I	V	V	S	L	S	L	T	F	S	V	S	V	V	F	F	V	G	A	I	V	G	W	I	S	V	S	E	I	Y	Y	S	R	M	T	G	L	N	E	S	S	E	I	S	E	G	T	Y	N	E	R	K
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 1w5c chain L Region: 69 - 81 Aligned: 13 Modelled: 13 Confidence: 22.3% Identity: 54% PDB header:photosynthesis Chain: L: PDB Molecule:cytochrome b559 beta subunit; PDBTitle: photosystem ii from thermosynechococcus elongatus Phyre2 PDB 2axt chain F domain 1 Region: 69 - 81 Aligned: 13 Modelled: 13 Confidence: 21.8% Identity: 54% Fold: Single transmembrane helix Superfamily: Cytochrome b559 subunits Family: Cytochrome b559 subunits Phyre2 PDB 1c2a chain A domain 1 Region: 7 - 20 Aligned: 14 Modelled: 14 Confidence: 19.2% Identity: 36% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Bowman-Birk inhibitor, BBI Family: Bowman-Birk inhibitor, BBI Phyre2 PDB 1fl2 chain A domain 2 Region: 5 - 36 Aligned: 32 Modelled: 32 Confidence: 15.0% Identity: 19% Fold: FAD/NAD(P)-binding domain Superfamily: FAD/NAD(P)-binding domain Family: FAD/NAD-linked reductases, N-terminal and central domains Phyre2 PDB 1j83 chain A Region: 94 - 109 Aligned: 16 Modelled: 16 Confidence: 14.3% Identity: 38% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: Family 17 carbohydrate binding module, CBM17 Phyre2 PDB 2fj8 chain A domain 1 Region: 7 - 20 Aligned: 14 Modelled: 14 Confidence: 13.8% Identity: 50% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Bowman-Birk inhibitor, BBI Family: Bowman-Birk inhibitor, BBI Phyre2 PDB 1efv chain A domain 2 Region: 3 - 35 Aligned: 33 Modelled: 33 Confidence: 11.1% Identity: 18% Fold: DHS-like NAD/FAD-binding domain Superfamily: DHS-like NAD/FAD-binding domain Family: C-terminal domain of the electron transfer flavoprotein alpha subunit Phyre2 PDB 1efp chain C Region: 8 - 45 Aligned: 38 Modelled: 38 Confidence: 11.0% Identity: 24% PDB header:electron transport Chain: C: PDB Molecule:protein (electron transfer flavoprotein); PDBTitle: electron transfer flavoprotein (etf) from paracoccus2 denitrificans Phyre2 PDB 1efp chain A domain 2 Region: 3 - 35 Aligned: 33 Modelled: 33 Confidence: 10.9% Identity: 18% Fold: DHS-like NAD/FAD-binding domain Superfamily: DHS-like NAD/FAD-binding domain Family: C-terminal domain of the electron transfer flavoprotein alpha subunit Phyre2 PDB 1tx6 chain J Region: 7 - 20 Aligned: 14 Modelled: 14 Confidence: 10.9% Identity: 50% PDB header:hydrolase/protein binding Chain: J: PDB Molecule:bowman-birk type trypsin inhibitor; PDBTitle: trypsin:bbi complex Phyre2 PDB 2bi8 chain A Region: 22 - 39 Aligned: 18 Modelled: 18 Confidence: 10.6% Identity: 39% PDB header:isomerase Chain: A: PDB Molecule:udp-galactopyranose mutase; PDBTitle: udp-galactopyranose mutase from klebsiella pneumoniae with2 reduced fad Phyre2 PDB 1w1n chain A Region: 5 - 12 Aligned: 8 Modelled: 8 Confidence: 9.5% Identity: 50% PDB header:transferase Chain: A: PDB Molecule:phosphatidylinositol 3-kinase tor1; PDBTitle: the solution structure of the fatc domain of the protein2 kinase tor1 from yeast Phyre2 PDB 1pbi chain A Region: 7 - 20 Aligned: 14 Modelled: 14 Confidence: 9.4% Identity: 29% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Bowman-Birk inhibitor, BBI Family: Bowman-Birk inhibitor, BBI Phyre2 PDB 2qn5 chain B Region: 7 - 18 Aligned: 12 Modelled: 11 Confidence: 7.6% Identity: 42% PDB header:hydrolase inhibitor/hydrolase Chain: B: PDB Molecule:bowman-birk type bran trypsin inhibitor; PDBTitle: crystal structure and functional study of the bowman-birk2 inhibitor from rice bran in complex with bovine trypsin Phyre2 PDB 2zyl chain A Region: 1 - 29 Aligned: 29 Modelled: 29 Confidence: 7.4% Identity: 17% PDB header:oxidoreductase Chain: A: PDB Molecule:possible oxidoreductase; PDBTitle: crystal structure of 3-ketosteroid-9-alpha-hydroxylase2 (ksha) from m. tuberculosis Phyre2 PDB 2pd0 chain D Region: 2 - 14 Aligned: 13 Modelled: 13 Confidence: 7.3% Identity: 38% PDB header:structural genomics, unknown function Chain: D: PDB Molecule:hypothetical protein; PDBTitle: protein cgd2_2020 from cryptosporidium parvum Phyre2 PDB 3cls chain D domain 2 Region: 3 - 35 Aligned: 33 Modelled: 33 Confidence: 7.3% Identity: 27% Fold: DHS-like NAD/FAD-binding domain Superfamily: DHS-like NAD/FAD-binding domain Family: C-terminal domain of the electron transfer flavoprotein alpha subunit Phyre2 PDB 2fqc chain A Region: 11 - 15 Aligned: 5 Modelled: 5 Confidence: 6.9% Identity: 80% PDB header:toxin Chain: A: PDB Molecule:conotoxin pl14a; PDBTitle: solution structure of conotoxin pl14a Phyre2 PDB 1zq1 chain D Region: 12 - 59 Aligned: 48 Modelled: 48 Confidence: 6.7% Identity: 8% PDB header:lyase Chain: D: PDB Molecule:glutamyl-trna(gln) amidotransferase subunit e; PDBTitle: structure of gatde trna-dependent amidotransferase from2 pyrococcus abyssi Phyre2 PDB 2bi7 chain A domain 1 Region: 22 - 40 Aligned: 19 Modelled: 19 Confidence: 6.7% Identity: 37% Fold: Nucleotide-binding domain Superfamily: Nucleotide-binding domain Family: UDP-galactopyranose mutase, N-terminal domain Phyre2 1 c1w5cL_ 2 d2axtf1 3 d1c2aa1 4 d1fl2a2 5 d1j83a_ 6 d2fj8a1 7 d1efva2 8 c1efpC_ 9 d1efpa2 10 c1tx6J_ 11 c2bi8A_ 12 c1w1nA_ 13 d1pbia_ 14 c2qn5B_ 15 c2zylA_ 16 c2pd0D_ 17 d3clsd2 18 c2fqcA_ 19 c1zq1D_ 20 d2bi7a1 21 22 23 24 25 26 27 28 29

Detailed template information

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

1 c1w5cL_ 22.3 54 PDB header:photosynthesis Chain: L: PDB Molecule:cytochrome b559 beta subunit; PDBTitle: photosystem ii from thermosynechococcus elongatus 2 d2axtf1 21.8 54 Fold:Single transmembrane helix Superfamily:Cytochrome b559 subunits Family:Cytochrome b559 subunits 3 d1c2aa1 19.2 36 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Bowman-Birk inhibitor, BBI Family:Bowman-Birk inhibitor, BBI 4 d1fl2a2 15.0 19 Fold:FAD/NAD(P)-binding domain Superfamily:FAD/NAD(P)-binding domain Family:FAD/NAD-linked reductases, N-terminal and central domains 5 d1j83a_ 14.3 38 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:Family 17 carbohydrate binding module, CBM17 6 d2fj8a1 13.8 50 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Bowman-Birk inhibitor, BBI Family:Bowman-Birk inhibitor, BBI 7 d1efva2 11.1 18 Fold:DHS-like NAD/FAD-binding domain Superfamily:DHS-like NAD/FAD-binding domain Family:C-terminal domain of the electron transfer flavoprotein alpha subunit 8 c1efpC_ 11.0 24 PDB header:electron transport Chain: C: PDB Molecule:protein (electron transfer flavoprotein); PDBTitle: electron transfer flavoprotein (etf) from paracoccus2 denitrificans 9 d1efpa2 10.9 18 Fold:DHS-like NAD/FAD-binding domain Superfamily:DHS-like NAD/FAD-binding domain Family:C-terminal domain of the electron transfer flavoprotein alpha subunit 10 c1tx6J_ 10.9 50 PDB header:hydrolase/protein binding Chain: J: PDB Molecule:bowman-birk type trypsin inhibitor; PDBTitle: trypsin:bbi complex 11 c2bi8A_ 10.6 39 PDB header:isomerase Chain: A: PDB Molecule:udp-galactopyranose mutase; PDBTitle: udp-galactopyranose mutase from klebsiella pneumoniae with2 reduced fad 12 c1w1nA_ 9.5 50 PDB header:transferase Chain: A: PDB Molecule:phosphatidylinositol 3-kinase tor1; PDBTitle: the solution structure of the fatc domain of the protein2 kinase tor1 from yeast 13 d1pbia_ 9.4 29 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Bowman-Birk inhibitor, BBI Family:Bowman-Birk inhibitor, BBI 14 c2qn5B_ 7.6 42 PDB header:hydrolase inhibitor/hydrolase Chain: B: PDB Molecule:bowman-birk type bran trypsin inhibitor; PDBTitle: crystal structure and functional study of the bowman-birk2 inhibitor from rice bran in complex with bovine trypsin 15 c2zylA_ 7.4 17 PDB header:oxidoreductase Chain: A: PDB Molecule:possible oxidoreductase; PDBTitle: crystal structure of 3-ketosteroid-9-alpha-hydroxylase2 (ksha) from m. tuberculosis 16 c2pd0D_ 7.3 38 PDB header:structural genomics, unknown function Chain: D: PDB Molecule:hypothetical protein; PDBTitle: protein cgd2_2020 from cryptosporidium parvum 17 d3clsd2 7.3 27 Fold:DHS-like NAD/FAD-binding domain Superfamily:DHS-like NAD/FAD-binding domain Family:C-terminal domain of the electron transfer flavoprotein alpha subunit 18 c2fqcA_ 6.9 80 PDB header:toxin Chain: A: PDB Molecule:conotoxin pl14a; PDBTitle: solution structure of conotoxin pl14a 19 c1zq1D_ 6.7 8 PDB header:lyase Chain: D: PDB Molecule:glutamyl-trna(gln) amidotransferase subunit e; PDBTitle: structure of gatde trna-dependent amidotransferase from2 pyrococcus abyssi 20 d2bi7a1 6.7 37 Fold:Nucleotide-binding domain Superfamily:Nucleotide-binding domain Family:UDP-galactopyranose mutase, N-terminal domain 21 d2d6fc3 not modelled 6.6 21 Fold:Glutamine synthetase/guanido kinase Superfamily:Glutamine synthetase/guanido kinase Family:GatB/GatE catalytic domain-like 22 d1cqxa2 not modelled 6.2 21 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Riboflavin synthase domain-like Family:Ferredoxin reductase FAD-binding domain-like 23 d1u97a_ not modelled 6.1 46 Fold:Cysteine alpha-hairpin motif Superfamily:Cysteine alpha-hairpin motif Family:COX17-like 24 d1pm6a_ not modelled 5.9 20 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Excisionase-like 25 d1qmva_ not modelled 5.8 23 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione peroxidase-like 26 c3fnvB_ not modelled 5.8 40 PDB header:metal binding protein Chain: B: PDB Molecule:cdgsh iron sulfur domain-containing protein 2; PDBTitle: crystal structure of miner1: the redox-active 2fe-2s protein causative2 in wolfram syndrome 2 27 c2pnvA_ not modelled 5.5 50 PDB header:membrane protein Chain: A: PDB Molecule:small conductance calcium-activated potassium PDBTitle: crystal structure of the leucine zipper domain of small-2 conductance ca2+-activated k+ (skca) channel from rattus3 norvegicus 28 c2rnbA_ not modelled 5.4 54 PDB header:metal transport Chain: A: PDB Molecule:cytochrome c oxidase copper chaperone; PDBTitle: solution structure of human cu(i)cox17 29 d2v1ra1 not modelled 5.3 31 Fold:SH3-like barrel Superfamily:SH3-domain Family:SH3-domain

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