Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	K	L	I	L	I	A	I	M	A	S	G	L	V	A	C	A	Q	S	T	A	P	Q	E	D	S	R	L	K	E	A	Y	S	A	C	I	N	T	A	Q	G	S	P	E	K	I	E	A	C	Q	S	V	L	N	V	L	K	K	E
Secondary structure
SS confidence
Disorder		?														?	?	?	?	?	?	?	?	?	?	?	?												?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.
Sequence		K	Q	H	Q	Q	F	A	D	Q	E	S	V	R	V	L	D	Y	Q	Q	C	L	R	A	T	Q	T	G	N	D	Q	A	V	K	A	D	C	D	K	V	W	Q	E	I	R	S	N	N	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 1b1x chain A domain 1 Region: 70 - 101 Aligned: 32 Modelled: 32 Confidence: 21.0% Identity: 22% Fold: Periplasmic binding protein-like II Superfamily: Periplasmic binding protein-like II Family: Transferrin Phyre2 PDB 2jpn chain A Region: 24 - 61 Aligned: 32 Modelled: 38 Confidence: 18.4% Identity: 28% PDB header:hydrolase Chain: A: PDB Molecule:atp-dependent dna helicase uvsw; PDBTitle: solution structure of t4 bacteriophage helicase uvsw.1 Phyre2 PDB 1ce2 chain A domain 1 Region: 43 - 104 Aligned: 58 Modelled: 62 Confidence: 15.1% Identity: 24% Fold: Periplasmic binding protein-like II Superfamily: Periplasmic binding protein-like II Family: Transferrin Phyre2 PDB 1ppj chain W Region: 97 - 106 Aligned: 10 Modelled: 10 Confidence: 14.8% Identity: 30% Fold: Single transmembrane helix Superfamily: Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family: Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 2b6d chain A domain 1 Region: 72 - 108 Aligned: 37 Modelled: 37 Confidence: 13.4% Identity: 11% Fold: Periplasmic binding protein-like II Superfamily: Periplasmic binding protein-like II Family: Transferrin Phyre2 PDB 3cx5 chain I domain 1 Region: 97 - 105 Aligned: 9 Modelled: 9 Confidence: 12.9% Identity: 22% Fold: Single transmembrane helix Superfamily: Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family: Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 1qr0 chain A domain 2 Region: 29 - 37 Aligned: 9 Modelled: 9 Confidence: 12.7% Identity: 22% Fold: 4'-phosphopantetheinyl transferase Superfamily: 4'-phosphopantetheinyl transferase Family: 4'-Phosphopantetheinyl transferase SFP Phyre2 PDB 1dtz chain A domain 1 Region: 72 - 101 Aligned: 30 Modelled: 30 Confidence: 12.6% Identity: 27% Fold: Periplasmic binding protein-like II Superfamily: Periplasmic binding protein-like II Family: Transferrin Phyre2 PDB 2hav chain A domain 1 Region: 72 - 108 Aligned: 37 Modelled: 37 Confidence: 12.4% Identity: 16% Fold: Periplasmic binding protein-like II Superfamily: Periplasmic binding protein-like II Family: Transferrin Phyre2 PDB 1ppj chain J Region: 97 - 106 Aligned: 10 Modelled: 10 Confidence: 11.2% Identity: 30% Fold: Single transmembrane helix Superfamily: Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family: Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 1iej chain A Region: 72 - 101 Aligned: 30 Modelled: 30 Confidence: 11.2% Identity: 23% Fold: Periplasmic binding protein-like II Superfamily: Periplasmic binding protein-like II Family: Transferrin Phyre2 PDB 1h76 chain A domain 1 Region: 72 - 101 Aligned: 30 Modelled: 30 Confidence: 10.8% Identity: 27% Fold: Periplasmic binding protein-like II Superfamily: Periplasmic binding protein-like II Family: Transferrin Phyre2 PDB 1oxj chain A domain 2 Region: 48 - 79 Aligned: 31 Modelled: 32 Confidence: 10.4% Identity: 13% Fold: alpha-alpha superhelix Superfamily: ARM repeat Family: PHAT domain Phyre2 PDB 1mse chain C Region: 23 - 35 Aligned: 13 Modelled: 13 Confidence: 10.3% Identity: 23% PDB header:dna binding protein/dna Chain: C: PDB Molecule:c-myb dna-binding domain; PDBTitle: solution structure of a specific dna complex of the myb dna-2 binding domain with cooperative recognition helices Phyre2 PDB 1jnf chain A domain 1 Region: 72 - 101 Aligned: 30 Modelled: 30 Confidence: 9.2% Identity: 27% Fold: Periplasmic binding protein-like II Superfamily: Periplasmic binding protein-like II Family: Transferrin Phyre2 PDB 1b1x chain A domain 2 Region: 72 - 100 Aligned: 29 Modelled: 29 Confidence: 8.3% Identity: 14% Fold: Periplasmic binding protein-like II Superfamily: Periplasmic binding protein-like II Family: Transferrin Phyre2 PDB 3osg chain A Region: 23 - 36 Aligned: 14 Modelled: 14 Confidence: 8.3% Identity: 43% PDB header:transcription/dna Chain: A: PDB Molecule:myb21; PDBTitle: the structure of protozoan parasite trichomonas vaginalis myb2 in2 complex with mre-1-12 dna Phyre2 PDB 1tfd chain A Region: 72 - 101 Aligned: 30 Modelled: 30 Confidence: 8.3% Identity: 27% Fold: Periplasmic binding protein-like II Superfamily: Periplasmic binding protein-like II Family: Transferrin Phyre2 PDB 2qq0 chain B Region: 87 - 104 Aligned: 18 Modelled: 18 Confidence: 7.8% Identity: 17% PDB header:transferase Chain: B: PDB Molecule:thymidine kinase; PDBTitle: thymidine kinase from thermotoga maritima in complex with2 thymidine + appnhp Phyre2 PDB 3nxb chain B Region: 45 - 66 Aligned: 22 Modelled: 22 Confidence: 7.6% Identity: 32% PDB header:transcription Chain: B: PDB Molecule:cat eye syndrome critical region protein 2; PDBTitle: crystal structure of the bromodomain of human cecr2 Phyre2 1 d1b1xa1 2 c2jpnA_ 3 d1ce2a1 4 d1ppjw_ 5 d2b6da1 6 d3cx5i1 7 d1qr0a2 8 d1dtza1 9 d2hava1 10 d1ppjj_ 11 d1ieja_ 12 d1h76a1 13 d1oxja2 14 c1mseC_ 15 d1jnfa1 16 d1b1xa2 17 c3osgA_ 18 d1tfda_ 19 c2qq0B_ 20 c3nxbB_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34

Detailed template information

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

1 d1b1xa1 21.0 22 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Transferrin 2 c2jpnA_ 18.4 28 PDB header:hydrolase Chain: A: PDB Molecule:atp-dependent dna helicase uvsw; PDBTitle: solution structure of t4 bacteriophage helicase uvsw.1 3 d1ce2a1 15.1 24 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Transferrin 4 d1ppjw_ 14.8 30 Fold:Single transmembrane helix Superfamily:Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family:Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 5 d2b6da1 13.4 11 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Transferrin 6 d3cx5i1 12.9 22 Fold:Single transmembrane helix Superfamily:Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family:Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 7 d1qr0a2 12.7 22 Fold:4'-phosphopantetheinyl transferase Superfamily:4'-phosphopantetheinyl transferase Family:4'-Phosphopantetheinyl transferase SFP 8 d1dtza1 12.6 27 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Transferrin 9 d2hava1 12.4 16 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Transferrin 10 d1ppjj_ 11.2 30 Fold:Single transmembrane helix Superfamily:Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family:Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 11 d1ieja_ 11.2 23 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Transferrin 12 d1h76a1 10.8 27 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Transferrin 13 d1oxja2 10.4 13 Fold:alpha-alpha superhelix Superfamily:ARM repeat Family:PHAT domain 14 c1mseC_ 10.3 23 PDB header:dna binding protein/dna Chain: C: PDB Molecule:c-myb dna-binding domain; PDBTitle: solution structure of a specific dna complex of the myb dna-2 binding domain with cooperative recognition helices 15 d1jnfa1 9.2 27 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Transferrin 16 d1b1xa2 8.3 14 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Transferrin 17 c3osgA_ 8.3 43 PDB header:transcription/dna Chain: A: PDB Molecule:myb21; PDBTitle: the structure of protozoan parasite trichomonas vaginalis myb2 in2 complex with mre-1-12 dna 18 d1tfda_ 8.3 27 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Transferrin 19 c2qq0B_ 7.8 17 PDB header:transferase Chain: B: PDB Molecule:thymidine kinase; PDBTitle: thymidine kinase from thermotoga maritima in complex with2 thymidine + appnhp 20 c3nxbB_ 7.6 32 PDB header:transcription Chain: B: PDB Molecule:cat eye syndrome critical region protein 2; PDBTitle: crystal structure of the bromodomain of human cecr2 21 c2yynA_ not modelled 7.4 23 PDB header:transcription Chain: A: PDB Molecule:transcription intermediary factor 1-alpha; PDBTitle: crystal sturcture of human bromodomain protein 22 d2d3ia2 not modelled 7.0 23 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Transferrin 23 d1u78a2 not modelled 6.5 44 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 24 c3mmyF_ not modelled 6.5 50 PDB header:nuclear protein Chain: F: PDB Molecule:nuclear pore complex protein nup98; PDBTitle: structural and functional analysis of the interaction between the2 nucleoporin nup98 and the mrna export factor rae1 25 d1h6gb1 not modelled 6.2 26 Fold:Four-helical up-and-down bundle Superfamily:alpha-catenin/vinculin-like Family:alpha-catenin/vinculin 26 d1mxaa1 not modelled 6.2 50 Fold:S-adenosylmethionine synthetase Superfamily:S-adenosylmethionine synthetase Family:S-adenosylmethionine synthetase 27 c1o8tA_ not modelled 6.1 38 PDB header:lipid transport Chain: A: PDB Molecule:apolipoprotein c-ii; PDBTitle: global structure and dynamics of human apolipoprotein cii2 in complex with micelles: evidence for increased mobility3 of the helix involvved in the activation of lipoprotein4 lipase. 28 d1gv2a2 not modelled 6.1 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain 29 d2pf1a2 not modelled 5.7 41 Fold:GLA-domain Superfamily:GLA-domain Family:GLA-domain 30 d1tkna_ not modelled 5.6 18 Fold:STAT-like Superfamily:CAPPD, an extracellular domain of amyloid beta A4 protein Family:CAPPD, an extracellular domain of amyloid beta A4 protein 31 d2p02a1 not modelled 5.4 50 Fold:S-adenosylmethionine synthetase Superfamily:S-adenosylmethionine synthetase Family:S-adenosylmethionine synthetase 32 d1a5ja1 not modelled 5.4 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain 33 d1qm4a1 not modelled 5.4 50 Fold:S-adenosylmethionine synthetase Superfamily:S-adenosylmethionine synthetase Family:S-adenosylmethionine synthetase 34 c1o4uA_ not modelled 5.3 15 PDB header:transferase Chain: A: PDB Molecule:type ii quinolic acid phosphoribosyltransferase; PDBTitle: crystal structure of a nicotinate nucleotide pyrophosphorylase2 (tm1645) from thermotoga maritima at 2.50 a resolution

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