Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	K	R	T	L	L	A	A	A	I	F	S	A	L	P	A	Y	A	G	L	T	S	I	T	A	G	Y	D	F	T	D	Y	S	G	D	H	G	N	R	N	L	A	Y	A	E	L	V	A	K	V	E	N	A	T	L	L	F	N	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?										?	?																?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	Q	G	R	R	D	Y	E	T	E	H	F	N	A	T	R	G	Q	G	A	V	W	Y	K	W	N	N	W	L	T	T	R	T	G	I	A	F	A	D	N	T	P	V	F	A	R	Q	D	F	R	Q	D	I	N	L	A	L	L	P	K
Secondary structure
SS confidence
Disorder				?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?																		?																							?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		T	L	F	T	T	G	Y	R	Y	T	K	Y	Y	D	D	V	E	V	D	A	W	Q	G	G	V	S	L	Y	T	G	P	V	I	T	S	Y	R	Y	T	H	Y	D	S	S	D	A	G	G	S	Y	S	N	M	I	S	V	R	L	N	D
Secondary structure
SS confidence
Disorder																																										?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		P	R	G	T	G	Y	T	Q	L	W	L	S	R	G	T	G	A	Y	T	Y	D	W	T	P	E	T	R	Y	G	S	M	K	S	V	S	L	Q	R	I	Q	P	L	T	E	Q	L	N	L	G	L	T	A	G	K	V	W	Y	D	T	P
Secondary structure
SS confidence
Disorder		?	?	?	?												?											?		?		?		?	?	?	?	?		?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.
Sequence		T	D	D	F	N	G	L	Q	L	A	A	R	L	T	W	K	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 1t16 chain A Region: 23 - 163 Aligned: 125 Modelled: 141 Confidence: 47.6% Identity: 22% Fold: Transmembrane beta-barrels Superfamily: Porins Family: Outer membrane protein transport protein Phyre2 PDB 1ew4 chain A Region: 188 - 218 Aligned: 31 Modelled: 31 Confidence: 44.5% Identity: 29% Fold: N domain of copper amine oxidase-like Superfamily: Frataxin/Nqo15-like Family: Frataxin-like Phyre2 PDB 3dwo chain X Region: 23 - 129 Aligned: 87 Modelled: 89 Confidence: 42.3% Identity: 24% PDB header:membrane protein Chain: X: PDB Molecule:probable outer membrane protein; PDBTitle: crystal structure of a pseudomonas aeruginosa fadl homologue Phyre2 PDB 3pam chain B Region: 93 - 128 Aligned: 36 Modelled: 35 Confidence: 35.1% Identity: 14% PDB header:transport protein Chain: B: PDB Molecule:transmembrane protein; PDBTitle: crystal structure of a domain of transmembrane protein of abc-type2 oligopeptide transport system from bartonella henselae str. houston-1 Phyre2 PDB 1ekg chain A Region: 188 - 218 Aligned: 31 Modelled: 31 Confidence: 28.4% Identity: 32% Fold: N domain of copper amine oxidase-like Superfamily: Frataxin/Nqo15-like Family: Frataxin-like Phyre2 PDB 2ga5 chain A domain 1 Region: 188 - 203 Aligned: 16 Modelled: 16 Confidence: 25.9% Identity: 25% Fold: N domain of copper amine oxidase-like Superfamily: Frataxin/Nqo15-like Family: Frataxin-like Phyre2 PDB 3lo4 chain B Region: 63 - 82 Aligned: 15 Modelled: 20 Confidence: 25.7% Identity: 53% PDB header:antimicrobial protein Chain: B: PDB Molecule:neutrophil defensin 1; PDBTitle: crystal structure of human alpha-defensin 1 (r24a mutant) Phyre2 PDB 3lo4 chain A Region: 63 - 82 Aligned: 15 Modelled: 20 Confidence: 25.7% Identity: 53% PDB header:antimicrobial protein Chain: A: PDB Molecule:neutrophil defensin 1; PDBTitle: crystal structure of human alpha-defensin 1 (r24a mutant) Phyre2 PDB 2fql chain A domain 1 Region: 188 - 203 Aligned: 16 Modelled: 16 Confidence: 23.7% Identity: 25% Fold: N domain of copper amine oxidase-like Superfamily: Frataxin/Nqo15-like Family: Frataxin-like Phyre2 PDB 1ibi chain A domain 1 Region: 230 - 239 Aligned: 10 Modelled: 10 Confidence: 20.8% Identity: 40% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: LIM domain Phyre2 PDB 2js3 chain B Region: 87 - 109 Aligned: 23 Modelled: 23 Confidence: 17.9% Identity: 35% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: nmr structure of protein q6n9a4_rhopa. northeast structural genomics2 consortium target rpt8 Phyre2 PDB 3fzy chain A Region: 8 - 74 Aligned: 56 Modelled: 67 Confidence: 16.9% Identity: 23% PDB header:toxin Chain: A: PDB Molecule:rtx toxin rtxa; PDBTitle: crystal structure of pre-cleavage form of cysteine protease domain2 from vibrio cholerae rtxa toxin Phyre2 PDB 1ctl chain A domain 1 Region: 230 - 239 Aligned: 10 Modelled: 10 Confidence: 14.6% Identity: 40% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: LIM domain Phyre2 PDB 3brz chain A Region: 23 - 131 Aligned: 97 Modelled: 105 Confidence: 13.8% Identity: 16% PDB header:transport protein Chain: A: PDB Molecule:todx; PDBTitle: crystal structure of the pseudomonas putida toluene2 transporter todx Phyre2 PDB 1u5s chain B domain 1 Region: 220 - 237 Aligned: 16 Modelled: 16 Confidence: 13.3% Identity: 25% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: LIM domain Phyre2 PDB 1g90 chain A Region: 113 - 154 Aligned: 42 Modelled: 42 Confidence: 11.5% Identity: 24% Fold: Transmembrane beta-barrels Superfamily: OMPA-like Family: Outer membrane protein Phyre2 PDB 3gny chain B Region: 63 - 82 Aligned: 15 Modelled: 20 Confidence: 10.8% Identity: 47% PDB header:antimicrobial protein Chain: B: PDB Molecule:neutrophil defensin 1; PDBTitle: crystal structure of human alpha-defensin 1 (hnp1) Phyre2 PDB 3lvx chain B Region: 63 - 82 Aligned: 15 Modelled: 20 Confidence: 10.8% Identity: 47% PDB header:antimicrobial protein Chain: B: PDB Molecule:neutrophil defensin 1; PDBTitle: crystal structure of human alpha-defensin 1 (i6a mutant) Phyre2 PDB 3lvx chain A Region: 63 - 82 Aligned: 15 Modelled: 20 Confidence: 10.8% Identity: 47% PDB header:antimicrobial protein Chain: A: PDB Molecule:neutrophil defensin 1; PDBTitle: crystal structure of human alpha-defensin 1 (i6a mutant) Phyre2 PDB 1dfn chain A Region: 63 - 82 Aligned: 15 Modelled: 20 Confidence: 10.6% Identity: 47% Fold: Defensin-like Superfamily: Defensin-like Family: Defensin Phyre2 1 d1t16a_ 2 d1ew4a_ 3 c3dwoX_ 4 c3pamB_ 5 d1ekga_ 6 d2ga5a1 7 c3lo4B_ 8 c3lo4A_ 9 d2fqla1 10 d1ibia1 11 c2js3B_ 12 c3fzyA_ 13 d1ctla1 14 c3brzA_ 15 d1u5sb1 16 d1g90a_ 17 c3gnyB_ 18 c3lvxB_ 19 c3lvxA_ 20 d1dfna_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43

Detailed template information

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

1 d1t16a_ 47.6 22 Fold:Transmembrane beta-barrels Superfamily:Porins Family:Outer membrane protein transport protein 2 d1ew4a_ 44.5 29 Fold:N domain of copper amine oxidase-like Superfamily:Frataxin/Nqo15-like Family:Frataxin-like 3 c3dwoX_ 42.3 24 PDB header:membrane protein Chain: X: PDB Molecule:probable outer membrane protein; PDBTitle: crystal structure of a pseudomonas aeruginosa fadl homologue 4 c3pamB_ 35.1 14 PDB header:transport protein Chain: B: PDB Molecule:transmembrane protein; PDBTitle: crystal structure of a domain of transmembrane protein of abc-type2 oligopeptide transport system from bartonella henselae str. houston-1 5 d1ekga_ 28.4 32 Fold:N domain of copper amine oxidase-like Superfamily:Frataxin/Nqo15-like Family:Frataxin-like 6 d2ga5a1 25.9 25 Fold:N domain of copper amine oxidase-like Superfamily:Frataxin/Nqo15-like Family:Frataxin-like 7 c3lo4B_ 25.7 53 PDB header:antimicrobial protein Chain: B: PDB Molecule:neutrophil defensin 1; PDBTitle: crystal structure of human alpha-defensin 1 (r24a mutant) 8 c3lo4A_ 25.7 53 PDB header:antimicrobial protein Chain: A: PDB Molecule:neutrophil defensin 1; PDBTitle: crystal structure of human alpha-defensin 1 (r24a mutant) 9 d2fqla1 23.7 25 Fold:N domain of copper amine oxidase-like Superfamily:Frataxin/Nqo15-like Family:Frataxin-like 10 d1ibia1 20.8 40 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 11 c2js3B_ 17.9 35 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: nmr structure of protein q6n9a4_rhopa. northeast structural genomics2 consortium target rpt8 12 c3fzyA_ 16.9 23 PDB header:toxin Chain: A: PDB Molecule:rtx toxin rtxa; PDBTitle: crystal structure of pre-cleavage form of cysteine protease domain2 from vibrio cholerae rtxa toxin 13 d1ctla1 14.6 40 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 14 c3brzA_ 13.8 16 PDB header:transport protein Chain: A: PDB Molecule:todx; PDBTitle: crystal structure of the pseudomonas putida toluene2 transporter todx 15 d1u5sb1 13.3 25 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 16 d1g90a_ 11.5 24 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 17 c3gnyB_ 10.8 47 PDB header:antimicrobial protein Chain: B: PDB Molecule:neutrophil defensin 1; PDBTitle: crystal structure of human alpha-defensin 1 (hnp1) 18 c3lvxB_ 10.8 47 PDB header:antimicrobial protein Chain: B: PDB Molecule:neutrophil defensin 1; PDBTitle: crystal structure of human alpha-defensin 1 (i6a mutant) 19 c3lvxA_ 10.8 47 PDB header:antimicrobial protein Chain: A: PDB Molecule:neutrophil defensin 1; PDBTitle: crystal structure of human alpha-defensin 1 (i6a mutant) 20 d1dfna_ 10.6 47 Fold:Defensin-like Superfamily:Defensin-like Family:Defensin 21 d1j8ra_ not modelled 10.3 27 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:PapG adhesin receptor-binding domain 22 d1k0ha_ not modelled 9.9 44 Fold:Phage tail proteins Superfamily:Phage tail proteins Family:gpFII-like 23 d1pbya5 not modelled 9.4 25 Fold:Streptavidin-like Superfamily:Quinohemoprotein amine dehydrogenase A chain, domain 3 Family:Quinohemoprotein amine dehydrogenase A chain, domain 3 24 c3eebB_ not modelled 9.3 18 PDB header:toxin Chain: B: PDB Molecule:rtx toxin rtxa; PDBTitle: structure of the v. cholerae rtx cysteine protease domain 25 c2pm4A_ not modelled 8.8 40 PDB header:antimicrobial protein Chain: A: PDB Molecule:neutrophil defensin 1 (hnp-1) (hp-1) (hp1) (defensin, alpha PDBTitle: human alpha-defensin 1 (multiple arg->lys mutant) 26 d2bbkl_ not modelled 8.7 22 Fold:Methylamine dehydrogenase, L chain Superfamily:Methylamine dehydrogenase, L chain Family:Methylamine dehydrogenase, L chain 27 d1qjpa_ not modelled 8.7 26 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 28 d1mdal_ not modelled 8.7 18 Fold:Methylamine dehydrogenase, L chain Superfamily:Methylamine dehydrogenase, L chain Family:Methylamine dehydrogenase, L chain 29 c3c75L_ not modelled 8.6 22 PDB header:oxidoreductase Chain: L: PDB Molecule:methylamine dehydrogenase light chain; PDBTitle: paracoccus versutus methylamine dehydrogenase in complex2 with amicyanin 30 d1qj8a_ not modelled 8.4 17 Fold:Transmembrane beta-barrels Superfamily:OMPA-like Family:Outer membrane protein 31 d1jmxa5 not modelled 8.3 18 Fold:Streptavidin-like Superfamily:Quinohemoprotein amine dehydrogenase A chain, domain 3 Family:Quinohemoprotein amine dehydrogenase A chain, domain 3 32 c3nb3C_ not modelled 7.4 26 PDB header:virus Chain: C: PDB Molecule:outer membrane protein a; PDBTitle: the host outer membrane proteins ompa and ompc are packed at specific2 sites in the shigella phage sf6 virion as structural components 33 c3lvuB_ not modelled 7.4 21 PDB header:transport protein Chain: B: PDB Molecule:abc transporter, periplasmic substrate-binding protein; PDBTitle: crystal structure of abc transporter, periplasmic substrate-binding2 protein spo2066 from silicibacter pomeroyi 34 d1bdsa_ not modelled 6.7 50 Fold:Defensin-like Superfamily:Defensin-like Family:Defensin 35 c3qraA_ not modelled 6.5 28 PDB header:cell invasion Chain: A: PDB Molecule:attachment invasion locus protein; PDBTitle: the crystal structure of ail, the attachment invasion locus protein of2 yersinia pestis 36 d1qdla_ not modelled 6.3 26 Fold:ADC synthase Superfamily:ADC synthase Family:ADC synthase 37 c2vcpE_ not modelled 6.0 44 PDB header:structural protein Chain: E: PDB Molecule:neural wiskott-aldrich syndrome protein; PDBTitle: crystal structure of n-wasp vc domain in complex with2 skeletal actin 38 c3h8aF_ not modelled 5.8 63 PDB header:lyase/protein binding Chain: F: PDB Molecule:rnase e; PDBTitle: crystal structure of e. coli enolase bound to its cognate rnase e2 recognition domain 39 d3eipa_ not modelled 5.8 44 Fold:FKBP-like Superfamily:Colicin E3 immunity protein Family:Colicin E3 immunity protein 40 d1imla1 not modelled 5.7 27 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 41 c3h8aE_ not modelled 5.7 56 PDB header:lyase/protein binding Chain: E: PDB Molecule:rnase e; PDBTitle: crystal structure of e. coli enolase bound to its cognate rnase e2 recognition domain 42 d1g8sa_ not modelled 5.5 14 Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:Fibrillarin homologue 43 d1pgja1 not modelled 5.5 19 Fold:6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like Family:Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase 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