Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	R	V	I	T	L	F	A	V	L	L	M	G	W	S	V	N	A	W	S	F	A	C	K	T	A	N	G	T	A	I	P	I	G	G	G	S	A	N	V	Y	V	N	L	A	P	V	V	N	V	G	Q	N	L	V	V	D	L	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?													?											?					?	?	?	?	?	?	?					?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	Q	I	F	C	H	N	D	Y	P	E	T	I	T	D	Y	V	T	L	Q	R	G	S	A	Y	G	G	V	L	S	N	F	S	G	T	V	K	Y	S	G	S	S	Y	P	F	P	T	T	S	E	T	P	R	V	V	Y	N	S	R	T
Secondary structure
SS confidence
Disorder																								?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		D	K	P	W	P	V	A	L	Y	L	T	P	V	S	S	A	G	G	V	A	I	K	A	G	S	L	I	A	V	L	I	L	R	Q	T	N	N	Y	N	S	D	D	F	Q	F	V	W	N	I	Y	A	N	N	D	V	V	V	P	T	G
Secondary structure
SS confidence
Disorder															?	?	?	?	?	?		?	?	?	?	?								?	?	?	?	?	?														?	?	?				?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		G	C	D	V	S	A	R	D	V	T	V	T	L	P	D	Y	P	G	S	V	P	I	P	L	T	V	Y	C	A	K	S	Q	N	L	G	Y	Y	L	S	G	T	T	A	D	A	G	N	S	I	F	T	N	T	A	S	F	S	P	A	Q
Secondary structure
SS confidence
Disorder		?			?	?	?	?	?				?			?	?	?	?	?																								?	?	?	?						?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		G	V	G	V	Q	L	T	R	N	G	T	I	I	P	A	N	N	T	V	S	L	G	A	V	G	T	S	A	V	S	L	G	L	T	A	N	Y	A	R	T	G	G	Q	V	T	A	G	N	V	Q	S	I	I	G	V	T	F	V	Y	Q
Secondary structure
SS confidence
Disorder															?				?	?	?	?	?	?	?		?														?		?	?	?		?														?
Disorder confidence
Sequence
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 1klf chain P Region: 22 - 300 Aligned: 279 Modelled: 279 Confidence: 100.0% Identity: 100% PDB header:chaperone/adhesin complex Chain: P: PDB Molecule:fimh protein; PDBTitle: fimh adhesin-fimc chaperone complex with d-mannose Phyre2 PDB 1ze3 chain H domain 1 Region: 180 - 300 Aligned: 121 Modelled: 121 Confidence: 100.0% Identity: 100% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 1uwf chain A domain 1 Region: 22 - 179 Aligned: 158 Modelled: 158 Confidence: 99.9% Identity: 100% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 3bwu chain F Region: 181 - 300 Aligned: 119 Modelled: 120 Confidence: 99.9% Identity: 24% PDB header:chaperone, structural, membrane protein Chain: F: PDB Molecule:protein fimf; PDBTitle: crystal structure of the ternary complex of fimd (n-terminal domain,2 fimdn) with fimc and the n-terminally truncated pilus subunit fimf3 (fimft) Phyre2 PDB 3jwn chain K Region: 169 - 300 Aligned: 132 Modelled: 132 Confidence: 99.9% Identity: 23% PDB header:protein binding/cell adhesion Chain: K: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 3jwn chain L Region: 169 - 300 Aligned: 132 Modelled: 132 Confidence: 99.9% Identity: 23% PDB header:protein binding/cell adhesion Chain: L: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 3jwn chain F Region: 169 - 300 Aligned: 132 Modelled: 132 Confidence: 99.9% Identity: 23% PDB header:protein binding/cell adhesion Chain: F: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 3jwn chain E Region: 169 - 300 Aligned: 132 Modelled: 132 Confidence: 99.9% Identity: 23% PDB header:protein binding/cell adhesion Chain: E: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 2jmr chain A Region: 169 - 300 Aligned: 132 Modelled: 132 Confidence: 99.9% Identity: 20% PDB header:cell adhesion Chain: A: PDB Molecule:fimf; PDBTitle: nmr structure of the e. coli type 1 pilus subunit fimf Phyre2 PDB 3bfw chain A Region: 179 - 299 Aligned: 118 Modelled: 121 Confidence: 99.9% Identity: 20% PDB header:structural protein/structural protein Chain: A: PDB Molecule:protein fimg; PDBTitle: crystal structure of truncated fimg (fimgt) in complex with the donor2 strand peptide of fimf (dsf) Phyre2 PDB 2j2z chain B domain 1 Region: 169 - 300 Aligned: 128 Modelled: 132 Confidence: 99.8% Identity: 18% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 2jty chain A Region: 169 - 300 Aligned: 131 Modelled: 132 Confidence: 99.8% Identity: 24% PDB header:structural protein Chain: A: PDB Molecule:type-1 fimbrial protein, a chain; PDBTitle: self-complemented variant of fima, the main subunit of type 1 pilus Phyre2 PDB 1pdk chain B Region: 177 - 300 Aligned: 122 Modelled: 124 Confidence: 99.8% Identity: 18% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 2uy6 chain B domain 1 Region: 169 - 300 Aligned: 128 Modelled: 132 Confidence: 99.8% Identity: 13% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 2w07 chain B Region: 176 - 300 Aligned: 110 Modelled: 125 Confidence: 99.7% Identity: 20% PDB header:cell adhesion Chain: B: PDB Molecule:minor pilin subunit papf; PDBTitle: structural determinants of polymerization reactivity of the2 p pilus adaptor subunit papf Phyre2 PDB 1n12 chain A Region: 180 - 299 Aligned: 118 Modelled: 120 Confidence: 99.4% Identity: 17% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 2wmp chain B Region: 179 - 299 Aligned: 110 Modelled: 121 Confidence: 91.2% Identity: 18% PDB header:chaperone Chain: B: PDB Molecule:papg protein; PDBTitle: structure of the e. coli chaperone papd in complex with the pilin2 domain of the papgii adhesin Phyre2 PDB 2jna chain A domain 1 Region: 1 - 22 Aligned: 22 Modelled: 22 Confidence: 32.8% Identity: 27% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 2noc chain A domain 1 Region: 1 - 23 Aligned: 23 Modelled: 23 Confidence: 13.9% Identity: 17% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 2oz4 chain A domain 1 Region: 187 - 225 Aligned: 39 Modelled: 39 Confidence: 6.8% Identity: 23% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: C2 set domains Phyre2 1 c1klfP_ 2 d1ze3h1 3 d1uwfa1 4 c3bwuF_ 5 c3jwnK_ 6 c3jwnL_ 7 c3jwnF_ 8 c3jwnE_ 9 c2jmrA_ 10 c3bfwA_ 11 d2j2zb1 12 c2jtyA_ 13 d1pdkb_ 14 d2uy6b1 15 c2w07B_ 16 d1n12a_ 17 c2wmpB_ 18 d2jnaa1 19 d2noca1 20 d2oz4a1 21 22

Detailed template information

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

1 c1klfP_ 100.0 100 PDB header:chaperone/adhesin complex Chain: P: PDB Molecule:fimh protein; PDBTitle: fimh adhesin-fimc chaperone complex with d-mannose 2 d1ze3h1 100.0 100 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 3 d1uwfa1 99.9 100 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 4 c3bwuF_ 99.9 24 PDB header:chaperone, structural, membrane protein Chain: F: PDB Molecule:protein fimf; PDBTitle: crystal structure of the ternary complex of fimd (n-terminal domain,2 fimdn) with fimc and the n-terminally truncated pilus subunit fimf3 (fimft) 5 c3jwnK_ 99.9 23 PDB header:protein binding/cell adhesion Chain: K: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 6 c3jwnL_ 99.9 23 PDB header:protein binding/cell adhesion Chain: L: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 7 c3jwnF_ 99.9 23 PDB header:protein binding/cell adhesion Chain: F: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 8 c3jwnE_ 99.9 23 PDB header:protein binding/cell adhesion Chain: E: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 9 c2jmrA_ 99.9 20 PDB header:cell adhesion Chain: A: PDB Molecule:fimf; PDBTitle: nmr structure of the e. coli type 1 pilus subunit fimf 10 c3bfwA_ 99.9 20 PDB header:structural protein/structural protein Chain: A: PDB Molecule:protein fimg; PDBTitle: crystal structure of truncated fimg (fimgt) in complex with the donor2 strand peptide of fimf (dsf) 11 d2j2zb1 99.8 18 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 12 c2jtyA_ 99.8 24 PDB header:structural protein Chain: A: PDB Molecule:type-1 fimbrial protein, a chain; PDBTitle: self-complemented variant of fima, the main subunit of type 1 pilus 13 d1pdkb_ 99.8 18 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 14 d2uy6b1 99.8 13 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 15 c2w07B_ 99.7 20 PDB header:cell adhesion Chain: B: PDB Molecule:minor pilin subunit papf; PDBTitle: structural determinants of polymerization reactivity of the2 p pilus adaptor subunit papf 16 d1n12a_ 99.4 17 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 17 c2wmpB_ 91.2 18 PDB header:chaperone Chain: B: PDB Molecule:papg protein; PDBTitle: structure of the e. coli chaperone papd in complex with the pilin2 domain of the papgii adhesin 18 d2jnaa1 32.8 27 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 19 d2noca1 13.9 17 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 20 d2oz4a1 6.8 23 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:C2 set domains 21 c3o0rC_ not modelled 6.3 20 PDB header:immune system/oxidoreductase Chain: C: PDB Molecule:nitric oxide reductase subunit c; PDBTitle: crystal structure of nitric oxide reductase from pseudomonas2 aeruginosa in complex with antibody fragment 22 c2l18A_ not modelled 6.0 43 PDB header:oxidoreductase Chain: A: PDB Molecule:arsenate reductase; PDBTitle: an arsenate reductase in the phosphate binding state

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