Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	N	K	P	F	Y	L	L	C	A	F	L	W	L	A	V	S	H	A	L	A	A	D	S	T	I	T	I	R	G	Y	V	R	D	N	G	C	S	V	A	A	E	S	T	N	F	T	V	D	L	M	E	N	A	A	K	Q	F	N
Secondary structure
SS confidence
Disorder		?	?	?	?													?	?	?	?	?	?																			?	?	?	?	?										?					?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		N	I	G	A	T	T	P	V	V	P	F	R	I	L	L	S	P	C	G	N	A	V	S	A	V	K	V	G	F	T	G	V	A	D	S	H	N	A	N	L	L	A	L	E	N	T	V	S	A	A	S	G	L	G	I	Q	L	L	N	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?														?										?	?	?	?	?	?	?						?	?	?		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.
Sequence		Q	Q	N	Q	I	P	L	N	A	P	S	S	A	L	S	W	T	T	L	T	P	G	K	P	N	T	L	N	F	Y	A	R	L	M	A	T	Q	V	P	V	T	A	G	H	I	N	A	T	A	T	F	T	L	E	Y	Q
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 3jwn chain K Region: 23 - 176 Aligned: 154 Modelled: 154 Confidence: 100.0% Identity: 99% PDB header:protein binding/cell adhesion Chain: K: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 3jwn chain E Region: 23 - 176 Aligned: 154 Modelled: 154 Confidence: 100.0% Identity: 99% PDB header:protein binding/cell adhesion Chain: E: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 3jwn chain L Region: 23 - 176 Aligned: 154 Modelled: 154 Confidence: 100.0% Identity: 99% 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: 23 - 176 Aligned: 154 Modelled: 154 Confidence: 100.0% Identity: 99% PDB header:protein binding/cell adhesion Chain: F: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 2jmr chain A Region: 23 - 176 Aligned: 154 Modelled: 154 Confidence: 100.0% Identity: 100% PDB header:cell adhesion Chain: A: PDB Molecule:fimf; PDBTitle: nmr structure of the e. coli type 1 pilus subunit fimf Phyre2 PDB 2jty chain A Region: 18 - 176 Aligned: 156 Modelled: 159 Confidence: 99.9% Identity: 30% 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: 33 - 176 Aligned: 144 Modelled: 144 Confidence: 99.9% Identity: 28% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 2j2z chain B domain 1 Region: 27 - 176 Aligned: 141 Modelled: 150 Confidence: 99.9% Identity: 25% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 2uy6 chain B domain 1 Region: 26 - 176 Aligned: 142 Modelled: 151 Confidence: 99.9% Identity: 25% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 3bwu chain F Region: 53 - 176 Aligned: 124 Modelled: 124 Confidence: 99.9% Identity: 95% 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 3bfw chain A Region: 35 - 175 Aligned: 131 Modelled: 141 Confidence: 99.9% Identity: 23% 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 1klf chain P Region: 26 - 176 Aligned: 133 Modelled: 151 Confidence: 99.8% Identity: 21% 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: 36 - 176 Aligned: 121 Modelled: 129 Confidence: 99.8% Identity: 25% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 2w07 chain B Region: 32 - 175 Aligned: 119 Modelled: 127 Confidence: 99.8% Identity: 24% 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: 36 - 175 Aligned: 131 Modelled: 140 Confidence: 99.5% Identity: 23% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 2wmp chain B Region: 40 - 175 Aligned: 119 Modelled: 136 Confidence: 86.5% Identity: 9% 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 - 24 Aligned: 23 Modelled: 24 Confidence: 12.5% Identity: 22% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 1 c3jwnK_ 2 c3jwnE_ 3 c3jwnL_ 4 c3jwnF_ 5 c2jmrA_ 6 c2jtyA_ 7 d1pdkb_ 8 d2j2zb1 9 d2uy6b1 10 c3bwuF_ 11 c3bfwA_ 12 c1klfP_ 13 d1ze3h1 14 c2w07B_ 15 d1n12a_ 16 c2wmpB_ 17 d2jnaa1

Detailed template information

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

1 c3jwnK_ 100.0 99 PDB header:protein binding/cell adhesion Chain: K: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 2 c3jwnE_ 100.0 99 PDB header:protein binding/cell adhesion Chain: E: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 3 c3jwnL_ 100.0 99 PDB header:protein binding/cell adhesion Chain: L: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 4 c3jwnF_ 100.0 99 PDB header:protein binding/cell adhesion Chain: F: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 5 c2jmrA_ 100.0 100 PDB header:cell adhesion Chain: A: PDB Molecule:fimf; PDBTitle: nmr structure of the e. coli type 1 pilus subunit fimf 6 c2jtyA_ 99.9 30 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 7 d1pdkb_ 99.9 28 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 8 d2j2zb1 99.9 25 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 9 d2uy6b1 99.9 25 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 10 c3bwuF_ 99.9 95 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) 11 c3bfwA_ 99.9 23 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) 12 c1klfP_ 99.8 21 PDB header:chaperone/adhesin complex Chain: P: PDB Molecule:fimh protein; PDBTitle: fimh adhesin-fimc chaperone complex with d-mannose 13 d1ze3h1 99.8 25 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 14 c2w07B_ 99.8 24 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 15 d1n12a_ 99.5 23 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 16 c2wmpB_ 86.5 9 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 17 d2jnaa1 12.5 22 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like

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

---

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