Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	R	L	H	K	R	F	L	L	A	T	F	C	A	L	F	T	A	T	L	Q	A	A	D	V	T	I	T	V	N	G	R	V	V	A	K	P	C	T	I	Q	T	K	E	A	N	V	N	L	G	D	L	Y	T	R	N	L	Q	Q
Secondary structure
SS confidence
Disorder		?	?	?	?														?	?	?	?	?	?		?																	?	?	?															?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		P	G	S	A	S	G	W	H	N	I	T	L	S	L	T	D	C	P	V	E	T	S	A	V	T	A	I	V	T	G	S	T	D	N	T	G	Y	Y	K	N	E	G	T	A	E	N	I	Q	I	E	L	R	D	D	Q	D	A	A	L	K
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?									?		?		?													?	?	?	?	?	?	?	?	?	?													?	?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.
Sequence		N	G	D	S	K	T	V	I	V	D	E	I	T	R	N	A	Q	F	P	L	K	A	R	A	I	T	V	N	G	N	A	S	Q	G	T	I	E	A	L	I	N	V	I	Y	T	W	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 L Region: 24 - 167 Aligned: 144 Modelled: 144 Confidence: 99.9% Identity: 22% PDB header:protein binding/cell adhesion Chain: L: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 3jwn chain K Region: 24 - 167 Aligned: 144 Modelled: 144 Confidence: 99.9% Identity: 22% PDB header:protein binding/cell adhesion Chain: K: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 3jwn chain F Region: 24 - 167 Aligned: 144 Modelled: 144 Confidence: 99.9% Identity: 22% 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: 24 - 167 Aligned: 144 Modelled: 144 Confidence: 99.9% Identity: 22% PDB header:protein binding/cell adhesion Chain: E: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh Phyre2 PDB 3bfw chain A Region: 36 - 166 Aligned: 131 Modelled: 131 Confidence: 99.9% Identity: 56% 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 2jmr chain A Region: 24 - 167 Aligned: 144 Modelled: 144 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 2jty chain A Region: 19 - 167 Aligned: 148 Modelled: 149 Confidence: 99.9% 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 2j2z chain B domain 1 Region: 27 - 167 Aligned: 139 Modelled: 141 Confidence: 99.9% Identity: 17% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 2uy6 chain B domain 1 Region: 27 - 167 Aligned: 139 Modelled: 141 Confidence: 99.9% Identity: 20% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 1pdk chain B Region: 34 - 167 Aligned: 134 Modelled: 134 Confidence: 99.9% Identity: 17% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 3bwu chain F Region: 36 - 167 Aligned: 120 Modelled: 132 Confidence: 99.8% Identity: 18% 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 1ze3 chain H domain 1 Region: 37 - 167 Aligned: 116 Modelled: 131 Confidence: 99.8% Identity: 19% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 1klf chain P Region: 32 - 167 Aligned: 121 Modelled: 127 Confidence: 99.8% Identity: 19% PDB header:chaperone/adhesin complex Chain: P: PDB Molecule:fimh protein; PDBTitle: fimh adhesin-fimc chaperone complex with d-mannose Phyre2 PDB 2w07 chain B Region: 33 - 166 Aligned: 118 Modelled: 134 Confidence: 99.7% Identity: 16% 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: 37 - 166 Aligned: 125 Modelled: 130 Confidence: 99.5% Identity: 14% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Bacterial adhesins Family: Pilus subunits Phyre2 PDB 2wmp chain B Region: 39 - 166 Aligned: 116 Modelled: 128 Confidence: 11.9% Identity: 12% 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 1ykh chain A domain 1 Region: 1 - 13 Aligned: 13 Modelled: 13 Confidence: 10.8% Identity: 31% Fold: Mediator hinge subcomplex-like Superfamily: Mediator hinge subcomplex-like Family: MED7 hinge region Phyre2 1 c3jwnL_ 2 c3jwnK_ 3 c3jwnF_ 4 c3jwnE_ 5 c3bfwA_ 6 c2jmrA_ 7 c2jtyA_ 8 d2j2zb1 9 d2uy6b1 10 d1pdkb_ 11 c3bwuF_ 12 d1ze3h1 13 c1klfP_ 14 c2w07B_ 15 d1n12a_ 16 c2wmpB_ 17 d1ykha1

Detailed template information

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

1 c3jwnL_ 99.9 22 PDB header:protein binding/cell adhesion Chain: L: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 2 c3jwnK_ 99.9 22 PDB header:protein binding/cell adhesion Chain: K: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 3 c3jwnF_ 99.9 22 PDB header:protein binding/cell adhesion Chain: F: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 4 c3jwnE_ 99.9 22 PDB header:protein binding/cell adhesion Chain: E: PDB Molecule:protein fimf; PDBTitle: complex of fimc, fimf, fimg and fimh 5 c3bfwA_ 99.9 56 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) 6 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 7 c2jtyA_ 99.9 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 8 d2j2zb1 99.9 17 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 9 d2uy6b1 99.9 20 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 10 d1pdkb_ 99.9 17 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 11 c3bwuF_ 99.8 18 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) 12 d1ze3h1 99.8 19 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 13 c1klfP_ 99.8 19 PDB header:chaperone/adhesin complex Chain: P: PDB Molecule:fimh protein; PDBTitle: fimh adhesin-fimc chaperone complex with d-mannose 14 c2w07B_ 99.7 16 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 14 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Pilus subunits 16 c2wmpB_ 11.9 12 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 d1ykha1 10.8 31 Fold:Mediator hinge subcomplex-like Superfamily:Mediator hinge subcomplex-like Family:MED7 hinge region

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