Phyre 2 Results for P0AF16

Email	l.a.kelley@imperial.ac.uk
Description	P0AF16
Date	Thu Jan 5 11:24:53 GMT 2012
Unique Job ID	424b3de1f60f30d3

Summary

Top model

Image coloured by rainbow N → C terminus

Model (left) based on template c3mkuA_

Top template information

PDB header:transport protein
Chain: A: PDB Molecule:multi antimicrobial extrusion protein (na(+)/drug
PDBTitle: structure of a cation-bound multidrug and toxin compound extrusion2 (mate) transporter

Confidence and coverage

Confidence:

100.0%

Coverage:

84%

428 residues ( 84% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.

3D viewing

Interactive 3D view in Jmol

Sequence analysis

Secondary structure and disorder prediction

1 . . . . . . . . 10 . . . . . . . . . 20 . . . . . . . . . 30 . . . . . . . . . 40 . . . . . . . . . 50 . . . . . . . . . 60

Sequence M N L L K S L A A V S S M T M F S R V L G F A R D A I V A R I F G A G M A T D A F F V A F K L P N L L R R I F A E G A F

Secondary structure

SS confidence

Disorder ? ?

Disorder confidence

. . . . . . . . . 70 . . . . . . . . . 80 . . . . . . . . . 90 . . . . . . . . . 100 . . . . . . . . . 110 . . . . . . . . . 120

Sequence S Q A F V P I L A E Y K S K Q G E D A T R V F V S Y V S G L L T L A L A V V T V A G M L A A P W V I M V T A P G F A D T

Secondary structure

SS confidence

Disorder
? ? ? ? ?

Disorder confidence

. . . . . . . . . 130 . . . . . . . . . 140 . . . . . . . . . 150 . . . . . . . . . 160 . . . . . . . . . 170 . . . . . . . . . 180

Sequence A D K F A L T S Q L L K I T F P Y I L L I S L A S L V G A I L N T W N R F S I P A F A P T L L N I S M I G F A L F A A P

Secondary structure

SS confidence

Disorder

Disorder confidence

. . . . . . . . . 190 . . . . . . . . . 200 . . . . . . . . . 210 . . . . . . . . . 220 . . . . . . . . . 230 . . . . . . . . . 240

Sequence Y F N P P V L A L A W A V T V G G V L Q L V Y Q L P H L K K I G M L V L P R I N F H D A G A M R V V K Q M G P A I L G V

Secondary structure

SS confidence

Disorder
?
? ?
? ?

Disorder confidence

. . . . . . . . . 250 . . . . . . . . . 260 . . . . . . . . . 270 . . . . . . . . . 280 . . . . . . . . . 290 . . . . . . . . . 300

Sequence S V S Q I S L I I N T I F A S F L A S G S V S W M Y Y A D R L M E F P S G V L G V A L G T I L L P S L S K S F A S G N H

Secondary structure

SS confidence

Disorder
? ? ?
? ?

Disorder confidence

. . . . . . . . . 310 . . . . . . . . . 320 . . . . . . . . . 330 . . . . . . . . . 340 . . . . . . . . . 350 . . . . . . . . . 360

Sequence D E Y N R L M D W G L R L C F L L A L P S A V A L G I L S G P L T V S L F Q Y G K F T A F D A L M T Q R A L I A Y S V G

Secondary structure

SS confidence

Disorder

Disorder confidence

. . . . . . . . . 370 . . . . . . . . . 380 . . . . . . . . . 390 . . . . . . . . . 400 . . . . . . . . . 410 . . . . . . . . . 420

Sequence L I G L I V V K V L A P G F Y S R Q D I K T P V K I A I V T L I L T Q L M N L A F I G P L K H A G L S L S I G L A A C L

Secondary structure

SS confidence

Disorder

Disorder confidence

. . . . . . . . . 430 . . . . . . . . . 440 . . . . . . . . . 450 . . . . . . . . . 460 . . . . . . . . . 470 . . . . . . . . . 480

Sequence N A S L L Y W Q L R K Q K I F T P Q P G W M A F L L R L V V A V L V M S G V L L G M L H I M P E W S L G T M P W R L L R

Secondary structure

SS confidence

Disorder
?
? ? ? ?
? ? ? ? ?

Disorder confidence

. . . . . . . . . 490 . . . . . . . . . 500 . . . . . . . . . 510 .

Sequence L M A V V L A G I A A Y F A A L A V L G F K V K E F A R R T V

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 3mku chain A

Region: 2 - 443
Aligned: 428
Modelled: 428
Confidence: 100.0%
Identity: 10%
PDB header:transport protein
Chain: A: PDB Molecule:multi antimicrobial extrusion protein (na(+)/drug
PDBTitle: structure of a cation-bound multidrug and toxin compound extrusion2 (mate) transporter

Phyre2

PDB 1pw4 chain A

Region: 73 - 511
Aligned: 426
Modelled: 439
Confidence: 83.7%
Identity: 7%
Fold: MFS general substrate transporter
Superfamily: MFS general substrate transporter
Family: Glycerol-3-phosphate transporter

Phyre2

PDB 3p5n chain A

Region: 389 - 509
Aligned: 121
Modelled: 121
Confidence: 10.7%
Identity: 12%
PDB header:transport protein
Chain: A: PDB Molecule:riboflavin uptake protein;
PDBTitle: structure and mechanism of the s component of a bacterial ecf2 transporter

Phyre2

PDB 1wrg chain A

Region: 72 - 110
Aligned: 39
Modelled: 39
Confidence: 5.8%
Identity: 10%
PDB header:membrane protein
Chain: A: PDB Molecule:light-harvesting protein b-880, beta chain;
PDBTitle: light-harvesting complex 1 beta subunit from wild-type2 rhodospirillum rubrum

Phyre2

Detailed template information

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

c3mkuA_

100.0

d1pw4a_

83.7

Fold:MFS general substrate transporter
Superfamily:MFS general substrate transporter
Family:Glycerol-3-phosphate transporter

c3p5nA_

10.7

PDB header:transport protein
Chain: A: PDB Molecule:riboflavin uptake protein;
PDBTitle: structure and mechanism of the s component of a bacterial ecf2 transporter

c1wrgA_

5.8

PDB header:membrane protein
Chain: A: PDB Molecule:light-harvesting protein b-880, beta chain;
PDBTitle: light-harvesting complex 1 beta subunit from wild-type2 rhodospirillum rubrum

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]

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

	1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence	M	N	L	L	K	S	L	A	A	V	S	S	M	T	M	F	S	R	V	L	G	F	A	R	D	A	I	V	A	R	I	F	G	A	G	M	A	T	D	A	F	F	V	A	F	K	L	P	N	L	L	R	R	I	F	A	E	G	A	F
Secondary structure
SS confidence
Disorder	?	?
Disorder confidence

	.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence	S	Q	A	F	V	P	I	L	A	E	Y	K	S	K	Q	G	E	D	A	T	R	V	F	V	S	Y	V	S	G	L	L	T	L	A	L	A	V	V	T	V	A	G	M	L	A	A	P	W	V	I	M	V	T	A	P	G	F	A	D	T
Secondary structure
SS confidence
Disorder													?	?	?	?	?
Disorder confidence

	.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence	A	D	K	F	A	L	T	S	Q	L	L	K	I	T	F	P	Y	I	L	L	I	S	L	A	S	L	V	G	A	I	L	N	T	W	N	R	F	S	I	P	A	F	A	P	T	L	L	N	I	S	M	I	G	F	A	L	F	A	A	P
Secondary structure
SS confidence
Disorder
Disorder confidence

	.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence	Y	F	N	P	P	V	L	A	L	A	W	A	V	T	V	G	G	V	L	Q	L	V	Y	Q	L	P	H	L	K	K	I	G	M	L	V	L	P	R	I	N	F	H	D	A	G	A	M	R	V	V	K	Q	M	G	P	A	I	L	G	V
Secondary structure
SS confidence
Disorder																															?			?	?					?	?
Disorder confidence

	.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence	S	V	S	Q	I	S	L	I	I	N	T	I	F	A	S	F	L	A	S	G	S	V	S	W	M	Y	Y	A	D	R	L	M	E	F	P	S	G	V	L	G	V	A	L	G	T	I	L	L	P	S	L	S	K	S	F	A	S	G	N	H
Secondary structure
SS confidence
Disorder															?	?	?																																									?	?
Disorder confidence

	.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence	D	E	Y	N	R	L	M	D	W	G	L	R	L	C	F	L	L	A	L	P	S	A	V	A	L	G	I	L	S	G	P	L	T	V	S	L	F	Q	Y	G	K	F	T	A	F	D	A	L	M	T	Q	R	A	L	I	A	Y	S	V	G
Secondary structure
SS confidence
Disorder
Disorder confidence

	.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence	L	I	G	L	I	V	V	K	V	L	A	P	G	F	Y	S	R	Q	D	I	K	T	P	V	K	I	A	I	V	T	L	I	L	T	Q	L	M	N	L	A	F	I	G	P	L	K	H	A	G	L	S	L	S	I	G	L	A	A	C	L
Secondary structure
SS confidence
Disorder
Disorder confidence

	.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence	N	A	S	L	L	Y	W	Q	L	R	K	Q	K	I	F	T	P	Q	P	G	W	M	A	F	L	L	R	L	V	V	A	V	L	V	M	S	G	V	L	L	G	M	L	H	I	M	P	E	W	S	L	G	T	M	P	W	R	L	L	R
Secondary structure
SS confidence
Disorder													?		?	?	?	?																															?	?	?	?	?
Disorder confidence

	.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510	.
Sequence	L	M	A	V	V	L	A	G	I	A	A	Y	F	A	A	L	A	V	L	G	F	K	V	K	E	F	A	R	R	T	V
Secondary structure
SS confidence
Disorder																													?	?	?
Disorder confidence