Phyre 2 Results for P31554

Email	l.a.kelley@imperial.ac.uk
Description	P31554
Date	Thu Jan 5 11:48:17 GMT 2012
Unique Job ID	9efc185c0e6496a9

Summary

Top model

Image coloured by rainbow N → C terminus

Model (left) based on template c2r1aD_

Top template information

PDB header:transport protein
Chain: D: PDB Molecule:protein yhbn;
PDBTitle: crystal structure of the periplasmic lipopolysaccharide transport2 protein lpta (yhbn), trigonal form

Confidence and coverage

Confidence:

99.3%

Coverage:

16%

123 residues ( 16% of your sequence) have been modelled with 99.3% confidence by the single highest scoring template.

Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.

309 residues ( 39%) could be modelled at >90% confidence using multiple-templates.

You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.

3D viewing

Interactive 3D view in Jmol

Sequence analysis

Secondary structure and disorder prediction

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

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

Secondary structure

SS confidence

Disorder ? ? ? ?
? ? ?
? ? ? ?
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?

Disorder confidence

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

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

Secondary structure

SS confidence

Disorder
? ? ? ? ? ?
?

Disorder confidence

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

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

Secondary structure

SS confidence

Disorder
? ? ?
?
? ?

Disorder confidence

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

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

Secondary structure

SS confidence

Disorder
?
? ?
?

Disorder confidence

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

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

Secondary structure

SS confidence

Disorder
?
? ? ? ?
?
?
? ? ? ? ? ? ?

Disorder confidence

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

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

Secondary structure

SS confidence

Disorder ? ? ? ? ? ? ? ?
? ? ? ? ?
? ? ?
? ? ? ? ? ?

Disorder confidence

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

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

Secondary structure

SS confidence

Disorder
?

Disorder confidence

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

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

Secondary structure

SS confidence

Disorder ? ? ?
? ?
?
? ? ? ? ? ? ? ? ? ? ? ? ? ?

Disorder confidence

. . . . . . . . . 490 . . . . . . . . . 500 . . . . . . . . . 510 . . . . . . . . . 520 . . . . . . . . . 530 . . . . . . . . . 540

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

Secondary structure

SS confidence

Disorder
? ?
?
?
?

Disorder confidence

. . . . . . . . . 550 . . . . . . . . . 560 . . . . . . . . . 570 . . . . . . . . . 580 . . . . . . . . . 590 . . . . . . . . . 600

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

Secondary structure

SS confidence

Disorder
?
? ? ? ? ? ?
? ? ? ? ? ?

Disorder confidence

. . . . . . . . . 610 . . . . . . . . . 620 . . . . . . . . . 630 . . . . . . . . . 640 . . . . . . . . . 650 . . . . . . . . . 660

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

Secondary structure

SS confidence

Disorder ? ? ? ? ? ? ? ?
?
? ?
?
?

Disorder confidence

. . . . . . . . . 670 . . . . . . . . . 680 . . . . . . . . . 690 . . . . . . . . . 700 . . . . . . . . . 710 . . . . . . . . . 720

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

Secondary structure

SS confidence

Disorder ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ?

Disorder confidence

. . . . . . . . . 730 . . . . . . . . . 740 . . . . . . . . . 750 . . . . . . . . . 760 . . . . . . . . . 770 . . . . . . . . . 780

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

Secondary structure

SS confidence

Disorder
? ? ? ? ? ? ? ? ? ?
? ? ? ? ? ? ? ? ? ?
?
? ? ?

Disorder confidence

. . . .

Sequence Q N T L

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 2r1a chain D

Region: 45 - 168
Aligned: 123
Modelled: 124
Confidence: 99.3%
Identity: 15%
PDB header:transport protein
Chain: D: PDB Molecule:protein yhbn;
PDBTitle: crystal structure of the periplasmic lipopolysaccharide transport2 protein lpta (yhbn), trigonal form

Phyre2

PDB 3my2 chain A

Region: 45 - 137
Aligned: 85
Modelled: 85
Confidence: 98.7%
Identity: 21%
PDB header:transport protein
Chain: A: PDB Molecule:lipopolysaccharide export system protein lptc;
PDBTitle: crystal structure of lptc

Phyre2

PDB 1t16 chain A

Region: 608 - 737
Aligned: 125
Modelled: 130
Confidence: 97.0%
Identity: 12%
Fold: Transmembrane beta-barrels
Superfamily: Porins
Family: Outer membrane protein transport protein

Phyre2

PDB 2k4t chain A

Region: 607 - 761
Aligned: 130
Modelled: 132
Confidence: 95.9%
Identity: 16%
PDB header:membrane protein,apoptosis
Chain: A: PDB Molecule:voltage-dependent anion-selective channel
PDBTitle: solution structure of human vdac-1 in ldao micelles

Phyre2

PDB 3brz chain A

Region: 575 - 759
Aligned: 183
Modelled: 185
Confidence: 95.9%
Identity: 11%
PDB header:transport protein
Chain: A: PDB Molecule:todx;
PDBTitle: crystal structure of the pseudomonas putida toluene2 transporter todx

Phyre2

PDB 3bry chain B

Region: 608 - 758
Aligned: 146
Modelled: 151
Confidence: 95.4%
Identity: 16%
PDB header:transport protein
Chain: B: PDB Molecule:tbux;
PDBTitle: crystal structure of the ralstonia pickettii toluene2 transporter tbux

Phyre2

PDB 2wjq chain A

Region: 558 - 759
Aligned: 193
Modelled: 202
Confidence: 81.7%
Identity: 9%
PDB header:transport protein
Chain: A: PDB Molecule:probable n-acetylneuraminic acid outer membrane channel
PDBTitle: nanc porin structure in hexagonal crystal form.

Phyre2

PDB 3dwo chain X

Region: 545 - 762
Aligned: 213
Modelled: 218
Confidence: 81.2%
Identity: 15%
PDB header:membrane protein
Chain: X: PDB Molecule:probable outer membrane protein;
PDBTitle: crystal structure of a pseudomonas aeruginosa fadl homologue

Phyre2

PDB 1p4t chain A

Region: 684 - 722
Aligned: 39
Modelled: 39
Confidence: 71.6%
Identity: 18%
Fold: Transmembrane beta-barrels
Superfamily: OMPA-like
Family: Outer membrane protein

Phyre2

PDB 2lhf chain A

Region: 684 - 722
Aligned: 39
Modelled: 39
Confidence: 70.1%
Identity: 23%
PDB header:membrane protein
Chain: A: PDB Molecule:outer membrane protein h1;
PDBTitle: solution structure of outer membrane protein h (oprh) from p.2 aeruginosa in dhpc micelles

Phyre2

PDB 1osm chain A

Region: 608 - 722
Aligned: 105
Modelled: 115
Confidence: 63.5%
Identity: 12%
Fold: Transmembrane beta-barrels
Superfamily: Porins
Family: Porin

Phyre2

PDB 2f1t chain B

Region: 583 - 733
Aligned: 151
Modelled: 151
Confidence: 62.5%
Identity: 9%
PDB header:membrane protein
Chain: B: PDB Molecule:outer membrane protein w;
PDBTitle: outer membrane protein ompw

Phyre2

PDB 2k0l chain A

Region: 575 - 722
Aligned: 148
Modelled: 148
Confidence: 58.3%
Identity: 13%
PDB header:membrane protein
Chain: A: PDB Molecule:outer membrane protein a;
PDBTitle: nmr structure of the transmembrane domain of the outer2 membrane protein a from klebsiella pneumoniae in dhpc3 micelles.

Phyre2

PDB 3qra chain A

Region: 629 - 759
Aligned: 117
Modelled: 131
Confidence: 45.5%
Identity: 17%
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

Phyre2

PDB 2zfg chain A domain 1

Region: 604 - 722
Aligned: 110
Modelled: 119
Confidence: 40.9%
Identity: 8%
Fold: Transmembrane beta-barrels
Superfamily: Porins
Family: Porin

Phyre2

PDB 2iwv chain D

Region: 546 - 758
Aligned: 200
Modelled: 212
Confidence: 39.2%
Identity: 11%
PDB header:ion channel
Chain: D: PDB Molecule:outer membrane protein g;
PDBTitle: structure of the monomeric outer membrane porin ompg in the2 open and closed conformation

Phyre2

PDB 1g90 chain A

Region: 629 - 759
Aligned: 126
Modelled: 131
Confidence: 37.6%
Identity: 19%
Fold: Transmembrane beta-barrels
Superfamily: OMPA-like
Family: Outer membrane protein

Phyre2

PDB 2x27 chain X

Region: 569 - 733
Aligned: 165
Modelled: 165
Confidence: 34.8%
Identity: 12%
PDB header:membrane protein
Chain: X: PDB Molecule:outer membrane protein oprg;
PDBTitle: crystal structure of the outer membrane protein oprg from2 pseudomonas aeruginosa

Phyre2

PDB 1qjp chain A

Region: 618 - 735
Aligned: 105
Modelled: 109
Confidence: 28.9%
Identity: 16%
Fold: Transmembrane beta-barrels
Superfamily: OMPA-like
Family: Outer membrane protein

Phyre2

PDB 1qj8 chain A

Region: 623 - 759
Aligned: 123
Modelled: 137
Confidence: 26.1%
Identity: 16%
Fold: Transmembrane beta-barrels
Superfamily: OMPA-like
Family: Outer membrane protein

Phyre2

Detailed template information

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

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	K	K	R	I	P	T	L	L	A	T	M	I	A	T	A	L	Y	S	Q	Q	G	L	A	A	D	L	A	S	Q	C	M	L	G	V	P	S	Y	D	R	P	L	V	Q	G	D	T	N	D	L	P	V	T	I	N	A	D	H	A	K
Secondary structure
SS confidence
Disorder	?	?	?	?														?	?	?		?	?	?	?		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence

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

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

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

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

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

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

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

	.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510	.	.	.	.	.	.	.	.	.	520	.	.	.	.	.	.	.	.	.	530	.	.	.	.	.	.	.	.	.	540
Sequence	V	M	P	Q	F	K	V	D	G	K	M	V	F	E	R	D	M	E	M	L	A	P	G	Y	T	Q	T	L	E	P	R	A	Q	Y	L	Y	V	P	Y	R	D	Q	S	D	I	Y	N	Y	D	S	S	L	L	Q	S	D	Y	S	G	L
Secondary structure
SS confidence
Disorder																		?	?																							?			?														?
Disorder confidence

	.	.	.	.	.	.	.	.	.	550	.	.	.	.	.	.	.	.	.	560	.	.	.	.	.	.	.	.	.	570	.	.	.	.	.	.	.	.	.	580	.	.	.	.	.	.	.	.	.	590	.	.	.	.	.	.	.	.	.	600
Sequence	F	R	D	R	T	Y	G	G	L	D	R	I	A	S	A	N	Q	V	T	T	G	V	T	S	R	I	Y	D	D	A	A	V	E	R	F	N	I	S	V	G	Q	I	Y	Y	F	T	E	S	R	T	G	D	D	N	I	T	W	E	N	D
Secondary structure
SS confidence
Disorder																													?																			?	?	?	?	?	?		?	?	?	?	?	?
Disorder confidence

	.	.	.	.	.	.	.	.	.	610	.	.	.	.	.	.	.	.	.	620	.	.	.	.	.	.	.	.	.	630	.	.	.	.	.	.	.	.	.	640	.	.	.	.	.	.	.	.	.	650	.	.	.	.	.	.	.	.	.	660
Sequence	D	K	T	G	S	L	V	W	A	G	D	T	Y	W	R	I	S	E	R	W	G	L	R	G	G	I	Q	Y	D	T	R	L	D	N	V	A	T	S	N	S	S	I	E	Y	R	R	D	E	D	R	L	V	Q	L	N	Y	R	Y	A	S
Secondary structure
SS confidence
Disorder	?	?	?	?	?	?	?	?											?													?	?		?														?
Disorder confidence

	.	.	.	.	.	.	.	.	.	670	.	.	.	.	.	.	.	.	.	680	.	.	.	.	.	.	.	.	.	690	.	.	.	.	.	.	.	.	.	700	.	.	.	.	.	.	.	.	.	710	.	.	.	.	.	.	.	.	.	720
Sequence	P	E	Y	I	Q	A	T	L	P	K	Y	Y	S	T	A	E	Q	Y	K	N	G	I	S	Q	V	G	A	V	A	S	W	P	I	A	D	R	W	S	I	V	G	A	Y	Y	Y	D	T	N	A	N	K	Q	A	D	S	M	L	G	V	Q
Secondary structure
SS confidence
Disorder	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?																																		?	?
Disorder confidence

	.	.	.	.	.	.	.	.	.	730	.	.	.	.	.	.	.	.	.	740	.	.	.	.	.	.	.	.	.	750	.	.	.	.	.	.	.	.	.	760	.	.	.	.	.	.	.	.	.	770	.	.	.	.	.	.	.	.	.	780
Sequence	Y	S	S	C	C	Y	A	I	R	V	G	Y	E	R	K	L	N	G	W	D	N	D	K	Q	H	A	V	Y	D	N	A	I	G	F	N	I	E	L	R	G	L	S	S	N	Y	G	L	G	T	Q	E	M	L	R	S	N	I	L	P	Y
Secondary structure
SS confidence
Disorder																		?	?	?	?	?	?	?	?	?	?												?	?	?	?	?	?	?	?	?	?								?		?	?	?
Disorder confidence

	.	.	.	.
Sequence	Q	N	T	L
Secondary structure
SS confidence
Disorder	?	?	?	?
Disorder confidence