Phyre 2 Results for P39414

Email	l.a.kelley@imperial.ac.uk
Description	P39414
Date	Thu Jan 5 12:00:49 GMT 2012
Unique Job ID	ea3c4a851388d80c

Summary

Top model

Image coloured by rainbow N → C terminus

Model (left) based on template c2w8aC_

Top template information

PDB header:membrane protein
Chain: C: PDB Molecule:glycine betaine transporter betp;
PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate

Confidence and coverage

Confidence:

34.8%

Coverage:

41%

199 residues ( 41% of your sequence) have been modelled with 34.8% confidence by the single highest scoring template.

You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.

Please note: You must be registered and logged in to use Phyrealarm.

3D viewing

Interactive 3D view in Jmol

Sequence analysis

Secondary structure and disorder prediction

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

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

Secondary structure

SS confidence

Disorder ? ? ? ? ?
?

Disorder confidence

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

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

Secondary structure

SS confidence

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

Disorder confidence

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

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

Secondary structure

SS confidence

Disorder
?
? ? ? ?

Disorder confidence

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

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

Secondary structure

SS confidence

Disorder ? ? ? ? ? ?
?
?
? ?

Disorder confidence

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

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

Secondary structure

SS confidence

Disorder
? ? ? ? ? ? ? ?
?
?

Disorder confidence

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

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

Secondary structure

SS confidence

Disorder
? ?
?

Disorder confidence

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

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

Secondary structure

SS confidence

Disorder
?
?
?

Disorder confidence

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

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

Secondary structure

SS confidence

Disorder

Disorder confidence

. . . . . . .

Sequence W M P V V L 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 2w8a chain C

Region: 7 - 281
Aligned: 199
Modelled: 226
Confidence: 34.8%
Identity: 15%
PDB header:membrane protein
Chain: C: PDB Molecule:glycine betaine transporter betp;
PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate

Phyre2

PDB 3d9s chain B

Region: 182 - 277
Aligned: 93
Modelled: 96
Confidence: 12.8%
Identity: 15%
PDB header:membrane protein
Chain: B: PDB Molecule:aquaporin-5;
PDBTitle: human aquaporin 5 (aqp5) - high resolution x-ray structure

Phyre2

PDB 1j4n chain A

Region: 182 - 270
Aligned: 86
Modelled: 89
Confidence: 10.2%
Identity: 17%
Fold: Aquaporin-like
Superfamily: Aquaporin-like
Family: Aquaporin-like

Phyre2

PDB 1ymg chain A

Region: 150 - 273
Aligned: 112
Modelled: 124
Confidence: 6.0%
Identity: 11%
PDB header:membrane protein
Chain: A: PDB Molecule:lens fiber major intrinsic protein;
PDBTitle: the channel architecture of aquaporin o at 2.2 angstrom resolution

Phyre2

PDB 1ymg chain A domain 1

Region: 150 - 273
Aligned: 112
Modelled: 124
Confidence: 6.0%
Identity: 11%
Fold: Aquaporin-like
Superfamily: Aquaporin-like
Family: Aquaporin-like

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	P	S	T	E	W	W	R	Y	L	A	P	L	A	V	I	A	I	I	A	L	L	P	V	P	A	G	L	E	N	H	T	W	L	Y	F	A	V	F	T	G	V	I	V	G	L	I	L	E	P	V	P	G	A	V	V	A	M	V
Secondary structure
SS confidence
Disorder	?	?	?	?	?																						?
Disorder confidence

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

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

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

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

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

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

	.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence	P	V	F	C	L	M	V	G	A	A	I	G	L	G	S	I	L	T	P	Y	A	T	G	P	S	P	I	Y	Y	G	S	G	Y	L	P	T	A	D	Y	W	R	L	G	A	I	F	G	L	I	F	L	V	L	L	V	I	T	G	L	L
Secondary structure
SS confidence
Disorder
Disorder confidence

	.	.	.	.	.	.	.
Sequence	W	M	P	V	V	L	L
Secondary structure
SS confidence
Disorder						?	?
Disorder confidence