Phyre 2 Results for P0AFA7

Email	l.a.kelley@imperial.ac.uk
Description	P0AFA7
Date	Thu Jan 5 11:25:45 GMT 2012
Unique Job ID	bc772c7cb77d723d

Summary

Top model

Image coloured by rainbow N → C terminus

Model (left) based on template d1nkza_

Top template information

Fold:Light-harvesting complex subunits
Superfamily:Light-harvesting complex subunits
Family:Light-harvesting complex subunits

Confidence and coverage

Confidence:

37.5%

Coverage:

31 residues ( 6% of your sequence) have been modelled with 37.5% 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 E I S W G R A L W R N F L G Q S P D W Y K L A L I I F L I V N P L I F L I S P F V A G W L L V A E F I F T L A M A L K

Secondary structure

SS confidence

Disorder ? ? ? ?
?

Disorder confidence

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

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

Secondary structure

SS confidence

Disorder

Disorder confidence

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

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

Secondary structure

SS confidence

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

Disorder confidence

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

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

Secondary structure

SS confidence

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

Disorder confidence

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

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

Secondary structure

SS confidence

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

Disorder confidence

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

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

Secondary structure

SS confidence

Disorder
? ? ?
? ?

Disorder confidence

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

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

Secondary structure

SS confidence

Disorder
? ?
? ?

Disorder confidence

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

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

Secondary structure

SS confidence

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

Disorder confidence

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

Sequence Y T L V L T L V G L L C V E F T L A P V T E W F M Q M G W I A 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 1nkz chain A

Region: 477 - 507
Aligned: 31
Modelled: 31
Confidence: 37.5%
Identity: 23%
Fold: Light-harvesting complex subunits
Superfamily: Light-harvesting complex subunits
Family: Light-harvesting complex subunits

Phyre2

PDB 1ijd chain A

Region: 477 - 507
Aligned: 31
Modelled: 31
Confidence: 37.3%
Identity: 23%
Fold: Light-harvesting complex subunits
Superfamily: Light-harvesting complex subunits
Family: Light-harvesting complex subunits

Phyre2

PDB 1j4n chain A

Region: 190 - 278
Aligned: 83
Modelled: 89
Confidence: 31.0%
Identity: 17%
Fold: Aquaporin-like
Superfamily: Aquaporin-like
Family: Aquaporin-like

Phyre2

PDB 1ppj chain C domain 1

Region: 117 - 246
Aligned: 91
Modelled: 91
Confidence: 11.1%
Identity: 20%
Fold: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
Superfamily: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
Family: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

Phyre2

PDB 3cx5 chain C domain 1

Region: 117 - 246
Aligned: 91
Modelled: 91
Confidence: 9.8%
Identity: 20%
Fold: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
Superfamily: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
Family: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

Phyre2

PDB 1f6g chain A

Region: 429 - 506
Aligned: 54
Modelled: 54
Confidence: 8.9%
Identity: 17%
Fold: Voltage-gated potassium channels
Superfamily: Voltage-gated potassium channels
Family: Voltage-gated potassium channels

Phyre2

PDB 2knc chain A

Region: 246 - 278
Aligned: 33
Modelled: 33
Confidence: 7.2%
Identity: 18%
PDB header:cell adhesion
Chain: A: PDB Molecule:integrin alpha-iib;
PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex

Phyre2

PDB 3d9s chain B

Region: 190 - 285
Aligned: 90
Modelled: 96
Confidence: 6.3%
Identity: 14%
PDB header:membrane protein
Chain: B: PDB Molecule:aquaporin-5;
PDBTitle: human aquaporin 5 (aqp5) - high resolution x-ray structure

Phyre2

PDB 1bcc chain C domain 2

Region: 117 - 246
Aligned: 91
Modelled: 91
Confidence: 6.1%
Identity: 21%
Fold: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
Superfamily: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
Family: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

Phyre2

PDB 2dxb chain R

Region: 11 - 22
Aligned: 12
Modelled: 12
Confidence: 5.9%
Identity: 67%
PDB header:hydrolase
Chain: R: PDB Molecule:thiocyanate hydrolase subunit gamma;
PDBTitle: recombinant thiocyanate hydrolase comprising partially-modified cobalt2 centers

Phyre2

PDB 3mk7 chain F

Region: 239 - 311
Aligned: 73
Modelled: 73
Confidence: 5.6%
Identity: 8%
PDB header:oxidoreductase
Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p;
PDBTitle: the structure of cbb3 cytochrome oxidase

Phyre2

PDB 1rc2 chain A

Region: 191 - 269
Aligned: 79
Modelled: 79
Confidence: 5.4%
Identity: 10%
Fold: Aquaporin-like
Superfamily: Aquaporin-like
Family: Aquaporin-like

Phyre2

PDB 2oar chain A domain 1

Region: 200 - 282
Aligned: 83
Modelled: 83
Confidence: 5.4%
Identity: 18%
Fold: Gated mechanosensitive channel
Superfamily: Gated mechanosensitive channel
Family: Gated mechanosensitive channel

Phyre2

PDB 3aag chain A

Region: 461 - 474
Aligned: 14
Modelled: 14
Confidence: 5.4%
Identity: 7%
PDB header:transferase
Chain: A: PDB Molecule:general glycosylation pathway protein;
PDBTitle: crystal structure of c. jejuni pglb c-terminal domain

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

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

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

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

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

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

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

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

	.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510	.	.	.
Sequence	Y	T	L	V	L	T	L	V	G	L	L	C	V	E	F	T	L	A	P	V	T	E	W	F	M	Q	M	G	W	I	A	T	L
Secondary structure
SS confidence
Disorder																													?	?	?	?	?
Disorder confidence