Phyre 2 Results for P39023

Email	l.a.kelley@imperial.ac.uk
Description	P39023
Date	Thu Apr 26 09:26:30 BST 2012
Unique Job ID	fe687422d43f91ad

Summary

Top model

Image coloured by rainbow N → C terminus

Model (left) based on template c3iz5C_

Top template information

PDB header:ribosome
Chain: C: PDB Molecule:60s ribosomal protein l3 (l3p);
PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome

Confidence and coverage

Confidence:

100.0%

Coverage:

96%

387 residues ( 96% 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 S H R K F S A P R H G S L G F L P R K R S S R H R G K V K S F P K D D P S K P V H L T A F L G Y K A G M T H I V R E V

Secondary structure

SS confidence

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

Disorder confidence

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

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

Secondary structure

SS confidence

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

Disorder confidence

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

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

Secondary structure

SS confidence

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

Disorder confidence

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

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

Secondary structure

SS confidence

Disorder
?
?
?
?
? ?

Disorder confidence

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

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

Secondary structure

SS confidence

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

Disorder confidence

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

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

Secondary structure

SS confidence

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

Disorder confidence

. . . . . . . . . 370 . . . . . . . . . 380 . . . . . . . . . 390 . . . . . . . . . 400 . . .

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

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 3iz5 chain C

Region: 1 - 393
Aligned: 387
Modelled: 393
Confidence: 100.0%
Identity: 68%
PDB header:ribosome
Chain: C: PDB Molecule:60s ribosomal protein l3 (l3p);
PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome

Phyre2

PDB 4a1a chain B

Region: 2 - 401
Aligned: 386
Modelled: 386
Confidence: 100.0%
Identity: 63%
PDB header:ribosome
Chain: B: PDB Molecule:ribosomal protein l3;
PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 3.

Phyre2

PDB 3jyw chain C

Region: 5 - 375
Aligned: 362
Modelled: 371
Confidence: 100.0%
Identity: 67%
PDB header:ribosome
Chain: C: PDB Molecule:60s ribosomal protein l3;
PDBTitle: structure of the 60s proteins for eukaryotic ribosome based on cryo-em2 map of thermomyces lanuginosus ribosome at 8.9a resolution

Phyre2

PDB 2zkr chain B

Region: 7 - 351
Aligned: 345
Modelled: 345
Confidence: 100.0%
Identity: 98%
PDB header:ribosomal protein/rna
Chain: B: PDB Molecule:rna expansion segment es4;
PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map

Phyre2

PDB 1s1i chain C

Region: 8 - 375
Aligned: 359
Modelled: 359
Confidence: 100.0%
Identity: 67%
PDB header:ribosome
Chain: C: PDB Molecule:60s ribosomal protein l3;
PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h.

Phyre2

PDB 1vqo chain B domain 1

Region: 7 - 375
Aligned: 329
Modelled: 333
Confidence: 100.0%
Identity: 37%
Fold: Reductase/isomerase/elongation factor common domain
Superfamily: Translation proteins
Family: Ribosomal protein L3

Phyre2

PDB 2gyc chain B domain 1

Region: 43 - 352
Aligned: 205
Modelled: 214
Confidence: 100.0%
Identity: 25%
Fold: Reductase/isomerase/elongation factor common domain
Superfamily: Translation proteins
Family: Ribosomal protein L3

Phyre2

PDB 2zjr chain B domain 1

Region: 43 - 354
Aligned: 202
Modelled: 214
Confidence: 100.0%
Identity: 25%
Fold: Reductase/isomerase/elongation factor common domain
Superfamily: Translation proteins
Family: Ribosomal protein L3

Phyre2

PDB 2j01 chain E domain 1

Region: 43 - 352
Aligned: 200
Modelled: 212
Confidence: 100.0%
Identity: 29%
Fold: Reductase/isomerase/elongation factor common domain
Superfamily: Translation proteins
Family: Ribosomal protein L3

Phyre2

PDB 2ftc chain C

Region: 44 - 354
Aligned: 208
Modelled: 219
Confidence: 100.0%
Identity: 21%
PDB header:ribosome
Chain: C: PDB Molecule:mitochondrial 39s ribosomal protein l3;
PDBTitle: structural model for the large subunit of the mammalian mitochondrial2 ribosome

Phyre2

PDB 3bbo chain F

Region: 134 - 353
Aligned: 152
Modelled: 152
Confidence: 100.0%
Identity: 29%
PDB header:ribosome
Chain: F: PDB Molecule:ribosomal protein l3;
PDBTitle: homology model for the spinach chloroplast 50s subunit fitted to 9.4a2 cryo-em map of the 70s chlororibosome

Phyre2

PDB 3ryk chain B

Region: 52 - 95
Aligned: 44
Modelled: 44
Confidence: 59.7%
Identity: 18%
PDB header:isomerase
Chain: B: PDB Molecule:dtdp-4-dehydrorhamnose 3,5-epimerase;
PDBTitle: 1.63 angstrom resolution crystal structure of dtdp-4-dehydrorhamnose2 3,5-epimerase (rfbc) from bacillus anthracis str. ames with tdp and3 ppi bound

Phyre2

PDB 1ep0 chain A

Region: 51 - 95
Aligned: 45
Modelled: 45
Confidence: 46.8%
Identity: 13%
Fold: Double-stranded beta-helix
Superfamily: RmlC-like cupins
Family: dTDP-sugar isomerase

Phyre2

PDB 1upi chain A

Region: 52 - 95
Aligned: 44
Modelled: 44
Confidence: 42.7%
Identity: 14%
PDB header:epimerase
Chain: A: PDB Molecule:dtdp-4-dehydrorhamnose 3,5-epimerase;
PDBTitle: mycobacterium tuberculosis rmlc epimerase (rv3465)

Phyre2

PDB 1wlt chain A domain 1

Region: 52 - 95
Aligned: 44
Modelled: 44
Confidence: 41.9%
Identity: 20%
Fold: Double-stranded beta-helix
Superfamily: RmlC-like cupins
Family: dTDP-sugar isomerase

Phyre2

PDB 1dzr chain A

Region: 52 - 95
Aligned: 44
Modelled: 44
Confidence: 41.4%
Identity: 20%
Fold: Double-stranded beta-helix
Superfamily: RmlC-like cupins
Family: dTDP-sugar isomerase

Phyre2

PDB 1oi6 chain A

Region: 52 - 95
Aligned: 44
Modelled: 44
Confidence: 35.5%
Identity: 18%
Fold: Double-stranded beta-helix
Superfamily: RmlC-like cupins
Family: dTDP-sugar isomerase

Phyre2

PDB 2ixc chain A domain 1

Region: 51 - 95
Aligned: 45
Modelled: 45
Confidence: 34.9%
Identity: 13%
Fold: Double-stranded beta-helix
Superfamily: RmlC-like cupins
Family: dTDP-sugar isomerase

Phyre2

PDB 2qtx chain L

Region: 194 - 223
Aligned: 28
Modelled: 30
Confidence: 34.4%
Identity: 29%
PDB header:rna binding protein
Chain: L: PDB Molecule:uncharacterized protein mj1435;
PDBTitle: crystal structure of an hfq-like protein from methanococcus2 jannaschii

Phyre2

PDB 2c0z chain A

Region: 52 - 95
Aligned: 44
Modelled: 44
Confidence: 33.1%
Identity: 16%
PDB header:isomerase
Chain: A: PDB Molecule:novw;
PDBTitle: the 1.6 a resolution crystal structure of novw: a 4-keto-6-2 deoxy sugar epimerase from the novobiocin biosynthetic3 gene cluster of streptomyces spheroides

Phyre2

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

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

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

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

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

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

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