BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 040416
(47 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|MM Chain m, Localization Of The Large Subunit Ribosomal Proteins
Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
Translating 80s Ribosome
Length = 92
Score = 75.9 bits (185), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 36/44 (81%), Positives = 38/44 (86%)
Query: 4 RKAVGIWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLREQTES 47
RKAVGIWGCKD KVKAGGAYT+N SAVT R TIRRLREQTE+
Sbjct: 49 RKAVGIWGCKDCGKVKAGGAYTMNTASAVTVRSTIRRLREQTEA 92
>pdb|1YSH|D Chain D, Localization And Dynamic Behavior Of Ribosomal Protein
L30e
Length = 73
Score = 57.0 bits (136), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 27/34 (79%), Positives = 28/34 (82%)
Query: 4 RKAVGIWGCKDSSKVKAGGAYTLNIGSAVTARVT 37
RKAVGIWGCKD KVKAGGAYT+N SAVT R T
Sbjct: 40 RKAVGIWGCKDCGKVKAGGAYTMNTASAVTVRST 73
>pdb|3ZF7|OO Chain o, High-resolution Cryo-electron Microscopy Structure Of
The Trypanosoma Brucei Ribosome
Length = 93
Score = 52.0 bits (123), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 26/44 (59%), Positives = 30/44 (68%)
Query: 4 RKAVGIWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLREQTES 47
RKAVGIW C SK AGGAYTL+ + T R T+RRLRE +S
Sbjct: 49 RKAVGIWRCDGCSKTVAGGAYTLSTPNNTTVRSTVRRLRELKQS 92
>pdb|3IZS|MM Chain m, Localization Of The Large Subunit Ribosomal Proteins
Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|GG Chain g, Yeast 80s Ribosome. This Entry Consists Of The 60s
Subunit Of The First 80s In The Asymmetric Unit.
pdb|3O5H|GG Chain g, Yeast 80s Ribosome. This Entry Consists Of The 60s
Subunit Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|PP Chain p, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|PP Chain p, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|PP Chain p, Cryo-Em Structure Of The 60s Ribosomal Subunit In
Complex With Arx1 And Rei1
Length = 92
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/44 (54%), Positives = 28/44 (63%)
Query: 4 RKAVGIWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLREQTES 47
R A GIW C K AGGAYT++ +A T R TIRRLRE E+
Sbjct: 49 RGAAGIWTCSCCKKTVAGGAYTVSTAAAATVRSTIRRLREMVEA 92
>pdb|1S1I|9 Chain 9, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex
From Yeast Obtained By Docking Atomic Models For Rna
And Protein Components Into A 11.7 A Cryo-Em Map. This
File, 1s1i, Contains 60s Subunit. The 40s Ribosomal
Subunit Is In File 1s1h
Length = 91
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/44 (54%), Positives = 28/44 (63%)
Query: 4 RKAVGIWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLREQTES 47
R A GIW C K AGGAYT++ +A T R TIRRLRE E+
Sbjct: 48 RGAAGIWTCSCCKKTVAGGAYTVSTAAAATVRSTIRRLREMVEA 91
>pdb|2ZKR|ZZ Chain z, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 92
Score = 46.2 bits (108), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/40 (57%), Positives = 27/40 (67%)
Query: 4 RKAVGIWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLRE 43
R+AVGIW C K AGGA+T N SAVT + IRRL+E
Sbjct: 49 RRAVGIWHCGSCMKTVAGGAWTYNTTSAVTVKSAIRRLKE 88
>pdb|4A17|Y Chain Y, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 2.
pdb|4A1A|Y Chain Y, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 3.
pdb|4A1C|Y Chain Y, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 4.
pdb|4A1E|Y Chain Y, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 1
Length = 103
Score = 45.1 bits (105), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 21/40 (52%), Positives = 27/40 (67%)
Query: 4 RKAVGIWGCKDSSKVKAGGAYTLNIGSAVTARVTIRRLRE 43
R AVGIW CK K+ AGGA+ L AVTA+ T+ RL++
Sbjct: 49 RAAVGIWKCKPCKKIIAGGAWELTTPPAVTAKTTMNRLKK 88
>pdb|3JYW|9 Chain 9, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus
Ribosome At 8.9a Resolution
Length = 72
Score = 33.9 bits (76), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 17/34 (50%), Positives = 20/34 (58%)
Query: 4 RKAVGIWGCKDSSKVKAGGAYTLNIGSAVTARVT 37
R A GIW C K AGGAYT++ +A T R T
Sbjct: 39 RGAAGIWTCSCCKKTVAGGAYTVSTAAAATVRST 72
>pdb|3EZ8|A Chain A, Crystal Structure Of Endoglucanase Cel9a From The
Thermoacidophilic Alicyclobacillus Acidocaldarius
pdb|3GZK|A Chain A, Structure Of A. Acidocaldarius Cellulase Cela
pdb|3H2W|A Chain A, Structure Of A. Acidocaldarius Cellulase Cela In Complex
With Cellobiose
pdb|3H3K|A Chain A, Structure Of A. Acidocaldarius Cellulase Cela In Complex
With Cellotetraose
pdb|3RX5|A Chain A, Structure Of Aacel9a In Complex With Cellotriose-Like
Isofagomine
pdb|3RX7|A Chain A, Structure Of Aacel9a In Complex With Cellotetraose-Like
Isofagomine
pdb|3RX8|A Chain A, Structure Of Aacel9a In Complex With Cellobiose-Like
Isofagomine
Length = 537
Score = 26.9 bits (58), Expect = 2.7, Method: Composition-based stats.
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 8 GIWGCKDSSKVKAGGAYTLNIGSAVTARVTIRR 40
G W D + ++ G YTL +G+ + ARV I R
Sbjct: 54 GNWYVGDFTALRVPGTYTLTVGT-LEARVVIHR 85
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.129 0.369
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,096,164
Number of Sequences: 62578
Number of extensions: 20940
Number of successful extensions: 56
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 48
Number of HSP's gapped (non-prelim): 10
length of query: 47
length of database: 14,973,337
effective HSP length: 20
effective length of query: 27
effective length of database: 13,721,777
effective search space: 370487979
effective search space used: 370487979
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)