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= 033538
(117 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|D Chain D, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 405
Score = 108 bits (270), Expect = 7e-25, Method: Compositional matrix adjust.
Identities = 62/117 (52%), Positives = 74/117 (63%)
Query: 1 MVNADLARIINSDEVQSVVRPIKTEVKRAXXXXXXXXXXXXXXXXXXYAKTARRMSLLAE 60
M NADL RIINSDEVQSVV+P+ EVKR Y TAR+M+ LAE
Sbjct: 289 MANADLGRIINSDEVQSVVKPLNKEVKRREKRKNPLKNVAAVLKLNPYFGTARKMATLAE 348
Query: 61 AQRVXXXXXXXXXXXXPITKEEAAAIKSAGKAWYQTMISDSDYTEFENFSKWLGVSQ 117
A R+ ++ EEAA +K+AGKAWY+TMISDSDY EF+NFSKWLGV+Q
Sbjct: 349 AARIKARKEKLDSKRTKLSPEEAAKVKAAGKAWYKTMISDSDYAEFDNFSKWLGVTQ 405
>pdb|4A17|C Chain C, 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|C Chain C, 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|C Chain C, 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|C Chain C, 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 = 410
Score = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 15/20 (75%), Positives = 19/20 (95%)
Query: 1 MVNADLARIINSDEVQSVVR 20
+ NAD+ARIINS+EVQSVV+
Sbjct: 290 LANADIARIINSNEVQSVVK 309
>pdb|3IZS|D Chain D, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|D Chain D, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|D Chain D, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|C Chain C, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|C Chain C, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|C Chain C, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 362
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 4 ADLARIINSDEVQSVVRP 21
+D+ RIINS E+QS +RP
Sbjct: 284 SDVTRIINSSEIQSAIRP 301
>pdb|2WW9|H Chain H, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound
To The Yeast 80s Ribosome
pdb|2WWA|H Chain H, Cryo-Em Structure Of Idle Yeast Ssh1 Complex Bound To The
Yeast 80s Ribosome
pdb|2WWB|H Chain H, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound To
The Actively Translating Wheat Germ 80s Ribosome
Length = 362
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 4 ADLARIINSDEVQSVVRP 21
+D+ RIINS E+QS +RP
Sbjct: 284 SDVTRIINSSEIQSAIRP 301
>pdb|1S1I|D Chain D, 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 = 361
Score = 30.0 bits (66), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 4 ADLARIINSDEVQSVVRP 21
+D+ RIINS E+QS +RP
Sbjct: 283 SDVTRIINSSEIQSAIRP 300
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
0.314 0.124 0.338
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,009,737
Number of Sequences: 62578
Number of extensions: 40509
Number of successful extensions: 95
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 89
Number of HSP's gapped (non-prelim): 6
length of query: 117
length of database: 14,973,337
effective HSP length: 80
effective length of query: 37
effective length of database: 9,967,097
effective search space: 368782589
effective search space used: 368782589
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)