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= psy5754
(67 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKR|NN Chain n, 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 = 297
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/60 (48%), Positives = 39/60 (65%), Gaps = 9/60 (15%)
Query: 1 MYKKAHENIRADPAHIKKEKKTPTVDSKGKIQKPKRWNKKKLTLAQRKERVSTAKANFLK 60
MYKKAH IR +P + KK KK K KRWN+ K++LAQ+K+RV+ KA+FL+
Sbjct: 239 MYKKAHAAIRENPVYEKKPKKE---------VKKKRWNRPKMSLAQKKDRVAQKKASFLR 289
>pdb|3IZR|Q Chain Q, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 304
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/48 (47%), Positives = 25/48 (52%), Gaps = 8/48 (16%)
Query: 1 MYKKAHENIRADPAHIKKEKKTPTVDSKGKIQKPKRWNKKKLTLAQRK 48
+YKK H IRADP K KK P KR+N KKLT QRK
Sbjct: 239 LYKKVHAAIRADPTMAKSTKKEPATH--------KRYNLKKLTYEQRK 278
>pdb|3ZF7|UU Chain u, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 308
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 27/46 (58%), Gaps = 6/46 (13%)
Query: 1 MYKKAHENIRADPAHIKKEKKTPTVDSKGKIQKPKRWNKKKLTLAQ 46
MYK+AH IRADP + +K+ P KPK++N KLT A+
Sbjct: 248 MYKRAHAAIRADPTKRRAKKERPAE------AKPKKYNTVKLTGAE 287
>pdb|4A17|M Chain M, 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|M Chain M, 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|M Chain M, 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|M Chain M, 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 = 301
Score = 33.1 bits (74), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 30/57 (52%), Gaps = 13/57 (22%)
Query: 1 MYKKAHENIRADPAHIKKEKKTPTVDSKGKIQKPKRWNKK----KLTLAQRKERVST 53
++ K H IR +P +K KK KPKR +KK KLT AQRK+RV T
Sbjct: 246 LFTKVHAEIRKNPERVKSTKKN---------DKPKRDHKKFYPTKLTAAQRKDRVKT 293
>pdb|3U5E|D Chain D, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|D Chain D, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|D Chain D, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 297
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 13/21 (61%), Positives = 14/21 (66%)
Query: 1 MYKKAHENIRADPAHIKKEKK 21
+Y AHE IRADPA EKK
Sbjct: 239 IYTSAHEAIRADPAFKPTEKK 259
>pdb|3IZS|Q Chain Q, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|E Chain E, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|E Chain E, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit
Length = 297
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 13/21 (61%), Positives = 14/21 (66%)
Query: 1 MYKKAHENIRADPAHIKKEKK 21
+Y AHE IRADPA EKK
Sbjct: 239 IYTSAHEAIRADPAFKPTEKK 259
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
0.309 0.123 0.340
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,859,419
Number of Sequences: 62578
Number of extensions: 53973
Number of successful extensions: 106
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 96
Number of HSP's gapped (non-prelim): 7
length of query: 67
length of database: 14,973,337
effective HSP length: 38
effective length of query: 29
effective length of database: 12,595,373
effective search space: 365265817
effective search space used: 365265817
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 45 (21.9 bits)