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= 035463
(65 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZ6|Y Chain Y, Localization Of The Small Subunit Ribosomal Proteins
Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
Translating 80s Ribosome
Length = 65
Score = 96.7 bits (239), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 47/51 (92%), Positives = 49/51 (96%)
Query: 1 MDSQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDI 51
MD+Q+K AVVVKVMGRTGSRGQVTQVRVKFLDDQNR IMRNVKGPVREGDI
Sbjct: 1 MDTQVKLAVVVKVMGRTGSRGQVTQVRVKFLDDQNRLIMRNVKGPVREGDI 51
>pdb|3IZB|Y Chain Y, Localization Of The Small Subunit Ribosomal Proteins
Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O2Z|R Chain R, Yeast 80s Ribosome. This Entry Consists Of The 40s
Subunit Of The First 80s In The Asymmetric Unit.
pdb|3O30|R Chain R, Yeast 80s Ribosome. This Entry Consists Of The 40s
Subunit Of The Second 80s In The Asymmetric Unit.
pdb|3U5C|CC Chain c, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|CC Chain c, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 67
Score = 68.6 bits (166), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 33/49 (67%), Positives = 41/49 (83%)
Query: 3 SQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRFIMRNVKGPVREGDI 51
+ + A V+KV+GRTGSRG VTQVRV+FL+D +R I+RNVKGPVRE DI
Sbjct: 5 TPVTLAKVIKVLGRTGSRGGVTQVRVEFLEDTSRTIVRNVKGPVRENDI 53
>pdb|3ZEY|Z Chain Z, High-resolution Cryo-electron Microscopy Structure Of
The Trypanosoma Brucei Ribosome
Length = 103
Score = 60.8 bits (146), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 29/53 (54%), Positives = 40/53 (75%), Gaps = 5/53 (9%)
Query: 4 QIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQ-----NRFIMRNVKGPVREGDI 51
Q + V++KV+GRTGSRG VTQVRV+ + ++ NR I+RNVKGP +EGD+
Sbjct: 37 QAQVGVIIKVLGRTGSRGNVTQVRVRLMAEEGSPEANRTIVRNVKGPCKEGDM 89
>pdb|1NY4|A Chain A, Solution Structure Of The 30s Ribosomal Protein S28e
From Pyrococcus Horikoshii. Northeast Structural
Genomics Consortium Target Jr19
Length = 82
Score = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/46 (56%), Positives = 36/46 (78%), Gaps = 2/46 (4%)
Query: 8 AVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDI 51
A V++++GRTG+ G VTQV+V+ L+ D+ R I RNV+GPVR GDI
Sbjct: 9 AEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRVGDI 54
>pdb|3J20|X Chain X, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 71
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/46 (56%), Positives = 36/46 (78%), Gaps = 2/46 (4%)
Query: 8 AVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDI 51
A V++++GRTG+ G VTQV+V+ L+ D+ R I RNV+GPVR GDI
Sbjct: 9 AEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRIGDI 54
>pdb|1NE3|A Chain A, Solution Structure Of Ribosomal Protein S28e From
Methanobacterium Thermoautotrophicum. Ontario Centre
For Structural Proteomics Target Mth0256_1_68;
Northeast Structural Genomics Target Tt744
Length = 68
Score = 49.3 bits (116), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 24/46 (52%), Positives = 33/46 (71%), Gaps = 2/46 (4%)
Query: 8 AVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDI 51
A V++V+ RTG G+V QV+ + LD D+ R + RNV GP+REGDI
Sbjct: 7 AEVIEVLKRTGMTGEVMQVKCRILDGRDKGRILTRNVMGPIREGDI 52
>pdb|2XZM|1 Chain 1, Crystal Structure Of The Eukaryotic 40s Ribosomal
Subunit In Complex With Initiation Factor 1. This File
Contains The 40s Subunit And Initiation Factor For
Molecule 1
pdb|2XZN|1 Chain 1, Crystal Structure Of The Eukaryotic 40s Ribosomal
Subunit In Complex With Initiation Factor 1. This File
Contains The 40s Subunit And Initiation Factor For
Molecule 2
Length = 68
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 34/51 (66%), Gaps = 2/51 (3%)
Query: 3 SQIKHAVVVKVMGRTGSRGQVTQVRVKFLD--DQNRFIMRNVKGPVREGDI 51
+ A ++ V+G+TGSRG +TQVRV + ++ R ++RNVKG R GD+
Sbjct: 4 EETTKARIMDVLGKTGSRGGITQVRVVLISGKEEGRQLIRNVKGACRVGDV 54
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
0.324 0.139 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,275,976
Number of Sequences: 62578
Number of extensions: 32165
Number of successful extensions: 98
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 86
Number of HSP's gapped (non-prelim): 7
length of query: 65
length of database: 14,973,337
effective HSP length: 36
effective length of query: 29
effective length of database: 12,720,529
effective search space: 368895341
effective search space used: 368895341
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)