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= 037546
(66 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 = 70.5 bits (171), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 38/52 (73%), Positives = 42/52 (80%), Gaps = 1/52 (1%)
Query: 1 MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDI 52
MDT K A V+KV+GRTGSRGQVTQVRV+F+DD R I RNVKGPVR GDI
Sbjct: 1 MDTQ-VKLAVVVKVMGRTGSRGQVTQVRVKFLDDQNRLIMRNVKGPVREGDI 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 = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 36/53 (67%), Positives = 40/53 (75%), Gaps = 1/53 (1%)
Query: 1 MDTGGP-KKATVIKVIGRTGSRGQVTQVRVQFMDDTKRQITRNVKGPVRVGDI 52
MD P A VIKV+GRTGSRG VTQVRV+F++DT R I RNVKGPVR DI
Sbjct: 1 MDNKTPVTLAKVIKVLGRTGSRGGVTQVRVEFLEDTSRTIVRNVKGPVRENDI 53
>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 = 53.1 bits (126), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 31/53 (58%), Positives = 39/53 (73%), Gaps = 4/53 (7%)
Query: 2 DTGGPKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDI 52
D G P A VI++IGRTG+ G VTQV+V+ ++ D R I RNV+GPVRVGDI
Sbjct: 4 DEGYP--AEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRVGDI 54
>pdb|3ZEY|Z Chain Z, High-resolution Cryo-electron Microscopy Structure Of
The Trypanosoma Brucei Ribosome
Length = 103
Score = 52.8 bits (125), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 27/47 (57%), Positives = 33/47 (70%), Gaps = 5/47 (10%)
Query: 11 VIKVIGRTGSRGQVTQVRVQFMD-----DTKRQITRNVKGPVRVGDI 52
+IKV+GRTGSRG VTQVRV+ M + R I RNVKGP + GD+
Sbjct: 43 IIKVLGRTGSRGNVTQVRVRLMAEEGSPEANRTIVRNVKGPCKEGDM 89
>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 = 52.4 bits (124), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 30/53 (56%), Positives = 39/53 (73%), Gaps = 4/53 (7%)
Query: 2 DTGGPKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDI 52
D G P A VI++IGRTG+ G VTQV+V+ ++ D R I RNV+GPVR+GDI
Sbjct: 4 DEGYP--AEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRIGDI 54
>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 = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/54 (50%), Positives = 37/54 (68%), Gaps = 2/54 (3%)
Query: 1 MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDI 52
M+T KA ++ V+G+TGSRG +TQVRV + + RQ+ RNVKG RVGD+
Sbjct: 1 MNTEETTKARIMDVLGKTGSRGGITQVRVVLISGKEEGRQLIRNVKGACRVGDV 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 = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/54 (50%), Positives = 35/54 (64%), Gaps = 4/54 (7%)
Query: 1 MDTGGPKKATVIKVIGRTGSRGQVTQVRVQFMD--DTKRQITRNVKGPVRVGDI 52
MD P A VI+V+ RTG G+V QV+ + +D D R +TRNV GP+R GDI
Sbjct: 1 MDDATP--AEVIEVLKRTGMTGEVMQVKCRILDGRDKGRILTRNVMGPIREGDI 52
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
0.319 0.137 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,435,494
Number of Sequences: 62578
Number of extensions: 34602
Number of successful extensions: 69
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: 57
Number of HSP's gapped (non-prelim): 7
length of query: 66
length of database: 14,973,337
effective HSP length: 37
effective length of query: 29
effective length of database: 12,657,951
effective search space: 367080579
effective search space used: 367080579
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)