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= 043767
(105 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|W Chain W, Localization Of The Large Subunit Ribosomal Proteins
Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
Translating 80s Ribosome
Length = 130
Score = 99.4 bits (246), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 49/60 (81%), Positives = 54/60 (90%), Gaps = 1/60 (1%)
Query: 30 TFTIDCAKPVEDKIMDIASLEKFLQERIKV-GGKAGALGDTVTVTRDKTKITVLSDSNFS 88
+F IDC+KPVEDKIM+IASLEKFLQERIKV GGKAG LGD+VTVTRDKTK+TV SD FS
Sbjct: 22 SFVIDCSKPVEDKIMEIASLEKFLQERIKVAGGKAGNLGDSVTVTRDKTKVTVTSDGAFS 81
>pdb|4A18|M Chain M, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|M Chain M, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|M Chain M, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|M Chain M, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2
Length = 118
Score = 64.3 bits (155), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 29/58 (50%), Positives = 40/58 (68%)
Query: 31 FTIDCAKPVEDKIMDIASLEKFLQERIKVGGKAGALGDTVTVTRDKTKITVLSDSNFS 88
F IDC++PVEDK++ I +FL+ +IKVGGK G LG+ +T++ D KI V S FS
Sbjct: 17 FKIDCSQPVEDKVILIGEFAEFLKSKIKVGGKLGNLGENITISNDDKKINVQSTIPFS 74
>pdb|3IZS|W Chain W, Localization Of The Large Subunit Ribosomal Proteins
Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3U5E|U Chain U, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|U Chain U, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|U Chain U, Cryo-Em Structure Of The 60s Ribosomal Subunit In
Complex With Arx1 And Rei1
Length = 121
Score = 60.8 bits (146), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 29/59 (49%), Positives = 39/59 (66%)
Query: 30 TFTIDCAKPVEDKIMDIASLEKFLQERIKVGGKAGALGDTVTVTRDKTKITVLSDSNFS 88
TFT+D + P E+ + D AS K+L + IKV G G LG+ VTVT D T +TV+S + FS
Sbjct: 14 TFTVDVSSPTENGVFDPASYAKYLIDHIKVEGAVGNLGNAVTVTEDGTVVTVVSTAKFS 72
>pdb|1MSK|A Chain A, Methionine Synthase (Activation Domain)
Length = 331
Score = 25.8 bits (55), Expect = 5.7, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 41 DKIMDIASLEKFLQERIKVG-GKAGALGDTVTVTRDKTKITVLSDSN 86
+ ++D S EK L R VG A +GD + + RD+T+ V++ S+
Sbjct: 85 NDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVINVSH 131
>pdb|1K7Y|A Chain A, E. Coli Meth C-Terminal Fragment (649-1227)
pdb|1K98|A Chain A, Adomet Complex Of Meth C-Terminal Fragment
Length = 577
Score = 25.4 bits (54), Expect = 7.9, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 41 DKIMDIASLEKFLQERIKVG-GKAGALGDTVTVTRDKTKITVLSDSN 86
+ ++D S EK L R VG A +GD + + RD+T+ V++ S+
Sbjct: 331 NDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVINVSH 377
>pdb|3BUL|A Chain A, E. Coli I690cG743C METH C-Terminal Fragment (649-1227)
pdb|3IV9|A Chain A, Structure Of The B12-Dependent Methionine Synthase (Meth)
C-Teminal Half In A "his-On" Conformation
pdb|3IVA|A Chain A, Structure Of The B12-Dependent Methionine Synthase (Meth)
C-Teminal Half With Adohcy Bound
Length = 579
Score = 25.4 bits (54), Expect = 8.0, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 41 DKIMDIASLEKFLQERIKVG-GKAGALGDTVTVTRDKTKITVLSDSN 86
+ ++D S EK L R VG A +GD + + RD+T+ V++ S+
Sbjct: 333 NDMLDKLSAEKTLNPRGVVGLFPANRVGDDIEIYRDETRTHVINVSH 379
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
0.313 0.128 0.350
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,808,068
Number of Sequences: 62578
Number of extensions: 48528
Number of successful extensions: 109
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 104
Number of HSP's gapped (non-prelim): 7
length of query: 105
length of database: 14,973,337
effective HSP length: 70
effective length of query: 35
effective length of database: 10,592,877
effective search space: 370750695
effective search space used: 370750695
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 45 (21.9 bits)