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= 002557
(908 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1RQ8|A Chain A, Solution Structure Of The Hypothetical Protein Sav1595
From Staphylococcus Aureus, A Putative Rna Binding
Protein
Length = 104
Score = 32.7 bits (73), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 42/88 (47%), Gaps = 4/88 (4%)
Query: 664 ITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKI 723
+T +++ R L + +G+ G+ + ++ + + REL+K+ V FD K++
Sbjct: 2 LTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKEL 61
Query: 724 ALALEAESGGVLVSVDKISKGYAMVVYR 751
A L + LV V G +V+YR
Sbjct: 62 AETLSEATRSELVQV----IGSMIVIYR 85
>pdb|1EH1|A Chain A, Ribosome Recycling Factor From Thermus Thermophilus
pdb|2V46|Y Chain Y, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
Trna-Fmet (Part 1 Of 4). This File Contains The 30s
Subunit, Mrna, P-Site Asl, E-Site Trna And Rrf For
Molecule 1.
pdb|2V48|Y Chain Y, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
Trna-Fmet (Part 3 Of 4). This File Contains The 30s
Subunit, Mrna, P-Site Asl, E-Site Trna And Rrf For
Molecule 2.
pdb|2QBE|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 50s Subunit Of The
First 70s Ribosome, With Rrf Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2QBG|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 50s Subunit Of The
Second 70s Ribosome, With Rrf Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2QBI|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 50s
Subunit Of The First 70s Ribosome, With Gentamicin And
Rrf Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2QBK|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 50s
Subunit Of The Second 70s Ribosome, With Gentamicin And
Rrf Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2Z4L|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
50s Subunit Of The First 70s Ribosome, With Paromomycin
And Rrf Bound. The Entire Crystal Structure Contains Two
70s Ribosomes And Is Described In Remark 400.
pdb|2Z4N|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
50s Subunit Of The Second 70s Ribosome, With Paromomycin
And Rrf Bound. The Entire Crystal Structure Contains Two
70s Ribosomes And Is Described In Remark 400.
pdb|3J0D|J Chain J, Models For The T. Thermophilus Ribosome Recycling Factor
Bound To The E. Coli Post-Termination Complex
pdb|3J0E|G Chain G, Models For The T. Thermophilus Ribosome Recycling Factor
And The E. Coli Elongation Factor G Bound To The E. Coli
Post-Termination Complex
Length = 185
Score = 30.8 bits (68), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 29/107 (27%), Positives = 46/107 (42%), Gaps = 18/107 (16%)
Query: 309 NMKRMHEILERKTGGLVIWRSGTAVSLYRGVSYEVPSVQLNKRIYKRNELPASSVSQATD 368
+M++ E+LE GL R+ A+ L+ V Y V LN+ P + V Q+ D
Sbjct: 13 HMQKSLEVLEHNLAGLRTGRANPALLLHLKVEYYGAHVPLNQIATVTAPDPRTLVVQSWD 72
Query: 369 ----KQIHKQI--------------SMSVNLETASEEQETDFVREVK 397
K I K I ++ +N+ +EE+ D VR V+
Sbjct: 73 QNALKAIEKAIRDSDLGLNPSNKGDALYINIPPLTEERRKDLVRAVR 119
>pdb|1LN4|A Chain A, Crystal Structure Of E. Coli Yhby
Length = 104
Score = 29.6 bits (65), Expect = 7.4, Method: Composition-based stats.
Identities = 25/90 (27%), Positives = 46/90 (51%), Gaps = 8/90 (8%)
Query: 664 ITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKK- 722
++ +++ + L +K +LLG G+ +G + + ++ EL+K VK+ T D+ K
Sbjct: 3 LSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIK--VKIATEDRETKT 60
Query: 723 -IALALEAESGGVLVSVDKISKGYAMVVYR 751
I A+ E+G V V G +V+YR
Sbjct: 61 LIVEAIVRETGACNVQV----IGKTLVLYR 86
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
0.315 0.132 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,822,979
Number of Sequences: 62578
Number of extensions: 992722
Number of successful extensions: 2356
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 2348
Number of HSP's gapped (non-prelim): 24
length of query: 908
length of database: 14,973,337
effective HSP length: 108
effective length of query: 800
effective length of database: 8,214,913
effective search space: 6571930400
effective search space used: 6571930400
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (26.2 bits)