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= psy9580
(71 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2AW4|3 Chain 3, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli At 3.5 A Resolution. This File
Contains The 50s Subunit Of One 70s Ribosome. The
Entire Crystal Structure Contains Two 70s Ribosomes And
Is Described In Remark 400.
pdb|2AWB|3 Chain 3, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli At 3.5 A Resolution. This File
Contains The 50s Subunit Of The Second 70s Ribosome.
The Entire Crystal Structure Contains Two 70s Ribosomes
And Is Described In Remark 400.
pdb|2I2T|3 Chain 3, Crystal Structure Of Ribosome With Messenger Rna And The
Anticodon Stem-Loop Of P-Site Trna. This File Contains
The 50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described
In Remark 400.
pdb|2I2V|3 Chain 3, Crystal Structure Of Ribosome With Messenger Rna And The
Anticodon Stem-Loop Of P-Site Trna. This File Contains
The 50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described
In Remark 400.
pdb|2J28|3 Chain 3, Model Of E. Coli Srp Bound To 70s Rncs
pdb|2QOV|3 Chain 3, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin. This
File Contains The 50s Subunit Of The First 70s
Ribosome. The Entire Crystal Structure Contains Two 70s
Ribosomes.
pdb|2QOX|3 Chain 3, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin. This
File Contains The 50s Subunit Of The Second 70s
Ribosome. The Entire Crystal Structure Contains Two 70s
Ribosomes.
pdb|2QOZ|3 Chain 3, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin And
Neomycin. This File Contains The 50s Subunit Of The
First 70s Ribosome, With Neomycin Bound. The Entire
Crystal Structure Contains Two 70s Ribosomes.
pdb|2QP1|3 Chain 3, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin And
Neomycin. This File Contains The 50s Subunit Of The
Second 70s Ribosome, With Neomycin Bound. The Entire
Crystal Structure Contains Two 70s Ribosomes.
pdb|2QAM|3 Chain 3, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Neomycin. This File
Contains The 50s Subunit Of The First 70s Ribosome,
With Neomycin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QAO|3 Chain 3, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Neomycin. This File
Contains The 50s Subunit Of The Second 70s Ribosome,
With Neomycin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBA|3 Chain 3, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin. This File
Contains The 50s Subunit Of The First 70s Ribosome,
With Gentamicin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBC|3 Chain 3, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin. This File
Contains The 50s Subunit Of The Second 70s Ribosome,
With Gentamicin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBE|3 Chain 3, 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|3 Chain 3, 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|3 Chain 3, 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|3 Chain 3, 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|3 Chain 3, 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|3 Chain 3, 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|2VHM|3 Chain 3, Structure Of Pdf Binding Helix In Complex With The
Ribosome (Part 1 Of 4)
pdb|2VHN|3 Chain 3, Structure Of Pdf Binding Helix In Complex With The
Ribosome. (Part 2 Of 4)
pdb|2RDO|3 Chain 3, 50s Subunit With Ef-G(Gdpnp) And Rrf Bound
pdb|3DF2|3 Chain 3, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Hygromycin B. This
File Contains The 50s Subunit Of The First 70s
Ribosome. The Entire Crystal Structure Contains Two 70s
Ribosomes.
pdb|3DF4|3 Chain 3, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Hygromycin B. This
File Contains The 50s Subunit Of The Second 70s
Ribosome. The Entire Crystal Structure Contains Two 70s
Ribosomes.
pdb|3BBX|3 Chain 3, The Hsp15 Protein Fitted Into The Low Resolution Cryo-Em
Map 50s.Nc-Trna.Hsp15 Complex
pdb|3FIK|3 Chain 3, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry
Consists Of The 50s Subunit.
pdb|3E1B|W Chain W, Structure Of The 50s Subunit Of E. Coli Ribosome In
Pre-Accommodation State
pdb|3E1D|W Chain W, Structure Of The 50s Subunit Of E. Coli Ribosome In
Post-Accommodation State
pdb|2WWQ|7 Chain 7, E.Coli 70s Ribosome Stalled During Translation Of Tnac
Leader Peptide. This File Contains The 50s, The P-Site
Trna And The Tnac Leader Peptide (Part 2 Of 2).
pdb|3OFQ|3 Chain 3, Crystal Structure Of The E. Coli Ribosome Bound To
Erythromycin. This File Contains The 50s Subunit Of The
Second 70s Ribosome.
pdb|3OFR|3 Chain 3, Crystal Structure Of The E. Coli Ribosome Bound To
Erythromycin. This File Contains The 50s Subunit Of The
First 70s Ribosome With Erthromycin Bound.
pdb|3OFC|3 Chain 3, Crystal Structure Of The E. Coli Ribosome Bound To
Chloramphenicol. This File Contains The 50s Subunit Of
The First 70s Ribosome With Chloramphenicol Bound.
pdb|3OFD|3 Chain 3, Crystal Structure Of The E. Coli Ribosome Bound To
Chloramphenicol. This File Contains The 50s Subunit Of
The Second 70s Ribosome.
pdb|3OFZ|3 Chain 3, Crystal Structure Of The E. Coli Ribosome Bound To
Clindamycin. This File Contains The 50s Subunit Of The
First 70s Ribosome Bound To Clindamycin.
pdb|3OG0|3 Chain 3, Crystal Structure Of The E. Coli Ribosome Bound To
Clindamycin. This File Contains The 50s Subunit Of The
Second 70s Ribosome.
pdb|3OAS|3 Chain 3, Crystal Structure Of The E. Coli Ribosome Bound To
Telithromycin. This File Contains The 50s Subunit Of
The Second 70s Ribosome.
pdb|3OAT|3 Chain 3, Crystal Structure Of The E. Coli Ribosome Bound To
Telithromycin. This File Contains The 50s Subunit Of
The First 70s Ribosome With Telithromycin Bound.
pdb|3J01|3 Chain 3, Structure Of The Ribosome-Secye Complex In The Membrane
Environment
pdb|3R8S|3 Chain 3, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
pdb|3R8T|3 Chain 3, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
pdb|3J0T|6 Chain 6, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class2 Of The Six
Classes)
pdb|3J0W|6 Chain 6, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 4a Of The Six
Classes)
pdb|3J0Y|6 Chain 6, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 4b Of The Six
Classes)
pdb|3J11|6 Chain 6, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 3 Of The Six
Classes)
pdb|3J12|6 Chain 6, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 5 Of The Six
Classes)
pdb|3J14|6 Chain 6, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 6 Of The Six
Classes)
pdb|3J19|3 Chain 3, Structure Of The Bacterial Ribosome Complexed By
Tmrna-Smpb And Ef-G During Translocation And
Mld-Loading (50s Subunit)
Length = 64
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/63 (47%), Positives = 35/63 (55%)
Query: 9 KIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLRGLASVHKSNIASVRAMM 68
KIKT A KRF G K A RHILTKK+TK KR LR A V K ++ V A +
Sbjct: 2 KIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACL 61
Query: 69 PNS 71
P +
Sbjct: 62 PYA 64
>pdb|1VS6|3 Chain 3, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With The Antibiotic
Kasugamyin At 3.5a Resolution. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described
In Remark 400.
pdb|1VS8|3 Chain 3, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With The Antibiotic
Kasugamyin At 3.5a Resolution. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described
In Remark 400.
pdb|3I1N|3 Chain 3, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1P|3 Chain 3, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1R|3 Chain 3, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1T|3 Chain 3, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I20|3 Chain 3, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I22|3 Chain 3, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3KCR|3 Chain 3, Ribosome-Secy Complex. This Entry 3kcr Contains 50s
Ribosomal Subnit. The 30s Ribosomal Subunit Can Be
Found In Pdb Entry 3kc4
pdb|1VT2|3 Chain 3, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 50s Subunit Of The
Second 70s Ribosome.
pdb|3ORB|3 Chain 3, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 50s Subunit Of The
First 70s Ribosome Bound To Cem-101.
pdb|3IZT|FF Chain f, Structural Insights Into Cognate Vs. Near-Cognate
Discrimination During Decoding. This Entry Contains The
Large Subunit Of A Ribosome Programmed With A
Near-Cognate Codon.
pdb|3IZU|FF Chain f, Structural Insights Into Cognate Vs. Near-Cognate
Discrimination During Decoding. This Entry Contains The
Large Subunit Of A Ribosome Programmed With A Cognate
Codon
pdb|3SGF|7 Chain 7, Crystal Structure Of Release Factor Rf3 Trapped In The
Gtp State On A Rotated Conformation Of The Ribosome
pdb|3UOS|7 Chain 7, Crystal Structure Of Release Factor Rf3 Trapped In The
Gtp State On A Rotated Conformation Of The Ribosome
(Without Viomycin)
pdb|4GAR|3 Chain 3, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
pdb|4GAU|3 Chain 3, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
Length = 65
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/63 (47%), Positives = 35/63 (55%)
Query: 9 KIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLRGLASVHKSNIASVRAMM 68
KIKT A KRF G K A RHILTKK+TK KR LR A V K ++ V A +
Sbjct: 3 KIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACL 62
Query: 69 PNS 71
P +
Sbjct: 63 PYA 65
>pdb|3BBO|5 Chain 5, Homology Model For The Spinach Chloroplast 50s Subunit
Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
Length = 159
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 38/62 (61%)
Query: 8 FKIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLRGLASVHKSNIASVRAM 67
+K+KT ++ KRF + G I R +A K+H+L KK+TK K +L L V +S+ +V
Sbjct: 90 YKMKTHKASAKRFRVTGKGKIVRRRAGKQHLLAKKNTKRKNRLSKLIQVDRSDYDNVIGA 149
Query: 68 MP 69
+P
Sbjct: 150 LP 151
>pdb|1Y9L|A Chain A, The X-Ray Structure Of An Secretion System Protein
pdb|1Y9T|A Chain A, Crystal Structure Of A Type Iii Secretion System Protein
Complexed With The Lipid,
1-Monohexanoyl-2-Hydroxy-Sn-Glycero-3-Phosphate
pdb|2JW1|A Chain A, Structural Characterization Of The Type Iii Pilotin-
Secretin Interaction In Shigella Flexneri By Nmr
Spectroscopy
Length = 115
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 1 MKELFSVFKIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKL-RGL 53
+KE+ F K + K F + GV+ +G IL +K +VK KL RG+
Sbjct: 62 VKEVDGCFMDAQKIAIDKLFSMLKDGVVLKGNKINDTILIEKDGEVKLKLIRGI 115
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
0.322 0.131 0.348
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,492,387
Number of Sequences: 62578
Number of extensions: 36725
Number of successful extensions: 98
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 90
Number of HSP's gapped (non-prelim): 12
length of query: 71
length of database: 14,973,337
effective HSP length: 41
effective length of query: 30
effective length of database: 12,407,639
effective search space: 372229170
effective search space used: 372229170
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 45 (21.9 bits)