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= 048067
(75 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2GYA|R Chain R, Structure Of The 50s Subunit Of A Pre-Translocational E.
Coli Ribosome Obtained By Fitting Atomic Models For Rna
And Protein Components Into Cryo-Em Map Emd-1056
pdb|2GYC|R Chain R, Structure Of The 50s Subunit Of A Secm-Stalled E. Coli
Ribosome Complex Obtained By Fitting Atomic Models For
Rna And Protein Components Into Cryo-Em Map Emd-1143
Length = 92
Score = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 26/44 (59%)
Query: 31 AASKLYGLEIEKVRTLNKQGMKKRREGCLVTGPNYKKAYRTLKK 74
A KL+ +E+E V TL +G KR + ++KKAY TLK+
Sbjct: 40 AVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDWKKAYVTLKE 83
>pdb|2J28|T Chain T, Model Of E. Coli Srp Bound To 70s Rncs
pdb|3IY9|T Chain T, Leishmania Tarentolae Mitochondrial Large Ribosomal
Subunit Model
pdb|3E1B|M Chain M, Structure Of The 50s Subunit Of E. Coli Ribosome In
Pre-Accommodation State
pdb|3E1D|M Chain M, Structure Of The 50s Subunit Of E. Coli Ribosome In
Post-Accommodation State
Length = 99
Score = 30.4 bits (67), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 26/44 (59%)
Query: 31 AASKLYGLEIEKVRTLNKQGMKKRREGCLVTGPNYKKAYRTLKK 74
A KL+ +E+E V TL +G KR + ++KKAY TLK+
Sbjct: 46 AVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDWKKAYVTLKE 89
>pdb|1P85|R Chain R, Real Space Refined Coordinates Of The 50s Subunit Fitted
Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp
State Of E. Coli 70s Ribosome
pdb|1P86|R Chain R, Real Space Refined Coordinates Of The 50s Subunit Fitted
Into The Low Resolution Cryo-Em Map Of The
Initiation-Like State Of E. Coli 70s Ribosome
pdb|2AW4|T Chain T, 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|T Chain T, 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|1VS6|T Chain T, 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|T Chain T, 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|2I2T|T Chain T, 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|T Chain T, 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|2QOV|T Chain T, 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|T Chain T, 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|T Chain T, 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|T Chain T, 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|T Chain T, 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|T Chain T, 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|T Chain T, 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|T Chain T, 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|T Chain T, 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|T Chain T, 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|T Chain T, 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|T Chain T, 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|T Chain T, 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|T Chain T, 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|T Chain T, Structure Of Pdf Binding Helix In Complex With The
Ribosome (Part 1 Of 4)
pdb|2VHN|T Chain T, Structure Of Pdf Binding Helix In Complex With The
Ribosome. (Part 2 Of 4)
pdb|2RDO|T Chain T, 50s Subunit With Ef-G(Gdpnp) And Rrf Bound
pdb|2VRH|B Chain B, Structure Of The E. Coli Trigger Factor Bound To A
Translating Ribosome
pdb|3DF2|T Chain T, 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|T Chain T, 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|T Chain T, The Hsp15 Protein Fitted Into The Low Resolution Cryo-Em
Map 50s.Nc-Trna.Hsp15 Complex
pdb|3I1N|T Chain T, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1P|T Chain T, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1R|T Chain T, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1T|T Chain T, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I20|T Chain T, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I22|T Chain T, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3KCR|T Chain T, Ribosome-Secy Complex. This Entry 3kcr Contains 50s
Ribosomal Subnit. The 30s Ribosomal Subunit Can Be
Found In Pdb Entry 3kc4
pdb|1VT2|T Chain T, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 50s Subunit Of The
Second 70s Ribosome.
pdb|3ORB|T Chain T, 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|U Chain U, 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|U Chain U, 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|3J01|T Chain T, Structure Of The Ribosome-Secye Complex In The Membrane
Environment
pdb|3SGF|X Chain X, Crystal Structure Of Release Factor Rf3 Trapped In The
Gtp State On A Rotated Conformation Of The Ribosome
pdb|3UOS|X Chain X, Crystal Structure Of Release Factor Rf3 Trapped In The
Gtp State On A Rotated Conformation Of The Ribosome
(Without Viomycin)
pdb|3J0T|V Chain V, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class2 Of The Six
Classes)
pdb|3J0W|V Chain V, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 4a Of The Six
Classes)
pdb|3J0Y|V Chain V, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 4b Of The Six
Classes)
pdb|3J11|V Chain V, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 3 Of The Six
Classes)
pdb|3J12|V Chain V, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 5 Of The Six
Classes)
pdb|3J14|V Chain V, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 6 Of The Six
Classes)
pdb|4GAR|T Chain T, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
pdb|4GAU|T Chain T, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
Length = 100
Score = 30.4 bits (67), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 26/44 (59%)
Query: 31 AASKLYGLEIEKVRTLNKQGMKKRREGCLVTGPNYKKAYRTLKK 74
A KL+ +E+E V TL +G KR + ++KKAY TLK+
Sbjct: 46 AVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDWKKAYVTLKE 89
>pdb|3FIK|T Chain T, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry
Consists Of The 50s Subunit.
pdb|2WWQ|T Chain T, 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|T Chain T, Crystal Structure Of The E. Coli Ribosome Bound To
Erythromycin. This File Contains The 50s Subunit Of The
Second 70s Ribosome.
pdb|3OFR|T Chain T, 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|T Chain T, 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|T Chain T, Crystal Structure Of The E. Coli Ribosome Bound To
Chloramphenicol. This File Contains The 50s Subunit Of
The Second 70s Ribosome.
pdb|3OFZ|T Chain T, 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|T Chain T, Crystal Structure Of The E. Coli Ribosome Bound To
Clindamycin. This File Contains The 50s Subunit Of The
Second 70s Ribosome.
pdb|3OAS|T Chain T, Crystal Structure Of The E. Coli Ribosome Bound To
Telithromycin. This File Contains The 50s Subunit Of
The Second 70s Ribosome.
pdb|3OAT|T Chain T, 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|3R8S|T Chain T, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
pdb|3R8T|T Chain T, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
pdb|3J19|T Chain T, Structure Of The Bacterial Ribosome Complexed By
Tmrna-Smpb And Ef-G During Translocation And
Mld-Loading (50s Subunit)
Length = 93
Score = 30.0 bits (66), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 26/44 (59%)
Query: 31 AASKLYGLEIEKVRTLNKQGMKKRREGCLVTGPNYKKAYRTLKK 74
A KL+ +E+E V TL +G KR + ++KKAY TLK+
Sbjct: 46 AVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDWKKAYVTLKE 89
>pdb|1MJH|A Chain A, Structure-Based Assignment Of The Biochemical Function
Of Hypothetical Protein Mj0577: A Test Case Of
Structural Genomics
pdb|1MJH|B Chain B, Structure-Based Assignment Of The Biochemical Function
Of Hypothetical Protein Mj0577: A Test Case Of
Structural Genomics
Length = 162
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 27/52 (51%)
Query: 11 KLLMPSSFENIKEIAFKTMHAASKLYGLEIEKVRTLNKQGMKKRREGCLVTG 62
K+L P+ F EIA K + A L E+ + ++++ +KKR L+ G
Sbjct: 7 KILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLG 58
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
0.320 0.135 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,043,760
Number of Sequences: 62578
Number of extensions: 62515
Number of successful extensions: 191
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 183
Number of HSP's gapped (non-prelim): 8
length of query: 75
length of database: 14,973,337
effective HSP length: 44
effective length of query: 31
effective length of database: 12,219,905
effective search space: 378817055
effective search space used: 378817055
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)