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= psy13112
(302 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1P6G|Q Chain Q, Real Space Refined Coordinates Of The 30s Subunit Fitted
Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp
State Of E. Coli 70s Ribosome
pdb|1P87|Q Chain Q, Real Space Refined Coordinates Of The 30s Subunit Fitted
Into The Low Resolution Cryo-Em Map Of The
Initiation-Like State Of E. Coli 70s Ribosome
pdb|2AVY|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli At 3.5 A Resolution. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2AW7|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli At 3.5 A Resolution. This File Contains
The 30s Subunit Of The Second 70s Ribosome. The Entire
Crystal Structure Contains Two 70s Ribosomes And Is
Described In Remark 400.
pdb|2I2P|Q Chain Q, Crystal Structure Of Ribosome With Messenger Rna And The
Anticodon Stem-Loop Of P-Site Trna. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2I2U|Q Chain Q, Crystal Structure Of Ribosome With Messenger Rna And The
Anticodon Stem-Loop Of P-Site Trna. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2QOU|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin. This
File Contains The 30s Subunit Of The First 70s Ribosome,
With Spectinomycin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes.
pdb|2QOW|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin. This
File Contains The 30s Subunit Of The Second 70s
Ribosome, With Spectinomycin Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|2QOY|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin And
Neomycin. This File Contains The 30s Subunit Of The
First 70s Ribosome, With Spectinomycin And Neomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes.
pdb|2QP0|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin And
Neomycin. This File Contains The 30s Subunit Of The
Second 70s Ribosome, With Spectinomycin And Neomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes.
pdb|2QAL|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Neomycin. This File
Contains The 30s Subunit Of The First 70s Ribosome, With
Neomycin Bound. The Entire Crystal Structure Contains
Two 70s Ribosomes And Is Described In Remark 400.
pdb|2QAN|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Neomycin. This File
Contains The 30s Subunit Of The Second 70s Ribosome,
With Neomycin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QB9|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin. This File
Contains The 30s Subunit Of The First 70s Ribosome, With
Gentamicin Bound. The Entire Crystal Structure Contains
Two 70s Ribosomes And Is Described In Remark 400.
pdb|2QBB|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin. This File
Contains The 30s Subunit Of The Second 70s Ribosome,
With Gentamicin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBD|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 30s Subunit Of The
First 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBF|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 30s Subunit Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBH|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 30s
Subunit Of The First 70s Ribosome, With Gentamicin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2QBJ|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 30s
Subunit Of The Second 70s Ribosome, With Gentamicin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2Z4K|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
30s Subunit Of The First 70s Ribosome, With Paromomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2Z4M|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
30s Subunit Of The Second 70s Ribosome, With Paromomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2VHO|Q Chain Q, Structure Of Pdf Binding Helix In Complex With The
Ribosome (Part 3 Of 4)
pdb|2VHP|Q Chain Q, Structure Of Pdf Binding Helix In Complex With The
Ribosome (Part 4 Of 4)
pdb|3DF1|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Hygromycin B. This File
Contains The 30s Subunit Of The First 70s Ribosome, With
Hygromycin B Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes.
pdb|3DF3|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Hygromycin B. This File
Contains The 30s Subunit Of The Second 70s Ribosome,
With Hygromycin B Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes.
pdb|3J00|Q Chain Q, Structure Of The Ribosome-Secye Complex In The Membrane
Environment
pdb|4ADV|Q Chain Q, Structure Of The E. Coli Methyltransferase Ksga Bound To
The E. Coli 30s Ribosomal Subunit
pdb|3J0U|T Chain T, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class2 Of The Six
Classes)
pdb|3J0V|T Chain T, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 4a Of The Six
Classes)
pdb|3J0X|T Chain T, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 4b Of The Six
Classes)
pdb|3J0Z|T Chain T, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 5 Of The Six
Classes)
pdb|3J10|T Chain T, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 6 Of The Six
Classes)
pdb|3J13|S Chain S, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 3 Of The Six
Classes)
Length = 83
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 174 GKYFPKFTVMYAHDPDKICKTGDIVLIEE 202
GK+ + T ++ HD + C GD+V I E
Sbjct: 34 GKFIKRTTKLHVHDENNECGIGDVVEIRE 62
>pdb|1VS5|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With The Antibiotic
Kasugamyin At 3.5a Resolution. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|1VS7|Q Chain Q, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With The Antibiotic
Kasugamyin At 3.5a Resolution. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|3E1A|J Chain J, Structure Of The 30s Subunit And The Trnas Of E. Coli
Ribosome In Pre- Accommodation State
pdb|3E1C|J Chain J, Structure Of The 30s Subunit And The Trnas Of E. Coli
Ribosome In Post-Accommodation State
pdb|3I1M|Q Chain Q, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1O|Q Chain Q, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1Q|Q Chain Q, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1S|Q Chain Q, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1Z|Q Chain Q, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I21|Q Chain Q, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3KC4|Q Chain Q, Ribosome-Secy Complex. This Entry 3kc4 Contains 30s
Ribosomal Subnit. The 50s Ribosomal Subunit Can Be Found
In Pdb Entry 3kcr
pdb|3OR9|Q Chain Q, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 30s Subunit Of The First
70s Ribosome.
pdb|3ORA|Q Chain Q, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 30s Subunit Of The
Second 70s Ribosome.
pdb|3IZV|U Chain U, Structural Insights Into Cognate Vs. Near-Cognate
Discrimination During Decoding. This Entry Contains The
Small Subunit Of A Ribosome Programmed With A
Near-Cognate Codon, AT-Site Trna, P-Site Trna, Mrna And
Ef-Tu
pdb|3IZW|U Chain U, Structural Insights Into Cognate Vs. Near-Cognate
Discrimination During Decoding.This Entry Contains The
Small Subunit Of A Ribosome Programmed With A Cognate
Codon, AT-Site Trna, P-Site Trna, Mrna And Ef-Tu
pdb|3SFS|Q Chain Q, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome
pdb|3UOQ|Q Chain Q, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome (Without
Viomycin)
pdb|4GAQ|Q Chain Q, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
pdb|4GAS|Q Chain Q, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
Length = 84
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 174 GKYFPKFTVMYAHDPDKICKTGDIVLIEE 202
GK+ + T ++ HD + C GD+V I E
Sbjct: 35 GKFIKRTTKLHVHDENNECGIGDVVEIRE 63
>pdb|2GY9|Q Chain Q, Structure Of The 30s 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|2GYB|Q Chain Q, Structure Of The 30s 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 = 79
Score = 27.7 bits (60), Expect = 8.5, Method: Composition-based stats.
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 174 GKYFPKFTVMYAHDPDKICKTGDIVLIEE 202
GK+ + T ++ HD + C GD+V I E
Sbjct: 30 GKFIKRTTKLHVHDENNECGIGDVVEIRE 58
>pdb|3FIH|Q Chain Q, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry
Consists Of The 30s Subunit, Trnas And The Ternary
Complex.
pdb|3IY8|Q Chain Q, Leishmania Tarentolae Mitonchondrial Ribosome Small
Subunit
pdb|2WWL|Q Chain Q, E.Coli 70s Ribosome Stalled During Translation Of Tnac
Leader Peptide. This File Contains The 30s, The P-Site
Trna And The Tnac Leader Peptide (Part 1 Of 2).
pdb|3OFO|Q Chain Q, Crystal Structure Of The E. Coli Ribosome Bound To
Erythromycin. This File Contains The 30s Subunit Of The
First 70s Ribosome.
pdb|3OFP|Q Chain Q, Crystal Structure Of The E. Coli Ribosome Bound To
Erythromycin. This File Contains The 30s Subunit Of The
Second 70s Ribosome.
pdb|3OFA|Q Chain Q, Crystal Structure Of The E. Coli Ribosome Bound To
Chloramphenicol. This File Contains The 30s Subunit Of
The First 70s Ribosome.
pdb|3OFB|Q Chain Q, Crystal Structure Of The E. Coli Ribosome Bound To
Chloramphenicol. This File Contains The 30s Subunit Of
The Second 70s Ribosome.
pdb|3OFX|Q Chain Q, Crystal Structure Of The E. Coli Ribosome Bound To
Clindamycin. This File Contains The 30s Subunit Of The
First 70s Ribosome.
pdb|3OFY|Q Chain Q, Crystal Structure Of The E. Coli Ribosome Bound To
Clindamycin. This File Contains The 30s Subunit Of The
Second 70s Ribosome
pdb|3OAQ|Q Chain Q, Crystal Structure Of The E. Coli Ribosome Bound To
Telithromycin. This File Contains The 30s Subunit Of The
First 70s Ribosome.
pdb|3OAR|Q Chain Q, Crystal Structure Of The E. Coli Ribosome Bound To
Telithromycin. This File Contains The 30s Subunit Of The
Second 70s Ribosome.
pdb|2YKR|Q Chain Q, 30s Ribosomal Subunit With Rsga Bound In The Presence Of
Gmppnp
pdb|4A2I|Q Chain Q, Cryo-Electron Microscopy Structure Of The 30s Subunit In
Complex With The Yjeq Biogenesis Factor
pdb|3J18|Q Chain Q, Structure Of The Bacterial Ribosome Complexed By
Tmrna-Smpb And Ef-G During Translocation And Mld-Loading
(30s Subunit)
pdb|4GD1|Q Chain Q, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
pdb|4GD2|Q Chain Q, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
Length = 80
Score = 27.7 bits (60), Expect = 9.3, Method: Composition-based stats.
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 174 GKYFPKFTVMYAHDPDKICKTGDIVLIEE 202
GK+ + T ++ HD + C GD+V I E
Sbjct: 32 GKFIKRTTKLHVHDENNECGIGDVVEIRE 60
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 0.138 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,779,465
Number of Sequences: 62578
Number of extensions: 420625
Number of successful extensions: 677
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 668
Number of HSP's gapped (non-prelim): 11
length of query: 302
length of database: 14,973,337
effective HSP length: 98
effective length of query: 204
effective length of database: 8,840,693
effective search space: 1803501372
effective search space used: 1803501372
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: 51 (24.3 bits)