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= 039022
(222 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1VLI|A Chain A, Crystal Structure Of Spore Coat Polysaccharide
Biosynthesis Protein Spse (Bsu37870) From Bacillus
Subtilis At 2.38 A Resolution
Length = 385
Score = 33.9 bits (76), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 38/83 (45%), Gaps = 10/83 (12%)
Query: 40 VMNRAKRGLFAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHAL 99
+ N A RG+F IQ G SED R KP R F ++ +R A+
Sbjct: 310 IRNFAYRGIFTTAPIQKGEAFSEDNIAVLRPGQKPQGLHPRFFE-LLTSGVR------AV 362
Query: 100 RCIDKAGGI--DEYLLK-TPYHK 119
R I GI D+ LLK +P+H+
Sbjct: 363 RDIPADTGIVWDDILLKDSPFHE 385
>pdb|3BBO|Y Chain Y, Homology Model For The Spinach Chloroplast 50s Subunit
Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
Length = 151
Score = 31.6 bits (70), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 49 FAGKHIQFGNRVSEDGGNKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAG 106
F GK N+VS +KT++ N+Q KR++ R+++++++T A++ I+K G
Sbjct: 80 FTGKKSNRANKVSHSN-HKTKKLQFVNLQYKRIWWEAGKRYVKLRLSTKAIKTIEKNG 136
>pdb|2QOV|Z Chain Z, 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|Z Chain Z, 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|Z Chain Z, 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|Z Chain Z, 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|Z Chain Z, 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|Z Chain Z, 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|Z Chain Z, 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|Z Chain Z, 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|Z Chain Z, 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|Z Chain Z, 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|Z Chain Z, 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|Z Chain Z, 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|Z Chain Z, 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|Z Chain Z, 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|3DF2|Z Chain Z, 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|Z Chain Z, 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|3I1N|X Chain X, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1P|X Chain X, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1R|X Chain X, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1T|X Chain X, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I20|X Chain X, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I22|X Chain X, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3KCR|X Chain X, Ribosome-Secy Complex. This Entry 3kcr Contains 50s
Ribosomal Subnit. The 30s Ribosomal Subunit Can Be Found
In Pdb Entry 3kc4
pdb|1VT2|X Chain X, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 50s Subunit Of The
Second 70s Ribosome.
pdb|3ORB|X Chain X, 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|Y Chain Y, 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|Y Chain Y, 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|1 Chain 1, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome
pdb|3UOS|1 Chain 1, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome (Without
Viomycin)
pdb|4GAR|X Chain X, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
pdb|4GAU|X Chain X, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
Length = 78
Score = 30.0 bits (66), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 66 NKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYL 112
N T+R + PN+ R + R + ++V+ +R IDK GID L
Sbjct: 23 NATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDKK-GIDTVL 68
>pdb|2I2T|X Chain X, 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|X Chain X, 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|3FIK|X Chain X, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry
Consists Of The 50s Subunit.
pdb|2WWQ|0 Chain 0, 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|X Chain X, Crystal Structure Of The E. Coli Ribosome Bound To
Erythromycin. This File Contains The 50s Subunit Of The
Second 70s Ribosome.
pdb|3OFR|X Chain X, 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|X Chain X, 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|X Chain X, Crystal Structure Of The E. Coli Ribosome Bound To
Chloramphenicol. This File Contains The 50s Subunit Of
The Second 70s Ribosome.
pdb|3OFZ|X Chain X, 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|X Chain X, Crystal Structure Of The E. Coli Ribosome Bound To
Clindamycin. This File Contains The 50s Subunit Of The
Second 70s Ribosome.
pdb|3OAS|X Chain X, Crystal Structure Of The E. Coli Ribosome Bound To
Telithromycin. This File Contains The 50s Subunit Of The
Second 70s Ribosome.
pdb|3OAT|X Chain X, 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|X Chain X, Structure Of The Ribosome-Secye Complex In The Membrane
Environment
pdb|3R8S|X Chain X, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
pdb|3R8T|X Chain X, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
pdb|3J0T|Z Chain Z, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class2 Of The Six
Classes)
pdb|3J0W|Z Chain Z, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 4a Of The Six
Classes)
pdb|3J0Y|Z Chain Z, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 4b Of The Six
Classes)
pdb|3J11|Z Chain Z, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 3 Of The Six
Classes)
pdb|3J12|Z Chain Z, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 5 Of The Six
Classes)
pdb|3J14|Z Chain Z, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 6 Of The Six
Classes)
pdb|3J19|X Chain X, Structure Of The Bacterial Ribosome Complexed By
Tmrna-Smpb And Ef-G During Translocation And Mld-Loading
(50s Subunit)
Length = 77
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 66 NKTRRNWKPNVQEKRLFSYIMDRHIRVKVTTHALRCIDKAGGIDEYL 112
N T+R + PN+ R + R + ++V+ +R IDK GID L
Sbjct: 22 NATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDKK-GIDTVL 67
>pdb|3QZE|A Chain A, Crystal Structure Of Dapa (Pa1010) At 1.6 A Resolution
pdb|3QZE|B Chain B, Crystal Structure Of Dapa (Pa1010) At 1.6 A Resolution
pdb|3QZE|C Chain C, Crystal Structure Of Dapa (Pa1010) At 1.6 A Resolution
pdb|3QZE|D Chain D, Crystal Structure Of Dapa (Pa1010) At 1.6 A Resolution
Length = 314
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 104 KAGGIDEYLLKTPYHKMDTEMGLY 127
K+GG D LL TPY+ T+ G+Y
Sbjct: 115 KSGGADACLLVTPYYNKPTQEGMY 138
>pdb|3NOE|A Chain A, Crystal Structure Of Dihydrodipicolinate Synthase From
Pseudomonas Aeruginosa
pdb|3NOE|B Chain B, Crystal Structure Of Dihydrodipicolinate Synthase From
Pseudomonas Aeruginosa
pdb|3PS7|A Chain A, Biochemical Studies And Crystal Structure Determination Of
Dihydrodipicolinate Synthase From Pseudomonas Aeruginosa
pdb|3PS7|B Chain B, Biochemical Studies And Crystal Structure Determination Of
Dihydrodipicolinate Synthase From Pseudomonas Aeruginosa
pdb|3PUO|A Chain A, Crystal Structure Of Dihydrodipicolinate Synthase From
Pseudomonas Aeruginosa(Psdhdps)complexed With L-Lysine
At 2.65a Resolution
pdb|3PUO|B Chain B, Crystal Structure Of Dihydrodipicolinate Synthase From
Pseudomonas Aeruginosa(Psdhdps)complexed With L-Lysine
At 2.65a Resolution
pdb|3S8H|A Chain A, Structure Of Dihydrodipicolinate Synthase Complexed With
3- Hydroxypropanoic Acid(Hpa)at 2.70 A Resolution
pdb|3S8H|B Chain B, Structure Of Dihydrodipicolinate Synthase Complexed With
3- Hydroxypropanoic Acid(Hpa)at 2.70 A Resolution
Length = 292
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 104 KAGGIDEYLLKTPYHKMDTEMGLY 127
K+GG D LL TPY+ T+ G+Y
Sbjct: 93 KSGGADACLLVTPYYNKPTQEGMY 116
>pdb|1Z47|A Chain A, Structure Of The Atpase Subunit Cysa Of The Putative
Sulfate Atp-Binding Cassette (Abc) Transporter From
Alicyclobacillus Acidocaldarius
pdb|1Z47|B Chain B, Structure Of The Atpase Subunit Cysa Of The Putative
Sulfate Atp-Binding Cassette (Abc) Transporter From
Alicyclobacillus Acidocaldarius
Length = 355
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 112 LLKTPYHKMDTEMGLYWKTKIEKLYEELGQTEVAFFTPEEEAKLE 156
L P+ +DT++ +T + ++++E+G T V F T ++E LE
Sbjct: 168 LFDEPFAAIDTQIRRELRTFVRQVHDEMGVTSV-FVTHDQEEALE 211
>pdb|1CII|A Chain A, Colicin Ia
Length = 602
Score = 27.7 bits (60), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 41 MNRAKRGL-FAGKHIQFGNRVSEDGGNKTRRNWKP 74
+NR RGL +AGK + ++E G NW+P
Sbjct: 510 LNRFSRGLGYAGKFTSLADWITEFGKAVRTENWRP 544
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
0.314 0.132 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,296,249
Number of Sequences: 62578
Number of extensions: 240566
Number of successful extensions: 612
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 601
Number of HSP's gapped (non-prelim): 16
length of query: 222
length of database: 14,973,337
effective HSP length: 95
effective length of query: 127
effective length of database: 9,028,427
effective search space: 1146610229
effective search space used: 1146610229
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: 49 (23.5 bits)