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= 037282
(56 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZ6|N Chain N, Localization Of The Small Subunit Ribosomal Proteins
Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
Translating 80s Ribosome
Length = 56
Score = 106 bits (264), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 47/56 (83%), Positives = 51/56 (91%)
Query: 1 MGHSNVWNSHPKTYGPGSRACRVCGNPHAIIRKYGLMCCRQCFRSNAKEIGFVKYR 56
MGHSNVWNSHPK YG GSR CRVCGN H +IRKYGLMCCRQCFRS+AK+IGF+KYR
Sbjct: 1 MGHSNVWNSHPKNYGAGSRVCRVCGNSHGLIRKYGLMCCRQCFRSDAKDIGFIKYR 56
>pdb|2ZKQ|NN Chain n, Structure Of A Mammalian Ribosomal 40s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 56
Score = 78.2 bits (191), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 34/54 (62%), Positives = 42/54 (77%)
Query: 1 MGHSNVWNSHPKTYGPGSRACRVCGNPHAIIRKYGLMCCRQCFRSNAKEIGFVK 54
MGH ++ SHP+ +G GSR+CRVC N H +IRKYGL CRQCFR AK+IGF+K
Sbjct: 1 MGHQQLYWSHPRKFGQGSRSCRVCSNRHGLIRKYGLNMCRQCFRQYAKDIGFIK 54
>pdb|3IZB|N Chain N, Localization Of The Small Subunit Ribosomal Proteins
Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O2Z|S Chain S, Yeast 80s Ribosome. This Entry Consists Of The 40s
Subunit Of The First 80s In The Asymmetric Unit.
pdb|3O30|S Chain S, Yeast 80s Ribosome. This Entry Consists Of The 40s
Subunit Of The Second 80s In The Asymmetric Unit.
pdb|3U5C|DD Chain d, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|DD Chain d, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 56
Score = 77.8 bits (190), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 35/56 (62%), Positives = 40/56 (71%)
Query: 1 MGHSNVWNSHPKTYGPGSRACRVCGNPHAIIRKYGLMCCRQCFRSNAKEIGFVKYR 56
M H NVW SHP+ YG GSR CRVC + +IRKYGL CRQCFR A +IGF K+R
Sbjct: 1 MAHENVWFSHPRRYGKGSRQCRVCSSHTGLIRKYGLNICRQCFREKANDIGFNKFR 56
>pdb|2XZM|N Chain N, Crystal Structure Of The Eukaryotic 40s Ribosomal
Subunit In Complex With Initiation Factor 1. This File
Contains The 40s Subunit And Initiation Factor For
Molecule 1
pdb|2XZN|N Chain N, Crystal Structure Of The Eukaryotic 40s Ribosomal
Subunit In Complex With Initiation Factor 1. This File
Contains The 40s Subunit And Initiation Factor For
Molecule 2
Length = 55
Score = 67.0 bits (162), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 28/53 (52%), Positives = 36/53 (67%)
Query: 4 SNVWNSHPKTYGPGSRACRVCGNPHAIIRKYGLMCCRQCFRSNAKEIGFVKYR 56
+ +W +HP+ YG S+ CRVCG +I KY +M CR+CFR A IGFVKYR
Sbjct: 3 NKLWRTHPRNYGKDSKECRVCGARQGLITKYEMMTCRRCFREQAPHIGFVKYR 55
>pdb|3JYV|N Chain N, Structure Of The 40s Rrna And Proteins And PE TRNA FOR
EUKARYOTIC Ribosome Based On Cryo-Em Map Of Thermomyces
Lanuginosus Ribosome At 8.9a Resolution
Length = 50
Score = 65.5 bits (158), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 29/50 (58%), Positives = 35/50 (70%)
Query: 5 NVWNSHPKTYGPGSRACRVCGNPHAIIRKYGLMCCRQCFRSNAKEIGFVK 54
NVW SHP+ +G GSR CRVC + ++RKY L CRQCFR A +IGF K
Sbjct: 1 NVWFSHPRRFGKGSRQCRVCSSHTGLVRKYDLNICRQCFREKANDIGFHK 50
>pdb|3ZEY|8 Chain 8, High-resolution Cryo-electron Microscopy Structure Of
The Trypanosoma Brucei Ribosome
Length = 57
Score = 62.0 bits (149), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 31/57 (54%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 1 MGHSNVWNSHPKT-YGPGSRACRVCGNPHAIIRKYGLMCCRQCFRSNAKEIGFVKYR 56
MGH W S + G GSR C +C N A+IRKY L CRQCFR NA IGF K R
Sbjct: 1 MGHLEQWRSRQRIGMGKGSRHCVICSNQKAVIRKYELNVCRQCFRENAANIGFSKLR 57
>pdb|3J20|P Chain P, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 56
Score = 49.7 bits (117), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 24/55 (43%), Positives = 31/55 (56%)
Query: 1 MGHSNVWNSHPKTYGPGSRACRVCGNPHAIIRKYGLMCCRQCFRSNAKEIGFVKY 55
M ++ P+ +G G+R C CG IIR GLM CR CFR A ++GF KY
Sbjct: 1 MAKADYNKRKPRKFGKGARRCIRCGQYGPIIRIQGLMLCRHCFREVAPKLGFRKY 55
>pdb|1S1H|N Chain N, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex
From Yeast Obtained By Docking Atomic Models For Rna
And Protein Components Into A 11.7 A Cryo-Em Map. This
File, 1s1h, Contains 40s Subunit. The 60s Ribosomal
Subunit Is In File 1s1i
Length = 36
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 21/36 (58%), Positives = 25/36 (69%)
Query: 21 CRVCGNPHAIIRKYGLMCCRQCFRSNAKEIGFVKYR 56
CRVC + ++RKY L CRQCFR A +IGF KYR
Sbjct: 1 CRVCSSHTGLVRKYDLNICRQCFREKANDIGFHKYR 36
>pdb|1K82|A Chain A, Crystal Structure Of E.Coli Formamidopyrimidine-Dna
Glycosylase (Fpg) Covalently Trapped With Dna
pdb|1K82|B Chain B, Crystal Structure Of E.Coli Formamidopyrimidine-Dna
Glycosylase (Fpg) Covalently Trapped With Dna
pdb|1K82|C Chain C, Crystal Structure Of E.Coli Formamidopyrimidine-Dna
Glycosylase (Fpg) Covalently Trapped With Dna
pdb|1K82|D Chain D, Crystal Structure Of E.Coli Formamidopyrimidine-Dna
Glycosylase (Fpg) Covalently Trapped With Dna
Length = 268
Score = 27.7 bits (60), Expect = 1.5, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 12 KTYGPGSRACRVCGNPHAIIR--KYGLMCCRQC 42
+ YG CRVCG P + + CRQC
Sbjct: 234 QVYGRKGEPCRVCGTPIVATKHAQRATFYCRQC 266
>pdb|2WR7|A Chain A, The Structure Of Influenza H2 Human Singapore
Hemagglutinin With Human Receptor
pdb|2WR7|B Chain B, The Structure Of Influenza H2 Human Singapore
Hemagglutinin With Human Receptor
pdb|2WR7|C Chain C, The Structure Of Influenza H2 Human Singapore
Hemagglutinin With Human Receptor
pdb|2WRB|A Chain A, The Structure Of Influenza H2 Human Singapore
Hemagglutinin With Avian Receptor
pdb|2WRB|B Chain B, The Structure Of Influenza H2 Human Singapore
Hemagglutinin With Avian Receptor
pdb|2WRB|C Chain C, The Structure Of Influenza H2 Human Singapore
Hemagglutinin With Avian Receptor
pdb|2WRC|A Chain A, The Structure Of Influenza H2 Human Singapore
Hemagglutinin
pdb|2WRC|B Chain B, The Structure Of Influenza H2 Human Singapore
Hemagglutinin
pdb|2WRC|C Chain C, The Structure Of Influenza H2 Human Singapore
Hemagglutinin
Length = 506
Score = 26.9 bits (58), Expect = 3.2, Method: Composition-based stats.
Identities = 12/21 (57%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 7 WNSHPKTYGPGSRACRVCGNP 27
W H T GSRAC V GNP
Sbjct: 137 WTQHTTT--GGSRACAVSGNP 155
>pdb|2WR3|A Chain A, Structure Of Influenza H2 Duck Ontario Hemagglutinin With
Avian Receptor
pdb|2WR3|B Chain B, Structure Of Influenza H2 Duck Ontario Hemagglutinin With
Avian Receptor
pdb|2WR3|C Chain C, Structure Of Influenza H2 Duck Ontario Hemagglutinin With
Avian Receptor
pdb|2WR4|A Chain A, Structure Of Influenza H2 Duck Ontario Hemagglutinin
With Human Receptor
pdb|2WR4|B Chain B, Structure Of Influenza H2 Duck Ontario Hemagglutinin
With Human Receptor
pdb|2WR4|C Chain C, Structure Of Influenza H2 Duck Ontario Hemagglutinin
With Human Receptor
pdb|2WR5|A Chain A, Structure Of Influenza H2 Duck Ontario Hemagglutinin
pdb|2WR5|B Chain B, Structure Of Influenza H2 Duck Ontario Hemagglutinin
pdb|2WR5|C Chain C, Structure Of Influenza H2 Duck Ontario Hemagglutinin
Length = 507
Score = 26.9 bits (58), Expect = 3.2, Method: Composition-based stats.
Identities = 12/21 (57%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 7 WNSHPKTYGPGSRACRVCGNP 27
W H T GSRAC V GNP
Sbjct: 137 WTQHTTT--GGSRACAVSGNP 155
>pdb|2WRD|A Chain A, Structure Of H2 Japan Hemagglutinin
pdb|2WRD|B Chain B, Structure Of H2 Japan Hemagglutinin
pdb|2WRD|C Chain C, Structure Of H2 Japan Hemagglutinin
Length = 505
Score = 26.9 bits (58), Expect = 3.3, Method: Composition-based stats.
Identities = 12/21 (57%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 7 WNSHPKTYGPGSRACRVCGNP 27
W H T GSRAC V GNP
Sbjct: 137 WTQHTTT--GGSRACAVSGNP 155
>pdb|1VS5|N Chain N, 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|N Chain N, 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|G Chain G, Structure Of The 30s Subunit And The Trnas Of E. Coli
Ribosome In Pre- Accommodation State
pdb|3E1C|G Chain G, Structure Of The 30s Subunit And The Trnas Of E. Coli
Ribosome In Post-Accommodation State
pdb|3I1M|N Chain N, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1O|N Chain N, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1Q|N Chain N, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1S|N Chain N, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1Z|N Chain N, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I21|N Chain N, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3KC4|N Chain N, Ribosome-Secy Complex. This Entry 3kc4 Contains 30s
Ribosomal Subnit. The 50s Ribosomal Subunit Can Be
Found In Pdb Entry 3kcr
pdb|3OR9|N Chain N, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 30s Subunit Of The
First 70s Ribosome.
pdb|3ORA|N Chain N, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 30s Subunit Of The
Second 70s Ribosome.
pdb|3IZV|R Chain R, 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|R Chain R, 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|N Chain N, Crystal Structure Of Release Factor Rf3 Trapped In The
Gtp State On A Rotated Conformation Of The Ribosome
pdb|3UOQ|N Chain N, Crystal Structure Of Release Factor Rf3 Trapped In The
Gtp State On A Rotated Conformation Of The Ribosome
(Without Viomycin)
pdb|4GAQ|N Chain N, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
pdb|4GAS|N Chain N, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
Length = 101
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 8/43 (18%)
Query: 2 GHSNVWN------SHPKTYGPGSRA--CRVCGNPHAIIRKYGL 36
+ WN + P+ P + CR G PH +RK+GL
Sbjct: 37 SDEDRWNAVLKLQTLPRDSSPSRQRNRCRQTGRPHGFLRKFGL 79
>pdb|1P6G|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, Structure Of Pdf Binding Helix In Complex With The
Ribosome (Part 3 Of 4)
pdb|2VHP|N Chain N, Structure Of Pdf Binding Helix In Complex With The
Ribosome (Part 4 Of 4)
pdb|3DF1|N Chain N, 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|N Chain N, 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|3OFO|N Chain N, Crystal Structure Of The E. Coli Ribosome Bound To
Erythromycin. This File Contains The 30s Subunit Of The
First 70s Ribosome.
pdb|3OFP|N Chain N, Crystal Structure Of The E. Coli Ribosome Bound To
Erythromycin. This File Contains The 30s Subunit Of The
Second 70s Ribosome.
pdb|3OFA|N Chain N, Crystal Structure Of The E. Coli Ribosome Bound To
Chloramphenicol. This File Contains The 30s Subunit Of
The First 70s Ribosome.
pdb|3OFB|N Chain N, Crystal Structure Of The E. Coli Ribosome Bound To
Chloramphenicol. This File Contains The 30s Subunit Of
The Second 70s Ribosome.
pdb|3OFX|N Chain N, Crystal Structure Of The E. Coli Ribosome Bound To
Clindamycin. This File Contains The 30s Subunit Of The
First 70s Ribosome.
pdb|3OFY|N Chain N, Crystal Structure Of The E. Coli Ribosome Bound To
Clindamycin. This File Contains The 30s Subunit Of The
Second 70s Ribosome
pdb|3OAQ|N Chain N, Crystal Structure Of The E. Coli Ribosome Bound To
Telithromycin. This File Contains The 30s Subunit Of
The First 70s Ribosome.
pdb|3OAR|N Chain N, Crystal Structure Of The E. Coli Ribosome Bound To
Telithromycin. This File Contains The 30s Subunit Of
The Second 70s Ribosome.
pdb|3J00|N Chain N, Structure Of The Ribosome-Secye Complex In The Membrane
Environment
pdb|2YKR|N Chain N, 30s Ribosomal Subunit With Rsga Bound In The Presence Of
Gmppnp
pdb|4A2I|N Chain N, Cryo-Electron Microscopy Structure Of The 30s Subunit In
Complex With The Yjeq Biogenesis Factor
pdb|4ADV|N Chain N, Structure Of The E. Coli Methyltransferase Ksga Bound To
The E. Coli 30s Ribosomal Subunit
pdb|3J0U|Q Chain Q, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class2 Of The Six
Classes)
pdb|3J0V|Q Chain Q, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 4a Of The Six
Classes)
pdb|3J0X|Q Chain Q, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 4b Of The Six
Classes)
pdb|3J0Z|Q Chain Q, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 5 Of The Six
Classes)
pdb|3J10|Q Chain Q, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 6 Of The Six
Classes)
pdb|3J13|P Chain P, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 3 Of The Six
Classes)
pdb|3J18|N Chain N, Structure Of The Bacterial Ribosome Complexed By
Tmrna-Smpb And Ef-G During Translocation And
Mld-Loading (30s Subunit)
pdb|4GD1|N Chain N, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
pdb|4GD2|N Chain N, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
Length = 100
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 21 CRVCGNPHAIIRKYGL 36
CR G PH +RK+GL
Sbjct: 63 CRQTGRPHGFLRKFGL 78
>pdb|3FIH|N Chain N, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry
Consists Of The 30s Subunit, Trnas And The Ternary
Complex.
pdb|2WWL|N Chain N, 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)
Length = 96
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 21 CRVCGNPHAIIRKYGL 36
CR G PH +RK+GL
Sbjct: 59 CRQTGRPHGFLRKFGL 74
>pdb|3QQI|A Chain A, Crystal Structure Of The Ha1 Receptor Binding Domain Of
H2 Hemagglutinin
pdb|3QQI|B Chain B, Crystal Structure Of The Ha1 Receptor Binding Domain Of
H2 Hemagglutinin
Length = 219
Score = 26.2 bits (56), Expect = 4.4, Method: Composition-based stats.
Identities = 12/21 (57%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 7 WNSHPKTYGPGSRACRVCGNP 27
W H T GSRAC V GNP
Sbjct: 77 WTQHTTT--GGSRACAVSGNP 95
>pdb|4HFU|A Chain A, Crystal Structure Of Fab 8m2 In Complex With A H2n2
Influenza Virus Hemagglutinin
pdb|4HG4|A Chain A, Crystal Structure Of Fab 2g1 In Complex With A H2n2
Influenza Virus Hemagglutinin
pdb|4HG4|B Chain B, Crystal Structure Of Fab 2g1 In Complex With A H2n2
Influenza Virus Hemagglutinin
pdb|4HG4|C Chain C, Crystal Structure Of Fab 2g1 In Complex With A H2n2
Influenza Virus Hemagglutinin
pdb|4HG4|D Chain D, Crystal Structure Of Fab 2g1 In Complex With A H2n2
Influenza Virus Hemagglutinin
pdb|4HG4|E Chain E, Crystal Structure Of Fab 2g1 In Complex With A H2n2
Influenza Virus Hemagglutinin
pdb|4HG4|F Chain F, Crystal Structure Of Fab 2g1 In Complex With A H2n2
Influenza Virus Hemagglutinin
pdb|4HG4|G Chain G, Crystal Structure Of Fab 2g1 In Complex With A H2n2
Influenza Virus Hemagglutinin
pdb|4HG4|H Chain H, Crystal Structure Of Fab 2g1 In Complex With A H2n2
Influenza Virus Hemagglutinin
pdb|4HG4|I Chain I, Crystal Structure Of Fab 2g1 In Complex With A H2n2
Influenza Virus Hemagglutinin
Length = 327
Score = 26.2 bits (56), Expect = 4.6, Method: Composition-based stats.
Identities = 12/21 (57%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 7 WNSHPKTYGPGSRACRVCGNP 27
W H T GSRAC V GNP
Sbjct: 124 WTQHTTT--GGSRACAVSGNP 142
>pdb|2GY9|N Chain N, 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|N Chain N, 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 = 61
Score = 26.2 bits (56), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 21 CRVCGNPHAIIRKYGL 36
CR G PH +RK+GL
Sbjct: 24 CRQTGRPHGFLRKFGL 39
>pdb|3KU5|A Chain A, Crystal Structure Of A H2n2 Influenza Virus Hemagglutinin,
Human Like
Length = 327
Score = 26.2 bits (56), Expect = 4.7, Method: Composition-based stats.
Identities = 12/21 (57%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 7 WNSHPKTYGPGSRACRVCGNP 27
W H T GSRAC V GNP
Sbjct: 124 WTQHTTT--GGSRACAVSGNP 142
>pdb|3KU6|A Chain A, Crystal Structure Of A H2n2 Influenza Virus Hemagglutinin,
226l228G
Length = 327
Score = 26.2 bits (56), Expect = 4.8, Method: Composition-based stats.
Identities = 12/21 (57%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 7 WNSHPKTYGPGSRACRVCGNP 27
W H T GSRAC V GNP
Sbjct: 124 WTQHTTT--GGSRACAVSGNP 142
>pdb|3KU3|A Chain A, Crystal Structure Of A H2n2 Influenza Virus Hemagglutinin,
Avian Like
pdb|3QQB|A Chain A, Crystal Structure Of Ha2 R106h Mutant Of H2 Hemagglutinin,
Neutral Ph Form
pdb|3QQE|A Chain A, Crystal Structure Of Ha2 R106h Mutant Of H2 Hemagglutinin,
Re- Neutralized Form
pdb|3QQO|A Chain A, Crystal Structure Of Ha2 R106h Mutant Of H2 Hemagglutinin,
Acidic Ph Form
pdb|3QQO|C Chain C, Crystal Structure Of Ha2 R106h Mutant Of H2 Hemagglutinin,
Acidic Ph Form
pdb|3QQO|E Chain E, Crystal Structure Of Ha2 R106h Mutant Of H2 Hemagglutinin,
Acidic Ph Form
pdb|4HF5|A Chain A, Crystal Structure Of Fab 8f8 In Complex A H2n2 Influenza
Virus Hemagglutinin
Length = 327
Score = 26.2 bits (56), Expect = 4.9, Method: Composition-based stats.
Identities = 12/21 (57%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 7 WNSHPKTYGPGSRACRVCGNP 27
W H T GSRAC V GNP
Sbjct: 124 WTQHTTT--GGSRACAVSGNP 142
>pdb|1R2Y|A Chain A, Mutm (Fpg) Bound To 8-Oxoguanine (Oxog) Containing Dna
pdb|1R2Z|A Chain A, Mutm (Fpg) Bound To 5,6-Dihydrouracil (Dhu) Containing Dna
Length = 274
Score = 25.8 bits (55), Expect = 7.1, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 2 GHSNVWNSHPKTYGPGSRACRVCGNP--HAIIRKYGLMCCRQCFR 44
G + + H YG C+ CG P ++ G C +C R
Sbjct: 230 GEAGTFQHHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 274
>pdb|1L1T|A Chain A, Mutm (Fpg) Bound To Abasic-Site Containing Dna
pdb|1L1Z|A Chain A, Mutm (Fpg) Covalent-Dna Intermediate
pdb|1L2B|A Chain A, Mutm (Fpg) Dna End-Product Structure
pdb|1L2C|A Chain A, Mutm (Fpg)-Dna Estranged Thymine Mismatch Recognition
Complex
pdb|1L2D|A Chain A, Mutm (fpg)-dna Estranged Guanine Mismatch Recognition
Complex
Length = 274
Score = 25.8 bits (55), Expect = 7.2, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 2 GHSNVWNSHPKTYGPGSRACRVCGNP--HAIIRKYGLMCCRQCFR 44
G + + H YG C+ CG P ++ G C +C R
Sbjct: 230 GEAGTFQHHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 274
>pdb|2F5N|A Chain A, Mutm Crosslinked To Undamaged Dna Sampling A:t Base Pair
Ic1
pdb|2F5O|A Chain A, Mutm Crosslinked To Undamaged Dna Sampling G:c Base Pair
Ic3
pdb|2F5P|A Chain A, Mutm Crosslinked To Undamaged Dna Sampling A:t Base Pair
Ic2
Length = 274
Score = 25.4 bits (54), Expect = 7.6, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 2 GHSNVWNSHPKTYGPGSRACRVCGNP--HAIIRKYGLMCCRQCFR 44
G + + H YG C+ CG P ++ G C +C R
Sbjct: 230 GEAGTFQHHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 274
>pdb|3JR4|A Chain A, Mutm Interrogating An Extrahelical G
pdb|3JR5|A Chain A, Mutm Lesion Recognition Control Complex With N174c
Crosslinking Site
Length = 273
Score = 25.4 bits (54), Expect = 7.7, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 2 GHSNVWNSHPKTYGPGSRACRVCGNP--HAIIRKYGLMCCRQCFR 44
G + + H YG C+ CG P ++ G C +C R
Sbjct: 229 GEAGTFQHHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
>pdb|3SAS|A Chain A, Mutm Slanted Complex 4 With R112a Mutation
pdb|3SAT|A Chain A, Mutm Slanted Complex 6 With R112a Mutation
pdb|3SAW|A Chain A, Mutm Slanted Complex 8 With R112a Mutation
Length = 273
Score = 25.4 bits (54), Expect = 7.8, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 2 GHSNVWNSHPKTYGPGSRACRVCGNP--HAIIRKYGLMCCRQCFR 44
G + + H YG C+ CG P ++ G C +C R
Sbjct: 229 GEAGTFQHHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
>pdb|3SAR|A Chain A, Mutm Slanted Complex 1
pdb|3SAU|A Chain A, Mutm Interrogation Complex 6
pdb|3SAV|A Chain A, Mutm Slanted Complex 8
Length = 273
Score = 25.4 bits (54), Expect = 8.0, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 2 GHSNVWNSHPKTYGPGSRACRVCGNP--HAIIRKYGLMCCRQCFR 44
G + + H YG C+ CG P ++ G C +C R
Sbjct: 229 GEAGTFQHHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
>pdb|2F5Q|A Chain A, Catalytically Inactive (E3q) Mutm Crosslinked To Oxog:c
Containing Dna Cc2
pdb|2F5S|A Chain A, Catalytically Inactive (e3q) Mutm Crosslinked To Oxog:c
Containing Dna Cc1
Length = 274
Score = 25.4 bits (54), Expect = 8.0, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 2 GHSNVWNSHPKTYGPGSRACRVCGNP--HAIIRKYGLMCCRQCFR 44
G + + H YG C+ CG P ++ G C +C R
Sbjct: 230 GEAGTFQHHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 274
>pdb|4G4N|A Chain A, Mutm Containing M77a Mutation Bound To Undamaged Dna
Length = 273
Score = 25.4 bits (54), Expect = 8.0, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 2 GHSNVWNSHPKTYGPGSRACRVCGNP--HAIIRKYGLMCCRQCFR 44
G + + H YG C+ CG P ++ G C +C R
Sbjct: 229 GEAGTFQHHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
>pdb|3U6C|A Chain A, Mutm Set 1 Apgo
pdb|3U6D|A Chain A, Mutm Set 1 Gpgo
pdb|3U6E|A Chain A, Mutm Set 1 Tpgo
pdb|3U6L|A Chain A, Mutm Set 2 Cpgo
pdb|3U6M|A Chain A, Structural Effects Of Sequence Context On Lesion
Recognition By Mutm
pdb|3U6O|A Chain A, Mutm Set 1 Apg
pdb|3U6P|A Chain A, Mutm Set 1 Gpg
pdb|3U6Q|A Chain A, Mutm Set 2 Apgo
pdb|3U6S|A Chain A, Mutm Set 1 Tpg
Length = 273
Score = 25.4 bits (54), Expect = 8.2, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 2 GHSNVWNSHPKTYGPGSRACRVCGNP--HAIIRKYGLMCCRQCFR 44
G + + H YG C+ CG P ++ G C +C R
Sbjct: 229 GEAGTFQHHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
>pdb|3GP1|A Chain A, Mutm Encountering An Intrahelical 8-Oxoguanine (Oxog)
Lesion In Ec3- V222p Complex
pdb|3SBJ|A Chain A, Mutm Slanted Complex 7
Length = 273
Score = 25.4 bits (54), Expect = 8.2, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 2 GHSNVWNSHPKTYGPGSRACRVCGNP--HAIIRKYGLMCCRQCFR 44
G + + H YG C+ CG P ++ G C +C R
Sbjct: 229 GEAGTFQHHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
>pdb|4G4R|A Chain A, Mutm Containing F114a Mutation Bound To Oxog-containing
Dna
Length = 273
Score = 25.4 bits (54), Expect = 8.2, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 2 GHSNVWNSHPKTYGPGSRACRVCGNP--HAIIRKYGLMCCRQCFR 44
G + + H YG C+ CG P ++ G C +C R
Sbjct: 229 GEAGTFQHHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
>pdb|4G4Q|A Chain A, Mutm Containing F114a Mutation Bound To Undamaged Dna
Length = 273
Score = 25.4 bits (54), Expect = 8.2, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 2 GHSNVWNSHPKTYGPGSRACRVCGNP--HAIIRKYGLMCCRQCFR 44
G + + H YG C+ CG P ++ G C +C R
Sbjct: 229 GEAGTFQHHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
>pdb|4G4O|A Chain A, Mutm Containing M77a Mutation Bound To Oxog-containing Dna
Length = 273
Score = 25.4 bits (54), Expect = 8.2, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 2 GHSNVWNSHPKTYGPGSRACRVCGNP--HAIIRKYGLMCCRQCFR 44
G + + H YG C+ CG P ++ G C +C R
Sbjct: 229 GEAGTFQHHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
>pdb|3GPY|A Chain A, Sequence-Matched Mutm Lesion Recognition Complex 3 (Lrc3)
pdb|3GQ4|A Chain A, Sequence-matched Mutm Lesion Recognition Complex 5 (lrc5)
Length = 273
Score = 25.4 bits (54), Expect = 8.2, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 2 GHSNVWNSHPKTYGPGSRACRVCGNP--HAIIRKYGLMCCRQCFR 44
G + + H YG C+ CG P ++ G C +C R
Sbjct: 229 GEAGTFQHHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
>pdb|3GPP|A Chain A, Mutm Encountering An Intrahelical 8-Oxoguanine (Oxog)
Lesion In Ec3- T224p Complex
pdb|3GQ5|A Chain A, Sequence-Matched Mutm Interrogation Complex 5 (Ic5)
Length = 273
Score = 25.4 bits (54), Expect = 8.2, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 2 GHSNVWNSHPKTYGPGSRACRVCGNP--HAIIRKYGLMCCRQCFR 44
G + + H YG C+ CG P ++ G C +C R
Sbjct: 229 GEAGTFQHHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
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
0.327 0.140 0.502
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,961,545
Number of Sequences: 62578
Number of extensions: 56339
Number of successful extensions: 203
Number of sequences better than 100.0: 37
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 191
Number of HSP's gapped (non-prelim): 37
length of query: 56
length of database: 14,973,337
effective HSP length: 28
effective length of query: 28
effective length of database: 13,221,153
effective search space: 370192284
effective search space used: 370192284
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)