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= 045338
(134 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|MM Chain m, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 92
Score = 182 bits (463), Expect = 3e-47, Method: Compositional matrix adjust.
Identities = 89/92 (96%), Positives = 92/92 (100%)
Query: 43 MTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDC 102
MTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGK+AVKRKAVGIWGCKDC
Sbjct: 1 MTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKFAVKRKAVGIWGCKDC 60
Query: 103 GKVKAGGAYTLNTASAVTVRSTIRRLREQTES 134
GKVKAGGAYT+NTASAVTVRSTIRRLREQTE+
Sbjct: 61 GKVKAGGAYTMNTASAVTVRSTIRRLREQTEA 92
>pdb|1YSH|D Chain D, Localization And Dynamic Behavior Of Ribosomal Protein
L30e
Length = 73
Score = 147 bits (372), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 71/73 (97%), Positives = 73/73 (100%)
Query: 52 IVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAY 111
IVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGK+AVKRKAVGIWGCKDCGKVKAGGAY
Sbjct: 1 IVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKFAVKRKAVGIWGCKDCGKVKAGGAY 60
Query: 112 TLNTASAVTVRST 124
T+NTASAVTVRST
Sbjct: 61 TMNTASAVTVRST 73
>pdb|2ZKR|ZZ Chain z, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 92
Score = 130 bits (327), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 63/88 (71%), Positives = 72/88 (81%)
Query: 43 MTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDC 102
M KRTKK GIVGKYGTRYGASLRK +KK+E+SQH+KY C FCGK +KR+AVGIW C C
Sbjct: 1 MAKRTKKVGIVGKYGTRYGASLRKMVKKIEISQHAKYTCSFCGKTKMKRRAVGIWHCGSC 60
Query: 103 GKVKAGGAYTLNTASAVTVRSTIRRLRE 130
K AGGA+T NT SAVTV+S IRRL+E
Sbjct: 61 MKTVAGGAWTYNTTSAVTVKSAIRRLKE 88
>pdb|3IZS|MM Chain m, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|GG Chain g, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|GG Chain g, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|PP Chain p, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|PP Chain p, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|PP Chain p, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 92
Score = 128 bits (321), Expect = 1e-30, Method: Compositional matrix adjust.
Identities = 61/92 (66%), Positives = 72/92 (78%)
Query: 43 MTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDC 102
M KRTKK GI GKYG RYG+SLR+Q+KK+E+ QH++Y C FCGK VKR A GIW C C
Sbjct: 1 MAKRTKKVGITGKYGVRYGSSLRRQVKKLEIQQHARYDCSFCGKKTVKRGAAGIWTCSCC 60
Query: 103 GKVKAGGAYTLNTASAVTVRSTIRRLREQTES 134
K AGGAYT++TA+A TVRSTIRRLRE E+
Sbjct: 61 KKTVAGGAYTVSTAAAATVRSTIRRLREMVEA 92
>pdb|3ZF7|OO Chain o, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 93
Score = 126 bits (316), Expect = 5e-30, Method: Compositional matrix adjust.
Identities = 58/92 (63%), Positives = 73/92 (79%)
Query: 43 MTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDC 102
M KRT K G++G+YG RYG++ RK+ KK+EVSQH+K+FC FCGK+A +RKAVGIW C C
Sbjct: 1 MAKRTVKMGVMGRYGARYGSNPRKRAKKLEVSQHAKHFCSFCGKFAFRRKAVGIWRCDGC 60
Query: 103 GKVKAGGAYTLNTASAVTVRSTIRRLREQTES 134
K AGGAYTL+T + TVRST+RRLRE +S
Sbjct: 61 SKTVAGGAYTLSTPNNTTVRSTVRRLRELKQS 92
>pdb|1S1I|9 Chain 9, 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,
1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is
In File 1s1h
Length = 91
Score = 125 bits (315), Expect = 6e-30, Method: Compositional matrix adjust.
Identities = 60/90 (66%), Positives = 71/90 (78%)
Query: 45 KRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGK 104
KRTKK GI GKYG RYG+SLR+Q+KK+E+ QH++Y C FCGK VKR A GIW C C K
Sbjct: 2 KRTKKVGITGKYGVRYGSSLRRQVKKLEIQQHARYDCSFCGKKTVKRGAAGIWTCSCCKK 61
Query: 105 VKAGGAYTLNTASAVTVRSTIRRLREQTES 134
AGGAYT++TA+A TVRSTIRRLRE E+
Sbjct: 62 TVAGGAYTVSTAAAATVRSTIRRLREMVEA 91
>pdb|4A17|Y Chain Y, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 2.
pdb|4A1A|Y Chain Y, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 3.
pdb|4A1C|Y Chain Y, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 4.
pdb|4A1E|Y Chain Y, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 1
Length = 103
Score = 119 bits (297), Expect = 6e-28, Method: Compositional matrix adjust.
Identities = 56/88 (63%), Positives = 68/88 (77%)
Query: 43 MTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDC 102
M KRT+K GI KYGTRYGASLRK +KK E++QH+KY C FCGK AVKR AVGIW CK C
Sbjct: 1 MAKRTQKVGITRKYGTRYGASLRKVVKKFEITQHAKYGCPFCGKVAVKRAAVGIWKCKPC 60
Query: 103 GKVKAGGAYTLNTASAVTVRSTIRRLRE 130
K+ AGGA+ L T AVT ++T+ RL++
Sbjct: 61 KKIIAGGAWELTTPPAVTAKTTMNRLKK 88
>pdb|3JYW|9 Chain 9, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 72
Score = 99.0 bits (245), Expect = 7e-22, Method: Compositional matrix adjust.
Identities = 46/71 (64%), Positives = 56/71 (78%)
Query: 54 GKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTL 113
GKYG RYG+SLR+Q+KK+E+ QH++Y C FCGK VKR A GIW C C K AGGAYT+
Sbjct: 2 GKYGVRYGSSLRRQVKKLEIQQHARYDCSFCGKKTVKRGAAGIWTCSCCKKTVAGGAYTV 61
Query: 114 NTASAVTVRST 124
+TA+A TVRST
Sbjct: 62 STAAAATVRST 72
>pdb|3J21|II Chain i, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 83
Score = 69.7 bits (169), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 33/76 (43%), Positives = 45/76 (59%)
Query: 47 TKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVK 106
TKK G G++G RYG +R+++ +E K+ C CG+ AVKR + GIW C+ CG
Sbjct: 4 TKKVGSAGRFGARYGLKIRRRVAAVEAKMRQKHTCPVCGRKAVKRISTGIWQCQKCGATF 63
Query: 107 AGGAYTLNTASAVTVR 122
AGGAY T + VR
Sbjct: 64 AGGAYLPVTPAGKAVR 79
>pdb|3CC2|Z Chain Z, The Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution With Rrna Sequence For The 23s Rrna And
Genome-Derived Sequences For R-Proteins
pdb|3CC4|Z Chain Z, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|Z Chain Z, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|Z Chain Z, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CMA|Z Chain Z, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|Z Chain Z, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|3I55|Z Chain Z, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|Z Chain Z, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
Length = 116
Score = 61.6 bits (148), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 44/84 (52%)
Query: 43 MTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDC 102
M ++ K G G++G RYG R+++ ++E + + C CG+ V R+ GIW C C
Sbjct: 25 MASKSGKTGSSGRFGARYGRVSRRRVAEIESEMNEDHACPNCGEDRVDRQGTGIWQCSYC 84
Query: 103 GKVKAGGAYTLNTASAVTVRSTIR 126
GG+Y T TVR +IR
Sbjct: 85 DYKFTGGSYKPETPGGKTVRRSIR 108
>pdb|3CPW|Y Chain Y, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|4ADX|Z Chain Z, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 92
Score = 61.2 bits (147), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 44/84 (52%)
Query: 43 MTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDC 102
M ++ K G G++G RYG R+++ ++E + + C CG+ V R+ GIW C C
Sbjct: 1 MASKSGKTGSSGRFGARYGRVSRRRVAEIESEMNEDHACPNCGEDRVDRQGTGIWQCSYC 60
Query: 103 GKVKAGGAYTLNTASAVTVRSTIR 126
GG+Y T TVR +IR
Sbjct: 61 DYKFTGGSYKPETPGGKTVRRSIR 84
>pdb|2QA4|Z Chain Z, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
Length = 92
Score = 60.8 bits (146), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 44/84 (52%)
Query: 43 MTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDC 102
M ++ K G G++G RYG R+++ ++E + + C CG+ V R+ GIW C C
Sbjct: 1 MASKSGKTGRSGRFGARYGRVSRRRVAEIESEMNEDHACPNCGEDRVDRQGTGIWQCSYC 60
Query: 103 GKVKAGGAYTLNTASAVTVRSTIR 126
GG+Y T TVR +IR
Sbjct: 61 DYKFTGGSYKPETPGGKTVRRSIR 84
>pdb|1FFK|W Chain W, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
Length = 73
Score = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 27/68 (39%), Positives = 38/68 (55%)
Query: 54 GKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTL 113
G++G RYG +R +++ +E+ KY C CG +KR + IW C CG AGGAYT
Sbjct: 3 GRFGPRYGLKIRVRVRDVEIKHKKKYKCPVCGFPKLKRASTSIWVCGHCGYKIAGGAYTP 62
Query: 114 NTASAVTV 121
T + V
Sbjct: 63 ETVAGKAV 70
>pdb|1YHQ|Z Chain Z, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|Z Chain Z, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|Z Chain Z, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|Z Chain Z, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|Z Chain Z, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|Z Chain Z, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|Z Chain Z, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|Z Chain Z, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|Z Chain Z, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|Z Chain Z, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|Z Chain Z, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|Z Chain Z, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|Z Chain Z, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|Z Chain Z, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|Z Chain Z, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|Z Chain Z, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|Z Chain Z, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|Z Chain Z, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|Z Chain Z, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
Length = 83
Score = 56.6 bits (135), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 39/73 (53%)
Query: 54 GKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTL 113
G++G RYG R+++ ++E + + C CG+ V R+ GIW C C GG+Y
Sbjct: 3 GRFGARYGRVSRRRVAEIESEMNEDHACPNCGEDRVDRQGTGIWQCSYCDYKFTGGSYKP 62
Query: 114 NTASAVTVRSTIR 126
T TVR +IR
Sbjct: 63 ETPGGKTVRRSIR 75
>pdb|1JJ2|Y Chain Y, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|Y Chain Y, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|1 Chain 1, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|1 Chain 1, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|1 Chain 1, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|1 Chain 1, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|1 Chain 1, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1K73|1 Chain 1, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|1 Chain 1, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|1 Chain 1, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|1 Chain 1, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|1 Chain 1, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|1 Chain 1, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|1 Chain 1, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|1 Chain 1, Crystal Structure Of Cca-Phe-Cap-Biotin Bound
Simultaneously At Half Occupancy To Both The A-Site And
P- Site Of The The 50s Ribosomal Subunit.
pdb|1QVF|Y Chain Y, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|Y Chain Y, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1W2B|Y Chain Y, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|3CXC|Y Chain Y, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
pdb|3OW2|Y Chain Y, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 73
Score = 52.4 bits (124), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 35/68 (51%)
Query: 54 GKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTL 113
G++G RYG +R ++ +E+ K+ C CG +KR GIW C CG AGG Y
Sbjct: 3 GRFGPRYGLKIRVRVADVEIKHKKKHKCPVCGFKKLKRAGTGIWMCGHCGYKIAGGCYQP 62
Query: 114 NTASAVTV 121
T + V
Sbjct: 63 ETVAGKAV 70
>pdb|1S72|Z Chain Z, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|2OTJ|Z Chain Z, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|Z Chain Z, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QEX|Z Chain Z, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
Length = 73
Score = 52.4 bits (124), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 36/69 (52%)
Query: 54 GKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTL 113
G++G RYG R+++ ++E + + C CG+ V R+ GIW C C GG+Y
Sbjct: 3 GRFGARYGRVSRRRVAEIESEMNEDHACPNCGEDRVDRQGTGIWQCSYCDYKFTGGSYKP 62
Query: 114 NTASAVTVR 122
T TVR
Sbjct: 63 ETPGGKTVR 71
>pdb|3G4S|Z Chain Z, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|Z Chain Z, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|Z Chain Z, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
Length = 73
Score = 52.4 bits (124), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 36/69 (52%)
Query: 54 GKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTL 113
G++G RYG R+++ ++E + + C CG+ V R+ GIW C C GG+Y
Sbjct: 3 GRFGARYGRVSRRRVAEIESEMNEDHACPNCGEDRVDRQGTGIWQCSYCDYKFTGGSYKP 62
Query: 114 NTASAVTVR 122
T TVR
Sbjct: 63 ETPGGKTVR 71
>pdb|3U7W|L Chain L, Crystal Structure Of Nih45-46 Fab
pdb|3U7Y|L Chain L, Structure Of Nih45-46 Fab In Complex With Gp120 Of
93th057 Hiv
Length = 210
Score = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 47 TKKAGIVGKY-GTRYGASLRKQIKKMEVSQHSKYFC---EFCGK 86
T+ AGI ++ G+R+GA I +E Y+C EF G+
Sbjct: 51 TRAAGIPDRFSGSRWGADYNLSISNLESGDFGVYYCQQYEFFGQ 94
>pdb|3MSR|A Chain A, The Crystal Structure Of An Amidohydrolase From Mycoplasma
Synoviae
Length = 363
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/34 (50%), Positives = 24/34 (70%), Gaps = 2/34 (5%)
Query: 42 KMTKRTK-KAGIVGKYGTRYGASLRKQIKKMEVS 74
+ KR+K KAGI+ K GT YGA R ++K +EV+
Sbjct: 142 PVVKRSKAKAGII-KAGTGYGAIDRLELKALEVA 174
>pdb|1CIC|A Chain A, Idiotope-Anti-Idiotope Fab-Fab Complex; D1.3-E225
Length = 214
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 47 TKKAGIVGKY-GTRYGASLRKQIKKMEVSQHSKYFCEFCGKYA 88
T+ G+ ++ G+ G I ++ + YFC+ CG Y
Sbjct: 53 TRHTGVPDRFTGSGSGTDFTLTISNVQSEDLADYFCQHCGSYP 95
>pdb|1Z4R|A Chain A, Human Gcn5 Acetyltransferase
Length = 168
Score = 26.9 bits (58), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 8/52 (15%)
Query: 38 VCFCKMTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAV 89
+ FC +T + G YG L +K+ + + YF + +YA+
Sbjct: 82 IVFCAVTSNEQVKG--------YGTHLMNHLKEYHIKHNILYFLTYADEYAI 125
>pdb|3RHB|A Chain A, Crystal Structure Of The Apo Form Of Glutaredoxin C5
From Arabidopsis Thaliana
pdb|3RHC|A Chain A, Crystal Structure Of The Holo Form Of Glutaredoxin C5
From Arabidopsis Thaliana
pdb|3RHC|B Chain B, Crystal Structure Of The Holo Form Of Glutaredoxin C5
From Arabidopsis Thaliana
Length = 113
Score = 26.6 bits (57), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 23/41 (56%)
Query: 56 YGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGI 96
+G+R S+RK + + V +SK +C +C + K +G+
Sbjct: 4 FGSRMEESIRKTVTENTVVIYSKTWCSYCTEVKTLFKRLGV 44
>pdb|3OVG|A Chain A, The Crystal Structure Of An Amidohydrolase From Mycoplasma
Synoviae With Zn Ion Bound
pdb|3OVG|B Chain B, The Crystal Structure Of An Amidohydrolase From Mycoplasma
Synoviae With Zn Ion Bound
pdb|3OVG|C Chain C, The Crystal Structure Of An Amidohydrolase From Mycoplasma
Synoviae With Zn Ion Bound
pdb|3OVG|D Chain D, The Crystal Structure Of An Amidohydrolase From Mycoplasma
Synoviae With Zn Ion Bound
pdb|3OVG|E Chain E, The Crystal Structure Of An Amidohydrolase From Mycoplasma
Synoviae With Zn Ion Bound
pdb|3OVG|F Chain F, The Crystal Structure Of An Amidohydrolase From Mycoplasma
Synoviae With Zn Ion Bound
Length = 363
Score = 26.2 bits (56), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 23/34 (67%), Gaps = 2/34 (5%)
Query: 42 KMTKRTK-KAGIVGKYGTRYGASLRKQIKKMEVS 74
+ KR+K KAGI+ GT YGA R ++K +EV+
Sbjct: 142 PVVKRSKAKAGIIXA-GTGYGAIDRLELKALEVA 174
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
0.323 0.132 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,189,358
Number of Sequences: 62578
Number of extensions: 98480
Number of successful extensions: 281
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 262
Number of HSP's gapped (non-prelim): 26
length of query: 134
length of database: 14,973,337
effective HSP length: 88
effective length of query: 46
effective length of database: 9,466,473
effective search space: 435457758
effective search space used: 435457758
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 46 (22.3 bits)