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= 031815
(152 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|X Chain X, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 152
Score = 211 bits (536), Expect = 2e-55, Method: Compositional matrix adjust.
Identities = 113/150 (75%), Positives = 118/150 (78%), Gaps = 1/150 (0%)
Query: 4 PKGETKKADPKVQ-ALKTAKAVKSGRTFKKAKKIRTSVTFHRPKTLKKDRNPKYPRISAP 62
PK KKAD K Q ALK AKAVKSG +K+KKIRTSVTFHRPKTLKK R+PKYPR+SAP
Sbjct: 3 PKAAVKKADGKTQQALKVAKAVKSGSIKRKSKKIRTSVTFHRPKTLKKARDPKYPRVSAP 62
Query: 63 PRNKLDHYQILKYPLTTESAMKKIEDNNTLVFXXXXXXXXXXXXXXXXXMYDIQAKKVNT 122
RNKLD YQILKYPLTTESAMKKIEDNNTLVF MYDIQAKKVNT
Sbjct: 63 GRNKLDQYQILKYPLTTESAMKKIEDNNTLVFIVDLKADKKKIKAAVKKMYDIQAKKVNT 122
Query: 123 LIRPDGTKKAYVRLTPDSDALDVANKIGII 152
LIRPDG KKAYV+LTPD DALDVANKIGII
Sbjct: 123 LIRPDGKKKAYVKLTPDYDALDVANKIGII 152
>pdb|2GO5|4 Chain 4, Structure Of Signal Recognition Particle Receptor (Sr) In
Complex With Signal Recognition Particle (Srp) And
Ribosome Nascent Chain Complex
pdb|2J37|4 Chain 4, Model Of Mammalian Srp Bound To 80s Rncs
Length = 152
Score = 191 bits (484), Expect = 2e-49, Method: Compositional matrix adjust.
Identities = 112/152 (73%), Positives = 114/152 (75%)
Query: 1 MAPPKGETKKADPKVQALKTAKAVKSGRTFKKAKKIRTSVTFHRPKTLKKDRNPKYPRIS 60
MAP KK D K QA K AKAVKSG K AKKIRTSVTFHRPKTL K R+PKYPRIS
Sbjct: 1 MAPKVAVAKKGDAKAQAAKVAKAVKSGSIKKTAKKIRTSVTFHRPKTLSKARDPKYPRIS 60
Query: 61 APPRNKLDHYQILKYPLTTESAMKKIEDNNTLVFXXXXXXXXXXXXXXXXXMYDIQAKKV 120
P RNKLD YQILKYPLTTESAMKKIEDNNTLVF MYDIQAKKV
Sbjct: 61 TPGRNKLDQYQILKYPLTTESAMKKIEDNNTLVFIVDLKADKKKIKAAVKKMYDIQAKKV 120
Query: 121 NTLIRPDGTKKAYVRLTPDSDALDVANKIGII 152
NTLIRPDG KKAYV+LTPD DALDVANKIGII
Sbjct: 121 NTLIRPDGKKKAYVKLTPDYDALDVANKIGII 152
>pdb|2ZKR|SS Chain s, 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 = 156
Score = 162 bits (411), Expect = 6e-41, Method: Compositional matrix adjust.
Identities = 86/126 (68%), Positives = 90/126 (71%)
Query: 27 GRTFKKAKKIRTSVTFHRPKTLKKDRNPKYPRISAPPRNKLDHYQILKYPLTTESAMKKI 86
G K KKIRTS TF RPKTL+ R PKYPR SAP RNKLDHY I+K+PLTTESAMKKI
Sbjct: 31 GVHSHKKKKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNKLDHYAIIKFPLTTESAMKKI 90
Query: 87 EDNNTLVFXXXXXXXXXXXXXXXXXMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVA 146
EDNNTLVF +YDI KVNTLIRPDG KKAYVRL PD DALDVA
Sbjct: 91 EDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYVRLAPDYDALDVA 150
Query: 147 NKIGII 152
NKIGII
Sbjct: 151 NKIGII 156
>pdb|2WW9|K Chain K, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound
To The Yeast 80s Ribosome
pdb|2WWA|K Chain K, Cryo-Em Structure Of Idle Yeast Ssh1 Complex Bound To The
Yeast 80s Ribosome
pdb|2WWB|K Chain K, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound To
The Actively Translating Wheat Germ 80s Ribosome
pdb|3IZS|X Chain X, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|W Chain W, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|W Chain W, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|X Chain X, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|X Chain X, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|X Chain X, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 142
Score = 131 bits (329), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 65/126 (51%), Positives = 83/126 (65%)
Query: 27 GRTFKKAKKIRTSVTFHRPKTLKKDRNPKYPRISAPPRNKLDHYQILKYPLTTESAMKKI 86
G KKA K+RTS TF PKTLK R PKY + P N+LD Y++++ P+T+E+AMKK+
Sbjct: 17 GTNGKKALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSYKVIEQPITSETAMKKV 76
Query: 87 EDNNTLVFXXXXXXXXXXXXXXXXXMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVA 146
ED N LVF +Y++ KVNTL+RP+GTKKAYVRLT D DALD+A
Sbjct: 77 EDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTKKAYVRLTADYDALDIA 136
Query: 147 NKIGII 152
N+IG I
Sbjct: 137 NRIGYI 142
>pdb|4A17|R Chain R, 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|R Chain R, 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|R Chain R, 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|R Chain R, 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 = 150
Score = 102 bits (254), Expect = 9e-23, Method: Compositional matrix adjust.
Identities = 61/140 (43%), Positives = 82/140 (58%), Gaps = 4/140 (2%)
Query: 16 QALKTAKAVKSGRTFKKAKKIRTSVTFHRPKTLKKDRNPKYPR-ISAPPR--NKLDHYQI 72
+A TAK K G + K K T V F RPKTL+ + PKY R + A + LD++ +
Sbjct: 12 KAKNTAKVAKKGSSITK-HKTYTGVRFFRPKTLQLAKAPKYSRTVRAHLKVSGHLDNHSV 70
Query: 73 LKYPLTTESAMKKIEDNNTLVFXXXXXXXXXXXXXXXXXMYDIQAKKVNTLIRPDGTKKA 132
+K PLTTE AMKK+ED NT+VF +Y+++ + VNTL G KKA
Sbjct: 71 VKTPLTTEKAMKKMEDENTMVFYVHNRSTKPQIKSAFEKLYNVKVRSVNTLNTITGNKKA 130
Query: 133 YVRLTPDSDALDVANKIGII 152
Y+RL DSD+L +ANKIG+I
Sbjct: 131 YIRLAADSDSLTLANKIGLI 150
>pdb|3ZF7|X Chain X, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 164
Score = 102 bits (253), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 53/112 (47%), Positives = 71/112 (63%), Gaps = 6/112 (5%)
Query: 41 TFHRPKTLKKDRNPKYPRISAPPRNKLDHYQILKYPLTTESAMKKIEDNNTLVFXXXXXX 100
T+ RP T+K N +SA +NK D ++I++YPLTT+ AMKKIE+NNTL F
Sbjct: 59 TYRRPATVKPSSN-----VSAI-KNKWDAFRIIRYPLTTDKAMKKIEENNTLTFIVDSRA 112
Query: 101 XXXXXXXXXXXMYDIQAKKVNTLIRPDGTKKAYVRLTPDSDALDVANKIGII 152
+Y ++ KVNTLIRPDG KKAY+RL+ DALD ANK+G++
Sbjct: 113 NKTEIKKAIRKLYQVKTVKVNTLIRPDGLKKAYIRLSASYDALDTANKMGLV 164
>pdb|1S1I|T Chain T, 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 = 83
Score = 92.0 bits (227), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 42/83 (50%), Positives = 57/83 (68%)
Query: 70 YQILKYPLTTESAMKKIEDNNTLVFXXXXXXXXXXXXXXXXXMYDIQAKKVNTLIRPDGT 129
Y++++ P+T+E+AMKK+ED N LVF +Y++ KVNTL+RP+GT
Sbjct: 1 YKVIEQPITSETAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGT 60
Query: 130 KKAYVRLTPDSDALDVANKIGII 152
KKAYVRLT D DALD+AN+IG I
Sbjct: 61 KKAYVRLTADYDALDIANRIGYI 83
>pdb|3JYW|T Chain T, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 80
Score = 88.6 bits (218), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 40/80 (50%), Positives = 55/80 (68%)
Query: 70 YQILKYPLTTESAMKKIEDNNTLVFXXXXXXXXXXXXXXXXXMYDIQAKKVNTLIRPDGT 129
Y++++ P+T+E+AMKK+ED N LVF +Y++ KVNTL+RP+GT
Sbjct: 1 YKVIEQPITSETAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGT 60
Query: 130 KKAYVRLTPDSDALDVANKI 149
KKAYVRLT D DALD+AN+I
Sbjct: 61 KKAYVRLTADYDALDIANRI 80
>pdb|3BBO|V Chain V, Homology Model For The Spinach Chloroplast 50s Subunit
Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
Length = 198
Score = 82.0 bits (201), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 40/90 (44%), Positives = 55/90 (61%)
Query: 63 PRNKLDHYQILKYPLTTESAMKKIEDNNTLVFXXXXXXXXXXXXXXXXXMYDIQAKKVNT 122
PR LD YQIL+ P+ TE+A+K I D N+L+F + ++ +KVNT
Sbjct: 105 PRRILDVYQILQSPIITEAAIKNIADENSLLFTVDVRADKKMIREAISNFFGVKVRKVNT 164
Query: 123 LIRPDGTKKAYVRLTPDSDALDVANKIGII 152
LIRPDGTKKAY+ L + +A ++A KIGI
Sbjct: 165 LIRPDGTKKAYIMLNKEYNASELAKKIGIF 194
>pdb|3J21|T Chain T, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 86
Score = 60.8 bits (146), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 48/85 (56%)
Query: 67 LDHYQILKYPLTTESAMKKIEDNNTLVFXXXXXXXXXXXXXXXXXMYDIQAKKVNTLIRP 126
+D Y+++ P+ TE A+ IE N L F +++++ +KVNTLI P
Sbjct: 1 MDPYKVIIRPVVTEKAISLIEKENKLTFIVDRRATKQDIKRAVEEIFNVKVEKVNTLITP 60
Query: 127 DGTKKAYVRLTPDSDALDVANKIGI 151
G KKAYV+L P+ A +VA ++G+
Sbjct: 61 RGEKKAYVKLKPEYSASEVAARLGL 85
>pdb|1FFK|P Chain P, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1GIY|T Chain T, Crystal Structure Of The Ribosome At 5.5 A Resolution.
This File, 1giy, Contains The 50s Ribosome Subunit. The
30s Ribosome Subunit, Three Trna, And Mrna Molecules Are
In The File 1gix
pdb|1JJ2|R Chain R, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|R Chain R, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|T Chain T, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|T Chain T, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|T Chain T, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|T Chain T, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|T Chain T, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1ML5|TT Chain t, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
pdb|1K73|T Chain T, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|T Chain T, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|T Chain T, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|T Chain T, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|T Chain T, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|T Chain T, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|T Chain T, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|T Chain T, 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|R Chain R, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|R Chain R, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1W2B|R Chain R, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|1YL3|T Chain T, Crystal Structure Of 70s Ribosome With Thrs Operator And
Trnas. Large Subunit. The Coordinates For The Small
Subunit Are In The Pdb Entry 1yl4.
pdb|2B66|X Chain X, 50s Ribosomal Subunit From A Crystal Structure Of Release
Factor Rf1, Trnas And Mrna Bound To The Ribosome. This
File Contains The 50s Subunit From A Crystal Structure
Of Release Factor Rf1, Trnas And Mrna Bound To The
Ribosome And Is Described In Remark 400
pdb|2B9N|X Chain X, 50s Ribosomal Subunit From A Crystal Structure Of Release
Factor Rf2, Trnas And Mrna Bound To The Ribosome. This
File Contains The 50s Subunit From A Crystal Structure
Of Release Factor Rf1, Trnas And Mrna Bound To The
Ribosome And Is Described In Remark 400.
pdb|2B9P|X Chain X, 50s Ribosomal Subunit From A Crystal Structure Of The
Ribosome In Complex With Trnas And Mrna With A Stop
Codon In The A-Site. This File Contains The 50s Subunit
From A Crystal Structure Of The Ribosome In Complex With
Trnas And Mrna With A Stop Codon In The A-Site And Is
Described In Remark 400.
pdb|3CXC|R Chain R, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
Length = 84
Score = 58.2 bits (139), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 43/83 (51%)
Query: 70 YQILKYPLTTESAMKKIEDNNTLVFXXXXXXXXXXXXXXXXXMYDIQAKKVNTLIRPDGT 129
+ ++K+P TE AM ++ N L F YD+ ++VNT DG
Sbjct: 2 WDVIKHPHVTEKAMNDMDFQNKLQFAVDDRASKGEVADAVEEQYDVTVEQVNTQNTMDGE 61
Query: 130 KKAYVRLTPDSDALDVANKIGII 152
KKA VRL+ D DA +VA++IG+
Sbjct: 62 KKAVVRLSEDDDAQEVASRIGVF 84
>pdb|1S72|S Chain S, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1YHQ|S Chain S, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|S Chain S, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|S Chain S, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|S Chain S, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|S Chain S, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|S Chain S, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|S Chain S, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|S Chain S, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|S Chain S, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|S Chain S, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|S Chain S, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|S Chain S, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|S Chain S, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|S Chain S, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|S Chain S, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|S Chain S, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|S Chain S, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|S Chain S, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|S Chain S, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|S Chain S, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|S Chain S, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|S Chain S, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|3CC2|S Chain S, 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|S Chain S, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|S Chain S, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|S Chain S, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|S Chain S, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|S Chain S, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|S Chain S, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|S Chain S, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|S Chain S, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|S Chain S, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|S Chain S, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|S Chain S, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|S Chain S, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|R Chain R, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|S Chain S, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|S Chain S, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|2QEX|S Chain S, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3I55|S Chain S, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|S Chain S, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
pdb|4ADX|S Chain S, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 85
Score = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 43/83 (51%)
Query: 70 YQILKYPLTTESAMKKIEDNNTLVFXXXXXXXXXXXXXXXXXMYDIQAKKVNTLIRPDGT 129
+ ++K+P TE AM ++ N L F YD+ ++VNT DG
Sbjct: 3 WDVIKHPHVTEKAMNDMDFQNKLQFAVDDRASKGEVADAVEEQYDVTVEQVNTQNTMDGE 62
Query: 130 KKAYVRLTPDSDALDVANKIGII 152
KKA VRL+ D DA +VA++IG+
Sbjct: 63 KKAVVRLSEDDDAQEVASRIGVF 85
>pdb|3G4S|S Chain S, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|S Chain S, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|S Chain S, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|3OW2|R Chain R, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 81
Score = 53.9 bits (128), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 41/80 (51%)
Query: 70 YQILKYPLTTESAMKKIEDNNTLVFXXXXXXXXXXXXXXXXXMYDIQAKKVNTLIRPDGT 129
+ ++K+P TE AM ++ N L F YD+ ++VNT DG
Sbjct: 2 WDVIKHPHVTEKAMNDMDFQNKLQFAVDDRASKGEVADAVEEQYDVTVEQVNTQNTMDGE 61
Query: 130 KKAYVRLTPDSDALDVANKI 149
KKA VRL+ D DA +VA++I
Sbjct: 62 KKAVVRLSEDDDAQEVASRI 81
>pdb|3ZF7|O Chain O, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 222
Score = 26.6 bits (57), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 15 VQALKTAKAVKSGRTFKKAKKIRTSVTFHRPKTLKK 50
V+ L+ A+ KSGR KK +K+R + R + LKK
Sbjct: 172 VEKLEAARIEKSGRHHKKMEKVRVAWKNARKEALKK 207
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 0.130 0.366
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,750,570
Number of Sequences: 62578
Number of extensions: 109158
Number of successful extensions: 199
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 169
Number of HSP's gapped (non-prelim): 20
length of query: 152
length of database: 14,973,337
effective HSP length: 90
effective length of query: 62
effective length of database: 9,341,317
effective search space: 579161654
effective search space used: 579161654
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: 47 (22.7 bits)