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= 048058
(157 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|D Chain D, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 405
Score = 241 bits (615), Expect = 1e-64, Method: Compositional matrix adjust.
Identities = 110/157 (70%), Positives = 130/157 (82%)
Query: 1 MAAAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSR 60
MA RPL++V++LEGDMATD SS++ L +V +A +RPD+V FVH +S N RQPYAVSR
Sbjct: 1 MATQTRPLVSVKALEGDMATDNSSSLALAEVFRAPLRPDVVRFVHRLLSCNKRQPYAVSR 60
Query: 61 KAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN 120
+AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTK WR+WHR++N
Sbjct: 61 RAGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKTWRKWHRRVN 120
Query: 121 VNQKRYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
V+ +R PSLV+ARGH+IETVPE+PLV
Sbjct: 121 VHLRRVAVASALAATSVPSLVLARGHRIETVPELPLV 157
>pdb|2ZKR|CC Chain c, 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 = 421
Score = 223 bits (568), Expect = 4e-59, Method: Compositional matrix adjust.
Identities = 105/155 (67%), Positives = 121/155 (78%), Gaps = 3/155 (1%)
Query: 3 AAARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKA 62
A ARPLI+V S +G+ + V LP V KA IRPDIV FVH+N+ KN+RQPYAVS A
Sbjct: 2 ACARPLISVYSEKGE---SSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELA 58
Query: 63 GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVN 122
GHQTSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCRGGRMFAPTK WRRWHR++N
Sbjct: 59 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTT 118
Query: 123 QKRYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
QKRY P+LVM++GH+IE VPE+PLV
Sbjct: 119 QKRYAICSALACLSLPALVMSKGHRIEEVPELPLV 153
>pdb|3ZF7|RR Chain r, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 374
Score = 193 bits (490), Expect = 4e-50, Method: Compositional matrix adjust.
Identities = 94/153 (61%), Positives = 113/153 (73%), Gaps = 3/153 (1%)
Query: 5 ARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGH 64
ARP ++V S D T LP V A IR D+V FVH+N++KNSRQPYAV+R +G
Sbjct: 3 ARPSVSVYSASEDKVV---GTCSLPAVFTAPIRHDVVQFVHTNMAKNSRQPYAVNRLSGM 59
Query: 65 QTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQK 124
+ SAESWGTGRAV+RIPR+ GGGT +G GAFGNMCRGGRMFAPTKI+RRWHRKIN++QK
Sbjct: 60 KHSAESWGTGRAVARIPRIHGGGTSMSGAGAFGNMCRGGRMFAPTKIFRRWHRKINLHQK 119
Query: 125 RYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
R+ P+LVM+RGHKIE V E+PLV
Sbjct: 120 RFAVVSALAASSLPALVMSRGHKIENVAEVPLV 152
>pdb|2WW9|H Chain H, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound
To The Yeast 80s Ribosome
pdb|2WWA|H Chain H, Cryo-Em Structure Of Idle Yeast Ssh1 Complex Bound To The
Yeast 80s Ribosome
pdb|2WWB|H Chain H, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound To
The Actively Translating Wheat Germ 80s Ribosome
Length = 362
Score = 179 bits (455), Expect = 4e-46, Method: Compositional matrix adjust.
Identities = 96/153 (62%), Positives = 116/153 (75%), Gaps = 3/153 (1%)
Query: 5 ARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGH 64
+RP +TV SL G+ +A +PLP V A IRPDIV V ++++KN RQ YAVS KAGH
Sbjct: 2 SRPQVTVHSLTGEATANA---LPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGH 58
Query: 65 QTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQK 124
QTSAESWGTGRAV+RIPRV GGGT R+GQGAFGNMCRGGRMFAPTK WR+W+ K+N N+K
Sbjct: 59 QTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEK 118
Query: 125 RYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
RY SLV+ARGH++E +PE+PLV
Sbjct: 119 RYATASAIAATAVASLVLARGHRVEKIPEIPLV 151
>pdb|3IZS|D Chain D, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|D Chain D, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|D Chain D, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|C Chain C, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|C Chain C, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|C Chain C, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 362
Score = 179 bits (455), Expect = 5e-46, Method: Compositional matrix adjust.
Identities = 96/153 (62%), Positives = 116/153 (75%), Gaps = 3/153 (1%)
Query: 5 ARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGH 64
+RP +TV SL G+ +A +PLP V A IRPDIV V ++++KN RQ YAVS KAGH
Sbjct: 2 SRPQVTVHSLTGEATANA---LPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGH 58
Query: 65 QTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQK 124
QTSAESWGTGRAV+RIPRV GGGT R+GQGAFGNMCRGGRMFAPTK WR+W+ K+N N+K
Sbjct: 59 QTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEK 118
Query: 125 RYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
RY SLV+ARGH++E +PE+PLV
Sbjct: 119 RYATASAIAATAVASLVLARGHRVEKIPEIPLV 151
>pdb|1S1I|D Chain D, 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 = 361
Score = 179 bits (455), Expect = 5e-46, Method: Compositional matrix adjust.
Identities = 96/153 (62%), Positives = 116/153 (75%), Gaps = 3/153 (1%)
Query: 5 ARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGH 64
+RP +TV SL G+ +A +PLP V A IRPDIV V ++++KN RQ YAVS KAGH
Sbjct: 1 SRPQVTVHSLTGEATANA---LPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGH 57
Query: 65 QTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQK 124
QTSAESWGTGRAV+RIPRV GGGT R+GQGAFGNMCRGGRMFAPTK WR+W+ K+N N+K
Sbjct: 58 QTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEK 117
Query: 125 RYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
RY SLV+ARGH++E +PE+PLV
Sbjct: 118 RYATASAIAATAVASLVLARGHRVEKIPEIPLV 150
>pdb|3JYW|D Chain D, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 257
Score = 174 bits (441), Expect = 2e-44, Method: Compositional matrix adjust.
Identities = 94/149 (63%), Positives = 113/149 (75%), Gaps = 3/149 (2%)
Query: 9 ITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSA 68
+TV SL G+ +A +PLP V A IRPDIV V ++++KN RQ YAVS KAGHQTSA
Sbjct: 2 VTVHSLTGEATANA---LPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQTSA 58
Query: 69 ESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYXX 128
ESWGTGRAV+RIPRV GGGT R+GQGAFGNMCRGGRMFAPTK WR+W+ K+N N+KRY
Sbjct: 59 ESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRYAT 118
Query: 129 XXXXXXXXXPSLVMARGHKIETVPEMPLV 157
SLV+ARGH++E +PE+PLV
Sbjct: 119 ASAIAATAVASLVLARGHRVEKIPEIPLV 147
>pdb|4A17|C Chain C, 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|C Chain C, 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|C Chain C, 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|C Chain C, 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 = 410
Score = 143 bits (360), Expect = 4e-35, Method: Compositional matrix adjust.
Identities = 77/157 (49%), Positives = 96/157 (61%), Gaps = 5/157 (3%)
Query: 5 ARPLITVQSLEGDMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRK--- 61
+RP I V + + ++ + LP V A IR DIV V ++++KN +Q V
Sbjct: 3 SRPQIHVHDAK-EANKQTATKLTLPAVFTAPIRTDIVHKVFTDLNKNRKQASGVKISTRG 61
Query: 62 -AGHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKIN 120
AG SAESWGTGRAV+RIPRV G GTHR+GQ AFGN CR GRMFAP K +RR HR++N
Sbjct: 62 TAGMGHSAESWGTGRAVARIPRVGGSGTHRSGQAAFGNQCRKGRMFAPLKTYRRVHRRVN 121
Query: 121 VNQKRYXXXXXXXXXXXPSLVMARGHKIETVPEMPLV 157
VNQKR+ LV ARGH+I V E+P V
Sbjct: 122 VNQKRHAVAAALAASALVPLVFARGHRISNVQELPYV 158
>pdb|3J21|D Chain D, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 255
Score = 53.5 bits (127), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 39/141 (27%), Positives = 59/141 (41%), Gaps = 4/141 (2%)
Query: 17 DMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRA 76
D+ + LP V RPD++ + QP AG + E+ G G +
Sbjct: 7 DLNGQPVGEIELPKVFFTPFRPDLIRRAVIASWTHRIQPQGRDPMAGKRRVTENIGKGHS 66
Query: 77 VSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYXXXXXXXXXX 136
++R+ R+ + AF RGGR P K+ + IN +KR
Sbjct: 67 MARVERLKTPPRY----AAFVPFARGGRRTHPPKVEKIIWEDINKKEKRLALMSAIAATA 122
Query: 137 XPSLVMARGHKIETVPEMPLV 157
LV ARGH I+ VP++PL+
Sbjct: 123 NYDLVRARGHIIDNVPQLPLI 143
>pdb|1JJ2|C Chain C, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|C Chain C, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|E Chain E, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|E Chain E, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|E Chain E, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|E Chain E, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|E Chain E, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1K73|E Chain E, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|E Chain E, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|E Chain E, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|E Chain E, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|E Chain E, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|E Chain E, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|E Chain E, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|E Chain E, 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|C Chain C, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|C Chain C, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1S72|C Chain C, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1W2B|C Chain C, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|1YHQ|C Chain C, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|C Chain C, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|C Chain C, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|C Chain C, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|C Chain C, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|C Chain C, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|C Chain C, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|C Chain C, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|C Chain C, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|C Chain C, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|C Chain C, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|C Chain C, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|C Chain C, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|C Chain C, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|C Chain C, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|C Chain C, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|C Chain C, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|C Chain C, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|C Chain C, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|C Chain C, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|C Chain C, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|C Chain C, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|2QEX|C Chain C, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3CXC|C Chain C, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
pdb|3OW2|C Chain C, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 246
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 38/141 (26%), Positives = 61/141 (43%), Gaps = 8/141 (5%)
Query: 17 DMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRA 76
D+ + V LPDV + +R D++G N +Q Y AG +T AES+G+GR
Sbjct: 7 DLDGNTDGEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESFGSGRG 66
Query: 77 VSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYXXXXXXXXXX 136
+ +P++ G R Q GR P K + +N +++
Sbjct: 67 QAHVPKLDGRA-RRVPQAV------KGRSAHPPKTEKDRSLDLNDKERQLAVRSALAATA 119
Query: 137 XPSLVMARGHKIETVPEMPLV 157
LV RGH+ + E+P+V
Sbjct: 120 DADLVADRGHEFDR-DEVPVV 139
>pdb|1FFK|C Chain C, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1GIY|F Chain F, 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|1ML5|FF Chain f, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
pdb|1YL3|F Chain F, 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|F Chain F, 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|F Chain F, 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|F Chain F, 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
Length = 246
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 38/141 (26%), Positives = 61/141 (43%), Gaps = 8/141 (5%)
Query: 17 DMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRA 76
D+ + V LPDV + +R D++G N +Q Y AG +T AES+G+GR
Sbjct: 7 DLDGNTDGEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESFGSGRG 66
Query: 77 VSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYXXXXXXXXXX 136
+ +P++ G R Q GR P K + +N +++
Sbjct: 67 QAHVPKLDGRA-RRVPQAV------KGRSAHPPKTEKDRSLDLNDKERQLAVRSALAATA 119
Query: 137 XPSLVMARGHKIETVPEMPLV 157
LV RGH+ + E+P+V
Sbjct: 120 DADLVADRGHEFDR-DEVPVV 139
>pdb|3CC2|C Chain C, 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|C Chain C, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|C Chain C, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|C Chain C, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|C Chain C, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|C Chain C, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|3G4S|C Chain C, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|C Chain C, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|C Chain C, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|3I55|C Chain C, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|C Chain C, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
pdb|4ADX|C Chain C, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 246
Score = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 38/141 (26%), Positives = 60/141 (42%), Gaps = 8/141 (5%)
Query: 17 DMATDASSTVPLPDVMKASIRPDIVGFVHSNISKNSRQPYAVSRKAGHQTSAESWGTGRA 76
D+ + V LPDV + +R D++G N +Q Y AG +T AES+G+GR
Sbjct: 7 DLDGNTDGEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESFGSGRG 66
Query: 77 VSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKIWRRWHRKINVNQKRYXXXXXXXXXX 136
+ +P+ G R Q GR P K + +N +++
Sbjct: 67 QAHVPK-QDGRARRVPQAV------KGRSAHPPKTEKDRSLDLNDKERQLAVRSALAATA 119
Query: 137 XPSLVMARGHKIETVPEMPLV 157
LV RGH+ + E+P+V
Sbjct: 120 DADLVADRGHEFDR-DEVPVV 139
>pdb|1PGL|2 Chain 2, Bean Pod Mottle Virus (Bpmv), Middle Component
Length = 370
Score = 27.3 bits (59), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 51 NSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGGG 87
N + P+ ++R G T + GT R+V R+P GGG
Sbjct: 186 NPQNPFVLNRWMGKLTFPQ--GTSRSVKRMPLSIGGG 220
>pdb|1PGW|2 Chain 2, Bean Pod Mottle Virus (Bpmv), Top Component
Length = 351
Score = 27.3 bits (59), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 51 NSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGGG 87
N + P+ ++R G T + GT R+V R+P GGG
Sbjct: 167 NPQNPFVLNRWMGKLTFPQ--GTSRSVKRMPLSIGGG 201
>pdb|1BMV|2 Chain 2, Protein-Rna Interactions In An Icosahedral Virus At 3.0
Angstroms Resolution
Length = 374
Score = 27.3 bits (59), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 51 NSRQPYAVSRKAGHQTSAESWGTGRAVSRIPRVPGGG 87
N + P+ ++R G T + GT R+V R+P GGG
Sbjct: 186 NPQNPFVLNRWMGKLTFPQ--GTSRSVKRMPLSIGGG 220
>pdb|3LMW|A Chain A, Crystal Structure Of Iota-Carrageenase Family Gh82 From
A. Fortis In Absence Of Chloride Ions
pdb|3LMW|B Chain B, Crystal Structure Of Iota-Carrageenase Family Gh82 From
A. Fortis In Absence Of Chloride Ions
Length = 473
Score = 26.2 bits (56), Expect = 8.9, Method: Composition-based stats.
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 63 GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAF 96
G+ TS +S RA++ I R P GGT G +
Sbjct: 33 GNDTSDDSNALQRAINAISRKPNGGTLLIPNGTY 66
>pdb|1H80|A Chain A, 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate-3,6-Anhydro-D-
Galactose-2-Sulfate 4 Galactohydrolase
pdb|1H80|B Chain B, 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate-3,6-Anhydro-D-
Galactose-2-Sulfate 4 Galactohydrolase
pdb|1KTW|A Chain A, Iota-carrageenase Complexed To Iota-carrageenan
Fragments
pdb|1KTW|B Chain B, Iota-carrageenase Complexed To Iota-carrageenan
Fragments
Length = 464
Score = 25.8 bits (55), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 63 GHQTSAESWGTGRAVSRIPRVPGGGTHRAGQGAF 96
G+ TS +S RA++ I R P GGT G +
Sbjct: 32 GNDTSDDSNALQRAINAISRKPNGGTLLIPNGTY 65
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.132 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,323,030
Number of Sequences: 62578
Number of extensions: 158501
Number of successful extensions: 284
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 265
Number of HSP's gapped (non-prelim): 18
length of query: 157
length of database: 14,973,337
effective HSP length: 91
effective length of query: 66
effective length of database: 9,278,739
effective search space: 612396774
effective search space used: 612396774
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)