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= psy5756
(360 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKR|NN Chain n, 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 = 297
Score = 319 bits (817), Expect = 2e-87, Method: Compositional matrix adjust.
Identities = 148/227 (65%), Positives = 179/227 (78%)
Query: 45 MGFVKVVKNKQYFKRYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDI 104
MGFVKVVKNK YFKRYQVKF+RRREGKTDYYARKRL++QDKNKYNTPKYR+IVR +N+DI
Sbjct: 1 MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI 60
Query: 105 TCQVAYSRIEGDHIICSAYSHELPKYGIKVGXXXXXXXXXXXXXXXXXXXXXXXXXXXXV 164
CQ+AY+RIEGD I+C+ Y+HELPKYG+KVG
Sbjct: 61 ICQIAYARIEGDMIVCARYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE 120
Query: 165 GCTEVTGEEFSVESVDKGPGAFRCYLDVGLMKTSTGAKVFGAMKGAVDGGLNIPHSVKRF 224
G EVTG+E++VES+D PGAF CYLD GL +T+TG KVFGA+KGAVDGGL+IPHS KRF
Sbjct: 121 GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF 180
Query: 225 PGYDNESKDFNAEIHRKHIFGLHVAEYMRQLSEEDDEAFKRQFSERV 271
PGYD+ESK+FNAE+HRKHI G +VA+YMR L EED++A+K+QFS+ +
Sbjct: 181 PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYI 227
>pdb|3IZR|Q Chain Q, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 304
Score = 235 bits (599), Expect = 3e-62, Method: Compositional matrix adjust.
Identities = 117/227 (51%), Positives = 152/227 (66%), Gaps = 4/227 (1%)
Query: 43 LEMGFVKVVKNKQYFKRYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNK 102
L+ GFVK K YFKR+QVKFKRRR+GKTDY AR RL QDKNKYNTPKYR + +NK
Sbjct: 3 LQGGFVKTQKTHAYFKRFQVKFKRRRQGKTDYRARIRLTNQDKNKYNTPKYRFV---TNK 59
Query: 103 DITCQVAYSRIEGDHIICSAYSHELPKYGIKVGXXXXXXXXXXXXXXXXXXXXXXXXXXX 162
DIT Q+ Y+ I GD ++ +AYSHELP+YG++VG
Sbjct: 60 DITAQIVYATIAGDIVMAAAYSHELPRYGLEVGLTNYAAAYCTGLLLARRVLTLRGLDQE 119
Query: 163 XVGCTEVTGEEFSVESVDKGPGAFRCYLDVGLMKTSTGAKVFGAMKGAVDGGLNIPHSVK 222
G E TGE++ VE D+ FR LDVGL++T+TG +VFGA+KGA+DGGL+IPHS K
Sbjct: 120 YEGNVEATGEDYYVEPADERR-PFRALLDVGLIRTTTGNRVFGALKGALDGGLDIPHSDK 178
Query: 223 RFPGYDNESKDFNAEIHRKHIFGLHVAEYMRQLSEEDDEAFKRQFSE 269
RF G+ + K +++IHRK+I+G HVA+YMR ++EE+ E F+ FSE
Sbjct: 179 RFAGFKKDEKQLDSDIHRKYIYGGHVADYMRSMAEEEPEKFQAHFSE 225
>pdb|3ZF7|UU Chain u, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 308
Score = 227 bits (579), Expect = 7e-60, Method: Compositional matrix adjust.
Identities = 106/220 (48%), Positives = 145/220 (65%), Gaps = 6/220 (2%)
Query: 45 MGFVKVVKNKQYFKRYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDI 104
M FVKVVKNK Y+KR+QVK++RRREGKTDY+AR+R+++QDK K+ TPKYRL+VR +N+D+
Sbjct: 1 MTFVKVVKNKAYYKRFQVKYRRRREGKTDYHARRRMVLQDKTKFGTPKYRLVVRITNRDV 60
Query: 105 TCQVAYSRIEGDHIICSAYSHELPKYGIKVGXXXXXXXXXXXXXXXXXXXXXXXXXXXXV 164
Q+ ++++ GD ++ +AYSHELP +GI+ G V
Sbjct: 61 IAQIVHAKVVGDEVVMAAYSHELPLFGIEHGLTNYAAAYATGLLVARRMLAKLGLAEKFV 120
Query: 165 GCTEVTGEEFSVESVDKGPG------AFRCYLDVGLMKTSTGAKVFGAMKGAVDGGLNIP 218
G EV G +V + D G F+ LDVGL +T+TGA+VFG +KGAVDGGL +P
Sbjct: 121 GVKEVDGSYAAVRTKDDDQGDDESRFPFKAILDVGLARTTTGARVFGVLKGAVDGGLAVP 180
Query: 219 HSVKRFPGYDNESKDFNAEIHRKHIFGLHVAEYMRQLSEE 258
H RFPGY+ ES NA++HR IFG HVA+Y++Q+ EE
Sbjct: 181 HRPNRFPGYNKESDALNAKVHRDRIFGRHVADYLKQVREE 220
>pdb|3U5E|D Chain D, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|D Chain D, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|D Chain D, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 297
Score = 219 bits (557), Expect = 2e-57, Method: Compositional matrix adjust.
Identities = 109/223 (48%), Positives = 144/223 (64%)
Query: 45 MGFVKVVKNKQYFKRYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDI 104
M F K K+ Y R+Q F+RRREGKTDYY RKRL+ Q K KYNTPKYRL+VRF+NKDI
Sbjct: 1 MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDI 60
Query: 105 TCQVAYSRIEGDHIICSAYSHELPKYGIKVGXXXXXXXXXXXXXXXXXXXXXXXXXXXXV 164
CQ+ S I GD ++ +AYSHELP+YGI G
Sbjct: 61 ICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQKLGLDETYK 120
Query: 165 GCTEVTGEEFSVESVDKGPGAFRCYLDVGLMKTSTGAKVFGAMKGAVDGGLNIPHSVKRF 224
G EV GE E+V+ GP F+ +LD+GL +T+TGA+VFGA+KGA DGGL +PHS RF
Sbjct: 121 GVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRF 180
Query: 225 PGYDNESKDFNAEIHRKHIFGLHVAEYMRQLSEEDDEAFKRQF 267
PG+D E+++ + E+ R +IFG HV++YM +L+++D+E F F
Sbjct: 181 PGWDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELF 223
>pdb|3IZS|Q Chain Q, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|E Chain E, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|E Chain E, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit
Length = 297
Score = 219 bits (557), Expect = 2e-57, Method: Compositional matrix adjust.
Identities = 109/223 (48%), Positives = 144/223 (64%)
Query: 45 MGFVKVVKNKQYFKRYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDI 104
M F K K+ Y R+Q F+RRREGKTDYY RKRL+ Q K KYNTPKYRL+VRF+NKDI
Sbjct: 1 MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDI 60
Query: 105 TCQVAYSRIEGDHIICSAYSHELPKYGIKVGXXXXXXXXXXXXXXXXXXXXXXXXXXXXV 164
CQ+ S I GD ++ +AYSHELP+YGI G
Sbjct: 61 ICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQRLGLDETYK 120
Query: 165 GCTEVTGEEFSVESVDKGPGAFRCYLDVGLMKTSTGAKVFGAMKGAVDGGLNIPHSVKRF 224
G EV GE E+V+ GP F+ +LD+GL +T+TGA+VFGA+KGA DGGL +PHS RF
Sbjct: 121 GVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRF 180
Query: 225 PGYDNESKDFNAEIHRKHIFGLHVAEYMRQLSEEDDEAFKRQF 267
PG+D E+++ + E+ R +IFG HV++YM +L+++D+E F F
Sbjct: 181 PGWDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELF 223
>pdb|4A17|M Chain M, 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|M Chain M, 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|M Chain M, 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|M Chain M, 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 = 301
Score = 217 bits (552), Expect = 1e-56, Method: Compositional matrix adjust.
Identities = 105/230 (45%), Positives = 144/230 (62%), Gaps = 5/230 (2%)
Query: 45 MGFVKVVKNKQYFKRYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDI 104
MGFVKV+K K YFKR+Q K++RRREG TDYYARKRLI+QDK+KYNTPKYRL+ R +N I
Sbjct: 1 MGFVKVLKTKAYFKRFQTKYRRRREGLTDYYARKRLIIQDKDKYNTPKYRLVARATNTRI 60
Query: 105 TCQVAYSRIEGDHIICSAYSHELPKYGIKVGXXXXXXXXXXXXXXXXXXXXXXXXXXXXV 164
Q+ Y+ ++ D ++C+A S+EL ++G+ G
Sbjct: 61 IAQIVYATLKCDRVLCAADSYELKRFGVSTGLASYAAAYATGLLLARRLLKQIGLDTVYA 120
Query: 165 GCTEVTGEEFSVESVDKGPGAFRCYLDVGLMKTSTGAKVFGAMKGAVDGGLNIPHSVKRF 224
G T+V G F+V+ K F+ LD GL++T+TG +VFG +KGA DGG+NIPHS RF
Sbjct: 121 GQTKVDGAYFNVDEDQKEKKPFKAILDAGLVRTTTGNRVFGVLKGACDGGINIPHSESRF 180
Query: 225 PGY-----DNESKDFNAEIHRKHIFGLHVAEYMRQLSEEDDEAFKRQFSE 269
PGY + ES + E H+ IFG H+ YM+ L + +EAF++QFS+
Sbjct: 181 PGYVRASDEGESSKYKPEDHKARIFGKHIDAYMKHLKGQSNEAFQKQFSK 230
>pdb|3JYW|E Chain E, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 237
Score = 212 bits (539), Expect = 3e-55, Method: Compositional matrix adjust.
Identities = 105/212 (49%), Positives = 139/212 (65%)
Query: 56 YFKRYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDITCQVAYSRIEG 115
Y R+Q F+RRREGKTDYY RKRL+ Q K KYNTPKYRL+VRF+NKDI CQ+ S I G
Sbjct: 2 YSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDIICQIISSTITG 61
Query: 116 DHIICSAYSHELPKYGIKVGXXXXXXXXXXXXXXXXXXXXXXXXXXXXVGCTEVTGEEFS 175
D ++ +AYSHELP+YGI G G EV GE
Sbjct: 62 DVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQRLGLDETYKGVEEVEGEYEL 121
Query: 176 VESVDKGPGAFRCYLDVGLMKTSTGAKVFGAMKGAVDGGLNIPHSVKRFPGYDNESKDFN 235
E+V+ GP F+ +LD+GL +T+TGA+VFGA+KGA DGGL +PHS RFPG+D E+++ +
Sbjct: 122 TEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRFPGWDFETEEID 181
Query: 236 AEIHRKHIFGLHVAEYMRQLSEEDDEAFKRQF 267
E+ R +IFG HV++YM +L+++D+E F F
Sbjct: 182 PELLRSYIFGGHVSQYMEELADDDEERFSELF 213
>pdb|1S1I|E Chain E, 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 = 222
Score = 211 bits (538), Expect = 4e-55, Method: Compositional matrix adjust.
Identities = 105/212 (49%), Positives = 139/212 (65%)
Query: 56 YFKRYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDITCQVAYSRIEG 115
Y R+Q F+RRREGKTDYY RKRL+ Q K KYNTPKYRL+VRF+NKDI CQ+ S I G
Sbjct: 2 YSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDIICQIISSTITG 61
Query: 116 DHIICSAYSHELPKYGIKVGXXXXXXXXXXXXXXXXXXXXXXXXXXXXVGCTEVTGEEFS 175
D ++ +AYSHELP+YGI G G EV GE
Sbjct: 62 DVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQRLGLDETYKGVEEVEGEYEL 121
Query: 176 VESVDKGPGAFRCYLDVGLMKTSTGAKVFGAMKGAVDGGLNIPHSVKRFPGYDNESKDFN 235
E+V+ GP F+ +LD+GL +T+TGA+VFGA+KGA DGGL +PHS RFPG+D E+++ +
Sbjct: 122 TEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRFPGWDFETEEID 181
Query: 236 AEIHRKHIFGLHVAEYMRQLSEEDDEAFKRQF 267
E+ R +IFG HV++YM +L+++D+E F F
Sbjct: 182 PELLRSYIFGGHVSQYMEELADDDEERFSELF 213
>pdb|1S72|N Chain N, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1YHQ|N Chain N, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|N Chain N, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|N Chain N, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|N Chain N, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|N Chain N, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|N Chain N, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|N Chain N, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|N Chain N, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|N Chain N, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|N Chain N, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|N Chain N, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|N Chain N, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|N Chain N, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|N Chain N, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|N Chain N, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|N Chain N, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|N Chain N, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|N Chain N, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|N Chain N, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|N Chain N, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|N Chain N, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|N Chain N, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|3CC2|N Chain N, 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|N Chain N, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|N Chain N, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|N Chain N, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|M Chain M, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|N Chain N, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|N Chain N, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|2QEX|N Chain N, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3I55|N Chain N, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|N Chain N, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
pdb|4ADX|N Chain N, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 187
Score = 80.9 bits (198), Expect = 9e-16, Method: Compositional matrix adjust.
Identities = 59/199 (29%), Positives = 87/199 (43%), Gaps = 47/199 (23%)
Query: 59 RYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDITCQVAYSRIEGDHI 118
RY+V +RRRE +TDY+ R RL+ + K RL+ R SNK + Q+ GD
Sbjct: 6 RYKVPMRRRREARTDYHQRLRLL-------KSGKPRLVARKSNKHVRAQLVTLGPNGDDT 58
Query: 119 ICSAYSHELPKYGIKVGXXXXXXXXXXXXXXXXXXXXXXXXXXXXVGCTEVTGEEFSVES 178
+ SA+S +L +YG + + +TG + +
Sbjct: 59 LASAHSSDLAEYGWEA-------------------------PTGNMPSAYLTGLLAGLRA 93
Query: 179 VDKGPGAFRCYLDVGLMKTSTGAKVFGAMKGAVDGGLNIPHSVKRFPGYDNESKDFNAEI 238
+ G LD+GL + G+KVF +GA+D GL+IPH + D A+
Sbjct: 94 QEA--GVEEAVLDIGLNSPTPGSKVFAIQEGAIDAGLDIPH-----------NDDVLADW 140
Query: 239 HRKHIFGLHVAEYMRQLSE 257
R G H+AEY QL E
Sbjct: 141 QRTR--GAHIAEYDEQLEE 157
>pdb|1FFK|K Chain K, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1GIY|Q Chain Q, 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|M Chain M, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|M Chain M, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|O Chain O, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|O Chain O, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|O Chain O, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|O Chain O, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|O Chain O, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1ML5|QQ Chain q, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
pdb|1K73|O Chain O, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|O Chain O, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|O Chain O, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|O Chain O, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|O Chain O, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|O Chain O, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|O Chain O, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|O Chain O, 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|M Chain M, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|M Chain M, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1W2B|M Chain M, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|1YL3|Q Chain Q, 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|S Chain S, 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|S Chain S, 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|S Chain S, 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|M Chain M, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
pdb|3G4S|N Chain N, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|N Chain N, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|N Chain N, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|3OW2|M Chain M, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 186
Score = 80.9 bits (198), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 59/199 (29%), Positives = 87/199 (43%), Gaps = 47/199 (23%)
Query: 59 RYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDITCQVAYSRIEGDHI 118
RY+V +RRRE +TDY+ R RL+ + K RL+ R SNK + Q+ GD
Sbjct: 5 RYKVPMRRRREARTDYHQRLRLL-------KSGKPRLVARKSNKHVRAQLVTLGPNGDDT 57
Query: 119 ICSAYSHELPKYGIKVGXXXXXXXXXXXXXXXXXXXXXXXXXXXXVGCTEVTGEEFSVES 178
+ SA+S +L +YG + + +TG + +
Sbjct: 58 LASAHSSDLAEYGWEA-------------------------PTGNMPSAYLTGLLAGLRA 92
Query: 179 VDKGPGAFRCYLDVGLMKTSTGAKVFGAMKGAVDGGLNIPHSVKRFPGYDNESKDFNAEI 238
+ G LD+GL + G+KVF +GA+D GL+IPH + D A+
Sbjct: 93 QEA--GVEEAVLDIGLNSPTPGSKVFAIQEGAIDAGLDIPH-----------NDDVLADW 139
Query: 239 HRKHIFGLHVAEYMRQLSE 257
R G H+AEY QL E
Sbjct: 140 QRTR--GAHIAEYDEQLEE 156
>pdb|3J21|O Chain O, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 203
Score = 68.9 bits (167), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 60/201 (29%), Positives = 87/201 (43%), Gaps = 48/201 (23%)
Query: 69 EGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDITCQVAYSRIEGDHIICSAYSHELP 128
EGKT+Y R +L+ + K RL+VR S Q+ +GD + SA++ EL
Sbjct: 16 EGKTNYRKRLKLL-------KSGKPRLVVRKSLNHHIAQIIVYDPKGDRTLVSAHTRELI 68
Query: 129 K-YGIKVGXXXXXXXXXXXXXXXXXXXXXXXXXXXXVGCTEVTGEEFSVESVDKGPGAFR 187
+ +G K + G ++ K G
Sbjct: 69 RDFGWK-------------------------GHCGNTPSAYLLGLLIGYKA--KQAGIEE 101
Query: 188 CYLDVGLMKTSTGAKVFGAMKGAVDGGLNIPHSVKRFPGYDNESKDFNAEIHRKHIFGLH 247
LD+GL G+ VF +KGAVD GLN+PHS + FP +E + I G H
Sbjct: 102 AILDIGLHPPVRGSSVFAVLKGAVDAGLNVPHSPEIFP---DEYR----------IRGEH 148
Query: 248 VAEYMRQLSEEDDEAFKRQFS 268
+AEY + L E+D+E F+RQF
Sbjct: 149 IAEYAKMLKEQDEEKFRRQFG 169
>pdb|4GMN|B Chain B, Structural Basis Of Rpl5 Recognition By Syo1
Length = 49
Score = 62.4 bits (150), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 29/41 (70%), Positives = 33/41 (80%)
Query: 45 MGFVKVVKNKQYFKRYQVKFKRRREGKTDYYARKRLIVQDK 85
M F K+VKN Y+ R+Q KFKRRR+GKTDYYARKRLI Q K
Sbjct: 1 MAFHKLVKNSAYYSRFQTKFKRRRQGKTDYYARKRLITQAK 41
>pdb|2OCA|A Chain A, The Crystal Structure Of T4 Uvsw
Length = 510
Score = 32.7 bits (73), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 34/133 (25%), Positives = 55/133 (41%), Gaps = 15/133 (11%)
Query: 10 SSLLQSLQTCDLPFGL----RCPEKRVFRSLKSF---FKP------LEMGFVKVVKNKQY 56
SS++ L C FGL R + + + + F FKP +E G V +K
Sbjct: 243 SSIISGLNNCMFKFGLSGSLRDGKANIMQYVGMFGEIFKPVTTSKLMEDGQVTELKINSI 302
Query: 57 FKRYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDITCQVAYSRIEGD 116
F RY +F + +GKT Y + I+ +K N +L ++ + KD V + +
Sbjct: 303 FLRYPDEFTTKLKGKT--YQEEIKIITGLSKRNKWIAKLAIKLAQKDENAFVMFKHVSHG 360
Query: 117 HIICSAYSHELPK 129
I +E K
Sbjct: 361 KAIFDLIKNEYDK 373
>pdb|3DMK|A Chain A, Crystal Structure Of Down Syndrome Cell Adhesion Molecule
(Dscam) Isoform 1.30.30, N-Terminal Eight Ig Domains
pdb|3DMK|B Chain B, Crystal Structure Of Down Syndrome Cell Adhesion Molecule
(Dscam) Isoform 1.30.30, N-Terminal Eight Ig Domains
pdb|3DMK|C Chain C, Crystal Structure Of Down Syndrome Cell Adhesion Molecule
(Dscam) Isoform 1.30.30, N-Terminal Eight Ig Domains
Length = 816
Score = 29.6 bits (65), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 7/84 (8%)
Query: 48 VKVVKNKQYFKRYQVKFKRRREGKTDYYARK-RLIVQDKNKYNTPKYRLIVRFSNKDITC 106
++ V + +K YQ + K R G+T A K RL++ + PK + +F K
Sbjct: 203 IREVGPEDGYKSYQCRTKHRLTGETRLSATKGRLVITEPISSAVPKVVSLAKFDMK---- 258
Query: 107 QVAYSRIEGDHIICSAYSHELPKY 130
YS ++C A + +P +
Sbjct: 259 --TYSGSSTMALLCPAQGYPVPVF 280
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
0.322 0.138 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,095,497
Number of Sequences: 62578
Number of extensions: 399027
Number of successful extensions: 733
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 702
Number of HSP's gapped (non-prelim): 19
length of query: 360
length of database: 14,973,337
effective HSP length: 100
effective length of query: 260
effective length of database: 8,715,537
effective search space: 2266039620
effective search space used: 2266039620
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)