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= psy11361
(200 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKR|RR Chain r, 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 = 184
Score = 236 bits (602), Expect = 6e-63, Method: Compositional matrix adjust.
Identities = 113/178 (63%), Positives = 134/178 (75%), Gaps = 15/178 (8%)
Query: 1 MGRYSKEPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPF 60
M RYS +P NPTKSCK+RGSNLRVHFKNTRETA+ I M +R+A K+LK+V Q +CVPF
Sbjct: 1 MVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLQKQCVPF 60
Query: 61 RRYNGGVGRCAQAKQWGTTQGRWPRKSADFLLQLLKNAESNADYRGLDTDRLVIEHIQVN 120
RRYNGGVGRCAQAKQWG TQGRWP+KSA+FLL +LKNAESNA+ +GLD D LVIEHIQVN
Sbjct: 61 RRYNGGVGRCAQAKQWGWTQGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVN 120
Query: 121 XXXXXXXXXXXAHGNYRGLDTDRLVIEHIQVNPYMSSPCHIEVILSERERVVAKPRED 178
AHG ++NPYMSSPCHIE+IL+E+E++V KP E+
Sbjct: 121 KAPKMRRRTYRAHG---------------RINPYMSSPCHIEMILTEKEQIVPKPEEE 163
>pdb|3IZR|V Chain V, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 171
Score = 182 bits (462), Expect = 9e-47, Method: Compositional matrix adjust.
Identities = 96/180 (53%), Positives = 117/180 (65%), Gaps = 16/180 (8%)
Query: 1 MGRYSKEPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPF 60
M +YS+E NPTKS KA G +LRVHFKNTRETA I K+PL +A ++L++V + +PF
Sbjct: 1 MVKYSREANNPTKSSKAMGRDLRVHFKNTRETAFAIRKLPLGKAKRYLEDVIAHKQAIPF 60
Query: 61 RRYNGGVGRCAQAK-QWGTTQGRWPRKSADFLLQLLKNAESNADYRGLDTDRLVIEHIQV 119
RRY GGVGR AQAK + QGRWP KSA F+L LLKNAESNA+ +GLD D L + HIQV
Sbjct: 61 RRYCGGVGRTAQAKSRHSNGQGRWPAKSARFILDLLKNAESNAEVKGLDVDTLYVSHIQV 120
Query: 120 NXXXXXXXXXXXAHGNYRGLDTDRLVIEHIQVNPYMSSPCHIEVILSERERVVAKPREDE 179
N AHG ++NPYMSSPCHIE+ILSE+E V K E +
Sbjct: 121 NQAQKQRRRTYRAHG---------------RINPYMSSPCHIELILSEKEEPVKKEPESQ 165
>pdb|2WW9|I Chain I, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound
To The Yeast 80s Ribosome
pdb|2WWA|I Chain I, Cryo-Em Structure Of Idle Yeast Ssh1 Complex Bound To The
Yeast 80s Ribosome
pdb|2WWB|I Chain I, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound To
The Actively Translating Wheat Germ 80s Ribosome
pdb|3O58|Q Chain Q, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|Q Chain Q, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|P 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|P 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|P Chain P, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 184
Score = 160 bits (404), Expect = 5e-40, Method: Compositional matrix adjust.
Identities = 79/179 (44%), Positives = 105/179 (58%), Gaps = 15/179 (8%)
Query: 1 MGRYSKEPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPF 60
M RY NP KS ARGS LRV FKNTRETA+ I+ L +A K+L+ V D +PF
Sbjct: 1 MARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPF 60
Query: 61 RRYNGGVGRCAQAKQWGTTQGRWPRKSADFLLQLLKNAESNADYRGLDTDRLVIEHIQVN 120
RR+N +GR AQ K++G T+ RWP KS F+ LL+NA +NA+ +GLD +L + HIQVN
Sbjct: 61 RRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQVN 120
Query: 121 XXXXXXXXXXXAHGNYRGLDTDRLVIEHIQVNPYMSSPCHIEVILSERERVVAKPREDE 179
AHG ++N Y SSP HIE++++E+E VAK E +
Sbjct: 121 QAPKQRRRTYRAHG---------------RINKYESSPSHIELVVTEKEEAVAKAAEKK 164
>pdb|3IZS|V Chain V, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
Length = 170
Score = 160 bits (404), Expect = 6e-40, Method: Compositional matrix adjust.
Identities = 79/179 (44%), Positives = 105/179 (58%), Gaps = 15/179 (8%)
Query: 1 MGRYSKEPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPF 60
M RY NP KS ARGS LRV FKNTRETA+ I+ L +A K+L+ V D +PF
Sbjct: 1 MARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPF 60
Query: 61 RRYNGGVGRCAQAKQWGTTQGRWPRKSADFLLQLLKNAESNADYRGLDTDRLVIEHIQVN 120
RR+N +GR AQ K++G T+ RWP KS F+ LL+NA +NA+ +GLD +L + HIQVN
Sbjct: 61 RRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQVN 120
Query: 121 XXXXXXXXXXXAHGNYRGLDTDRLVIEHIQVNPYMSSPCHIEVILSERERVVAKPREDE 179
AHG ++N Y SSP HIE++++E+E VAK E +
Sbjct: 121 QAPKQRRRTYRAHG---------------RINKYESSPSHIELVVTEKEEAVAKAAEKK 164
>pdb|1S1I|N Chain N, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
Yeast Obtained By Docking Atomic Models For Rna And
Protein Components Into A 11.7 A Cryo-Em Map. This File,
1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is
In File 1s1h
Length = 183
Score = 157 bits (397), Expect = 3e-39, Method: Compositional matrix adjust.
Identities = 78/178 (43%), Positives = 104/178 (58%), Gaps = 15/178 (8%)
Query: 2 GRYSKEPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFR 61
RY NP KS ARGS LRV FKNTRETA+ I+ L +A K+L+ V D +PFR
Sbjct: 1 ARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPFR 60
Query: 62 RYNGGVGRCAQAKQWGTTQGRWPRKSADFLLQLLKNAESNADYRGLDTDRLVIEHIQVNX 121
R+N +GR AQ K++G T+ RWP KS F+ LL+NA +NA+ +GLD +L + HIQVN
Sbjct: 61 RFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQVNQ 120
Query: 122 XXXXXXXXXXAHGNYRGLDTDRLVIEHIQVNPYMSSPCHIEVILSERERVVAKPREDE 179
AHG ++N Y SSP HIE++++E+E VAK E +
Sbjct: 121 APKQRRRTYRAHG---------------RINKYESSPSHIELVVTEKEEAVAKAAEKK 163
>pdb|3ZF7|R Chain R, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 166
Score = 153 bits (386), Expect = 8e-38, Method: Compositional matrix adjust.
Identities = 73/177 (41%), Positives = 110/177 (62%), Gaps = 15/177 (8%)
Query: 1 MGRYSKEPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPF 60
M YS++P+ +K+ KA+ ++LR H+KNT ETA I+ M LR+A + + V + C+PF
Sbjct: 1 MVHYSRKPQVSSKTAKAKIADLRCHYKNTFETANVINGMKLRKAQQLYRQVLAKTRCIPF 60
Query: 61 RRYNGGVGRCAQAKQWGTTQGRWPRKSADFLLQLLKNAESNADYRGLDTDRLVIEHIQVN 120
+RYNG +G AQAK+WG T+GRWPRKS +L LLKNAE+NA +GLD ++VI+H+QV+
Sbjct: 61 KRYNGKIGNTAQAKEWGQTKGRWPRKSVVAMLSLLKNAEANAIEKGLDPGKMVIKHVQVD 120
Query: 121 XXXXXXXXXXXAHGNYRGLDTDRLVIEHIQVNPYMSSPCHIEVILSERERVVAKPRE 177
AHG ++ PYM SPCH+++ +++ + V P+
Sbjct: 121 QAPRVRRRTFRAHG---------------RITPYMRSPCHVQLFMTQPQERVPVPKS 162
>pdb|3JYW|N Chain N, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 150
Score = 147 bits (370), Expect = 5e-36, Method: Compositional matrix adjust.
Identities = 72/165 (43%), Positives = 97/165 (58%), Gaps = 15/165 (9%)
Query: 4 YSKEPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRY 63
Y NP KS ARGS LRV FKNTRETA+ I+ L +A K+L+ V D +PFRR+
Sbjct: 1 YGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPFRRF 60
Query: 64 NGGVGRCAQAKQWGTTQGRWPRKSADFLLQLLKNAESNADYRGLDTDRLVIEHIQVNXXX 123
N +GR AQ K++G T+ RWP KS F+ LL+NA +NA+ +GLD +L + HIQVN
Sbjct: 61 NSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQVNQAP 120
Query: 124 XXXXXXXXAHGNYRGLDTDRLVIEHIQVNPYMSSPCHIEVILSER 168
AHG ++N Y SSP HIE++++E+
Sbjct: 121 KQRRRTYRAHG---------------RINKYESSPSHIELVVTEK 150
>pdb|4A17|Q Chain Q, 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|Q Chain Q, 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|Q Chain Q, 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|Q Chain Q, 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 = 183
Score = 143 bits (360), Expect = 7e-35, Method: Compositional matrix adjust.
Identities = 76/182 (41%), Positives = 103/182 (56%), Gaps = 20/182 (10%)
Query: 1 MGR--YSKEPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECV 58
MG+ YS+EP N K+ K S+LRVHFKNT E + I + L A ++LK V D+ C+
Sbjct: 1 MGKTNYSREPANQAKAVKTSASDLRVHFKNTYEVVRAIKGLNLENAKRYLKAVIDRKRCI 60
Query: 59 PFRRYNGGVGRCAQAKQWGTTQGRWPRKSADFLLQLLKNAESNADYRGLDTDRLVIEHIQ 118
PF R+ G +GR AQA ++G TQGRWP KS +L LL N +NA + L+T LVI+H Q
Sbjct: 61 PFTRFTGCIGRTAQAHEFGRTQGRWPVKSVKVILGLLDNLSANAQAKSLNTANLVIQHGQ 120
Query: 119 VNXXXXXXXXXXXAHGNYRGLDTDRLVIEHIQVNPYMSSPCHIEVILSERERVVAKPRED 178
VN AHG ++NPY++S CH+E+ E V AK R++
Sbjct: 121 VNRAQKGRRRTYRAHG---------------RINPYLNSGCHVEIFAQE---VAAKVRKE 162
Query: 179 EP 180
P
Sbjct: 163 AP 164
>pdb|1S72|R Chain R, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1YHQ|R Chain R, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|R Chain R, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|R Chain R, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|R Chain R, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJN|R Chain R, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|R Chain R, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|R Chain R, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|R Chain R, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|R Chain R, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|R Chain R, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|R Chain R, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|R Chain R, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|R Chain R, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|R Chain R, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|R Chain R, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|R Chain R, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|R Chain R, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|R Chain R, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|R Chain R, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|R Chain R, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|R Chain R, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|3CC2|R Chain R, 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|R Chain R, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|R Chain R, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|Q Chain Q, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|R Chain R, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|R Chain R, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|2QEX|R Chain R, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3I55|R Chain R, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|R Chain R, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
pdb|4ADX|R Chain R, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 155
Score = 72.8 bits (177), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 42/150 (28%), Positives = 76/150 (50%), Gaps = 3/150 (2%)
Query: 4 YSKEPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRY 63
YS E +P + KA ++ FK+++ A+ I A+ +L+ V + + VPF+++
Sbjct: 5 YSVEA-DPDTTAKAMLRERQMSFKHSKAIAREIKGKTAGEAVDYLEAVIEGDQPVPFKQH 63
Query: 64 NGGVGRCAQAKQWGTTQGRWPRKSADFLLQLLKNAESNADYRGLDTDRLVIEHIQVNXXX 123
N GVG ++ W GR+P K++ L LL+NA NAD++G D + + I+H+ +
Sbjct: 64 NSGVGHKSKVDGWDA--GRYPEKASKAFLDLLENAVGNADHQGFDGEAMTIKHVAAHKVG 121
Query: 124 XXXXXXXXAHGNYRGLDTDRLVIEHIQVNP 153
A G ++ ++ +E I P
Sbjct: 122 EQQGRKPRAMGRASAWNSPQVDVELILEEP 151
>pdb|1FFK|O Chain O, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1JJ2|Q Chain Q, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|Q Chain Q, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|S Chain S, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|S Chain S, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|S Chain S, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|S Chain S, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|S Chain S, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1K73|S Chain S, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|S Chain S, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|S Chain S, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|S Chain S, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|S Chain S, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|S Chain S, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|S Chain S, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|S Chain S, 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|Q Chain Q, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|Q Chain Q, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1W2B|Q Chain Q, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|3CXC|Q Chain Q, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
Length = 154
Score = 72.8 bits (177), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 42/150 (28%), Positives = 76/150 (50%), Gaps = 3/150 (2%)
Query: 4 YSKEPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRY 63
YS E +P + KA ++ FK+++ A+ I A+ +L+ V + + VPF+++
Sbjct: 4 YSVEA-DPDTTAKAMLRERQMSFKHSKAIAREIKGKTAGEAVDYLEAVIEGDQPVPFKQH 62
Query: 64 NGGVGRCAQAKQWGTTQGRWPRKSADFLLQLLKNAESNADYRGLDTDRLVIEHIQVNXXX 123
N GVG ++ W GR+P K++ L LL+NA NAD++G D + + I+H+ +
Sbjct: 63 NSGVGHKSKVDGWDA--GRYPEKASKAFLDLLENAVGNADHQGFDGEAMTIKHVAAHKVG 120
Query: 124 XXXXXXXXAHGNYRGLDTDRLVIEHIQVNP 153
A G ++ ++ +E I P
Sbjct: 121 EQQGRKPRAMGRASAWNSPQVDVELILEEP 150
>pdb|3G4S|R Chain R, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|R Chain R, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|R Chain R, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|3OW2|Q Chain Q, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 150
Score = 72.4 bits (176), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 42/150 (28%), Positives = 76/150 (50%), Gaps = 3/150 (2%)
Query: 4 YSKEPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRY 63
YS E +P + KA ++ FK+++ A+ I A+ +L+ V + + VPF+++
Sbjct: 4 YSVEA-DPDTTAKAMLRERQMSFKHSKAIAREIKGKTAGEAVDYLEAVIEGDQPVPFKQH 62
Query: 64 NGGVGRCAQAKQWGTTQGRWPRKSADFLLQLLKNAESNADYRGLDTDRLVIEHIQVNXXX 123
N GVG ++ W GR+P K++ L LL+NA NAD++G D + + I+H+ +
Sbjct: 63 NSGVGHKSKVDGWDA--GRYPEKASKAFLDLLENAVGNADHQGFDGEAMTIKHVAAHKVG 120
Query: 124 XXXXXXXXAHGNYRGLDTDRLVIEHIQVNP 153
A G ++ ++ +E I P
Sbjct: 121 EQQGRKPRAMGRASAWNSPQVDVELILEEP 150
>pdb|1YJ9|R Chain R, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
Length = 152
Score = 72.0 bits (175), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 37/114 (32%), Positives = 65/114 (57%), Gaps = 3/114 (2%)
Query: 4 YSKEPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRY 63
YS E +P + KA ++ FK+++ A+ I A+ +L+ V + + VPF+++
Sbjct: 5 YSVEA-DPDTTAKAMLRERQMSFKHSKAIAREIKGKTAGEAVDYLEAVIEGDQPVPFKQH 63
Query: 64 NGGVGRCAQAKQWGTTQGRWPRKSADFLLQLLKNAESNADYRGLDTDRLVIEHI 117
N GVG ++ W GR+P K++ L LL+NA NAD++G D + + I+H+
Sbjct: 64 NSGVGHKSKVDGWDA--GRYPEKASKAFLDLLENAVGNADHQGFDGEAMTIKHV 115
>pdb|3J21|S Chain S, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 155
Score = 60.1 bits (144), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 47/167 (28%), Positives = 74/167 (44%), Gaps = 18/167 (10%)
Query: 4 YSKEPRNPTKSCKARGSNLRVHFKNTRETAKTISKMPLRRAIKFLKNVKDQLECVPFRRY 63
YS + +P + +A +LR+ K E + + M L A+++L +V VP +RY
Sbjct: 7 YSFQNFDPKRMARASARDLRISPKLAVEVCRELRGMMLNDALRYLDDVIALKRPVPLKRY 66
Query: 64 NGGVGRCAQAKQWGTTQGRWPRKSADFLLQLLKNAESNADYRGLDTDRLVIEHIQVNXXX 123
N G K +G GR+P K A + ++L N ++NA +GLD D+L I HI +
Sbjct: 67 NDSQGH-KPGKGFGP--GRYPVKVAKAIKKVLLNVKNNAVQKGLDPDKLKIIHIAAHKGP 123
Query: 124 XXXXXXXXAHGNYRGLDTDRLVIEHIQVNPYMSSPCHIEVILSERER 170
A G + P+ HIEV++ E R
Sbjct: 124 VLRGWYPRAFG---------------RATPFNEQTTHIEVVVEEIRR 155
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 0.135 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,855,658
Number of Sequences: 62578
Number of extensions: 164948
Number of successful extensions: 366
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 331
Number of HSP's gapped (non-prelim): 13
length of query: 200
length of database: 14,973,337
effective HSP length: 94
effective length of query: 106
effective length of database: 9,091,005
effective search space: 963646530
effective search space used: 963646530
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: 49 (23.5 bits)