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= 025449
(252 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 274 bits (701), Expect = 3e-74, Method: Compositional matrix adjust.
Identities = 131/162 (80%), Positives = 146/162 (90%), Gaps = 3/162 (1%)
Query: 2 AFAKAQKSKAYFKRYQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDIT 61
F K QK+ AYFKR+QVK+KRRR+GKTDYRARIRL NQDKNKYNTPKYRFV TNKDIT
Sbjct: 6 GFVKTQKTHAYFKRFQVKFKRRRQGKTDYRARIRLTNQDKNKYNTPKYRFV---TNKDIT 62
Query: 62 AQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEG 121
AQI+ A+IAGDIV+A+AY+HELPRYGLEVGLTNYAAAYCTGLLLARRVL + +D EYEG
Sbjct: 63 AQIVYATIAGDIVMAAAYSHELPRYGLEVGLTNYAAAYCTGLLLARRVLTLRGLDQEYEG 122
Query: 122 HVEATGEDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALK 163
+VEATGEDY VEP + RRPFRALLDVGL++TTTGNRVFGALK
Sbjct: 123 NVEATGEDYYVEPADERRPFRALLDVGLIRTTTGNRVFGALK 164
>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 = 205 bits (521), Expect = 2e-53, Method: Compositional matrix adjust.
Identities = 107/164 (65%), Positives = 128/164 (78%), Gaps = 1/164 (0%)
Query: 1 MAFAKAQKSKAYFKRYQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDI 60
M F K K+KAYFKRYQVK++RRREGKTDY AR RL+ QDKNKYNTPKYR +VR TN+DI
Sbjct: 1 MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI 60
Query: 61 TAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYE 120
QI A I GD+++ + YAHELP+YG++VGLTNYAAAYCTGLLLARR+L MD YE
Sbjct: 61 ICQIAYARIEGDMIVCARYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE 120
Query: 121 GHVEATGEDYSVEPTENRR-PFRALLDVGLVKTTTGNRVFGALK 163
G VE TG++Y+VE + + F LD GL +TTTGN+VFGALK
Sbjct: 121 GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALK 164
>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 = 197 bits (501), Expect = 4e-51, Method: Compositional matrix adjust.
Identities = 103/164 (62%), Positives = 122/164 (74%), Gaps = 1/164 (0%)
Query: 1 MAFAKAQKSKAYFKRYQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDI 60
MAF K KS AY R+Q ++RRREGKTDY R RL+ Q K KYNTPKYR VVRFTNKDI
Sbjct: 1 MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDI 60
Query: 61 TAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYE 120
QIIS++I GD+VLA+AY+HELPRYG+ GLTN+AAAY TGLL+ARR L+ L +D Y+
Sbjct: 61 ICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQKLGLDETYK 120
Query: 121 GHVEATGEDYSVEPTEN-RRPFRALLDVGLVKTTTGNRVFGALK 163
G E GE E E+ RPF+ LD+GL +TTTG RVFGALK
Sbjct: 121 GVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALK 164
>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 = 197 bits (501), Expect = 5e-51, Method: Compositional matrix adjust.
Identities = 103/164 (62%), Positives = 122/164 (74%), Gaps = 1/164 (0%)
Query: 1 MAFAKAQKSKAYFKRYQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDI 60
MAF K KS AY R+Q ++RRREGKTDY R RL+ Q K KYNTPKYR VVRFTNKDI
Sbjct: 1 MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDI 60
Query: 61 TAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYE 120
QIIS++I GD+VLA+AY+HELPRYG+ GLTN+AAAY TGLL+ARR L+ L +D Y+
Sbjct: 61 ICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQRLGLDETYK 120
Query: 121 GHVEATGEDYSVEPTEN-RRPFRALLDVGLVKTTTGNRVFGALK 163
G E GE E E+ RPF+ LD+GL +TTTG RVFGALK
Sbjct: 121 GVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALK 164
>pdb|3ZF7|UU Chain u, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 308
Score = 192 bits (488), Expect = 2e-49, Method: Compositional matrix adjust.
Identities = 97/170 (57%), Positives = 123/170 (72%), Gaps = 7/170 (4%)
Query: 1 MAFAKAQKSKAYFKRYQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDI 60
M F K K+KAY+KR+QVKY+RRREGKTDY AR R++ QDK K+ TPKYR VVR TN+D+
Sbjct: 1 MTFVKVVKNKAYYKRFQVKYRRRREGKTDYHARRRMVLQDKTKFGTPKYRLVVRITNRDV 60
Query: 61 TAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYE 120
AQI+ A + GD V+ +AY+HELP +G+E GLTNYAAAY TGLL+ARR+L L + ++
Sbjct: 61 IAQIVHAKVVGDEVVMAAYSHELPLFGIEHGLTNYAAAYATGLLVARRMLAKLGLAEKFV 120
Query: 121 GHVEATG-------EDYSVEPTENRRPFRALLDVGLVKTTTGNRVFGALK 163
G E G +D E+R PF+A+LDVGL +TTTG RVFG LK
Sbjct: 121 GVKEVDGSYAAVRTKDDDQGDDESRFPFKAILDVGLARTTTGARVFGVLK 170
>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 = 189 bits (481), Expect = 1e-48, Method: Compositional matrix adjust.
Identities = 96/164 (58%), Positives = 121/164 (73%), Gaps = 1/164 (0%)
Query: 1 MAFAKAQKSKAYFKRYQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDI 60
M F K K+KAYFKR+Q KY+RRREG TDY AR RLI QDK+KYNTPKYR V R TN I
Sbjct: 1 MGFVKVLKTKAYFKRFQTKYRRRREGLTDYYARKRLIIQDKDKYNTPKYRLVARATNTRI 60
Query: 61 TAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYE 120
AQI+ A++ D VL +A ++EL R+G+ GL +YAAAY TGLLLARR+LK + +D Y
Sbjct: 61 IAQIVYATLKCDRVLCAADSYELKRFGVSTGLASYAAAYATGLLLARRLLKQIGLDTVYA 120
Query: 121 GHVEATGEDYSV-EPTENRRPFRALLDVGLVKTTTGNRVFGALK 163
G + G ++V E + ++PF+A+LD GLV+TTTGNRVFG LK
Sbjct: 121 GQTKVDGAYFNVDEDQKEKKPFKAILDAGLVRTTTGNRVFGVLK 164
>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 = 186 bits (473), Expect = 7e-48, Method: Compositional matrix adjust.
Identities = 97/154 (62%), Positives = 116/154 (75%), Gaps = 1/154 (0%)
Query: 11 AYFKRYQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIA 70
AY R+Q ++RRREGKTDY R RL+ Q K KYNTPKYR VVRFTNKDI QIIS++I
Sbjct: 1 AYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDIICQIISSTIT 60
Query: 71 GDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDY 130
GD+VLA+AY+HELPRYG+ GLTN+AAAY TGLL+ARR L+ L +D Y+G E GE
Sbjct: 61 GDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQRLGLDETYKGVEEVEGEYE 120
Query: 131 SVEPTEN-RRPFRALLDVGLVKTTTGNRVFGALK 163
E E+ RPF+ LD+GL +TTTG RVFGALK
Sbjct: 121 LTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALK 154
>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 = 186 bits (473), Expect = 9e-48, Method: Compositional matrix adjust.
Identities = 97/154 (62%), Positives = 116/154 (75%), Gaps = 1/154 (0%)
Query: 11 AYFKRYQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIA 70
AY R+Q ++RRREGKTDY R RL+ Q K KYNTPKYR VVRFTNKDI QIIS++I
Sbjct: 1 AYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDIICQIISSTIT 60
Query: 71 GDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDY 130
GD+VLA+AY+HELPRYG+ GLTN+AAAY TGLL+ARR L+ L +D Y+G E GE
Sbjct: 61 GDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQRLGLDETYKGVEEVEGEYE 120
Query: 131 SVEPTEN-RRPFRALLDVGLVKTTTGNRVFGALK 163
E E+ RPF+ LD+GL +TTTG RVFGALK
Sbjct: 121 LTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALK 154
>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 = 79.7 bits (195), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 52/149 (34%), Positives = 71/149 (47%), Gaps = 33/149 (22%)
Query: 11 AYFKRYQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIA 70
A RY+V +RRRE +TDY R+RL+ + K R V R +NK + AQ+++
Sbjct: 2 ATGPRYKVPMRRRREARTDYHQRLRLLK-------SGKPRLVARKSNKHVRAQLVTLGPN 54
Query: 71 GDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDY 130
GD LASA++ +L YG E N +AY TGLL R E VE
Sbjct: 55 GDDTLASAHSSDLAEYGWEAPTGNMPSAYLTGLLAGLRA---------QEAGVE------ 99
Query: 131 SVEPTENRRPFRALLDVGLVKTTTGNRVF 159
A+LD+GL T G++VF
Sbjct: 100 -----------EAVLDIGLNSPTPGSKVF 117
>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 = 79.7 bits (195), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 52/149 (34%), Positives = 71/149 (47%), Gaps = 33/149 (22%)
Query: 11 AYFKRYQVKYKRRREGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIA 70
A RY+V +RRRE +TDY R+RL+ + K R V R +NK + AQ+++
Sbjct: 1 ATGPRYKVPMRRRREARTDYHQRLRLLK-------SGKPRLVARKSNKHVRAQLVTLGPN 53
Query: 71 GDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDY 130
GD LASA++ +L YG E N +AY TGLL R E VE
Sbjct: 54 GDDTLASAHSSDLAEYGWEAPTGNMPSAYLTGLLAGLRA---------QEAGVE------ 98
Query: 131 SVEPTENRRPFRALLDVGLVKTTTGNRVF 159
A+LD+GL T G++VF
Sbjct: 99 -----------EAVLDIGLNSPTPGSKVF 116
>pdb|4GMN|B Chain B, Structural Basis Of Rpl5 Recognition By Syo1
Length = 49
Score = 51.6 bits (122), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 26/42 (61%), Positives = 31/42 (73%)
Query: 1 MAFAKAQKSKAYFKRYQVKYKRRREGKTDYRARIRLINQDKN 42
MAF K K+ AY+ R+Q K+KRRR+GKTDY AR RLI Q K
Sbjct: 1 MAFHKLVKNSAYYSRFQTKFKRRRQGKTDYYARKRLITQAKG 42
>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 = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 43/140 (30%), Positives = 59/140 (42%), Gaps = 34/140 (24%)
Query: 25 EGKTDYRARIRLINQDKNKYNTPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELP 84
EGKT+YR R++L+ K R VVR + AQII GD L SA+ EL
Sbjct: 16 EGKTNYRKRLKLLKSGKP-------RLVVRKSLNHHIAQIIVYDPKGDRTLVSAHTRELI 68
Query: 85 R-YGLEVGLTNYAAAYCTGLLLARRVLKMLEMDAEYEGHVEATGEDYSVEPTENRRPFRA 143
R +G + N +AY GLL+ + + +E A
Sbjct: 69 RDFGWKGHCGNTPSAYLLGLLIGYKA------------------KQAGIE--------EA 102
Query: 144 LLDVGLVKTTTGNRVFGALK 163
+LD+GL G+ VF LK
Sbjct: 103 ILDIGLHPPVRGSSVFAVLK 122
>pdb|1OVY|A Chain A, Solution Structure Of Ribosomal Protein L18 From Bacillus
Stearothermophilus
Length = 120
Score = 31.2 bits (69), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 34/66 (51%), Gaps = 4/66 (6%)
Query: 46 TPKYRFVVRFTNKDITAQIISASIAGDIVLASAYAHELPRYGLEVGLTNYAAAYCTGLLL 105
T + R V +NK I AQII + + IV AS E +GL+ N AA G L+
Sbjct: 26 TERPRLSVFRSNKHIYAQIIDDTKSATIVSASTLDKE---FGLD-STNNIEAAKKVGELV 81
Query: 106 ARRVLK 111
A+R L+
Sbjct: 82 AKRALE 87
>pdb|3S52|A Chain A, Crystal Structure Of A Putative Fumarylacetoacetate
Hydrolase Family Protein From Yersinia Pestis Co92
pdb|3S52|B Chain B, Crystal Structure Of A Putative Fumarylacetoacetate
Hydrolase Family Protein From Yersinia Pestis Co92
pdb|3S52|C Chain C, Crystal Structure Of A Putative Fumarylacetoacetate
Hydrolase Family Protein From Yersinia Pestis Co92
pdb|3S52|D Chain D, Crystal Structure Of A Putative Fumarylacetoacetate
Hydrolase Family Protein From Yersinia Pestis Co92
Length = 221
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 24/46 (52%)
Query: 102 GLLLARRVLKMLEMDAEYEGHVEATGEDYSVEPTENRRPFRALLDV 147
G LL V K++ + + Y H++ G SVEP +P AL D+
Sbjct: 12 GALLDFPVNKVVCVGSNYAEHIKEXGSTASVEPVLFIKPETALCDI 57
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 0.137 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,048,360
Number of Sequences: 62578
Number of extensions: 214189
Number of successful extensions: 582
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: 553
Number of HSP's gapped (non-prelim): 18
length of query: 252
length of database: 14,973,337
effective HSP length: 97
effective length of query: 155
effective length of database: 8,903,271
effective search space: 1380007005
effective search space used: 1380007005
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 50 (23.9 bits)