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= 021064
(318 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|SS Chain s, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 319
Score = 419 bits (1077), Expect = e-118, Method: Compositional matrix adjust.
Identities = 208/272 (76%), Positives = 243/272 (89%)
Query: 1 MVVKASKAEKKIAYDAKLCQLLEEYTQILVAAADNVGSNQLQNIRRGLRGDSVVLMGKNT 60
M +K +KAEKK+AYD KLCQLL+EYT++L+A ADNVGSNQLQ IR+GLRGDS+VLMGKNT
Sbjct: 1 MAIKRTKAEKKVAYDKKLCQLLDEYTKVLIAVADNVGSNQLQEIRKGLRGDSIVLMGKNT 60
Query: 61 MMKRTIRMHAEKTGNTAFLNLIPLLQGNVGLIFTKGDLXXXXXXXXXXXXGAPARVGLVA 120
+++R I++HA+ TGN FL L+PLL GNVGLIFTKGDL GAPARVGLVA
Sbjct: 61 LIRRCIKVHADNTGNKEFLELMPLLVGNVGLIFTKGDLKEVREEVAKYKVGAPARVGLVA 120
Query: 121 PIDVVVPPGNTGLDPSQTSFFQVLNIPTKINKGTVEIITPVELIRKGDKVGSSEAALLAK 180
P+DVVVPPGNTGLDPSQTSFFQVLNIPTKINKGTVEIITPVELI+KGDKVGSSE+ALLAK
Sbjct: 121 PVDVVVPPGNTGLDPSQTSFFQVLNIPTKINKGTVEIITPVELIKKGDKVGSSESALLAK 180
Query: 181 LGIRPFSYGLVVQSVYENGSVYSPEVLDLSEDDLVEKFASSVSMVTALALAISYPTLAAA 240
LGIRPFSYGLV+ +VY++GSV+SPEVLDL+EDDL+EKFAS VSMV +++LAISYPT+AAA
Sbjct: 181 LGIRPFSYGLVITNVYDSGSVFSPEVLDLTEDDLMEKFASGVSMVASVSLAISYPTIAAA 240
Query: 241 PHMFVNAYKNVVAVALATEYSFPQADKVKEYL 272
PHMF+N YKNV+AVA+ TEYS+P ADK+KEYL
Sbjct: 241 PHMFLNGYKNVLAVAVETEYSYPHADKIKEYL 272
>pdb|2ZKR|GG Chain g, 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 = 317
Score = 265 bits (676), Expect = 3e-71, Method: Compositional matrix adjust.
Identities = 136/270 (50%), Positives = 185/270 (68%), Gaps = 2/270 (0%)
Query: 4 KASKAEKKIAYDAKLCQLLEEYTQILVAAADNVGSNQLQNIRRGLRGDSVVLMGKNTMMK 63
+ +A K Y K+ QLL++Y + + ADNVGS Q+Q IR LRG +VVLMGKNTMM+
Sbjct: 3 REDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKAVVLMGKNTMMR 62
Query: 64 RTIRMHAEKTGNTAFLNLIPLLQGNVGLIFTKGDLXXXXXXXXXXXXGAPARVGLVAPID 123
+ IR H E N A L+P ++GNVG +FTK DL A AR G +AP +
Sbjct: 63 KAIRGHLEN--NPALEKLLPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCE 120
Query: 124 VVVPPGNTGLDPSQTSFFQVLNIPTKINKGTVEIITPVELIRKGDKVGSSEAALLAKLGI 183
V VP NTGL P +TSFFQ L I TKI++GT+EI++ V+LI+ GDKVG+SEA LL L I
Sbjct: 121 VTVPAQNTGLGPEKTSFFQALGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNI 180
Query: 184 RPFSYGLVVQSVYENGSVYSPEVLDLSEDDLVEKFASSVSMVTALALAISYPTLAAAPHM 243
PFS+GLV+Q V++NGS+Y+PEVLD++E+ L +F V V ++ L I YPT+A+ PH
Sbjct: 181 SPFSFGLVIQQVFDNGSIYNPEVLDITEETLHSRFLEGVRNVASVCLQIGYPTVASVPHS 240
Query: 244 FVNAYKNVVAVALATEYSFPQADKVKEYLA 273
+N YK V+A+++ T+Y+FP A+KVK +LA
Sbjct: 241 IINGYKRVLALSVETDYTFPLAEKVKAFLA 270
>pdb|3IZS|SS Chain s, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3J16|G Chain G, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
Length = 312
Score = 220 bits (560), Expect = 9e-58, Method: Compositional matrix adjust.
Identities = 118/260 (45%), Positives = 170/260 (65%), Gaps = 2/260 (0%)
Query: 9 EKKIAYDAKLCQLLEEYTQILVAAADNVGSNQLQNIRRGLRGDSVVLMGKNTMMKRTIRM 68
EKK Y AKL + LEEY + V DNV S Q+ +R+ LRG +VVLMGKNTM++R IR
Sbjct: 6 EKKAEYFAKLREYLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIRG 65
Query: 69 HAEKTGNTAFLNLIPLLQGNVGLIFTKGDLXXXXXXXXXXXXGAPARVGLVAPIDVVVPP 128
+ F L+P ++GNVG +FT L APAR G VAP D+ V
Sbjct: 66 FLSDLPD--FEKLLPFVKGNVGFVFTNEPLTEIKNVIVSNRVAAPARAGAVAPEDIWVRA 123
Query: 129 GNTGLDPSQTSFFQVLNIPTKINKGTVEIITPVELIRKGDKVGSSEAALLAKLGIRPFSY 188
NTG++P +TSFFQ L +PTKI +GT+EI++ V+++ G+KVG SEA+LL L I PF++
Sbjct: 124 VNTGMEPGKTSFFQALGVPTKIARGTIEIVSDVKVVDAGNKVGQSEASLLNLLNISPFTF 183
Query: 189 GLVVQSVYENGSVYSPEVLDLSEDDLVEKFASSVSMVTALALAISYPTLAAAPHMFVNAY 248
GL V VY+NG V+ +LD+++++LV F S+VS + +++LAI YPTL + H +N Y
Sbjct: 184 GLTVVQVYDNGQVFPSSILDITDEELVSHFVSAVSTIASISLAIGYPTLPSVGHTLINNY 243
Query: 249 KNVVAVALATEYSFPQADKV 268
K+++AVA+A Y +P+ + +
Sbjct: 244 KDLLAVAIAASYHYPEIEDL 263
>pdb|3O5H|M Chain M, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit
Length = 312
Score = 217 bits (552), Expect = 7e-57, Method: Compositional matrix adjust.
Identities = 117/260 (45%), Positives = 169/260 (65%), Gaps = 2/260 (0%)
Query: 9 EKKIAYDAKLCQLLEEYTQILVAAADNVGSNQLQNIRRGLRGDSVVLMGKNTMMKRTIRM 68
EKK Y AKL + LEEY + V DNV S Q+ +R+ LRG +VVLMGKNTM++R IR
Sbjct: 6 EKKAEYFAKLREYLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIRG 65
Query: 69 HAEKTGNTAFLNLIPLLQGNVGLIFTKGDLXXXXXXXXXXXXGAPARVGLVAPIDVVVPP 128
+ F L+P ++G VG +FT L APAR G VAP D+ V
Sbjct: 66 FLSDLPD--FEKLLPFVKGYVGFVFTNEPLTEIKNVIVSNRVAAPARAGAVAPEDIWVRA 123
Query: 129 GNTGLDPSQTSFFQVLNIPTKINKGTVEIITPVELIRKGDKVGSSEAALLAKLGIRPFSY 188
NTG++P +TSFFQ L +PTKI +GT+EI++ V+++ G+KVG SEA+LL L I PF++
Sbjct: 124 VNTGMEPGKTSFFQALGVPTKIARGTIEIVSDVKVVDAGNKVGQSEASLLNLLNISPFTF 183
Query: 189 GLVVQSVYENGSVYSPEVLDLSEDDLVEKFASSVSMVTALALAISYPTLAAAPHMFVNAY 248
GL V VY+NG V+ +LD+++++LV F S+VS + +++LAI YPTL + H +N Y
Sbjct: 184 GLTVVQVYDNGQVFPSSILDITDEELVSHFVSAVSTIASISLAIGYPTLPSVGHTLINNY 243
Query: 249 KNVVAVALATEYSFPQADKV 268
K+++AVA+A Y +P+ + +
Sbjct: 244 KDLLAVAIAASYHYPEIEDL 263
>pdb|3U5I|QQ Chain q, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|QQ Chain q, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 312
Score = 192 bits (487), Expect = 2e-49, Method: Compositional matrix adjust.
Identities = 110/260 (42%), Positives = 154/260 (59%), Gaps = 2/260 (0%)
Query: 9 EKKIAYDAKLCQLLEEYTQILVAAADNVGSNQLQNIRRGLRGDSVVLMGKNTMMKRTIRM 68
EKK Y AKL + LEEY + V DNV S Q+ +R+ LRG +VVLMGKNTM++R IR
Sbjct: 6 EKKAEYFAKLREYLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIRG 65
Query: 69 HAEKTGNTAFLNLIPLLQGNVGLIFTKGDLXXXXXXXXXXXXGAPARVGLVAPIDVVVPP 128
+ F L+P ++GNVG +FT L APAR G VAP D+ V
Sbjct: 66 FLSDLPD--FEKLLPFVKGNVGFVFTNEPLTEIKNVIVSNRVAAPARAGAVAPEDIWVRA 123
Query: 129 GNTGLDPSQTSFFQVLNIPTKINKGTVEIITPVELIRKGDKVGSSEAALLAKLGIRPFSY 188
NTG++P +TSFFQ L +PTKI +GT+EI++ V+++ G+KVG SEA+LL L I PF++
Sbjct: 124 VNTGMEPGKTSFFQALGVPTKIARGTIEIVSDVKVVDAGNKVGQSEASLLNLLNISPFTF 183
Query: 189 GLVVQSVYENGSVYSPEVLDLSEDDLVEKFASSVSMVTALALAISYPTLAAAPHMFVNAY 248
GL V VY+NG V+ +++LAI YPTL + H +N Y
Sbjct: 184 GLTVVQVYDNGQVFPXXXXXXXXXXXXXXXXXXXXXXXSISLAIGYPTLPSVGHTLINNY 243
Query: 249 KNVVAVALATEYSFPQADKV 268
K+++AVA+A Y +P+ + +
Sbjct: 244 KDLLAVAIAASYHYPEIEDL 263
>pdb|3CC2|G Chain G, 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|G Chain G, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|G Chain G, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|G Chain G, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|G Chain G, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3G4S|G Chain G, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|G Chain G, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|G Chain G, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|3I55|G Chain G, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|G Chain G, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
Length = 348
Score = 108 bits (271), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 69/256 (26%), Positives = 127/256 (49%), Gaps = 7/256 (2%)
Query: 10 KKIAYDAKLCQLLEEYTQILVAAADNVGSNQLQNIRRGLRGDSVVLMGKNTMMKRTIRMH 69
K+ DA + +++E Y + V + S QLQ++RR L G + + + +NT+++R +
Sbjct: 16 KQEEVDA-IVEMIESYESVGVVNIAGIPSRQLQDMRRDLHGTAELRVSRNTLLERAL--- 71
Query: 70 AEKTGNTAFLNLIPLLQGNVGLIFTKGDLXXXXXXXXXXXXGAPARVGLVAPIDVVVPPG 129
+ +L + G VGLI T + AP G VAP D+V+P G
Sbjct: 72 --DDVDDGLEDLNGYITGQVGLIGTDDNPFSLFQELEASKTPAPIGAGEVAPNDIVIPEG 129
Query: 130 NTGLDPSQ-TSFFQVLNIPTKINKGTVEIITPVELIRKGDKVGSSEAALLAKLGIRPFSY 188
+TG+DP Q + +I +G++++++ ++ G++V + +L +LGI P
Sbjct: 130 DTGVDPGPFVGELQSVGADARIQEGSIQVLSDSTVLDTGEEVSQELSNVLNELGIEPKEV 189
Query: 189 GLVVQSVYENGSVYSPEVLDLSEDDLVEKFASSVSMVTALALAISYPTLAAAPHMFVNAY 248
GL +++V+ +G ++ PE L+L D+ ++ L++ YPT AP M +A
Sbjct: 190 GLDLRAVFADGVLFEPEELELDIDEYRSDIQAAAGRAFNLSVNADYPTATTAPTMLQSAR 249
Query: 249 KNVVAVALATEYSFPQ 264
N ++AL P+
Sbjct: 250 GNAKSLALQAAIEDPE 265
>pdb|1JJ2|G Chain G, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|G Chain G, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|I Chain I, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|I Chain I, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|I Chain I, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|I Chain I, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|I Chain I, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1K73|I Chain I, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|I Chain I, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|I Chain I, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|I Chain I, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|I Chain I, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|I Chain I, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|I Chain I, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|I Chain I, 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|G Chain G, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|G Chain G, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1S72|G Chain G, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1W2B|G Chain G, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|1YHQ|G Chain G, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|G Chain G, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|G Chain G, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|G Chain G, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|G Chain G, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|G Chain G, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|G Chain G, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|G Chain G, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|G Chain G, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|G Chain G, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|G Chain G, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|G Chain G, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|G Chain G, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|G Chain G, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|G Chain G, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|G Chain G, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|G Chain G, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|G Chain G, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|G Chain G, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|G Chain G, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|G Chain G, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|G Chain G, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|3CME|G Chain G, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|2QEX|G Chain G, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3CXC|G Chain G, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
Length = 348
Score = 107 bits (266), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 68/256 (26%), Positives = 126/256 (49%), Gaps = 7/256 (2%)
Query: 10 KKIAYDAKLCQLLEEYTQILVAAADNVGSNQLQNIRRGLRGDSVVLMGKNTMMKRTIRMH 69
K+ DA + +++E Y + V + S QLQ++RR L G + + + +NT+++R +
Sbjct: 16 KQEEVDA-IVEMIESYESVGVVNIAGIPSRQLQDMRRDLHGTAELRVSRNTLLERAL--- 71
Query: 70 AEKTGNTAFLNLIPLLQGNVGLIFTKGDLXXXXXXXXXXXXGAPARVGLVAPIDVVVPPG 129
+ +L + G VGLI T + AP G VAP D+V+P G
Sbjct: 72 --DDVDDGLEDLNGYITGQVGLIGTDDNPFSLFQELEASKTPAPIGAGEVAPNDIVIPEG 129
Query: 130 NTGLDPSQ-TSFFQVLNIPTKINKGTVEIITPVELIRKGDKVGSSEAALLAKLGIRPFSY 188
+TG+DP Q + +I +G++++++ ++ G++V + +L +LGI P
Sbjct: 130 DTGVDPGPFVGELQSVGADARIQEGSIQVLSDSTVLDTGEEVSQELSNVLNELGIEPKEV 189
Query: 189 GLVVQSVYENGSVYSPEVLDLSEDDLVEKFASSVSMVTALALAISYPTLAAAPHMFVNAY 248
GL +++V+ +G ++ PE L+L D+ ++ L++ YPT AP M +
Sbjct: 190 GLDLRAVFADGVLFEPEELELDIDEYRSDIQAAAGRAFNLSVNADYPTATTAPTMLQSDR 249
Query: 249 KNVVAVALATEYSFPQ 264
N ++AL P+
Sbjct: 250 GNAKSLALQAAIEDPE 265
>pdb|3A1Y|G Chain G, The Structure Of Protein Complex
Length = 284
Score = 105 bits (262), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 76/258 (29%), Positives = 124/258 (48%), Gaps = 2/258 (0%)
Query: 5 ASKAEKKIAYDAKLCQLLEEYTQILVAAADNVGSNQLQNIRRGLRGDSVVL-MGKNTMMK 63
A AE K +L +L++ Y I + ++ + L +RR +R + +L + +NT+++
Sbjct: 2 AHVAEWKKKEVEELAKLIKSYPVIALVDVSSMPAYPLSQMRRLIRENGGLLRVSRNTLIE 61
Query: 64 RTIRMHAEKTGNTAFLNLIPLLQGNVGLIFTKGDLXXXXXXXXXXXXGAPARVGLVAPID 123
I+ A++ G L+ + G++ T + APA+ G V P D
Sbjct: 62 LAIKKAAKELGKPELEKLVEYIDRGAGILVTNMNPFKLYKFLQQNRQPAPAKPGAVVPKD 121
Query: 124 VVVPPGNTGLDPSQ-TSFFQVLNIPTKINKGTVEIITPVELIRKGDKVGSSEAALLAKLG 182
VVVP G T L P Q L IP +I KG V I +++ G+ + A +L LG
Sbjct: 122 VVVPAGPTPLAPGPIVGQMQALGIPARIEKGKVTIQKDTTVLKAGEVITPELANILNALG 181
Query: 183 IRPFSYGLVVQSVYENGSVYSPEVLDLSEDDLVEKFASSVSMVTALALAISYPTLAAAPH 242
I+P GL V +VYE+G VY+P+VL + E + ++ + LA+ I+YPT
Sbjct: 182 IQPLEVGLDVLAVYEDGIVYTPDVLAIDEQEYIDMLQKAYMHAFNLAVNIAYPTPETIEA 241
Query: 243 MFVNAYKNVVAVALATEY 260
+ A+ N VA+ Y
Sbjct: 242 IIQKAFLNAKTVAIEAGY 259
>pdb|3J21|KK Chain k, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 339
Score = 103 bits (256), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 72/258 (27%), Positives = 126/258 (48%), Gaps = 2/258 (0%)
Query: 5 ASKAEKKIAYDAKLCQLLEEYTQILVAAADNVGSNQLQNIRRGLRGDSVVL-MGKNTMMK 63
A AE K +L L++ Y + + ++ + L +RR +R ++ +L + +NT+++
Sbjct: 2 AHVAEWKKKEVEELANLIKSYPVVALVDVSSMPAYPLSQMRRLIRENNGLLRVSRNTLIE 61
Query: 64 RTIRMHAEKTGNTAFLNLIPLLQGNVGLIFTKGDLXXXXXXXXXXXXGAPARVGLVAPID 123
I+ A++ G LI ++G G++ T + APA+ G P D
Sbjct: 62 LAIKKVAQELGKPELEKLINYIEGGAGILVTTMNPFKLYKFLQQNRQPAPAKPGAKVPKD 121
Query: 124 VVVPPGNTGLDPSQ-TSFFQVLNIPTKINKGTVEIITPVELIRKGDKVGSSEAALLAKLG 182
VV+P G T L P Q + IP +I +G V I +++ G+++ A +L LG
Sbjct: 122 VVIPAGPTSLAPGPIVGQMQAMGIPARIERGKVTIQKDTVVLKAGEEITPELANILNALG 181
Query: 183 IRPFSYGLVVQSVYENGSVYSPEVLDLSEDDLVEKFASSVSMVTALALAISYPTLAAAPH 242
I+P GL + +VYE+G +Y+P+VL + E + + + LA+ I+YPT
Sbjct: 182 IQPLEVGLDLLAVYEDGIIYTPDVLAIDESEYINMLQKAYMHAFNLAVNIAYPTPQTIEA 241
Query: 243 MFVNAYKNVVAVALATEY 260
+ A+ N AVA+ Y
Sbjct: 242 IIQKAFLNAKAVAVEAGY 259
>pdb|3JSY|A Chain A, N-Terminal Fragment Of Ribosomal Protein L10 From
Methanococ Jannaschii
pdb|3JSY|B Chain B, N-Terminal Fragment Of Ribosomal Protein L10 From
Methanococ Jannaschii
Length = 213
Score = 84.0 bits (206), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 56/182 (30%), Positives = 94/182 (51%), Gaps = 1/182 (0%)
Query: 35 NVGSNQLQNIRRGLRGDSVVLMGKNTMMKRTIRMHAEKTGNTAFLNLIPLLQGNVGLIFT 94
+V + QLQ IR +R + M +NT++ R ++ AE+ N L ++ ++ T
Sbjct: 29 DVPAPQLQEIRDKIRDKVKLRMSRNTLIIRALKEAAEELNNPKLAELANYVERGAAILVT 88
Query: 95 KGDLXXXXXXXXXXXXGAPARVGLVAPIDVVVPPGNTGLDPSQ-TSFFQVLNIPTKINKG 153
+ AP R G +AP D+ V G+TG+ P + + IP I KG
Sbjct: 89 DMNPFKLYKLLEENKSPAPVRGGQIAPCDIKVEKGSTGMPPGPFLGELKSVGIPAAIEKG 148
Query: 154 TVEIITPVELIRKGDKVGSSEAALLAKLGIRPFSYGLVVQSVYENGSVYSPEVLDLSEDD 213
+ I +++KG+ V AA+L +LGI+P GL + +VYE+G +Y+P+VL + E+
Sbjct: 149 KIAIKEDKVVVKKGEVVSPKLAAVLDRLGIKPIKVGLNILAVYEDGIIYTPDVLKVDEEK 208
Query: 214 LV 215
L+
Sbjct: 209 LL 210
>pdb|3JYW|8 Chain 8, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus
Ribosome At 8.9a Resolution
Length = 118
Score = 81.6 bits (200), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 41/86 (47%), Positives = 54/86 (62%), Gaps = 2/86 (2%)
Query: 9 EKKIAYDAKLCQLLEEYTQILVAAADNVGSNQLQNIRRGLRGDSVVLMGKNTMMKRTIRM 68
EKK Y AKL + LEEY + V DNV S Q+ +R+ LRG +VVLMGKNTM++R IR
Sbjct: 4 EKKAEYFAKLREYLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIRG 63
Query: 69 HAEKTGNTAFLNLIPLLQGNVGLIFT 94
+ F L+P ++G VG +FT
Sbjct: 64 FLSDLPD--FEKLLPFVKGYVGFVFT 87
>pdb|3OW2|G Chain G, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 62
Score = 35.8 bits (81), Expect = 0.033, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 30/49 (61%)
Query: 18 LCQLLEEYTQILVAAADNVGSNQLQNIRRGLRGDSVVLMGKNTMMKRTI 66
+ +++E Y + V + S QLQ++RR L G + + + +NT+++R +
Sbjct: 12 IVEMIESYESVGVVNIAGIPSRQLQDMRRDLHGTAELRVSRNTLLERAL 60
>pdb|3NET|A Chain A, Crystal Structure Of Histidyl-Trna Synthetase From Nostoc
Sp. Pcc 7120
pdb|3NET|B Chain B, Crystal Structure Of Histidyl-Trna Synthetase From Nostoc
Sp. Pcc 7120
Length = 465
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 35/72 (48%), Gaps = 9/72 (12%)
Query: 138 TSFFQVLNIPTKINKGTVEIITPVELIRKGDKVGSSEAAL-LAKLGIRPFSYGLVVQSVY 196
T FFQ LNI K + II +E K+G ++ L L K GI P ++ V
Sbjct: 191 TGFFQSLNISETQIKSCISIIDNLE------KIGEAKVKLELEKEGINPEQTQKIIDFVK 244
Query: 197 ENGSVYSPEVLD 208
+GSV +VLD
Sbjct: 245 IDGSV--DDVLD 254
>pdb|2Q88|A Chain A, Crystal Structure Of Ehub In Complex With Ectoine
pdb|2Q89|A Chain A, Crystal Structure Of Ehub In Complex With Hydroxyectoine
Length = 257
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 17/64 (26%)
Query: 124 VVVPPGNTGLDPSQTSFFQVLNIP--------TKINKGTVEIITPVE---------LIRK 166
+VVP G +GL Q V ++P +K N VE++ PVE RK
Sbjct: 150 IVVPDGQSGLKMLQDGRIDVYSLPVLSINDLVSKANDPNVEVLAPVEGAPVYCDGAAFRK 209
Query: 167 GDKV 170
GD+
Sbjct: 210 GDEA 213
>pdb|3AQ1|B Chain B, Open State Monomer Of A Group Ii Chaperonin From
Methanococcoides Burtonii
Length = 500
Score = 28.1 bits (61), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 6/47 (12%)
Query: 176 ALLAKLGIRPFSYGLVVQSVYENGS------VYSPEVLDLSEDDLVE 216
AL G+ P + ++S +E G+ VY+ EV+D+ E+D++E
Sbjct: 401 ALAENAGLDPIDIMVELRSQHEKGNKNAGLNVYTGEVVDMWENDVIE 447
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
0.320 0.135 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,258,001
Number of Sequences: 62578
Number of extensions: 310048
Number of successful extensions: 811
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 782
Number of HSP's gapped (non-prelim): 19
length of query: 318
length of database: 14,973,337
effective HSP length: 99
effective length of query: 219
effective length of database: 8,778,115
effective search space: 1922407185
effective search space used: 1922407185
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: 51 (24.3 bits)