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= 036252
(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 = 424 bits (1091), Expect = e-119, Method: Compositional matrix adjust.
Identities = 216/319 (67%), Positives = 258/319 (80%), Gaps = 1/319 (0%)
Query: 1 MATRLSKAEKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKNT 60
MA + +KAEKK+AYD +LC+LL+EY+++LI ADNVGSNQLQ IR GLR SIVLMGKNT
Sbjct: 1 MAIKRTKAEKKVAYDKKLCQLLDEYTKVLIAVADNVGSNQLQEIRKGLRGDSIVLMGKNT 60
Query: 61 MMKRSIRLHAERTGNRDLLNLIPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGLVA 120
+++R I++HA+ TGN++ L L+PLL GNVG+IFTKGDLKEV +EV+K+KV APARVGLVA
Sbjct: 61 LIRRCIKVHADNTGNKEFLELMPLLVGNVGLIFTKGDLKEVREEVAKYKVGAPARVGLVA 120
Query: 121 PIDVVVPPGNTGLDPSQTSFFQVLNIPTKINKGTVEIITPVELIKKGDRVGSSESALLSK 180
P+DVVVPPGNTGLDPSQTSFFQVLNIPTKINKGTVEIITPVELIKKGD+VGSSESALL+K
Sbjct: 121 PVDVVVPPGNTGLDPSQTSFFQVLNIPTKINKGTVEIITPVELIKKGDKVGSSESALLAK 180
Query: 181 LAIKPFSYGLIVMSVYENGSVYSPEVLDLTEDDIATKFLEAVSRVASLALSIRYPTIAAA 240
L I+PFSYGL++ +VY++GSV+SPEVLDLTEDD+ KF VS VAS++L+I YPTIAAA
Sbjct: 181 LGIRPFSYGLVITNVYDSGSVFSPEVLDLTEDDLMEKFASGVSMVASVSLAISYPTIAAA 240
Query: 241 PHFFINGYKNVLSFAVATEYSFSQADKVKEYLKDPSKFXXXX-XXXXXXXXXXXXXXXXX 299
PH F+NGYKNVL+ AV TEYS+ ADK+KEYLKDPSKF
Sbjct: 241 PHMFLNGYKNVLAVAVETEYSYPHADKIKEYLKDPSKFAVAAPVAADSGAAAPSAAKEEE 300
Query: 300 XXXXXXXXSDDDMGLSLFD 318
SD D+G+SLFD
Sbjct: 301 KKEEPEEESDGDLGMSLFD 319
>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 = 288 bits (738), Expect = 2e-78, Method: Compositional matrix adjust.
Identities = 145/275 (52%), Positives = 199/275 (72%), Gaps = 2/275 (0%)
Query: 4 RLSKAEKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKNTMMK 63
R +A K Y ++ +LL++Y + IV ADNVGS Q+Q IR LR ++VLMGKNTMM+
Sbjct: 3 REDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKAVVLMGKNTMMR 62
Query: 64 RSIRLHAERTGNRDLLNLIPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGLVAPID 123
++IR H E N L L+P ++GNVG +FTK DL E+ D + +KV A AR G +AP +
Sbjct: 63 KAIRGHLEN--NPALEKLLPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCE 120
Query: 124 VVVPPGNTGLDPSQTSFFQVLNIPTKINKGTVEIITPVELIKKGDRVGSSESALLSKLAI 183
V VP NTGL P +TSFFQ L I TKI++GT+EI++ V+LIK GD+VG+SE+ LL+ L I
Sbjct: 121 VTVPAQNTGLGPEKTSFFQALGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNI 180
Query: 184 KPFSYGLIVMSVYENGSVYSPEVLDLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHF 243
PFS+GL++ V++NGS+Y+PEVLD+TE+ + ++FLE V VAS+ L I YPT+A+ PH
Sbjct: 181 SPFSFGLVIQQVFDNGSIYNPEVLDITEETLHSRFLEGVRNVASVCLQIGYPTVASVPHS 240
Query: 244 FINGYKNVLSFAVATEYSFSQADKVKEYLKDPSKF 278
INGYK VL+ +V T+Y+F A+KVK +L DPS F
Sbjct: 241 IINGYKRVLALSVETDYTFPLAEKVKAFLADPSAF 275
>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 = 226 bits (576), Expect = 1e-59, Method: Compositional matrix adjust.
Identities = 125/310 (40%), Positives = 195/310 (62%), Gaps = 3/310 (0%)
Query: 9 EKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKNTMMKRSIRL 68
EKK Y A+L + LEEY + +V DNV S Q+ +R LR ++VLMGKNTM++R+IR
Sbjct: 6 EKKAEYFAKLREYLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIR- 64
Query: 69 HAERTGNRDLLNLIPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGLVAPIDVVVPP 128
+ D L+P ++GNVG +FT L E+ + + ++VAAPAR G VAP D+ V
Sbjct: 65 -GFLSDLPDFEKLLPFVKGNVGFVFTNEPLTEIKNVIVSNRVAAPARAGAVAPEDIWVRA 123
Query: 129 GNTGLDPSQTSFFQVLNIPTKINKGTVEIITPVELIKKGDRVGSSESALLSKLAIKPFSY 188
NTG++P +TSFFQ L +PTKI +GT+EI++ V+++ G++VG SE++LL+ L I PF++
Sbjct: 124 VNTGMEPGKTSFFQALGVPTKIARGTIEIVSDVKVVDAGNKVGQSEASLLNLLNISPFTF 183
Query: 189 GLIVMSVYENGSVYSPEVLDLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFINGY 248
GL V+ VY+NG V+ +LD+T++++ + F+ AVS +AS++L+I YPT+ + H IN Y
Sbjct: 184 GLTVVQVYDNGQVFPSSILDITDEELVSHFVSAVSTIASISLAIGYPTLPSVGHTLINNY 243
Query: 249 KNVLSFAVATEYSFSQADKVKEYLKDPSKFXXXXXXXXXXXXXXXXXXXXXXXXXXXXXS 308
K++L+ A+A Y + + + + + +++P K+ S
Sbjct: 244 KDLLAVAIAASYHYPEIEDLVDRIENPEKY-AAAAPAATSAASGDAAPAEEAAAEEEEES 302
Query: 309 DDDMGLSLFD 318
DDDMG LFD
Sbjct: 303 DDDMGFGLFD 312
>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 = 223 bits (568), Expect = 1e-58, Method: Compositional matrix adjust.
Identities = 124/310 (40%), Positives = 194/310 (62%), Gaps = 3/310 (0%)
Query: 9 EKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKNTMMKRSIRL 68
EKK Y A+L + LEEY + +V DNV S Q+ +R LR ++VLMGKNTM++R+IR
Sbjct: 6 EKKAEYFAKLREYLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIR- 64
Query: 69 HAERTGNRDLLNLIPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGLVAPIDVVVPP 128
+ D L+P ++G VG +FT L E+ + + ++VAAPAR G VAP D+ V
Sbjct: 65 -GFLSDLPDFEKLLPFVKGYVGFVFTNEPLTEIKNVIVSNRVAAPARAGAVAPEDIWVRA 123
Query: 129 GNTGLDPSQTSFFQVLNIPTKINKGTVEIITPVELIKKGDRVGSSESALLSKLAIKPFSY 188
NTG++P +TSFFQ L +PTKI +GT+EI++ V+++ G++VG SE++LL+ L I PF++
Sbjct: 124 VNTGMEPGKTSFFQALGVPTKIARGTIEIVSDVKVVDAGNKVGQSEASLLNLLNISPFTF 183
Query: 189 GLIVMSVYENGSVYSPEVLDLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFINGY 248
GL V+ VY+NG V+ +LD+T++++ + F+ AVS +AS++L+I YPT+ + H IN Y
Sbjct: 184 GLTVVQVYDNGQVFPSSILDITDEELVSHFVSAVSTIASISLAIGYPTLPSVGHTLINNY 243
Query: 249 KNVLSFAVATEYSFSQADKVKEYLKDPSKFXXXXXXXXXXXXXXXXXXXXXXXXXXXXXS 308
K++L+ A+A Y + + + + + +++P K+ S
Sbjct: 244 KDLLAVAIAASYHYPEIEDLVDRIENPEKY-AAAAPAATSAASGDAAPAEEAAAEEEEES 302
Query: 309 DDDMGLSLFD 318
DDDMG LFD
Sbjct: 303 DDDMGFGLFD 312
>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 = 197 bits (502), Expect = 5e-51, Method: Compositional matrix adjust.
Identities = 117/310 (37%), Positives = 177/310 (57%), Gaps = 3/310 (0%)
Query: 9 EKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKNTMMKRSIRL 68
EKK Y A+L + LEEY + +V DNV S Q+ +R LR ++VLMGKNTM++R+IR
Sbjct: 6 EKKAEYFAKLREYLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIRG 65
Query: 69 HAERTGNRDLLNLIPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGLVAPIDVVVPP 128
D L+P ++GNVG +FT L E+ + + ++VAAPAR G VAP D+ V
Sbjct: 66 FLSDL--PDFEKLLPFVKGNVGFVFTNEPLTEIKNVIVSNRVAAPARAGAVAPEDIWVRA 123
Query: 129 GNTGLDPSQTSFFQVLNIPTKINKGTVEIITPVELIKKGDRVGSSESALLSKLAIKPFSY 188
NTG++P +TSFFQ L +PTKI +GT+EI++ V+++ G++VG SE++LL+ L I PF++
Sbjct: 124 VNTGMEPGKTSFFQALGVPTKIARGTIEIVSDVKVVDAGNKVGQSEASLLNLLNISPFTF 183
Query: 189 GLIVMSVYENGSVYSPEVLDLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFINGY 248
GL V+ VY+NG V+ S++L+I YPT+ + H IN Y
Sbjct: 184 GLTVVQVYDNGQVFPXXXXXXXXXXXXXXXXXXXXXXXSISLAIGYPTLPSVGHTLINNY 243
Query: 249 KNVLSFAVATEYSFSQADKVKEYLKDPSKFXXXXXXXXXXXXXXXXXXXXXXXXXXXXXS 308
K++L+ A+A Y + + + + + +++P K+ S
Sbjct: 244 KDLLAVAIAASYHYPEIEDLVDRIENPEKY-AAAAPAATSAASGDAAPAEEAAAEEEEES 302
Query: 309 DDDMGLSLFD 318
DDDMG LFD
Sbjct: 303 DDDMGFGLFD 312
>pdb|3A1Y|G Chain G, The Structure Of Protein Complex
Length = 284
Score = 109 bits (273), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 75/255 (29%), Positives = 130/255 (50%), Gaps = 2/255 (0%)
Query: 8 AEKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVL-MGKNTMMKRSI 66
AE K L KL++ Y I +V ++ + L +R +R++ +L + +NT+++ +I
Sbjct: 5 AEWKKKEVEELAKLIKSYPVIALVDVSSMPAYPLSQMRRLIRENGGLLRVSRNTLIELAI 64
Query: 67 RLHAERTGNRDLLNLIPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGLVAPIDVVV 126
+ A+ G +L L+ + G++ T + ++ + +++ APA+ G V P DVVV
Sbjct: 65 KKAAKELGKPELEKLVEYIDRGAGILVTNMNPFKLYKFLQQNRQPAPAKPGAVVPKDVVV 124
Query: 127 PPGNTGLDPSQ-TSFFQVLNIPTKINKGTVEIITPVELIKKGDRVGSSESALLSKLAIKP 185
P G T L P Q L IP +I KG V I ++K G+ + + +L+ L I+P
Sbjct: 125 PAGPTPLAPGPIVGQMQALGIPARIEKGKVTIQKDTTVLKAGEVITPELANILNALGIQP 184
Query: 186 FSYGLIVMSVYENGSVYSPEVLDLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFI 245
GL V++VYE+G VY+P+VL + E + +A +LA++I YPT
Sbjct: 185 LEVGLDVLAVYEDGIVYTPDVLAIDEQEYIDMLQKAYMHAFNLAVNIAYPTPETIEAIIQ 244
Query: 246 NGYKNVLSFAVATEY 260
+ N + A+ Y
Sbjct: 245 KAFLNAKTVAIEAGY 259
>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 = 107 bits (268), Expect = 6e-24, Method: Compositional matrix adjust.
Identities = 71/248 (28%), Positives = 127/248 (51%), Gaps = 7/248 (2%)
Query: 10 KKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKNTMMKRSIRLH 69
K+ DA + +++E Y + +V + S QLQ +R L + + + +NT+++R+ L
Sbjct: 16 KQEEVDA-IVEMIESYESVGVVNIAGIPSRQLQDMRRDLHGTAELRVSRNTLLERA--LD 72
Query: 70 AERTGNRDLLNLIPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGLVAPIDVVVPPG 129
G DL I G VG+I T + + E+ K AP G VAP D+V+P G
Sbjct: 73 DVDDGLEDLNGYI---TGQVGLIGTDDNPFSLFQELEASKTPAPIGAGEVAPNDIVIPEG 129
Query: 130 NTGLDPSQ-TSFFQVLNIPTKINKGTVEIITPVELIKKGDRVGSSESALLSKLAIKPFSY 188
+TG+DP Q + +I +G++++++ ++ G+ V S +L++L I+P
Sbjct: 130 DTGVDPGPFVGELQSVGADARIQEGSIQVLSDSTVLDTGEEVSQELSNVLNELGIEPKEV 189
Query: 189 GLIVMSVYENGSVYSPEVLDLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFINGY 248
GL + +V+ +G ++ PE L+L D+ + A R +L+++ YPT AP +
Sbjct: 190 GLDLRAVFADGVLFEPEELELDIDEYRSDIQAAAGRAFNLSVNADYPTATTAPTMLQSAR 249
Query: 249 KNVLSFAV 256
N S A+
Sbjct: 250 GNAKSLAL 257
>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 (267), Expect = 8e-24, Method: Compositional matrix adjust.
Identities = 71/248 (28%), Positives = 127/248 (51%), Gaps = 7/248 (2%)
Query: 10 KKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKNTMMKRSIRLH 69
K+ DA + +++E Y + +V + S QLQ +R L + + + +NT+++R+ L
Sbjct: 16 KQEEVDA-IVEMIESYESVGVVNIAGIPSRQLQDMRRDLHGTAELRVSRNTLLERA--LD 72
Query: 70 AERTGNRDLLNLIPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGLVAPIDVVVPPG 129
G DL I G VG+I T + + E+ K AP G VAP D+V+P G
Sbjct: 73 DVDDGLEDLNGYI---TGQVGLIGTDDNPFSLFQELEASKTPAPIGAGEVAPNDIVIPEG 129
Query: 130 NTGLDPSQ-TSFFQVLNIPTKINKGTVEIITPVELIKKGDRVGSSESALLSKLAIKPFSY 188
+TG+DP Q + +I +G++++++ ++ G+ V S +L++L I+P
Sbjct: 130 DTGVDPGPFVGELQSVGADARIQEGSIQVLSDSTVLDTGEEVSQELSNVLNELGIEPKEV 189
Query: 189 GLIVMSVYENGSVYSPEVLDLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFINGY 248
GL + +V+ +G ++ PE L+L D+ + A R +L+++ YPT AP +
Sbjct: 190 GLDLRAVFADGVLFEPEELELDIDEYRSDIQAAAGRAFNLSVNADYPTATTAPTMLQSDR 249
Query: 249 KNVLSFAV 256
N S A+
Sbjct: 250 GNAKSLAL 257
>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 = 106 bits (265), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 70/255 (27%), Positives = 131/255 (51%), Gaps = 2/255 (0%)
Query: 8 AEKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVL-MGKNTMMKRSI 66
AE K L L++ Y + +V ++ + L +R +R+++ +L + +NT+++ +I
Sbjct: 5 AEWKKKEVEELANLIKSYPVVALVDVSSMPAYPLSQMRRLIRENNGLLRVSRNTLIELAI 64
Query: 67 RLHAERTGNRDLLNLIPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGLVAPIDVVV 126
+ A+ G +L LI ++G G++ T + ++ + +++ APA+ G P DVV+
Sbjct: 65 KKVAQELGKPELEKLINYIEGGAGILVTTMNPFKLYKFLQQNRQPAPAKPGAKVPKDVVI 124
Query: 127 PPGNTGLDPSQ-TSFFQVLNIPTKINKGTVEIITPVELIKKGDRVGSSESALLSKLAIKP 185
P G T L P Q + IP +I +G V I ++K G+ + + +L+ L I+P
Sbjct: 125 PAGPTSLAPGPIVGQMQAMGIPARIERGKVTIQKDTVVLKAGEEITPELANILNALGIQP 184
Query: 186 FSYGLIVMSVYENGSVYSPEVLDLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPHFFI 245
GL +++VYE+G +Y+P+VL + E + +A +LA++I YPT
Sbjct: 185 LEVGLDLLAVYEDGIIYTPDVLAIDESEYINMLQKAYMHAFNLAVNIAYPTPQTIEAIIQ 244
Query: 246 NGYKNVLSFAVATEY 260
+ N + AV Y
Sbjct: 245 KAFLNAKAVAVEAGY 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 = 90.1 bits (222), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 65/208 (31%), Positives = 111/208 (53%), Gaps = 1/208 (0%)
Query: 8 AEKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKNTMMKRSIR 67
A KI L L++ + IV +V + QLQ IR +RD + M +NT++ R+++
Sbjct: 2 APWKIEEVKTLKGLIKSKPVVAIVDMMDVPAPQLQEIRDKIRDKVKLRMSRNTLIIRALK 61
Query: 68 LHAERTGNRDLLNLIPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPARVGLVAPIDVVVP 127
AE N L L ++ ++ T + ++ + ++K AP R G +AP D+ V
Sbjct: 62 EAAEELNNPKLAELANYVERGAAILVTDMNPFKLYKLLEENKSPAPVRGGQIAPCDIKVE 121
Query: 128 PGNTGLDPSQ-TSFFQVLNIPTKINKGTVEIITPVELIKKGDRVGSSESALLSKLAIKPF 186
G+TG+ P + + IP I KG + I ++KKG+ V +A+L +L IKP
Sbjct: 122 KGSTGMPPGPFLGELKSVGIPAAIEKGKIAIKEDKVVVKKGEVVSPKLAAVLDRLGIKPI 181
Query: 187 SYGLIVMSVYENGSVYSPEVLDLTEDDI 214
GL +++VYE+G +Y+P+VL + E+ +
Sbjct: 182 KVGLNILAVYEDGIIYTPDVLKVDEEKL 209
>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 = 79.3 bits (194), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 40/95 (42%), Positives = 58/95 (61%), Gaps = 2/95 (2%)
Query: 9 EKKIAYDARLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKNTMMKRSIRL 68
EKK Y A+L + LEEY + +V DNV S Q+ +R LR ++VLMGKNTM++R+IR
Sbjct: 4 EKKAEYFAKLREYLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIRG 63
Query: 69 HAERTGNRDLLNLIPLLQGNVGMIFTKGDLKEVSD 103
+ D L+P ++G VG +FT L E+ +
Sbjct: 64 FL--SDLPDFEKLLPFVKGYVGFVFTNEPLTEIKN 96
>pdb|3MM1|A Chain A, Dye-Decolorizing Peroxidase (Dyp) D171n
pdb|3MM3|A Chain A, Dye-Decolorizing Peroxidase (Dyp) D171n In Complex With
Cyanide
Length = 442
Score = 31.2 bits (69), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 183 IKPFSYGLIVMSVYENGSVYSPEVLDLTEDDIATKFLEAVSRVASLALSIRYPTIAAAPH 242
+ PF+ G + V+ GS + LD DDI++ F ++++V +L+ S R A H
Sbjct: 109 VAPFT-GTTIHGVFLIGSDQD-DFLDQFTDDISSTFGSSITQVQALSGSARPGDQAGHEH 166
Query: 243 F-FING 247
F F+NG
Sbjct: 167 FGFLNG 172
>pdb|3G6S|A Chain A, Crystal Structure Of The
EndonucleaseEXONUCLEASEPHOSPHATASE (BVU_0621) FROM
Bacteroides Vulgatus. Northeast Structural Genomics
Consortium Target Bvr56d
Length = 267
Score = 30.8 bits (68), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 17 RLCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKN 59
R+C+ ++++ ++ IV V NQ Q +RAGL ++ + +G++
Sbjct: 29 RVCQFIKDH-ELDIVGXQEVLHNQFQDLRAGLPEYDGIGVGRD 70
>pdb|1F45|B Chain B, Human Interleukin-12
pdb|3HMX|B Chain B, Crystal Structure Of Ustekinumab FabIL-12 Complex
Length = 197
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 148 TKINKGTVEIITPVELIKKGDRVGSSESALL---SKLAIKPFSY--GLIVMSVYENGSVY 202
TK TVE P+EL K + S E++ + S LA + S+ L + S+YE+ +Y
Sbjct: 53 TKDKTSTVEACLPLELTKNESCLNSRETSFITNGSCLASRKTSFMMALCLSSIYEDLKMY 112
Query: 203 SPE 205
E
Sbjct: 113 QVE 115
>pdb|3OW2|G Chain G, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 62
Score = 28.9 bits (63), Expect = 3.7, Method: Composition-based stats.
Identities = 12/49 (24%), Positives = 29/49 (59%)
Query: 18 LCKLLEEYSQILIVAADNVGSNQLQHIRAGLRDHSIVLMGKNTMMKRSI 66
+ +++E Y + +V + S QLQ +R L + + + +NT+++R++
Sbjct: 12 IVEMIESYESVGVVNIAGIPSRQLQDMRRDLHGTAELRVSRNTLLERAL 60
>pdb|3PJ0|A Chain A, Crystal Structure Of A Putative L-Allo-Threonine Aldolase
(Lmo0305) From Listeria Monocytogenes Egd-E At 1.80 A
Resolution
pdb|3PJ0|B Chain B, Crystal Structure Of A Putative L-Allo-Threonine Aldolase
(Lmo0305) From Listeria Monocytogenes Egd-E At 1.80 A
Resolution
pdb|3PJ0|C Chain C, Crystal Structure Of A Putative L-Allo-Threonine Aldolase
(Lmo0305) From Listeria Monocytogenes Egd-E At 1.80 A
Resolution
pdb|3PJ0|D Chain D, Crystal Structure Of A Putative L-Allo-Threonine Aldolase
(Lmo0305) From Listeria Monocytogenes Egd-E At 1.80 A
Resolution
Length = 359
Score = 28.1 bits (61), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 66 IRLHAERTGNRDLLNLIPLLQGNVGMIFTKGDLKEVSDEVSKHKVAAPAR 115
+ +H E+ G ++L + PLL G + T D+K + + VS + P R
Sbjct: 100 LEIH-EQDGLKELQQITPLLLGTANQLLTIDDIKSLREPVSSVLIELPQR 148
>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 = 28.1 bits (61), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 8/47 (17%)
Query: 124 VVVPPGNTGLDPSQTSFFQVLNIP--------TKINKGTVEIITPVE 162
+VVP G +GL Q V ++P +K N VE++ PVE
Sbjct: 150 IVVPDGQSGLKMLQDGRIDVYSLPVLSINDLVSKANDPNVEVLAPVE 196
>pdb|1MQS|A Chain A, Crystal Structure Of Sly1p In Complex With An N-Terminal
Peptide Of Sed5p
Length = 671
Score = 27.7 bits (60), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 144 LNIPTKINKGTVEIITPVELIKKGDRVGSSESA 176
L+ P K+ G+ I TP E + + R+G+S S+
Sbjct: 635 LHNPKKVXYGSTAITTPAEFLNEISRLGASNSS 667
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
0.317 0.134 0.369
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,924,109
Number of Sequences: 62578
Number of extensions: 305181
Number of successful extensions: 846
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 814
Number of HSP's gapped (non-prelim): 28
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)