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= psy17475
(346 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 360 bits (923), Expect = e-100, Method: Compositional matrix adjust.
Identities = 179/257 (69%), Positives = 213/257 (82%), Gaps = 2/257 (0%)
Query: 1 QLVDEYPKCFVVGADNVGSRQFQNIRQSLEGLGVVLMGKNTMMRKAIRGHLEHNPGLERL 60
QL+D+YPKCF+VGADNVGS+Q Q IR SL G VVLMGKNTMMRKAIRGHLE+NP LE+L
Sbjct: 19 QLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKAVVLMGKNTMMRKAIRGHLENNPALEKL 78
Query: 61 LPHIKGNVGFVFTRGDLNEVREKLLENKVQAPARNGAIAPCPVTIPAQNTGLGPEKTSFF 120
LPHI+GNVGFVFT+ DL E+R+ LL NKV A AR GAIAPC VT+PAQNTGLGPEKTSFF
Sbjct: 79 LPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCEVTVPAQNTGLGPEKTSFF 138
Query: 121 QALSIPTKISKGTIEIINDVHILKEGD--SSREATLLNMLNISPFSYGLIIKMVYDSGTI 178
QAL I TKIS+GTIEI++DV ++K GD + EATLLNMLNISPFS+GL+I+ V+D+G+I
Sbjct: 139 QALGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLVIQQVFDNGSI 198
Query: 179 FAPQILDIRPEDLRVKFLEGVATLASVCLSIGYPTVASVPHSIVNGFKNVLAVAAATEVD 238
+ P++LDI E L +FLEGV +ASVCL IGYPTVASVPHSI+NG+K VLA++ T+
Sbjct: 199 YNPEVLDITEETLHSRFLEGVRNVASVCLQIGYPTVASVPHSIINGYKRVLALSVETDYT 258
Query: 239 FEQAKTVKEFLKDPSKF 255
F A+ VK FL DPS F
Sbjct: 259 FPLAEKVKAFLADPSAF 275
Score = 90.9 bits (224), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 42/72 (58%), Positives = 56/72 (77%)
Query: 275 RFSRNAETDLNDVHILKEGDKVGPSEATLLNMLNISPFSYGLIIKMVYDSGTIFAPQILD 334
+ SR L+DV ++K GDKVG SEATLLNMLNISPFS+GL+I+ V+D+G+I+ P++LD
Sbjct: 146 KISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLVIQQVFDNGSIYNPEVLD 205
Query: 335 IRPEDLRVKFLE 346
I E L +FLE
Sbjct: 206 ITEETLHSRFLE 217
>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 = 275 bits (702), Expect = 3e-74, Method: Compositional matrix adjust.
Identities = 141/259 (54%), Positives = 186/259 (71%), Gaps = 4/259 (1%)
Query: 1 QLVDEYPKCFVVGADNVGSRQFQNIRQSLEGLGVVLMGKNTMMRKAIRGHLEHNPGLE-- 58
QL+DEY K + ADNVGS Q Q IR+ L G +VLMGKNT++R+ I+ H ++ E
Sbjct: 20 QLLDEYTKVLIAVADNVGSNQLQEIRKGLRGDSIVLMGKNTLIRRCIKVHADNTGNKEFL 79
Query: 59 RLLPHIKGNVGFVFTRGDLNEVREKLLENKVQAPARNGAIAPCPVTIPAQNTGLGPEKTS 118
L+P + GNVG +FT+GDL EVRE++ + KV APAR G +AP V +P NTGL P +TS
Sbjct: 80 ELMPLLVGNVGLIFTKGDLKEVREEVAKYKVGAPARVGLVAPVDVVVPPGNTGLDPSQTS 139
Query: 119 FFQALSIPTKISKGTIEIINDVHILKEGD--SSREATLLNMLNISPFSYGLIIKMVYDSG 176
FFQ L+IPTKI+KGT+EII V ++K+GD S E+ LL L I PFSYGL+I VYDSG
Sbjct: 140 FFQVLNIPTKINKGTVEIITPVELIKKGDKVGSSESALLAKLGIRPFSYGLVITNVYDSG 199
Query: 177 TIFAPQILDIRPEDLRVKFLEGVATLASVCLSIGYPTVASVPHSIVNGFKNVLAVAAATE 236
++F+P++LD+ +DL KF GV+ +ASV L+I YPT+A+ PH +NG+KNVLAVA TE
Sbjct: 200 SVFSPEVLDLTEDDLMEKFASGVSMVASVSLAISYPTIAAAPHMFLNGYKNVLAVAVETE 259
Query: 237 VDFEQAKTVKEFLKDPSKF 255
+ A +KE+LKDPSKF
Sbjct: 260 YSYPHADKIKEYLKDPSKF 278
Score = 75.1 bits (183), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 33/58 (56%), Positives = 45/58 (77%)
Query: 287 VHILKEGDKVGPSEATLLNMLNISPFSYGLIIKMVYDSGTIFAPQILDIRPEDLRVKF 344
V ++K+GDKVG SE+ LL L I PFSYGL+I VYDSG++F+P++LD+ +DL KF
Sbjct: 161 VELIKKGDKVGSSESALLAKLGIRPFSYGLVITNVYDSGSVFSPEVLDLTEDDLMEKF 218
>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 = 242 bits (617), Expect = 2e-64, Method: Compositional matrix adjust.
Identities = 127/257 (49%), Positives = 183/257 (71%), Gaps = 2/257 (0%)
Query: 1 QLVDEYPKCFVVGADNVGSRQFQNIRQSLEGLGVVLMGKNTMMRKAIRGHLEHNPGLERL 60
+ ++EY FVVG DNV S+Q +R+ L G VVLMGKNTM+R+AIRG L P E+L
Sbjct: 17 EYLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIRGFLSDLPDFEKL 76
Query: 61 LPHIKGNVGFVFTRGDLNEVREKLLENKVQAPARNGAIAPCPVTIPAQNTGLGPEKTSFF 120
LP +KGNVGFVFT L E++ ++ N+V APAR GA+AP + + A NTG+ P KTSFF
Sbjct: 77 LPFVKGNVGFVFTNEPLTEIKNVIVSNRVAAPARAGAVAPEDIWVRAVNTGMEPGKTSFF 136
Query: 121 QALSIPTKISKGTIEIINDVHILKEGD--SSREATLLNMLNISPFSYGLIIKMVYDSGTI 178
QAL +PTKI++GTIEI++DV ++ G+ EA+LLN+LNISPF++GL + VYD+G +
Sbjct: 137 QALGVPTKIARGTIEIVSDVKVVDAGNKVGQSEASLLNLLNISPFTFGLTVVQVYDNGQV 196
Query: 179 FAPQILDIRPEDLRVKFLEGVATLASVCLSIGYPTVASVPHSIVNGFKNVLAVAAATEVD 238
F ILDI E+L F+ V+T+AS+ L+IGYPT+ SV H+++N +K++LAVA A
Sbjct: 197 FPSSILDITDEELVSHFVSAVSTIASISLAIGYPTLPSVGHTLINNYKDLLAVAIAASYH 256
Query: 239 FEQAKTVKEFLKDPSKF 255
+ + + + + +++P K+
Sbjct: 257 YPEIEDLVDRIENPEKY 273
Score = 70.1 bits (170), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 33/71 (46%), Positives = 49/71 (69%)
Query: 275 RFSRNAETDLNDVHILKEGDKVGPSEATLLNMLNISPFSYGLIIKMVYDSGTIFAPQILD 334
+ +R ++DV ++ G+KVG SEA+LLN+LNISPF++GL + VYD+G +F ILD
Sbjct: 144 KIARGTIEIVSDVKVVDAGNKVGQSEASLLNLLNISPFTFGLTVVQVYDNGQVFPSSILD 203
Query: 335 IRPEDLRVKFL 345
I E+L F+
Sbjct: 204 ITDEELVSHFV 214
>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 = 239 bits (610), Expect = 2e-63, Method: Compositional matrix adjust.
Identities = 126/257 (49%), Positives = 182/257 (70%), Gaps = 2/257 (0%)
Query: 1 QLVDEYPKCFVVGADNVGSRQFQNIRQSLEGLGVVLMGKNTMMRKAIRGHLEHNPGLERL 60
+ ++EY FVVG DNV S+Q +R+ L G VVLMGKNTM+R+AIRG L P E+L
Sbjct: 17 EYLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIRGFLSDLPDFEKL 76
Query: 61 LPHIKGNVGFVFTRGDLNEVREKLLENKVQAPARNGAIAPCPVTIPAQNTGLGPEKTSFF 120
LP +KG VGFVFT L E++ ++ N+V APAR GA+AP + + A NTG+ P KTSFF
Sbjct: 77 LPFVKGYVGFVFTNEPLTEIKNVIVSNRVAAPARAGAVAPEDIWVRAVNTGMEPGKTSFF 136
Query: 121 QALSIPTKISKGTIEIINDVHILKEGD--SSREATLLNMLNISPFSYGLIIKMVYDSGTI 178
QAL +PTKI++GTIEI++DV ++ G+ EA+LLN+LNISPF++GL + VYD+G +
Sbjct: 137 QALGVPTKIARGTIEIVSDVKVVDAGNKVGQSEASLLNLLNISPFTFGLTVVQVYDNGQV 196
Query: 179 FAPQILDIRPEDLRVKFLEGVATLASVCLSIGYPTVASVPHSIVNGFKNVLAVAAATEVD 238
F ILDI E+L F+ V+T+AS+ L+IGYPT+ SV H+++N +K++LAVA A
Sbjct: 197 FPSSILDITDEELVSHFVSAVSTIASISLAIGYPTLPSVGHTLINNYKDLLAVAIAASYH 256
Query: 239 FEQAKTVKEFLKDPSKF 255
+ + + + + +++P K+
Sbjct: 257 YPEIEDLVDRIENPEKY 273
Score = 70.1 bits (170), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 33/71 (46%), Positives = 49/71 (69%)
Query: 275 RFSRNAETDLNDVHILKEGDKVGPSEATLLNMLNISPFSYGLIIKMVYDSGTIFAPQILD 334
+ +R ++DV ++ G+KVG SEA+LLN+LNISPF++GL + VYD+G +F ILD
Sbjct: 144 KIARGTIEIVSDVKVVDAGNKVGQSEASLLNLLNISPFTFGLTVVQVYDNGQVFPSSILD 203
Query: 335 IRPEDLRVKFL 345
I E+L F+
Sbjct: 204 ITDEELVSHFV 214
>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 = 214 bits (546), Expect = 4e-56, Method: Compositional matrix adjust.
Identities = 117/257 (45%), Positives = 169/257 (65%), Gaps = 2/257 (0%)
Query: 1 QLVDEYPKCFVVGADNVGSRQFQNIRQSLEGLGVVLMGKNTMMRKAIRGHLEHNPGLERL 60
+ ++EY FVVG DNV S+Q +R+ L G VVLMGKNTM+R+AIRG L P E+L
Sbjct: 17 EYLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIRGFLSDLPDFEKL 76
Query: 61 LPHIKGNVGFVFTRGDLNEVREKLLENKVQAPARNGAIAPCPVTIPAQNTGLGPEKTSFF 120
LP +KGNVGFVFT L E++ ++ N+V APAR GA+AP + + A NTG+ P KTSFF
Sbjct: 77 LPFVKGNVGFVFTNEPLTEIKNVIVSNRVAAPARAGAVAPEDIWVRAVNTGMEPGKTSFF 136
Query: 121 QALSIPTKISKGTIEIINDVHILKEGD--SSREATLLNMLNISPFSYGLIIKMVYDSGTI 178
QAL +PTKI++GTIEI++DV ++ G+ EA+LLN+LNISPF++GL + VYD+G +
Sbjct: 137 QALGVPTKIARGTIEIVSDVKVVDAGNKVGQSEASLLNLLNISPFTFGLTVVQVYDNGQV 196
Query: 179 FAPQILDIRPEDLRVKFLEGVATLASVCLSIGYPTVASVPHSIVNGFKNVLAVAAATEVD 238
F S+ L+IGYPT+ SV H+++N +K++LAVA A
Sbjct: 197 FPXXXXXXXXXXXXXXXXXXXXXXXSISLAIGYPTLPSVGHTLINNYKDLLAVAIAASYH 256
Query: 239 FEQAKTVKEFLKDPSKF 255
+ + + + + +++P K+
Sbjct: 257 YPEIEDLVDRIENPEKY 273
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 26/54 (48%), Positives = 40/54 (74%)
Query: 275 RFSRNAETDLNDVHILKEGDKVGPSEATLLNMLNISPFSYGLIIKMVYDSGTIF 328
+ +R ++DV ++ G+KVG SEA+LLN+LNISPF++GL + VYD+G +F
Sbjct: 144 KIARGTIEIVSDVKVVDAGNKVGQSEASLLNLLNISPFTFGLTVVQVYDNGQVF 197
>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 = 101 bits (251), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 65/241 (26%), Positives = 123/241 (51%), Gaps = 8/241 (3%)
Query: 1 QLVDEYPKCFVVGADNVGSRQFQNIRQSLEGLGVVLMGKNTMMRKAIRGHLEHNPGLERL 60
++++ Y VV + SRQ Q++R+ L G + + +NT++ +A+ + + GLE L
Sbjct: 25 EMIESYESVGVVNIAGIPSRQLQDMRRDLHGTAELRVSRNTLLERALD---DVDDGLEDL 81
Query: 61 LPHIKGNVGFVFTRGDLNEVREKLLENKVQAPARNGAIAPCPVTIPAQNTGLGPEK-TSF 119
+I G VG + T + + ++L +K AP G +AP + IP +TG+ P
Sbjct: 82 NGYITGQVGLIGTDDNPFSLFQELEASKTPAPIGAGEVAPNDIVIPEGDTGVDPGPFVGE 141
Query: 120 FQALSIPTKISKGTIEIINDVHILKEGD--SSREATLLNMLNISPFSYGLIIKMVYDSGT 177
Q++ +I +G+I++++D +L G+ S + +LN L I P GL ++ V+ G
Sbjct: 142 LQSVGADARIQEGSIQVLSDSTVLDTGEEVSQELSNVLNELGIEPKEVGLDLRAVFADGV 201
Query: 178 IFAPQILDIRPEDLRVKFLEGVATLASVCLSIGYPTVASVPHSIVNGFKNV--LAVAAAT 235
+F P+ L++ ++ R ++ ++ YPT + P + + N LA+ AA
Sbjct: 202 LFEPEELELDIDEYRSDIQAAAGRAFNLSVNADYPTATTAPTMLQSARGNAKSLALQAAI 261
Query: 236 E 236
E
Sbjct: 262 E 262
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 33/58 (56%)
Query: 284 LNDVHILKEGDKVGPSEATLLNMLNISPFSYGLIIKMVYDSGTIFAPQILDIRPEDLR 341
L+D +L G++V + +LN L I P GL ++ V+ G +F P+ L++ ++ R
Sbjct: 159 LSDSTVLDTGEEVSQELSNVLNELGIEPKEVGLDLRAVFADGVLFEPEELELDIDEYR 216
>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 = 101 bits (251), Expect = 8e-22, Method: Compositional matrix adjust.
Identities = 79/293 (26%), Positives = 139/293 (47%), Gaps = 10/293 (3%)
Query: 2 LVDEYPKCFVVGADNVGSRQFQNIRQSL-EGLGVVLMGKNTMMRKAIRGHLEH--NPGLE 58
L+ YP +V ++ + +R+ + E G++ + +NT++ AI+ + P LE
Sbjct: 18 LIKSYPVVALVDVSSMPAYPLSQMRRLIRENNGLLRVSRNTLIELAIKKVAQELGKPELE 77
Query: 59 RLLPHIKGNVGFVFTRGDLNEVREKLLENKVQAPARNGAIAPCPVTIPAQNTGLGPEK-T 117
+L+ +I+G G + T + ++ + L +N+ APA+ GA P V IPA T L P
Sbjct: 78 KLINYIEGGAGILVTTMNPFKLYKFLQQNRQPAPAKPGAKVPKDVVIPAGPTSLAPGPIV 137
Query: 118 SFFQALSIPTKISKGTIEIINDVHILKEGD--SSREATLLNMLNISPFSYGLIIKMVYDS 175
QA+ IP +I +G + I D +LK G+ + A +LN L I P GL + VY+
Sbjct: 138 GQMQAMGIPARIERGKVTIQKDTVVLKAGEEITPELANILNALGIQPLEVGLDLLAVYED 197
Query: 176 GTIFAPQILDIRPEDLRVKFLEGVATLA-SVCLSIGYPTVASVPHSIVNGFKNVLAVAAA 234
G I+ P +L I E + L+ A ++ ++I YPT ++ I F N A A A
Sbjct: 198 GIIYTPDVLAID-ESEYINMLQKAYMHAFNLAVNIAYPTPQTIEAIIQKAFLN--AKAVA 254
Query: 235 TEVDFEQAKTVKEFLKDPSKFLXXXXXXXXXXXXSNRSEERFSRNAETDLNDV 287
E + +T+ + + + + +++E S A+ + V
Sbjct: 255 VEAGYITKETISDIIGRAIRAMLLLAQQLPEDVLDEKTKELLSAQAQVSVAQV 307
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 32/61 (52%)
Query: 275 RFSRNAETDLNDVHILKEGDKVGPSEATLLNMLNISPFSYGLIIKMVYDSGTIFAPQILD 334
R R T D +LK G+++ P A +LN L I P GL + VY+ G I+ P +L
Sbjct: 148 RIERGKVTIQKDTVVLKAGEEITPELANILNALGIQPLEVGLDLLAVYEDGIIYTPDVLA 207
Query: 335 I 335
I
Sbjct: 208 I 208
>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 = 100 bits (250), Expect = 8e-22, Method: Compositional matrix adjust.
Identities = 65/241 (26%), Positives = 123/241 (51%), Gaps = 8/241 (3%)
Query: 1 QLVDEYPKCFVVGADNVGSRQFQNIRQSLEGLGVVLMGKNTMMRKAIRGHLEHNPGLERL 60
++++ Y VV + SRQ Q++R+ L G + + +NT++ +A+ + + GLE L
Sbjct: 25 EMIESYESVGVVNIAGIPSRQLQDMRRDLHGTAELRVSRNTLLERALD---DVDDGLEDL 81
Query: 61 LPHIKGNVGFVFTRGDLNEVREKLLENKVQAPARNGAIAPCPVTIPAQNTGLGPEK-TSF 119
+I G VG + T + + ++L +K AP G +AP + IP +TG+ P
Sbjct: 82 NGYITGQVGLIGTDDNPFSLFQELEASKTPAPIGAGEVAPNDIVIPEGDTGVDPGPFVGE 141
Query: 120 FQALSIPTKISKGTIEIINDVHILKEGD--SSREATLLNMLNISPFSYGLIIKMVYDSGT 177
Q++ +I +G+I++++D +L G+ S + +LN L I P GL ++ V+ G
Sbjct: 142 LQSVGADARIQEGSIQVLSDSTVLDTGEEVSQELSNVLNELGIEPKEVGLDLRAVFADGV 201
Query: 178 IFAPQILDIRPEDLRVKFLEGVATLASVCLSIGYPTVASVPHSIVNGFKNV--LAVAAAT 235
+F P+ L++ ++ R ++ ++ YPT + P + + N LA+ AA
Sbjct: 202 LFEPEELELDIDEYRSDIQAAAGRAFNLSVNADYPTATTAPTMLQSDRGNAKSLALQAAI 261
Query: 236 E 236
E
Sbjct: 262 E 262
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 33/58 (56%)
Query: 284 LNDVHILKEGDKVGPSEATLLNMLNISPFSYGLIIKMVYDSGTIFAPQILDIRPEDLR 341
L+D +L G++V + +LN L I P GL ++ V+ G +F P+ L++ ++ R
Sbjct: 159 LSDSTVLDTGEEVSQELSNVLNELGIEPKEVGLDLRAVFADGVLFEPEELELDIDEYR 216
>pdb|3A1Y|G Chain G, The Structure Of Protein Complex
Length = 284
Score = 99.4 bits (246), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 72/257 (28%), Positives = 124/257 (48%), Gaps = 12/257 (4%)
Query: 1 QLVDEYPKCFVVGADNVGSRQFQNIRQSL-EGLGVVLMGKNTMMRKAIRGHLEH--NPGL 57
+L+ YP +V ++ + +R+ + E G++ + +NT++ AI+ + P L
Sbjct: 17 KLIKSYPVIALVDVSSMPAYPLSQMRRLIRENGGLLRVSRNTLIELAIKKAAKELGKPEL 76
Query: 58 ERLLPHIKGNVGFVFTRGDLNEVREKLLENKVQAPARNGAIAPCPVTIPAQNTGLGPEK- 116
E+L+ +I G + T + ++ + L +N+ APA+ GA+ P V +PA T L P
Sbjct: 77 EKLVEYIDRGAGILVTNMNPFKLYKFLQQNRQPAPAKPGAVVPKDVVVPAGPTPLAPGPI 136
Query: 117 TSFFQALSIPTKISKGTIEIINDVHILKEGD--SSREATLLNMLNISPFSYGLIIKMVYD 174
QAL IP +I KG + I D +LK G+ + A +LN L I P GL + VY+
Sbjct: 137 VGQMQALGIPARIEKGKVTIQKDTTVLKAGEVITPELANILNALGIQPLEVGLDVLAVYE 196
Query: 175 SGTIFAPQILDIRPEDLRVKFLEGVATLASVCLSIGYPTVASVPHSIVNGFKNVLAVAAA 234
G ++ P +L I ++ + ++ ++I YPT ++ I F N A
Sbjct: 197 DGIVYTPDVLAIDEQEYIDMLQKAYMHAFNLAVNIAYPTPETIEAIIQKAFLN------A 250
Query: 235 TEVDFEQAKTVKEFLKD 251
V E KE ++D
Sbjct: 251 KTVAIEAGYITKETIQD 267
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 31/61 (50%)
Query: 275 RFSRNAETDLNDVHILKEGDKVGPSEATLLNMLNISPFSYGLIIKMVYDSGTIFAPQILD 334
R + T D +LK G+ + P A +LN L I P GL + VY+ G ++ P +L
Sbjct: 148 RIEKGKVTIQKDTTVLKAGEVITPELANILNALGIQPLEVGLDVLAVYEDGIVYTPDVLA 207
Query: 335 I 335
I
Sbjct: 208 I 208
>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 = 95.5 bits (236), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 45/87 (51%), Positives = 59/87 (67%)
Query: 1 QLVDEYPKCFVVGADNVGSRQFQNIRQSLEGLGVVLMGKNTMMRKAIRGHLEHNPGLERL 60
+ ++EY FVVG DNV S+Q +R+ L G VVLMGKNTM+R+AIRG L P E+L
Sbjct: 15 EYLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIRGFLSDLPDFEKL 74
Query: 61 LPHIKGNVGFVFTRGDLNEVREKLLEN 87
LP +KG VGFVFT L E++ ++ N
Sbjct: 75 LPFVKGYVGFVFTNEPLTEIKNVIVSN 101
>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 = 82.4 bits (202), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 60/195 (30%), Positives = 95/195 (48%), Gaps = 5/195 (2%)
Query: 2 LVDEYPKCFVVGADNVGSRQFQNIRQSLEGLGVVLMGKNTMMRKAIRGHLE--HNPGLER 59
L+ P +V +V + Q Q IR + + M +NT++ +A++ E +NP L
Sbjct: 15 LIKSKPVVAIVDMMDVPAPQLQEIRDKIRDKVKLRMSRNTLIIRALKEAAEELNNPKLAE 74
Query: 60 LLPHIKGNVGFVFTRGDLNEVREKLLENKVQAPARNGAIAPCPVTIPAQNTGLGPEK-TS 118
L +++ + T + ++ + L ENK AP R G IAPC + + +TG+ P
Sbjct: 75 LANYVERGAAILVTDMNPFKLYKLLEENKSPAPVRGGQIAPCDIKVEKGSTGMPPGPFLG 134
Query: 119 FFQALSIPTKISKGTIEIIND--VHILKEGDSSREATLLNMLNISPFSYGLIIKMVYDSG 176
+++ IP I KG I I D V E S + A +L+ L I P GL I VY+ G
Sbjct: 135 ELKSVGIPAAIEKGKIAIKEDKVVVKKGEVVSPKLAAVLDRLGIKPIKVGLNILAVYEDG 194
Query: 177 TIFAPQILDIRPEDL 191
I+ P +L + E L
Sbjct: 195 IIYTPDVLKVDEEKL 209
Score = 35.4 bits (80), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 23/43 (53%)
Query: 298 PSEATLLNMLNISPFSYGLIIKMVYDSGTIFAPQILDIRPEDL 340
P A +L+ L I P GL I VY+ G I+ P +L + E L
Sbjct: 167 PKLAAVLDRLGIKPIKVGLNILAVYEDGIIYTPDVLKVDEEKL 209
>pdb|3QPQ|L Chain L, Crystal Structure Of Anti-Tlr3 Antibody C1068 Fab
pdb|3QPQ|E Chain E, Crystal Structure Of Anti-Tlr3 Antibody C1068 Fab
pdb|3QPQ|C Chain C, Crystal Structure Of Anti-Tlr3 Antibody C1068 Fab
pdb|3QPQ|I Chain I, Crystal Structure Of Anti-Tlr3 Antibody C1068 Fab
pdb|3ULU|E Chain E, Structure Of Quaternary Complex Of Human Tlr3ecd With
Three Fabs (Form1)
pdb|3ULV|E Chain E, Structure Of Quaternary Complex Of Human Tlr3ecd With
Three Fabs (Form2)
Length = 215
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 5/79 (6%)
Query: 161 SPFSYGLIIKMVYDSGTIFAPQILDIRPEDLRVKFLEGVATLASVC-LSIGYPTVASVPH 219
+PF++G K+ GT+ AP + P D ++K G A++ VC L+ YP A V
Sbjct: 94 TPFTFGSGTKLELKRGTVAAPSVFIFPPSDEQLK--SGTASV--VCLLNNFYPREAKVQW 149
Query: 220 SIVNGFKNVLAVAAATEVD 238
+ N ++ + + TE D
Sbjct: 150 KVDNALQSGNSQESVTEQD 168
>pdb|3OW2|G Chain G, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 62
Score = 33.5 bits (75), Expect = 0.19, Method: Composition-based stats.
Identities = 13/47 (27%), Positives = 28/47 (59%)
Query: 1 QLVDEYPKCFVVGADNVGSRQFQNIRQSLEGLGVVLMGKNTMMRKAI 47
++++ Y VV + SRQ Q++R+ L G + + +NT++ +A+
Sbjct: 14 EMIESYESVGVVNIAGIPSRQLQDMRRDLHGTAELRVSRNTLLERAL 60
>pdb|3D45|A Chain A, Crystal Structure Of Mouse Parn In Complex With M7gpppg
pdb|3D45|B Chain B, Crystal Structure Of Mouse Parn In Complex With M7gpppg
Length = 507
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 19/28 (67%), Gaps = 1/28 (3%)
Query: 79 EVREKLLENKVQAPARNGAIAPCPVTIP 106
++RE+ E + QA GA+A CPVTIP
Sbjct: 143 QLREQFDEKRSQANGA-GALAKCPVTIP 169
>pdb|1X0U|A Chain A, Crystal Structure Of The Carboxyl Transferase Subunit Of
Putative Pcc Of Sulfolobus Tokodaii
pdb|1X0U|B Chain B, Crystal Structure Of The Carboxyl Transferase Subunit Of
Putative Pcc Of Sulfolobus Tokodaii
pdb|1X0U|C Chain C, Crystal Structure Of The Carboxyl Transferase Subunit Of
Putative Pcc Of Sulfolobus Tokodaii
pdb|1X0U|D Chain D, Crystal Structure Of The Carboxyl Transferase Subunit Of
Putative Pcc Of Sulfolobus Tokodaii
pdb|1X0U|E Chain E, Crystal Structure Of The Carboxyl Transferase Subunit Of
Putative Pcc Of Sulfolobus Tokodaii
pdb|1X0U|F Chain F, Crystal Structure Of The Carboxyl Transferase Subunit Of
Putative Pcc Of Sulfolobus Tokodaii
Length = 522
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 44/97 (45%), Gaps = 11/97 (11%)
Query: 11 VVGADNVGSRQFQNIRQSLEGLGVV---------LMGKNTMMRKAIRGHLEHNPGLERLL 61
VVG ++ G + Q SLEG G V ++ + T+M G ++P L +
Sbjct: 129 VVGINDSGGARIQEGALSLEGYGAVFKMNVMASGVIPQITIMAGPAAGGAVYSPALTDFI 188
Query: 62 PHIKGNVGFVFTRGDLNEVREKLLENKVQAPARNGAI 98
IKG+ ++F G E+ + +L +V GA+
Sbjct: 189 IMIKGDAYYMFVTGP--EITKVVLGEEVSFQDLGGAV 223
>pdb|2CE7|A Chain A, Edta Treated
pdb|2CE7|B Chain B, Edta Treated
pdb|2CE7|C Chain C, Edta Treated
pdb|2CE7|D Chain D, Edta Treated
pdb|2CE7|E Chain E, Edta Treated
pdb|2CE7|F Chain F, Edta Treated
pdb|2CEA|A Chain A, Cell Division Protein Ftsh
pdb|2CEA|B Chain B, Cell Division Protein Ftsh
pdb|2CEA|C Chain C, Cell Division Protein Ftsh
pdb|2CEA|D Chain D, Cell Division Protein Ftsh
pdb|2CEA|E Chain E, Cell Division Protein Ftsh
pdb|2CEA|F Chain F, Cell Division Protein Ftsh
Length = 476
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 225 FKNVLAVAAATEVDFEQAKTVKEFLKDPSKF 255
FK+V E E+ K V EFLKDPSKF
Sbjct: 15 FKDV----GGAEEAIEELKEVVEFLKDPSKF 41
>pdb|3KDS|E Chain E, Apo-ftsh Crystal Structure
pdb|3KDS|F Chain F, Apo-ftsh Crystal Structure
pdb|3KDS|G Chain G, Apo-ftsh Crystal Structure
Length = 465
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 225 FKNVLAVAAATEVDFEQAKTVKEFLKDPSKF 255
FK+V E E+ K V EFLKDPSKF
Sbjct: 15 FKDV----GGAEEAIEELKEVVEFLKDPSKF 41
>pdb|1JMY|A Chain A, Truncated Recombinant Human Bile Salt Stimulated Lipase
Length = 522
Score = 28.1 bits (61), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 7/82 (8%)
Query: 146 GDSSREATLLNMLNISPFSYGLIIKMVYDSGTIFAPQILDIRPEDLRVKFLE------GV 199
G+S+ A++ ++ +SP++ GLI + + SG +P ++ P K E G
Sbjct: 192 GESAGGASV-SLQTLSPYNKGLIRRAISQSGVALSPWVIQKNPLFWAKKVAEKVGCPVGD 250
Query: 200 ATLASVCLSIGYPTVASVPHSI 221
A + CL + P ++ + +
Sbjct: 251 AARMAQCLKVTDPRALTLAYKV 272
>pdb|1F6W|A Chain A, Structure Of The Catalytic Domain Of Human Bile Salt
Activated Lipase
Length = 533
Score = 28.1 bits (61), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 39/82 (47%), Gaps = 7/82 (8%)
Query: 146 GDSSREATLLNMLNISPFSYGLIIKMVYDSGTIFAPQILDIRPEDLRVKFLE------GV 199
G+S+ A++ ++ +SP++ GLI + + SG +P ++ P K E G
Sbjct: 192 GESAGGASV-SLQTLSPYNKGLIRRAISQSGVALSPWVIQKNPLFWAKKVAEKVGCPVGD 250
Query: 200 ATLASVCLSIGYPTVASVPHSI 221
A + CL + P ++ + +
Sbjct: 251 AARMAQCLKVTDPRALTLAYKV 272
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 0.138 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,540,398
Number of Sequences: 62578
Number of extensions: 377009
Number of successful extensions: 947
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 898
Number of HSP's gapped (non-prelim): 35
length of query: 346
length of database: 14,973,337
effective HSP length: 100
effective length of query: 246
effective length of database: 8,715,537
effective search space: 2144022102
effective search space used: 2144022102
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)