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= psy13118
(286 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKR|CC Chain c, 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 = 421
Score = 247 bits (631), Expect = 5e-66, Method: Compositional matrix adjust.
Identities = 113/143 (79%), Positives = 128/143 (89%)
Query: 16 VGVARPLITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGH 75
+ ARPLI+VYSEK E +G+ VTLP+VFKAPIRPD+VNFVH NL KN+RQPYAVS+ AGH
Sbjct: 1 MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH 60
Query: 76 QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQR 135
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCR GRMFAPT+ WRRWHR+VN Q+
Sbjct: 61 QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK 120
Query: 136 RYAMVSAIAASSVPALVMSKGHQ 158
RYA+ SA+A S+PALVMSKGH+
Sbjct: 121 RYAICSALACLSLPALVMSKGHR 143
Score = 216 bits (551), Expect = 1e-56, Method: Compositional matrix adjust.
Identities = 102/157 (64%), Positives = 121/157 (77%), Gaps = 11/157 (7%)
Query: 127 HRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARIPRVRGGGTHRSGQ 186
H + N R+ VS +A GHQTSAESWGTGRAVARIPRVRGGGTHRSGQ
Sbjct: 41 HTNLRKNNRQPYAVSELA-----------GHQTSAESWGTGRAVARIPRVRGGGTHRSGQ 89
Query: 187 GAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHMIQDVPE 246
GAFGNMCR GRMFAPT+ WRRWHR+VN Q+RYA+ SA+A S+PALVMSKGH I++VPE
Sbjct: 90 GAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKRYAICSALACLSLPALVMSKGHRIEEVPE 149
Query: 247 FPLVVSDKIQEYKKTKQATIFLHRIKAWNDVLKVQSS 283
PLVV DK++ YKKTK+A + L ++KAWND+ KV +S
Sbjct: 150 LPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIKKVYAS 186
>pdb|3ZF7|RR Chain r, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 374
Score = 204 bits (519), Expect = 4e-53, Method: Compositional matrix adjust.
Identities = 94/140 (67%), Positives = 118/140 (84%)
Query: 19 ARPLITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTS 78
ARP ++VYS + T +LP+VF APIR DVV FVH N++KN RQPYAV++ +G + S
Sbjct: 3 ARPSVSVYSASEDKVVGTCSLPAVFTAPIRHDVVQFVHTNMAKNSRQPYAVNRLSGMKHS 62
Query: 79 AESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYA 138
AESWGTGRAVARIPR+ GGGT SG GAFGNMCR GRMFAPT+I+RRWHRK+N++Q+R+A
Sbjct: 63 AESWGTGRAVARIPRIHGGGTSMSGAGAFGNMCRGGRMFAPTKIFRRWHRKINLHQKRFA 122
Query: 139 MVSAIAASSVPALVMSKGHQ 158
+VSA+AASS+PALVMS+GH+
Sbjct: 123 VVSALAASSLPALVMSRGHK 142
Score = 182 bits (463), Expect = 1e-46, Method: Compositional matrix adjust.
Identities = 84/128 (65%), Positives = 106/128 (82%)
Query: 156 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVN 215
G + SAESWGTGRAVARIPR+ GGGT SG GAFGNMCR GRMFAPT+I+RRWHRK+N++
Sbjct: 58 GMKHSAESWGTGRAVARIPRIHGGGTSMSGAGAFGNMCRGGRMFAPTKIFRRWHRKINLH 117
Query: 216 QRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKAWN 275
Q+R+A+VSA+AASS+PALVMS+GH I++V E PLVV D ++ Y+KTK+A FL + A +
Sbjct: 118 QKRFAVVSALAASSLPALVMSRGHKIENVAEVPLVVEDGVRAYEKTKEAMTFLKTVGAID 177
Query: 276 DVLKVQSS 283
DV +V S
Sbjct: 178 DVNRVNDS 185
>pdb|3IZR|D Chain D, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 405
Score = 200 bits (509), Expect = 6e-52, Method: Compositional matrix adjust.
Identities = 93/142 (65%), Positives = 118/142 (83%), Gaps = 3/142 (2%)
Query: 20 RPLITVYSEKNE---PTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQ 76
RPL++V + + + ++ L VF+AP+RPDVV FVH+ LS N RQPYAVS+ AGHQ
Sbjct: 6 RPLVSVKALEGDMATDNSSSLALAEVFRAPLRPDVVRFVHRLLSCNKRQPYAVSRRAGHQ 65
Query: 77 TSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRR 136
TSAESWGTGRAV+RIPRV GGGTHR+GQGAFGNMCR GRMFAPT+ WR+WHR+VNV+ RR
Sbjct: 66 TSAESWGTGRAVSRIPRVPGGGTHRAGQGAFGNMCRGGRMFAPTKTWRKWHRRVNVHLRR 125
Query: 137 YAMVSAIAASSVPALVMSKGHQ 158
A+ SA+AA+SVP+LV+++GH+
Sbjct: 126 VAVASALAATSVPSLVLARGHR 147
Score = 185 bits (470), Expect = 2e-47, Method: Compositional matrix adjust.
Identities = 94/168 (55%), Positives = 120/168 (71%), Gaps = 13/168 (7%)
Query: 118 APTR--IWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARIPR 175
AP R + R HR ++ N+R+ VS A GHQTSAESWGTGRAV+RIPR
Sbjct: 34 APLRPDVVRFVHRLLSCNKRQPYAVSRRA-----------GHQTSAESWGTGRAVSRIPR 82
Query: 176 VRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVM 235
V GGGTHR+GQGAFGNMCR GRMFAPT+ WR+WHR+VNV+ RR A+ SA+AA+SVP+LV+
Sbjct: 83 VPGGGTHRAGQGAFGNMCRGGRMFAPTKTWRKWHRRVNVHLRRVAVASALAATSVPSLVL 142
Query: 236 SKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKAWNDVLKVQSS 283
++GH I+ VPE PLV+SD + +KT QA L ++ A+ D K + S
Sbjct: 143 ARGHRIETVPELPLVISDSAESIEKTSQAIKILKQVGAYADAEKAKDS 190
>pdb|3IZS|D Chain D, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|D Chain D, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|D Chain D, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|C Chain C, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|C Chain C, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|C Chain C, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 362
Score = 160 bits (405), Expect = 7e-40, Method: Compositional matrix adjust.
Identities = 92/141 (65%), Positives = 116/141 (82%)
Query: 18 VARPLITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQT 77
++RP +TV+S E T + LP+VF APIRPD+V+ V +++KN RQ YAVS+ AGHQT
Sbjct: 1 MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT 60
Query: 78 SAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRY 137
SAESWGTGRAVARIPRV GGGT RSGQGAFGNMCR GRMFAPT+ WR+W+ KVN N++RY
Sbjct: 61 SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY 120
Query: 138 AMVSAIAASSVPALVMSKGHQ 158
A SAIAA++V +LV+++GH+
Sbjct: 121 ATASAIAATAVASLVLARGHR 141
Score = 134 bits (338), Expect = 4e-32, Method: Compositional matrix adjust.
Identities = 85/147 (57%), Positives = 107/147 (72%), Gaps = 11/147 (7%)
Query: 130 VNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAF 189
VN N+R+ VS A GHQTSAESWGTGRAVARIPRV GGGT RSGQGAF
Sbjct: 42 VNKNKRQAYAVSEKA-----------GHQTSAESWGTGRAVARIPRVGGGGTGRSGQGAF 90
Query: 190 GNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPL 249
GNMCR GRMFAPT+ WR+W+ KVN N++RYA SAIAA++V +LV+++GH ++ +PE PL
Sbjct: 91 GNMCRGGRMFAPTKTWRKWNVKVNHNEKRYATASAIAATAVASLVLARGHRVEKIPEIPL 150
Query: 250 VVSDKIQEYKKTKQATIFLHRIKAWND 276
VVS ++ +KTK+A L + A +D
Sbjct: 151 VVSTDLESIQKTKEAVAALKAVGAHSD 177
>pdb|2WW9|H Chain H, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound
To The Yeast 80s Ribosome
pdb|2WWA|H Chain H, Cryo-Em Structure Of Idle Yeast Ssh1 Complex Bound To The
Yeast 80s Ribosome
pdb|2WWB|H Chain H, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound To
The Actively Translating Wheat Germ 80s Ribosome
Length = 362
Score = 160 bits (405), Expect = 7e-40, Method: Compositional matrix adjust.
Identities = 92/141 (65%), Positives = 116/141 (82%)
Query: 18 VARPLITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQT 77
++RP +TV+S E T + LP+VF APIRPD+V+ V +++KN RQ YAVS+ AGHQT
Sbjct: 1 MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT 60
Query: 78 SAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRY 137
SAESWGTGRAVARIPRV GGGT RSGQGAFGNMCR GRMFAPT+ WR+W+ KVN N++RY
Sbjct: 61 SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY 120
Query: 138 AMVSAIAASSVPALVMSKGHQ 158
A SAIAA++V +LV+++GH+
Sbjct: 121 ATASAIAATAVASLVLARGHR 141
Score = 134 bits (338), Expect = 4e-32, Method: Compositional matrix adjust.
Identities = 85/147 (57%), Positives = 107/147 (72%), Gaps = 11/147 (7%)
Query: 130 VNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAF 189
VN N+R+ VS A GHQTSAESWGTGRAVARIPRV GGGT RSGQGAF
Sbjct: 42 VNKNKRQAYAVSEKA-----------GHQTSAESWGTGRAVARIPRVGGGGTGRSGQGAF 90
Query: 190 GNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPL 249
GNMCR GRMFAPT+ WR+W+ KVN N++RYA SAIAA++V +LV+++GH ++ +PE PL
Sbjct: 91 GNMCRGGRMFAPTKTWRKWNVKVNHNEKRYATASAIAATAVASLVLARGHRVEKIPEIPL 150
Query: 250 VVSDKIQEYKKTKQATIFLHRIKAWND 276
VVS ++ +KTK+A L + A +D
Sbjct: 151 VVSTDLESIQKTKEAVAALKAVGAHSD 177
>pdb|1S1I|D Chain D, 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 = 361
Score = 160 bits (405), Expect = 8e-40, Method: Compositional matrix adjust.
Identities = 92/140 (65%), Positives = 115/140 (82%)
Query: 19 ARPLITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTS 78
+RP +TV+S E T + LP+VF APIRPD+V+ V +++KN RQ YAVS+ AGHQTS
Sbjct: 1 SRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQTS 60
Query: 79 AESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYA 138
AESWGTGRAVARIPRV GGGT RSGQGAFGNMCR GRMFAPT+ WR+W+ KVN N++RYA
Sbjct: 61 AESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRYA 120
Query: 139 MVSAIAASSVPALVMSKGHQ 158
SAIAA++V +LV+++GH+
Sbjct: 121 TASAIAATAVASLVLARGHR 140
Score = 134 bits (338), Expect = 4e-32, Method: Compositional matrix adjust.
Identities = 85/147 (57%), Positives = 107/147 (72%), Gaps = 11/147 (7%)
Query: 130 VNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAF 189
VN N+R+ VS A GHQTSAESWGTGRAVARIPRV GGGT RSGQGAF
Sbjct: 41 VNKNKRQAYAVSEKA-----------GHQTSAESWGTGRAVARIPRVGGGGTGRSGQGAF 89
Query: 190 GNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPL 249
GNMCR GRMFAPT+ WR+W+ KVN N++RYA SAIAA++V +LV+++GH ++ +PE PL
Sbjct: 90 GNMCRGGRMFAPTKTWRKWNVKVNHNEKRYATASAIAATAVASLVLARGHRVEKIPEIPL 149
Query: 250 VVSDKIQEYKKTKQATIFLHRIKAWND 276
VVS ++ +KTK+A L + A +D
Sbjct: 150 VVSTDLESIQKTKEAVAALKAVGAHSD 176
>pdb|3JYW|D Chain D, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 257
Score = 155 bits (391), Expect = 3e-38, Method: Compositional matrix adjust.
Identities = 90/138 (65%), Positives = 112/138 (81%)
Query: 23 ITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESW 82
+TV+S E T + LP+VF APIRPD+V+ V +++KN RQ YAVS+ AGHQTSAESW
Sbjct: 2 VTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQTSAESW 61
Query: 83 GTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSA 142
GTGRAVARIPRV GGGT RSGQGAFGNMCR GRMFAPT+ WR+W+ KVN N++RYA SA
Sbjct: 62 GTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRYATASA 121
Query: 143 IAASSVPALVMSKGHQTS 160
IAA++V +LV+++GH+
Sbjct: 122 IAATAVASLVLARGHRVE 139
Score = 133 bits (335), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 85/147 (57%), Positives = 107/147 (72%), Gaps = 11/147 (7%)
Query: 130 VNVNQRRYAMVSAIAASSVPALVMSKGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAF 189
VN N+R+ VS A GHQTSAESWGTGRAVARIPRV GGGT RSGQGAF
Sbjct: 38 VNKNKRQAYAVSEKA-----------GHQTSAESWGTGRAVARIPRVGGGGTGRSGQGAF 86
Query: 190 GNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPL 249
GNMCR GRMFAPT+ WR+W+ KVN N++RYA SAIAA++V +LV+++GH ++ +PE PL
Sbjct: 87 GNMCRGGRMFAPTKTWRKWNVKVNHNEKRYATASAIAATAVASLVLARGHRVEKIPEIPL 146
Query: 250 VVSDKIQEYKKTKQATIFLHRIKAWND 276
VVS ++ +KTK+A L + A +D
Sbjct: 147 VVSTDLESIQKTKEAVAALKAVGAHSD 173
>pdb|4A17|C Chain C, 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|C Chain C, 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|C Chain C, 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|C Chain C, 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 = 410
Score = 155 bits (391), Expect = 4e-38, Method: Compositional matrix adjust.
Identities = 78/128 (60%), Positives = 99/128 (77%), Gaps = 2/128 (1%)
Query: 156 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVN 215
GH SAESWGTGRAVARIPRV G GTHRSGQ AFGN CR GRMFAP + +RR HR+VNVN
Sbjct: 66 GH--SAESWGTGRAVARIPRVGGSGTHRSGQAAFGNQCRKGRMFAPLKTYRRVHRRVNVN 123
Query: 216 QRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKAWN 275
Q+R+A+ +A+AAS++ LV ++GH I +V E P V D ++ Y+KTKQA FL R+ A++
Sbjct: 124 QKRHAVAAALAASALVPLVFARGHRISNVQELPYVFDDSVESYEKTKQAVAFLKRVGAYD 183
Query: 276 DVLKVQSS 283
DVL+V +
Sbjct: 184 DVLRVAET 191
Score = 147 bits (372), Expect = 5e-36, Method: Compositional matrix adjust.
Identities = 101/223 (45%), Positives = 132/223 (59%), Gaps = 35/223 (15%)
Query: 18 VARPLITVYS--EKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVS----K 71
+RP I V+ E N+ T +TLP+VF APIR D+V+ V +L+KN +Q V
Sbjct: 2 TSRPQIHVHDAKEANKQTATKLTLPAVFTAPIRTDIVHKVFTDLNKNRKQASGVKISTRG 61
Query: 72 DAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVN 131
AG SAESWGTGRAVARIPRV G GTHRSGQ AFGN CR GRMFAP + +RR HR+VN
Sbjct: 62 TAGMGHSAESWGTGRAVARIPRVGGSGTHRSGQAAFGNQCRKGRMFAPLKTYRRVHRRVN 121
Query: 132 VNQRRYAMVSAIAASSVPALVMSKGH------------QTSAESW-GTGRAVARIPRVRG 178
VNQ+R+A+ +A+AAS++ LV ++GH S ES+ T +AVA + RV
Sbjct: 122 VNQKRHAVAAALAASALVPLVFARGHRISNVQELPYVFDDSVESYEKTKQAVAFLKRV-- 179
Query: 179 GGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAM 221
GA+ ++ R A T+ R K + RRY +
Sbjct: 180 --------GAYDDVLR----VAETKALRAGQGK--LRNRRYKL 208
>pdb|3J21|D Chain D, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 255
Score = 75.1 bits (183), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 37/128 (28%), Positives = 73/128 (57%), Gaps = 4/128 (3%)
Query: 156 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVN 215
G + E+ G G ++AR+ R++ + AF R GR P ++ + +N
Sbjct: 53 GKRRVTENIGKGHSMARVERLKTPPRY----AAFVPFARGGRRTHPPKVEKIIWEDINKK 108
Query: 216 QRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKAWN 275
++R A++SAIAA++ LV ++GH+I +VP+ PL+V D +Q+ +KT++ ++ W+
Sbjct: 109 EKRLALMSAIAATANYDLVRARGHIIDNVPQLPLIVVDDLQKVQKTRETREIFKKLGIWD 168
Query: 276 DVLKVQSS 283
D+++ +
Sbjct: 169 DIVRAKEK 176
Score = 59.3 bits (142), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 39/135 (28%), Positives = 67/135 (49%), Gaps = 5/135 (3%)
Query: 23 ITVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESW 82
+ V+ +P G+ + LP VF P RPD++ + QP AG + E+
Sbjct: 3 VKVFDLNGQPVGE-IELPKVFFTPFRPDLIRRAVIASWTHRIQPQGRDPMAGKRRVTENI 61
Query: 83 GTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSA 142
G G ++AR+ R++ + AF R GR P ++ + +N ++R A++SA
Sbjct: 62 GKGHSMARVERLKTPPRY----AAFVPFARGGRRTHPPKVEKIIWEDINKKEKRLALMSA 117
Query: 143 IAASSVPALVMSKGH 157
IAA++ LV ++GH
Sbjct: 118 IAATANYDLVRARGH 132
>pdb|1FFK|C Chain C, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1GIY|F Chain F, 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|1ML5|FF Chain f, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
pdb|1YL3|F Chain F, 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|F Chain F, 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|F Chain F, 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|F Chain F, 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
Length = 246
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 42/135 (31%), Positives = 68/135 (50%), Gaps = 8/135 (5%)
Query: 24 TVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWG 83
T+Y G+ V LP VF+ P+R D++ + N +Q Y + AG +T AES+G
Sbjct: 4 TIYDLDGNTDGE-VDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESFG 62
Query: 84 TGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAI 143
+GR A +P++ G R Q GR P + + +N +R+ A+ SA+
Sbjct: 63 SGRGQAHVPKL-DGRARRVPQAV------KGRSAHPPKTEKDRSLDLNDKERQLAVRSAL 115
Query: 144 AASSVPALVMSKGHQ 158
AA++ LV +GH+
Sbjct: 116 AATADADLVADRGHE 130
Score = 48.1 bits (113), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 38/128 (29%), Positives = 63/128 (49%), Gaps = 8/128 (6%)
Query: 156 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVN 215
G +T AES+G+GR A +P++ G R Q GR P + + +N
Sbjct: 53 GLRTPAESFGSGRGQAHVPKL-DGRARRVPQAV------KGRSAHPPKTEKDRSLDLNDK 105
Query: 216 QRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKAWN 275
+R+ A+ SA+AA++ LV +GH D E P+VVSD ++ KT++ L +
Sbjct: 106 ERQLAVRSALAATADADLVADRGHEF-DRDEVPVVVSDDFEDLVKTQEVVSLLEALDVHA 164
Query: 276 DVLKVQSS 283
D+ + +
Sbjct: 165 DIDRADET 172
>pdb|1JJ2|C Chain C, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|C Chain C, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|E Chain E, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|E Chain E, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|E Chain E, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|E Chain E, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|E Chain E, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1K73|E Chain E, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|E Chain E, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|E Chain E, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|E Chain E, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|E Chain E, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|E Chain E, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|E Chain E, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|E Chain E, 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|C Chain C, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|C Chain C, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1S72|C Chain C, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1W2B|C Chain C, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|1YHQ|C Chain C, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|C Chain C, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|C Chain C, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|C Chain C, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|C Chain C, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|C Chain C, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|C Chain C, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|C Chain C, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|C Chain C, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|C Chain C, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|C Chain C, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|C Chain C, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|C Chain C, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|C Chain C, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|C Chain C, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|C Chain C, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|C Chain C, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|C Chain C, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|C Chain C, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|C Chain C, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|C Chain C, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|C Chain C, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|2QEX|C Chain C, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3CXC|C Chain C, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
pdb|3OW2|C Chain C, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 246
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 42/135 (31%), Positives = 68/135 (50%), Gaps = 8/135 (5%)
Query: 24 TVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWG 83
T+Y G+ V LP VF+ P+R D++ + N +Q Y + AG +T AES+G
Sbjct: 4 TIYDLDGNTDGE-VDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESFG 62
Query: 84 TGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAI 143
+GR A +P++ G R Q GR P + + +N +R+ A+ SA+
Sbjct: 63 SGRGQAHVPKL-DGRARRVPQAV------KGRSAHPPKTEKDRSLDLNDKERQLAVRSAL 115
Query: 144 AASSVPALVMSKGHQ 158
AA++ LV +GH+
Sbjct: 116 AATADADLVADRGHE 130
Score = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 38/128 (29%), Positives = 63/128 (49%), Gaps = 8/128 (6%)
Query: 156 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVN 215
G +T AES+G+GR A +P++ G R Q GR P + + +N
Sbjct: 53 GLRTPAESFGSGRGQAHVPKL-DGRARRVPQAV------KGRSAHPPKTEKDRSLDLNDK 105
Query: 216 QRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKAWN 275
+R+ A+ SA+AA++ LV +GH D E P+VVSD ++ KT++ L +
Sbjct: 106 ERQLAVRSALAATADADLVADRGHEF-DRDEVPVVVSDDFEDLVKTQEVVSLLEALDVHA 164
Query: 276 DVLKVQSS 283
D+ + +
Sbjct: 165 DIDRADET 172
>pdb|3CC2|C Chain C, 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|C Chain C, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|C Chain C, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|C Chain C, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|C Chain C, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|C Chain C, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|3G4S|C Chain C, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|C Chain C, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|C Chain C, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|3I55|C Chain C, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|C Chain C, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
pdb|4ADX|C Chain C, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 246
Score = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 42/135 (31%), Positives = 68/135 (50%), Gaps = 8/135 (5%)
Query: 24 TVYSEKNEPTGQTVTLPSVFKAPIRPDVVNFVHQNLSKNHRQPYAVSKDAGHQTSAESWG 83
T+Y G+ V LP VF+ P+R D++ + N +Q Y + AG +T AES+G
Sbjct: 4 TIYDLDGNTDGE-VDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESFG 62
Query: 84 TGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVNQRRYAMVSAI 143
+GR A +P+ + G R Q GR P + + +N +R+ A+ SA+
Sbjct: 63 SGRGQAHVPK-QDGRARRVPQAV------KGRSAHPPKTEKDRSLDLNDKERQLAVRSAL 115
Query: 144 AASSVPALVMSKGHQ 158
AA++ LV +GH+
Sbjct: 116 AATADADLVADRGHE 130
Score = 47.4 bits (111), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 38/128 (29%), Positives = 63/128 (49%), Gaps = 8/128 (6%)
Query: 156 GHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRAGRMFAPTRIWRRWHRKVNVN 215
G +T AES+G+GR A +P+ + G R Q GR P + + +N
Sbjct: 53 GLRTPAESFGSGRGQAHVPK-QDGRARRVPQAV------KGRSAHPPKTEKDRSLDLNDK 105
Query: 216 QRRYAMVSAIAASSVPALVMSKGHMIQDVPEFPLVVSDKIQEYKKTKQATIFLHRIKAWN 275
+R+ A+ SA+AA++ LV +GH D E P+VVSD ++ KT++ L +
Sbjct: 106 ERQLAVRSALAATADADLVADRGHEF-DRDEVPVVVSDDFEDLVKTQEVVSLLEALDVHA 164
Query: 276 DVLKVQSS 283
D+ + +
Sbjct: 165 DIDRADET 172
>pdb|3BBO|G Chain G, Homology Model For The Spinach Chloroplast 50s Subunit
Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
Length = 293
Score = 31.2 bits (69), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 38/74 (51%), Gaps = 13/74 (17%)
Query: 83 GTGRAVARIPRVRGGG--------THRSGQGAFGNMCR--AGRMFAPTRIWRRWHRKVNV 132
GT + R VRGGG T R+ +G+ G+ R G +F P R W K+N
Sbjct: 98 GTASTLTRA-EVRGGGRKPYPQKKTGRARRGSQGSPLRPGGGVIFGPKP--RDWTIKMNK 154
Query: 133 NQRRYAMVSAIAAS 146
+RR A+ +AIA++
Sbjct: 155 KERRLALSTAIASA 168
Score = 31.2 bits (69), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 38/74 (51%), Gaps = 13/74 (17%)
Query: 165 GTGRAVARIPRVRGGG--------THRSGQGAFGNMCR--AGRMFAPTRIWRRWHRKVNV 214
GT + R VRGGG T R+ +G+ G+ R G +F P R W K+N
Sbjct: 98 GTASTLTRA-EVRGGGRKPYPQKKTGRARRGSQGSPLRPGGGVIFGPKP--RDWTIKMNK 154
Query: 215 NQRRYAMVSAIAAS 228
+RR A+ +AIA++
Sbjct: 155 KERRLALSTAIASA 168
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
0.322 0.132 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,677,463
Number of Sequences: 62578
Number of extensions: 354870
Number of successful extensions: 733
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 697
Number of HSP's gapped (non-prelim): 29
length of query: 286
length of database: 14,973,337
effective HSP length: 98
effective length of query: 188
effective length of database: 8,840,693
effective search space: 1662050284
effective search space used: 1662050284
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 bits)