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= 029857
(186 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|P Chain P, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 204
Score = 308 bits (788), Expect = 1e-84, Method: Compositional matrix adjust.
Identities = 149/186 (80%), Positives = 161/186 (86%)
Query: 1 MRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXXXXXXXXXXXXXXXXXX 60
MRF+QRVRCWEYRQ P+IVR+TRPTRPDKARRLGYKAKQ
Sbjct: 19 MRFVQRVRCWEYRQQPAIVRLTRPTRPDKARRLGYKAKQGYVVYRVRVRRGGRKRPVPKG 78
Query: 61 IVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAA 120
IVYGKP +QG+TQLKFQR+KRSVAEERAGRKLGGL+VLNSYW+NEDSTYKYFE+ILVD A
Sbjct: 79 IVYGKPKHQGITQLKFQRNKRSVAEERAGRKLGGLRVLNSYWVNEDSTYKYFEIILVDVA 138
Query: 121 HNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHHKARPSRRATWKRNQTL 180
H+AIRNDPRINW+CKPVHKHRELRGLTSAGKKYRGLRGKGH HHKARPSRRATWKRNQT+
Sbjct: 139 HSAIRNDPRINWLCKPVHKHRELRGLTSAGKKYRGLRGKGHTHHKARPSRRATWKRNQTV 198
Query: 181 SLRRYR 186
SLRRYR
Sbjct: 199 SLRRYR 204
>pdb|3IZS|P Chain P, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|O Chain O, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|O Chain O, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|N Chain N, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|N Chain N, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|N Chain N, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 204
Score = 223 bits (568), Expect = 4e-59, Method: Compositional matrix adjust.
Identities = 115/186 (61%), Positives = 127/186 (68%), Gaps = 1/186 (0%)
Query: 1 MRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXXXXXXXXXXXXXXXXXX 60
+RFLQRVR WEYRQ I R RPTRPDKARRLGYKAKQ
Sbjct: 19 LRFLQRVRVWEYRQKNVIHRAARPTRPDKARRLGYKAKQGFVIYRVRVRRGNRKRPVPKG 78
Query: 61 IVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAA 120
YGKPTNQGV +LK+QRS R+ AEER GR+ L+VLNSYW+N+DSTYKYFEVILVD
Sbjct: 79 ATYGKPTNQGVNELKYQRSLRATAEERVGRRAANLRVLNSYWVNQDSTYKYFEVILVDPQ 138
Query: 121 HNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHHKARPSRRATWKRNQTL 180
H AIR D R NWIC PVHKHRE RGLT+ GKK RG+ KGH + + RR TWKR TL
Sbjct: 139 HKAIRRDARYNWICDPVHKHREARGLTATGKKSRGI-NKGHKFNNTKAGRRKTWKRQNTL 197
Query: 181 SLRRYR 186
SL RYR
Sbjct: 198 SLWRYR 203
>pdb|1S1I|L Chain L, 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 = 203
Score = 223 bits (568), Expect = 5e-59, Method: Compositional matrix adjust.
Identities = 115/186 (61%), Positives = 127/186 (68%), Gaps = 1/186 (0%)
Query: 1 MRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXXXXXXXXXXXXXXXXXX 60
+RFLQRVR WEYRQ I R RPTRPDKARRLGYKAKQ
Sbjct: 18 LRFLQRVRVWEYRQKNVIHRAARPTRPDKARRLGYKAKQGFVIYRVRVRRGNRKRPVPKG 77
Query: 61 IVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAA 120
YGKPTNQGV +LK+QRS R+ AEER GR+ L+VLNSYW+N+DSTYKYFEVILVD
Sbjct: 78 ATYGKPTNQGVNELKYQRSLRATAEERVGRRAANLRVLNSYWVNQDSTYKYFEVILVDPQ 137
Query: 121 HNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHHKARPSRRATWKRNQTL 180
H AIR D R NWIC PVHKHRE RGLT+ GKK RG+ KGH + + RR TWKR TL
Sbjct: 138 HKAIRRDARYNWICDPVHKHREARGLTATGKKSRGI-NKGHKFNNTKAGRRKTWKRQNTL 196
Query: 181 SLRRYR 186
SL RYR
Sbjct: 197 SLWRYR 202
>pdb|2ZKR|MM Chain m, 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 = 204
Score = 219 bits (557), Expect = 1e-57, Method: Compositional matrix adjust.
Identities = 115/187 (61%), Positives = 128/187 (68%), Gaps = 2/187 (1%)
Query: 1 MRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXXXXXXXXXXXXXXXXXX 60
MRFL RVRCW+YRQ ++ R RPTRPDKARRLGYKAKQ
Sbjct: 19 MRFLLRVRCWQYRQLSALHRAPRPTRPDKARRLGYKAKQGYVIYRIRVRRGGRKRPVPKG 78
Query: 61 IVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAA 120
YGKP + GV QLKF RS +SVAEERAGR G L+VLNSYW+ EDSTYK+FEVIL+D
Sbjct: 79 ATYGKPVHHGVNQLKFARSLQSVAEERAGRHCGALRVLNSYWVGEDSTYKFFEVILIDPF 138
Query: 121 HNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGH-LHHKARPSRRATWKRNQT 179
H AIR +P WI KPVHKHRE+RGLTSAG+K RGL GKGH HH SRRA W+R T
Sbjct: 139 HKAIRRNPDTQWITKPVHKHREMRGLTSAGRKSRGL-GKGHKFHHTIGGSRRAAWRRRNT 197
Query: 180 LSLRRYR 186
L L RYR
Sbjct: 198 LQLHRYR 204
>pdb|3JYW|L Chain L, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 192
Score = 212 bits (540), Expect = 9e-56, Method: Compositional matrix adjust.
Identities = 108/176 (61%), Positives = 120/176 (68%), Gaps = 1/176 (0%)
Query: 1 MRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXXXXXXXXXXXXXXXXXX 60
+RFLQRVR WEYRQ I R RPTRPDKARRLGYKAKQ
Sbjct: 18 LRFLQRVRVWEYRQKNVIHRAARPTRPDKARRLGYKAKQGFVIYRVRVRRGNRKRPVPKG 77
Query: 61 IVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAA 120
YGKPTNQGV +LK+QRS R+ AEER GR+ L+VLNSYW+N+DSTYKYFEVILVD
Sbjct: 78 ATYGKPTNQGVNELKYQRSLRATAEERVGRRAANLRVLNSYWVNQDSTYKYFEVILVDPQ 137
Query: 121 HNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHHKARPSRRATWKR 176
H AIR D R NWIC PVHKHRE RGLT+ GKK RG+ KGH + + RR TWKR
Sbjct: 138 HKAIRRDARYNWICDPVHKHREARGLTATGKKSRGI-NKGHKFNNTKAGRRKTWKR 192
>pdb|4A17|L Chain L, 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|L Chain L, 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|L Chain L, 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|L Chain L, 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 = 204
Score = 210 bits (534), Expect = 5e-55, Method: Compositional matrix adjust.
Identities = 104/186 (55%), Positives = 127/186 (68%)
Query: 1 MRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXXXXXXXXXXXXXXXXXX 60
M F+ R+R WEYRQ P I + +R +RPDKAR+LGYK K
Sbjct: 19 MSFILRLRTWEYRQLPVIHKASRSSRPDKARKLGYKNKDGYAIWRVRVRRGGRKRPVSKG 78
Query: 61 IVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAA 120
IVYGKP++ G+ QLKF R+ RS AEER G+++ L+VLNSYW+ +D TYK++EVIL D +
Sbjct: 79 IVYGKPSSVGINQLKFARNLRSCAEERVGKRVPELRVLNSYWVGQDGTYKFYEVILADPS 138
Query: 121 HNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHHKARPSRRATWKRNQTL 180
HNAIRNDPRINWIC+ HKHRELRGLTSAG+K RGLR KGH R SR+ W+ Q L
Sbjct: 139 HNAIRNDPRINWICESAHKHRELRGLTSAGRKGRGLRVKGHRAKSLRTSRKGNWRARQML 198
Query: 181 SLRRYR 186
LRRYR
Sbjct: 199 KLRRYR 204
>pdb|3ZF7|Q Chain Q, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 221
Score = 185 bits (470), Expect = 1e-47, Method: Compositional matrix adjust.
Identities = 93/169 (55%), Positives = 111/169 (65%)
Query: 1 MRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXXXXXXXXXXXXXXXXXX 60
MRF+QRVR WE+R +IVR+ RPTRP+KAR +GYK KQ
Sbjct: 36 MRFIQRVRAWEFRHQHTIVRLRRPTRPEKARMVGYKTKQGYVVFRVRVRRGGRKRPVHKG 95
Query: 61 IVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAA 120
I YGKP GV K ++ R VAE+R G+K G L+VLNSYW+N DST+ ++EV+ VD
Sbjct: 96 ITYGKPNTAGVLGRKLNKNNRVVAEQRLGKKYGNLRVLNSYWVNADSTFLWYEVVAVDPM 155
Query: 121 HNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHHKARPS 169
H AIR DPRINWI VHKHRE RGLTSAG+K+RGLR KGH K RPS
Sbjct: 156 HRAIRRDPRINWIVNAVHKHREQRGLTSAGRKHRGLRQKGHKASKLRPS 204
>pdb|3J21|M Chain M, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 194
Score = 133 bits (335), Expect = 6e-32, Method: Compositional matrix adjust.
Identities = 77/170 (45%), Positives = 99/170 (58%), Gaps = 2/170 (1%)
Query: 4 LQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXXXXXXXXXXXXXXXXXXIVY 63
L + R ++R+ P +VR+ RPTR D+AR LGY+AKQ
Sbjct: 22 LLKQRMIKWRREPVVVRIERPTRLDRARALGYQAKQGYVIVRVRVRKGGRKRPRWKG--G 79
Query: 64 GKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAAHNA 123
KP+ G + ++S + +AEE+A RK L+VLNSYW+ ED YK+FEVI+VD H
Sbjct: 80 RKPSKMGQVKYSPKKSLQWIAEEKAARKFPNLEVLNSYWVGEDGMYKWFEVIMVDPHHPV 139
Query: 124 IRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHHKARPSRRAT 173
I++DP+I WI HK R RGLTSAGKK RGLR KG K RPS RA
Sbjct: 140 IKSDPKIAWIALKHHKGRVFRGLTSAGKKGRGLRNKGKGAEKVRPSIRAN 189
>pdb|1JJ2|L Chain L, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|L Chain L, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|N Chain N, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|N Chain N, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|N Chain N, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|N Chain N, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|N Chain N, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1K73|N Chain N, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|N Chain N, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|N Chain N, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|N Chain N, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|N Chain N, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|N Chain N, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|N Chain N, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|N Chain N, 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|L Chain L, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|L Chain L, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1W2B|L Chain L, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|3CXC|L Chain L, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
pdb|3OW2|L Chain L, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 194
Score = 120 bits (301), Expect = 5e-28, Method: Compositional matrix adjust.
Identities = 69/166 (41%), Positives = 96/166 (57%), Gaps = 2/166 (1%)
Query: 8 RCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXXXXXXXXXXXXXXXXXXIVYGKPT 67
R E+R P++VR+ RPTR D+AR LGYKAKQ K
Sbjct: 27 RMQEWRNEPAVVRIERPTRLDRARSLGYKAKQGIIVVRVAIRKGSSRRTRFNKGRRSK-- 84
Query: 68 NQGVTQLKFQRSKRSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAAHNAIRND 127
V ++ +++ + +AEERA RK L+VLNSY + ED +K+ EVIL+D H AI++D
Sbjct: 85 RMMVNRITRKKNIQRIAEERANRKFPNLRVLNSYSVGEDGRHKWHEVILIDPDHPAIKSD 144
Query: 128 PRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHHKARPSRRAT 173
+++WI + H+ R RGLTSAG++ RGLRG+G K RPS R
Sbjct: 145 DQLSWISRTRHRLRTFRGLTSAGRRCRGLRGQGKGSEKVRPSLRVN 190
>pdb|1FFK|I Chain I, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
Length = 194
Score = 120 bits (300), Expect = 5e-28, Method: Compositional matrix adjust.
Identities = 73/176 (41%), Positives = 101/176 (57%), Gaps = 18/176 (10%)
Query: 8 RCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXXXXXXXXXXXXXXXXXXIVYGKPT 67
R ++R+ P++VR+ RPTR D+AR LGYKAK+
Sbjct: 27 RLQKWRREPAVVRIPRPTRLDRARALGYKAKKGIIVVRVRIRRGGRRATR---------P 77
Query: 68 NQGVTQLKFQRSKRS-------VAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAA 120
N+G K ++R +AEERA RK ++VLNSYW+ ED YK+FEVILVD
Sbjct: 78 NKGRKSKKMMVNRRPRKKNLQWIAEERANRKYPNMEVLNSYWVGEDGRYKWFEVILVDRD 137
Query: 121 HNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHHKARPSRRATWKR 176
H AI++DP+++W+ + + R RGLTSAG+K RGLR KG K RPS RA +++
Sbjct: 138 HPAIKSDPQLSWVSR--TRGRVYRGLTSAGRKARGLRRKGRGAEKVRPSLRANFRK 191
>pdb|1VQ9|M Chain M, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|M Chain M, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|M Chain M, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|M Chain M, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|M Chain M, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|M Chain M, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
Length = 195
Score = 116 bits (290), Expect = 9e-27, Method: Compositional matrix adjust.
Identities = 71/170 (41%), Positives = 91/170 (53%), Gaps = 2/170 (1%)
Query: 4 LQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXXXXXXXXXXXXXXXXXXIVY 63
LQ R E+R ++ R+ RPTR DKAR GYKAKQ
Sbjct: 24 LQWQRQQEWRNEGAVERIERPTRLDKARSQGYKAKQGVIVARVSVRKGSARKRRHKAGRR 83
Query: 64 GKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAAHNA 123
K QGVT++ ++ + VAEERA R L+VLNSY + +D K+ EVIL+D H A
Sbjct: 84 SK--RQGVTRITRRKDIQRVAEERASRTFPNLRVLNSYSVGQDGRQKWHEVILIDPNHPA 141
Query: 124 IRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHHKARPSRRAT 173
I+ND ++WIC R RGLT AG++ RGL GKG K RPS R+
Sbjct: 142 IQNDDDLSWICADDQADRVFRGLTGAGRRNRGLSGKGKGSEKTRPSLRSN 191
>pdb|3CC2|M Chain M, 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|M Chain M, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|M Chain M, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|M Chain M, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|M Chain M, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|M Chain M, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|M Chain M, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|M Chain M, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|M Chain M, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|M Chain M, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|M Chain M, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|M Chain M, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|M Chain M, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|L Chain L, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|M Chain M, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|M Chain M, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|4ADX|M Chain M, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 196
Score = 116 bits (290), Expect = 9e-27, Method: Compositional matrix adjust.
Identities = 71/170 (41%), Positives = 91/170 (53%), Gaps = 2/170 (1%)
Query: 4 LQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXXXXXXXXXXXXXXXXXXIVY 63
LQ R E+R ++ R+ RPTR DKAR GYKAKQ
Sbjct: 24 LQWQRQQEWRNEGAVERIERPTRLDKARSQGYKAKQGVIVARVSVRKGSARKRRHKAGRR 83
Query: 64 GKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAAHNA 123
K QGVT++ ++ + VAEERA R L+VLNSY + +D K+ EVIL+D H A
Sbjct: 84 SK--RQGVTRITRRKDIQRVAEERASRTFPNLRVLNSYSVGQDGRQKWHEVILIDPNHPA 141
Query: 124 IRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHHKARPSRRAT 173
I+ND ++WIC R RGLT AG++ RGL GKG K RPS R+
Sbjct: 142 IQNDDDLSWICADDQADRVFRGLTGAGRRNRGLSGKGKGSEKTRPSLRSN 191
>pdb|2QA4|M Chain M, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|2QEX|M Chain M, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
Length = 196
Score = 116 bits (290), Expect = 9e-27, Method: Compositional matrix adjust.
Identities = 71/170 (41%), Positives = 91/170 (53%), Gaps = 2/170 (1%)
Query: 4 LQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXXXXXXXXXXXXXXXXXXIVY 63
LQ R E+R ++ R+ RPTR DKAR GYKAKQ
Sbjct: 24 LQWQRQQEWRNEGAVERIERPTRLDKARSQGYKAKQGVIVARVSVRKGSARKRRHKAGRR 83
Query: 64 GKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAAHNA 123
K QGVT++ ++ + VAEERA R L+VLNSY + +D K+ EVIL+D H A
Sbjct: 84 SK--RQGVTRITRRKDIQRVAEERASRTFPNLRVLNSYSVGQDGRQKWHEVILIDPNHPA 141
Query: 124 IRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHHKARPSRRAT 173
I+ND ++WIC R RGLT AG++ RGL GKG K RPS R+
Sbjct: 142 IQNDDDLSWICADDQADRVFRGLTGAGRRNRGLSGKGKGSEKTRPSLRSN 191
>pdb|1YI2|M Chain M, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|M Chain M, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|M Chain M, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|M Chain M, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|M Chain M, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|M Chain M, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
Length = 195
Score = 116 bits (290), Expect = 9e-27, Method: Compositional matrix adjust.
Identities = 71/170 (41%), Positives = 91/170 (53%), Gaps = 2/170 (1%)
Query: 4 LQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXXXXXXXXXXXXXXXXXXIVY 63
LQ R E+R ++ R+ RPTR DKAR GYKAKQ
Sbjct: 24 LQWQRQQEWRNEGAVERIERPTRLDKARSQGYKAKQGVIVARVSVRKGSARKRRHKAGRR 83
Query: 64 GKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAAHNA 123
K QGVT++ ++ + VAEERA R L+VLNSY + +D K+ EVIL+D H A
Sbjct: 84 SK--RQGVTRITRRKDIQRVAEERASRTFPNLRVLNSYSVGQDGRQKWHEVILIDPNHPA 141
Query: 124 IRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHHKARPSRRAT 173
I+ND ++WIC R RGLT AG++ RGL GKG K RPS R+
Sbjct: 142 IQNDDDLSWICADDQADRVFRGLTGAGRRNRGLSGKGKGSEKTRPSLRSN 191
>pdb|1S72|M Chain M, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1VQ4|M Chain M, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|M Chain M, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|M Chain M, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|M Chain M, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|M Chain M, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQN|M Chain M, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|M Chain M, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|M Chain M, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
Length = 194
Score = 115 bits (289), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 71/170 (41%), Positives = 91/170 (53%), Gaps = 2/170 (1%)
Query: 4 LQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXXXXXXXXXXXXXXXXXXIVY 63
LQ R E+R ++ R+ RPTR DKAR GYKAKQ
Sbjct: 23 LQWQRQQEWRNEGAVERIERPTRLDKARSQGYKAKQGVIVARVSVRKGSARKRRHKAGRR 82
Query: 64 GKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAAHNA 123
K QGVT++ ++ + VAEERA R L+VLNSY + +D K+ EVIL+D H A
Sbjct: 83 SK--RQGVTRITRRKDIQRVAEERASRTFPNLRVLNSYSVGQDGRQKWHEVILIDPNHPA 140
Query: 124 IRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHHKARPSRRAT 173
I+ND ++WIC R RGLT AG++ RGL GKG K RPS R+
Sbjct: 141 IQNDDDLSWICADDQADRVFRGLTGAGRRNRGLSGKGKGSEKTRPSLRSN 190
>pdb|3G4S|M Chain M, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|M Chain M, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|M Chain M, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|3I55|M Chain M, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|M Chain M, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
Length = 194
Score = 115 bits (289), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 71/170 (41%), Positives = 91/170 (53%), Gaps = 2/170 (1%)
Query: 4 LQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXXXXXXXXXXXXXXXXXXIVY 63
LQ R E+R ++ R+ RPTR DKAR GYKAKQ
Sbjct: 23 LQWQRQQEWRNEGAVERIERPTRLDKARSQGYKAKQGVIVARVSVRKGSARKRRHKAGRR 82
Query: 64 GKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAAHNA 123
K QGVT++ ++ + VAEERA R L+VLNSY + +D K+ EVIL+D H A
Sbjct: 83 SK--RQGVTRITRRKDIQRVAEERASRTFPNLRVLNSYSVGQDGRQKWHEVILIDPNHPA 140
Query: 124 IRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHHKARPSRRAT 173
I+ND ++WIC R RGLT AG++ RGL GKG K RPS R+
Sbjct: 141 IQNDDDLSWICADDQADRVFRGLTGAGRRNRGLSGKGKGSEKTRPSLRSN 190
>pdb|1YHQ|M Chain M, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
Length = 194
Score = 115 bits (289), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 71/170 (41%), Positives = 91/170 (53%), Gaps = 2/170 (1%)
Query: 4 LQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXXXXXXXXXXXXXXXXXXIVY 63
LQ R E+R ++ R+ RPTR DKAR GYKAKQ
Sbjct: 23 LQWQRQQEWRNEGAVERIERPTRLDKARSQGYKAKQGVIVARVSVRKGSARKRRHKAGRR 82
Query: 64 GKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLKVLNSYWINEDSTYKYFEVILVDAAHNA 123
K QGVT++ ++ + VAEERA R L+VLNSY + +D K+ EVIL+D H A
Sbjct: 83 SK--RQGVTRITRRKDIQRVAEERASRTFPNLRVLNSYSVGQDGRQKWHEVILIDPNHPA 140
Query: 124 IRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHHKARPSRRAT 173
I+ND ++WIC R RGLT AG++ RGL GKG K RPS R+
Sbjct: 141 IQNDDDLSWICADDQADRVFRGLTGAGRRNRGLSGKGKGSEKTRPSLRSN 190
>pdb|3N71|A Chain A, Crystal Structure Of Cardiac Specific Histone
Methyltransferase Smyd1
Length = 490
Score = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 22/94 (23%), Positives = 42/94 (44%), Gaps = 19/94 (20%)
Query: 94 GLKVLNSYWINEDSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKY 153
GLK +W + VI + A++A+ D IN++C K +E K +
Sbjct: 20 GLKATKEFWAAD--------VIFAERAYSAVVFDSLINFVCHTCFKRQE--------KLH 63
Query: 154 RGLRGKGHLHHKARPSRRATW--KRNQTLSLRRY 185
R + K H+ R ++ W +N+ ++++Y
Sbjct: 64 RCGQCK-FAHYCDRTCQKDAWLNHKNECAAIKKY 96
>pdb|2VZN|A Chain A, Crystal Structure Of The Major Allergen From Fire Ant
Venom, Sol I 3
pdb|2VZN|B Chain B, Crystal Structure Of The Major Allergen From Fire Ant
Venom, Sol I 3
Length = 218
Score = 27.3 bits (59), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 12/49 (24%)
Query: 110 KYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRG 158
+Y V DA +AI V+KH ELR ++GK+ RG G
Sbjct: 32 EYSNVGFTDAEKDAI------------VNKHNELRQRVASGKEMRGTNG 68
>pdb|1ZXM|A Chain A, Human Topo Iia Atpase/amp-pnp
pdb|1ZXM|B Chain B, Human Topo Iia Atpase/amp-pnp
pdb|1ZXN|A Chain A, Human Dna Topoisomerase Iia AtpaseADP
pdb|1ZXN|B Chain B, Human Dna Topoisomerase Iia AtpaseADP
pdb|1ZXN|C Chain C, Human Dna Topoisomerase Iia AtpaseADP
pdb|1ZXN|D Chain D, Human Dna Topoisomerase Iia AtpaseADP
Length = 400
Score = 26.9 bits (58), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 109 YKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGK 151
YK F+ ILV+AA N R DP+++ I + L + + GK
Sbjct: 54 YKIFDEILVNAADNKQR-DPKMSCIRVTIDPENNLISIWNNGK 95
>pdb|2JY9|A Chain A, Nmr Structure Of Putative Trna Hydrolase Domain From
Salmonella Typhimurium. Northeast Structural Genomics
Consortium Target Str220
Length = 148
Score = 26.6 bits (57), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 20 RVTRPTRPDKARRLGYKAKQ 39
R TRPTR K RRL KA++
Sbjct: 106 RATRPTRASKERRLSSKAQK 125
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.323 0.136 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,119,262
Number of Sequences: 62578
Number of extensions: 175427
Number of successful extensions: 336
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 296
Number of HSP's gapped (non-prelim): 24
length of query: 186
length of database: 14,973,337
effective HSP length: 93
effective length of query: 93
effective length of database: 9,153,583
effective search space: 851283219
effective search space used: 851283219
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: 48 (23.1 bits)