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= 029295
(195 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 = 316 bits (810), Expect = 4e-87, Method: Compositional matrix adjust.
Identities = 158/204 (77%), Positives = 170/204 (83%), Gaps = 9/204 (4%)
Query: 1 MGAYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXX 60
MGAYKYVSELWR+KQSDVMRF+QRVRCWEYRQ P+IVR+TRPTRPDKARRLGYKAKQ
Sbjct: 1 MGAYKYVSELWRRKQSDVMRFVQRVRCWEYRQQPAIVRLTRPTRPDKARRLGYKAKQGYV 60
Query: 61 XXXXXXXXXXXXXXXXXXIVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLK------ 114
IVYGKP +QG+TQLKFQR+KRSVAEERAGRKLGGL+
Sbjct: 61 VYRVRVRRGGRKRPVPKGIVYGKPKHQGITQLKFQRNKRSVAEERAGRKLGGLRVLNSYW 120
Query: 115 ---DSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHL 171
DSTYKYFE+ILVD AH+AIRNDPRINW+CKPVHKHRELRGLTSAGKKYRGLRGKGH
Sbjct: 121 VNEDSTYKYFEIILVDVAHSAIRNDPRINWLCKPVHKHRELRGLTSAGKKYRGLRGKGHT 180
Query: 172 HHKARPSRRATWKRNQTLSLRRYR 195
HHKARPSRRATWKRNQT+SLRRYR
Sbjct: 181 HHKARPSRRATWKRNQTVSLRRYR 204
>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 = 228 bits (581), Expect = 2e-60, Method: Compositional matrix adjust.
Identities = 124/205 (60%), Positives = 137/205 (66%), Gaps = 11/205 (5%)
Query: 1 MGAYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXX 60
MGAYKY+ ELWRKKQSDVMRFL RVRCW+YRQ ++ R RPTRPDKARRLGYKAKQ
Sbjct: 1 MGAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRLGYKAKQGYV 60
Query: 61 XXXXXXXXXXXXXXXXXXIVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLK------ 114
YGKP + GV QLKF RS +SVAEERAGR G L+
Sbjct: 61 IYRIRVRRGGRKRPVPKGATYGKPVHHGVNQLKFARSLQSVAEERAGRHCGALRVLNSYW 120
Query: 115 ---DSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGH- 170
DSTYK+FEVIL+D H AIR +P WI KPVHKHRE+RGLTSAG+K RGL GKGH
Sbjct: 121 VGEDSTYKFFEVILIDPFHKAIRRNPDTQWITKPVHKHREMRGLTSAGRKSRGL-GKGHK 179
Query: 171 LHHKARPSRRATWKRNQTLSLRRYR 195
HH SRRA W+R TL L RYR
Sbjct: 180 FHHTIGGSRRAAWRRRNTLQLHRYR 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 = 227 bits (578), Expect = 4e-60, Method: Compositional matrix adjust.
Identities = 123/204 (60%), Positives = 134/204 (65%), Gaps = 10/204 (4%)
Query: 1 MGAYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXX 60
MGAYKY+ EL RKKQSDV+RFLQRVR WEYRQ I R RPTRPDKARRLGYKAKQ
Sbjct: 1 MGAYKYLEELQRKKQSDVLRFLQRVRVWEYRQKNVIHRAARPTRPDKARRLGYKAKQGFV 60
Query: 61 XXXXXXXXXXXXXXXXXXIVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLK------ 114
YGKPTNQGV +LK+QRS R+ AEER GR+ L+
Sbjct: 61 IYRVRVRRGNRKRPVPKGATYGKPTNQGVNELKYQRSLRATAEERVGRRAANLRVLNSYW 120
Query: 115 ---DSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHL 171
DSTYKYFEVILVD H AIR D R NWIC PVHKHRE RGLT+ GKK RG+ KGH
Sbjct: 121 VNQDSTYKYFEVILVDPQHKAIRRDARYNWICDPVHKHREARGLTATGKKSRGI-NKGHK 179
Query: 172 HHKARPSRRATWKRNQTLSLRRYR 195
+ + RR TWKR TLSL RYR
Sbjct: 180 FNNTKAGRRKTWKRQNTLSLWRYR 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 = 224 bits (571), Expect = 2e-59, Method: Compositional matrix adjust.
Identities = 122/203 (60%), Positives = 133/203 (65%), Gaps = 10/203 (4%)
Query: 2 GAYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXX 61
GAYKY+ EL RKKQSDV+RFLQRVR WEYRQ I R RPTRPDKARRLGYKAKQ
Sbjct: 1 GAYKYLEELQRKKQSDVLRFLQRVRVWEYRQKNVIHRAARPTRPDKARRLGYKAKQGFVI 60
Query: 62 XXXXXXXXXXXXXXXXXIVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLK------- 114
YGKPTNQGV +LK+QRS R+ AEER GR+ L+
Sbjct: 61 YRVRVRRGNRKRPVPKGATYGKPTNQGVNELKYQRSLRATAEERVGRRAANLRVLNSYWV 120
Query: 115 --DSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLH 172
DSTYKYFEVILVD H AIR D R NWIC PVHKHRE RGLT+ GKK RG+ KGH
Sbjct: 121 NQDSTYKYFEVILVDPQHKAIRRDARYNWICDPVHKHREARGLTATGKKSRGI-NKGHKF 179
Query: 173 HKARPSRRATWKRNQTLSLRRYR 195
+ + RR TWKR TLSL RYR
Sbjct: 180 NNTKAGRRKTWKRQNTLSLWRYR 202
>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 = 219 bits (559), Expect = 6e-58, Method: Compositional matrix adjust.
Identities = 113/204 (55%), Positives = 136/204 (66%), Gaps = 9/204 (4%)
Query: 1 MGAYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXX 60
MGAYKY+ ELWRKKQSD+M F+ R+R WEYRQ P I + +R +RPDKAR+LGYK K
Sbjct: 1 MGAYKYLEELWRKKQSDLMSFILRLRTWEYRQLPVIHKASRSSRPDKARKLGYKNKDGYA 60
Query: 61 XXXXXXXXXXXXXXXXXXIVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLK------ 114
IVYGKP++ G+ QLKF R+ RS AEER G+++ L+
Sbjct: 61 IWRVRVRRGGRKRPVSKGIVYGKPSSVGINQLKFARNLRSCAEERVGKRVPELRVLNSYW 120
Query: 115 ---DSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHL 171
D TYK++EVIL D +HNAIRNDPRINWIC+ HKHRELRGLTSAG+K RGLR KGH
Sbjct: 121 VGQDGTYKFYEVILADPSHNAIRNDPRINWICESAHKHRELRGLTSAGRKGRGLRVKGHR 180
Query: 172 HHKARPSRRATWKRNQTLSLRRYR 195
R SR+ W+ Q L LRRYR
Sbjct: 181 AKSLRTSRKGNWRARQMLKLRRYR 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 = 213 bits (543), Expect = 4e-56, Method: Compositional matrix adjust.
Identities = 115/193 (59%), Positives = 126/193 (65%), Gaps = 10/193 (5%)
Query: 2 GAYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXX 61
GAYKY+ EL RKKQSDV+RFLQRVR WEYRQ I R RPTRPDKARRLGYKAKQ
Sbjct: 1 GAYKYLEELQRKKQSDVLRFLQRVRVWEYRQKNVIHRAARPTRPDKARRLGYKAKQGFVI 60
Query: 62 XXXXXXXXXXXXXXXXXIVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLK------- 114
YGKPTNQGV +LK+QRS R+ AEER GR+ L+
Sbjct: 61 YRVRVRRGNRKRPVPKGATYGKPTNQGVNELKYQRSLRATAEERVGRRAANLRVLNSYWV 120
Query: 115 --DSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLH 172
DSTYKYFEVILVD H AIR D R NWIC PVHKHRE RGLT+ GKK RG+ KGH
Sbjct: 121 NQDSTYKYFEVILVDPQHKAIRRDARYNWICDPVHKHREARGLTATGKKSRGI-NKGHKF 179
Query: 173 HKARPSRRATWKR 185
+ + RR TWKR
Sbjct: 180 NNTKAGRRKTWKR 192
>pdb|3ZF7|Q Chain Q, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 221
Score = 187 bits (476), Expect = 3e-48, Method: Compositional matrix adjust.
Identities = 97/187 (51%), Positives = 119/187 (63%), Gaps = 9/187 (4%)
Query: 1 MGAYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXX 60
MG++ Y++ELW+KK SDVMRF+QRVR WE+R +IVR+ RPTRP+KAR +GYK KQ
Sbjct: 18 MGSFMYLNELWKKKSSDVMRFIQRVRAWEFRHQHTIVRLRRPTRPEKARMVGYKTKQGYV 77
Query: 61 XXXXXXXXXXXXXXXXXXIVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLK------ 114
I YGKP GV K ++ R VAE+R G+K G L+
Sbjct: 78 VFRVRVRRGGRKRPVHKGITYGKPNTAGVLGRKLNKNNRVVAEQRLGKKYGNLRVLNSYW 137
Query: 115 ---DSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHL 171
DST+ ++EV+ VD H AIR DPRINWI VHKHRE RGLTSAG+K+RGLR KGH
Sbjct: 138 VNADSTFLWYEVVAVDPMHRAIRRDPRINWIVNAVHKHREQRGLTSAGRKHRGLRQKGHK 197
Query: 172 HHKARPS 178
K RPS
Sbjct: 198 ASKLRPS 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 = 122 bits (307), Expect = 9e-29, Method: Compositional matrix adjust.
Identities = 77/191 (40%), Positives = 102/191 (53%), Gaps = 11/191 (5%)
Query: 1 MGAYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXX 60
MG YKY+ E W+ + + L + R ++R+ P +VR+ RPTR D+AR LGY+AKQ
Sbjct: 1 MGMYKYIREAWKSPKKSYVGELLKQRMIKWRREPVVVRIERPTRLDRARALGYQAKQGYV 60
Query: 61 XXXXXXXXXXXXXXXXXXIVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLK------ 114
KP+ G + ++S + +AEE+A RK L+
Sbjct: 61 IVRVRVRKGGRKRPRWKG--GRKPSKMGQVKYSPKKSLQWIAEEKAARKFPNLEVLNSYW 118
Query: 115 ---DSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHL 171
D YK+FEVI+VD H I++DP+I WI HK R RGLTSAGKK RGLR KG
Sbjct: 119 VGEDGMYKWFEVIMVDPHHPVIKSDPKIAWIALKHHKGRVFRGLTSAGKKGRGLRNKGKG 178
Query: 172 HHKARPSRRAT 182
K RPS RA
Sbjct: 179 AEKVRPSIRAN 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 = 110 bits (275), Expect = 6e-25, Method: Compositional matrix adjust.
Identities = 69/189 (36%), Positives = 100/189 (52%), Gaps = 11/189 (5%)
Query: 3 AYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXX 62
AY Y+ E W++ + + L R E+R P++VR+ RPTR D+AR LGYKAKQ
Sbjct: 4 AYSYIREAWKRPKEGQIAELMWHRMQEWRNEPAVVRIERPTRLDRARSLGYKAKQGIIVV 63
Query: 63 XXXXXXXXXXXXXXXXIVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLK-------- 114
K V ++ +++ + +AEERA RK L+
Sbjct: 64 RVAIRKGSSRRTRFNKGRRSK--RMMVNRITRKKNIQRIAEERANRKFPNLRVLNSYSVG 121
Query: 115 -DSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHH 173
D +K+ EVIL+D H AI++D +++WI + H+ R RGLTSAG++ RGLRG+G
Sbjct: 122 EDGRHKWHEVILIDPDHPAIKSDDQLSWISRTRHRLRTFRGLTSAGRRCRGLRGQGKGSE 181
Query: 174 KARPSRRAT 182
K RPS R
Sbjct: 182 KVRPSLRVN 190
>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 = 106 bits (265), Expect = 6e-24, Method: Compositional matrix adjust.
Identities = 70/189 (37%), Positives = 92/189 (48%), Gaps = 11/189 (5%)
Query: 3 AYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXX 62
AY Y+ + W+ + LQ R E+R ++ R+ RPTR DKAR GYKAKQ
Sbjct: 5 AYSYIRDAWKNPGDGQLAELQWQRQQEWRNEGAVERIERPTRLDKARSQGYKAKQGVIVA 64
Query: 63 XXXXXXXXXXXXXXXXIVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLK-------- 114
K QGVT++ ++ + VAEERA R L+
Sbjct: 65 RVSVRKGSARKRRHKAGRRSK--RQGVTRITRRKDIQRVAEERASRTFPNLRVLNSYSVG 122
Query: 115 -DSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHH 173
D K+ EVIL+D H AI+ND ++WIC R RGLT AG++ RGL GKG
Sbjct: 123 QDGRQKWHEVILIDPNHPAIQNDDDLSWICADDQADRVFRGLTGAGRRNRGLSGKGKGSE 182
Query: 174 KARPSRRAT 182
K RPS R+
Sbjct: 183 KTRPSLRSN 191
>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 = 106 bits (265), Expect = 7e-24, Method: Compositional matrix adjust.
Identities = 70/189 (37%), Positives = 92/189 (48%), Gaps = 11/189 (5%)
Query: 3 AYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXX 62
AY Y+ + W+ + LQ R E+R ++ R+ RPTR DKAR GYKAKQ
Sbjct: 4 AYSYIRDAWKNPGDGQLAELQWQRQQEWRNEGAVERIERPTRLDKARSQGYKAKQGVIVA 63
Query: 63 XXXXXXXXXXXXXXXXIVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLK-------- 114
K QGVT++ ++ + VAEERA R L+
Sbjct: 64 RVSVRKGSARKRRHKAGRRSK--RQGVTRITRRKDIQRVAEERASRTFPNLRVLNSYSVG 121
Query: 115 -DSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHH 173
D K+ EVIL+D H AI+ND ++WIC R RGLT AG++ RGL GKG
Sbjct: 122 QDGRQKWHEVILIDPNHPAIQNDDDLSWICADDQADRVFRGLTGAGRRNRGLSGKGKGSE 181
Query: 174 KARPSRRAT 182
K RPS R+
Sbjct: 182 KTRPSLRSN 190
>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 = 106 bits (264), Expect = 8e-24, Method: Compositional matrix adjust.
Identities = 70/189 (37%), Positives = 91/189 (48%), Gaps = 11/189 (5%)
Query: 3 AYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXX 62
AY Y+ + W + LQ R E+R ++ R+ RPTR DKAR GYKAKQ
Sbjct: 5 AYSYIRDAWENPGDGQLAELQWQRQQEWRNEGAVERIERPTRLDKARSQGYKAKQGVIVA 64
Query: 63 XXXXXXXXXXXXXXXXIVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLK-------- 114
K QGVT++ ++ + VAEERA R L+
Sbjct: 65 RVSVRKGSARKRRHKAGRRSK--RQGVTRITRRKDIQRVAEERASRTFPNLRVLNSYSVG 122
Query: 115 -DSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHH 173
D K+ EVIL+D H AI+ND ++WIC R RGLT AG++ RGL GKG
Sbjct: 123 QDGRQKWHEVILIDPNHPAIQNDDDLSWICADDQADRVFRGLTGAGRRNRGLSGKGKGSE 182
Query: 174 KARPSRRAT 182
K RPS R+
Sbjct: 183 KTRPSLRSN 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 = 106 bits (264), Expect = 9e-24, Method: Compositional matrix adjust.
Identities = 70/189 (37%), Positives = 91/189 (48%), Gaps = 11/189 (5%)
Query: 3 AYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXX 62
AY Y+ + W + LQ R E+R ++ R+ RPTR DKAR GYKAKQ
Sbjct: 5 AYSYIRDAWENPGDGQLAELQWQRQQEWRNEGAVERIERPTRLDKARSQGYKAKQGVIVA 64
Query: 63 XXXXXXXXXXXXXXXXIVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLK-------- 114
K QGVT++ ++ + VAEERA R L+
Sbjct: 65 RVSVRKGSARKRRHKAGRRSK--RQGVTRITRRKDIQRVAEERASRTFPNLRVLNSYSVG 122
Query: 115 -DSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHH 173
D K+ EVIL+D H AI+ND ++WIC R RGLT AG++ RGL GKG
Sbjct: 123 QDGRQKWHEVILIDPNHPAIQNDDDLSWICADDQADRVFRGLTGAGRRNRGLSGKGKGSE 182
Query: 174 KARPSRRAT 182
K RPS R+
Sbjct: 183 KTRPSLRSN 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 = 106 bits (264), Expect = 9e-24, Method: Compositional matrix adjust.
Identities = 70/189 (37%), Positives = 91/189 (48%), Gaps = 11/189 (5%)
Query: 3 AYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXX 62
AY Y+ + W + LQ R E+R ++ R+ RPTR DKAR GYKAKQ
Sbjct: 4 AYSYIRDAWENPGDGQLAELQWQRQQEWRNEGAVERIERPTRLDKARSQGYKAKQGVIVA 63
Query: 63 XXXXXXXXXXXXXXXXIVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLK-------- 114
K QGVT++ ++ + VAEERA R L+
Sbjct: 64 RVSVRKGSARKRRHKAGRRSK--RQGVTRITRRKDIQRVAEERASRTFPNLRVLNSYSVG 121
Query: 115 -DSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHH 173
D K+ EVIL+D H AI+ND ++WIC R RGLT AG++ RGL GKG
Sbjct: 122 QDGRQKWHEVILIDPNHPAIQNDDDLSWICADDQADRVFRGLTGAGRRNRGLSGKGKGSE 181
Query: 174 KARPSRRAT 182
K RPS R+
Sbjct: 182 KTRPSLRSN 190
>pdb|1YHQ|M Chain M, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
Length = 194
Score = 106 bits (264), Expect = 9e-24, Method: Compositional matrix adjust.
Identities = 70/189 (37%), Positives = 91/189 (48%), Gaps = 11/189 (5%)
Query: 3 AYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXX 62
AY Y+ + W + LQ R E+R ++ R+ RPTR DKAR GYKAKQ
Sbjct: 4 AYSYIRDAWENPGDGQLAELQWQRQQEWRNEGAVERIERPTRLDKARSQGYKAKQGVIVA 63
Query: 63 XXXXXXXXXXXXXXXXIVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLK-------- 114
K QGVT++ ++ + VAEERA R L+
Sbjct: 64 RVSVRKGSARKRRHKAGRRSK--RQGVTRITRRKDIQRVAEERASRTFPNLRVLNSYSVG 121
Query: 115 -DSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHH 173
D K+ EVIL+D H AI+ND ++WIC R RGLT AG++ RGL GKG
Sbjct: 122 QDGRQKWHEVILIDPNHPAIQNDDDLSWICADDQADRVFRGLTGAGRRNRGLSGKGKGSE 181
Query: 174 KARPSRRAT 182
K RPS R+
Sbjct: 182 KTRPSLRSN 190
>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 = 106 bits (264), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 70/189 (37%), Positives = 91/189 (48%), Gaps = 11/189 (5%)
Query: 3 AYKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXX 62
AY Y+ + W + LQ R E+R ++ R+ RPTR DKAR GYKAKQ
Sbjct: 5 AYSYIRDAWENPGDGQLAELQWQRQQEWRNEGAVERIERPTRLDKARSQGYKAKQGVIVA 64
Query: 63 XXXXXXXXXXXXXXXXIVYGKPTNQGVTQLKFQRSKRSVAEERAGRKLGGLK-------- 114
K QGVT++ ++ + VAEERA R L+
Sbjct: 65 RVSVRKGSARKRRHKAGRRSK--RQGVTRITRRKDIQRVAEERASRTFPNLRVLNSYSVG 122
Query: 115 -DSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRGKGHLHH 173
D K+ EVIL+D H AI+ND ++WIC R RGLT AG++ RGL GKG
Sbjct: 123 QDGRQKWHEVILIDPNHPAIQNDDDLSWICADDQADRVFRGLTGAGRRNRGLSGKGKGSE 182
Query: 174 KARPSRRAT 182
K RPS R+
Sbjct: 183 KTRPSLRSN 191
>pdb|1FFK|I Chain I, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
Length = 194
Score = 101 bits (252), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 71/198 (35%), Positives = 102/198 (51%), Gaps = 27/198 (13%)
Query: 4 YKYVSELWRKKQSDVMRFLQRVRCWEYRQHPSIVRVTRPTRPDKARRLGYKAKQXXXXXX 63
Y Y+ E W++ + L R ++R+ P++VR+ RPTR D+AR LGYKAK+
Sbjct: 5 YAYIREAWKRPYEGYVGELMWHRLQKWRREPAVVRIPRPTRLDRARALGYKAKKGIIVVR 64
Query: 64 XXXXXXXXXXXXXXXIVYGKPTNQGVTQLKFQRSKRS-------VAEERAGRKLGGLK-- 114
N+G K ++R +AEERA RK ++
Sbjct: 65 VRIRRGGRRATR---------PNKGRKSKKMMVNRRPRKKNLQWIAEERANRKYPNMEVL 115
Query: 115 -------DSTYKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRG 167
D YK+FEVILVD H AI++DP+++W+ + + R RGLTSAG+K RGLR
Sbjct: 116 NSYWVGEDGRYKWFEVILVDRDHPAIKSDPQLSWVSR--TRGRVYRGLTSAGRKARGLRR 173
Query: 168 KGHLHHKARPSRRATWKR 185
KG K RPS RA +++
Sbjct: 174 KGRGAEKVRPSLRANFRK 191
>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 = 5.0, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 12/49 (24%)
Query: 119 KYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGKKYRGLRG 167
+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 = 27.3 bits (59), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 118 YKYFEVILVDAAHNAIRNDPRINWICKPVHKHRELRGLTSAGK 160
YK F+ ILV+AA N R DP+++ I + L + + GK
Sbjct: 54 YKIFDEILVNAADNKQR-DPKMSCIRVTIDPENNLISIWNNGK 95
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 0.135 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,346,203
Number of Sequences: 62578
Number of extensions: 183981
Number of successful extensions: 445
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 389
Number of HSP's gapped (non-prelim): 23
length of query: 195
length of database: 14,973,337
effective HSP length: 94
effective length of query: 101
effective length of database: 9,091,005
effective search space: 918191505
effective search space used: 918191505
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)