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= 034411
(95 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|LL Chain l, Localization Of The Large Subunit Ribosomal Proteins
Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
Translating 80s Ribosome
Length = 94
Score = 174 bits (441), Expect = 1e-44, Method: Compositional matrix adjust.
Identities = 83/94 (88%), Positives = 89/94 (94%)
Query: 1 MGKGTGSFGKRRNKTHTLCVRCGRRSFHIQKSRCSACAYPAARVRKYNWSVKAIRRKTTG 60
MGKGTGSFGKRRNKTHTLCVRCGRRSFH+QKS CS+C YPAAR+RKYNWSVKAIRRKTTG
Sbjct: 1 MGKGTGSFGKRRNKTHTLCVRCGRRSFHLQKSTCSSCGYPAARIRKYNWSVKAIRRKTTG 60
Query: 61 TGRMRYLRHVPRRFKSNFREGTEAAPRKKNVAAS 94
TGRMRY+RHVPRRFKSNFREGTEA PRK+ AA+
Sbjct: 61 TGRMRYMRHVPRRFKSNFREGTEATPRKRAAAAN 94
>pdb|3IZS|LL Chain l, Localization Of The Large Subunit Ribosomal Proteins
Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|DD Chain d, Yeast 80s Ribosome. This Entry Consists Of The 60s
Subunit Of The First 80s In The Asymmetric Unit.
pdb|3O5H|DD Chain d, Yeast 80s Ribosome. This Entry Consists Of The 60s
Subunit Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|JJ Chain j, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|JJ Chain j, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|JJ Chain j, Cryo-Em Structure Of The 60s Ribosomal Subunit In
Complex With Arx1 And Rei1
Length = 88
Score = 127 bits (318), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 59/84 (70%), Positives = 68/84 (80%)
Query: 1 MGKGTGSFGKRRNKTHTLCVRCGRRSFHIQKSRCSACAYPAARVRKYNWSVKAIRRKTTG 60
MGKGT SFGKR NK+HTLC RCGRRSFH+QK CS+C YPAA+ R YNW KA RR TTG
Sbjct: 1 MGKGTPSFGKRHNKSHTLCNRCGRRSFHVQKKTCSSCGYPAAKTRSYNWGAKAKRRHTTG 60
Query: 61 TGRMRYLRHVPRRFKSNFREGTEA 84
TGRMRYL+HV RRFK+ F+ G+ +
Sbjct: 61 TGRMRYLKHVSRRFKNGFQTGSAS 84
>pdb|1S1I|Y Chain Y, 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 = 87
Score = 124 bits (312), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 58/83 (69%), Positives = 67/83 (80%)
Query: 2 GKGTGSFGKRRNKTHTLCVRCGRRSFHIQKSRCSACAYPAARVRKYNWSVKAIRRKTTGT 61
GKGT SFGKR NK+HTLC RCGRRSFH+QK CS+C YPAA+ R YNW KA RR TTGT
Sbjct: 1 GKGTPSFGKRHNKSHTLCNRCGRRSFHVQKKTCSSCGYPAAKTRSYNWGAKAKRRHTTGT 60
Query: 62 GRMRYLRHVPRRFKSNFREGTEA 84
GRMRYL+HV RRFK+ F+ G+ +
Sbjct: 61 GRMRYLKHVSRRFKNGFQTGSAS 83
>pdb|2ZKR|2 Chain 2, 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 = 97
Score = 120 bits (302), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 59/88 (67%), Positives = 68/88 (77%)
Query: 1 MGKGTGSFGKRRNKTHTLCVRCGRRSFHIQKSRCSACAYPAARVRKYNWSVKAIRRKTTG 60
M KGT SFGKRRNKTHTLC RCG +++H+QKS C C YPA R RKYNWS KA RR TTG
Sbjct: 1 MTKGTSSFGKRRNKTHTLCRRCGSKAYHLQKSTCGKCGYPAKRKRKYNWSAKAKRRNTTG 60
Query: 61 TGRMRYLRHVPRRFKSNFREGTEAAPRK 88
TGRMR+L+ V RRF+ FREGT P++
Sbjct: 61 TGRMRHLKIVYRRFRHGFREGTTPKPKR 88
>pdb|4A18|A Chain A, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|A Chain A, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|A Chain A, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|A Chain A, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2
Length = 94
Score = 103 bits (256), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 50/90 (55%), Positives = 66/90 (73%), Gaps = 1/90 (1%)
Query: 1 MGKGTGSFGKRRNKTHTLCVRCGRRSFHIQKSRCSACAYPAARVRKYN-WSVKAIRRKTT 59
M +GT +FGKR KTHTLC RCG+ ++H QK RC+AC YP A++R+Y+ W K RK
Sbjct: 1 MTRGTPAFGKRHQKTHTLCRRCGKATYHKQKLRCAACGYPDAKMRRYDGWGQKVRDRKGQ 60
Query: 60 GTGRMRYLRHVPRRFKSNFREGTEAAPRKK 89
GTGRMRY++ + RR K+ FR GT+AAP+ K
Sbjct: 61 GTGRMRYMKTIARRAKNGFRSGTQAAPKVK 90
>pdb|3ZF7|NN Chain n, High-resolution Cryo-electron Microscopy Structure Of
The Trypanosoma Brucei Ribosome
Length = 84
Score = 87.4 bits (215), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 48/84 (57%), Positives = 64/84 (76%)
Query: 1 MGKGTGSFGKRRNKTHTLCVRCGRRSFHIQKSRCSACAYPAARVRKYNWSVKAIRRKTTG 60
M KGT S G+R +TH LC RCGR ++H+Q RC+ACAYP A+ R+YNWSVKAI+R+ TG
Sbjct: 1 MTKGTTSMGQRHGRTHILCRRCGRNAYHVQWERCAACAYPRAQRRRYNWSVKAIKRRRTG 60
Query: 61 TGRMRYLRHVPRRFKSNFREGTEA 84
TGR RYL+ V RR +++F+ +A
Sbjct: 61 TGRCRYLKVVHRRIRNHFKTDIKA 84
>pdb|3JYW|Y Chain Y, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus
Ribosome At 8.9a Resolution
Length = 52
Score = 84.7 bits (208), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 38/52 (73%), Positives = 42/52 (80%)
Query: 2 GKGTGSFGKRRNKTHTLCVRCGRRSFHIQKSRCSACAYPAARVRKYNWSVKA 53
GKGT SFGKR NK+HTLC RCGRRSFH+QK CS+C YPAA+ R YNW KA
Sbjct: 1 GKGTPSFGKRHNKSHTLCNRCGRRSFHVQKKTCSSCGYPAAKTRSYNWGAKA 52
>pdb|1S72|1 Chain 1, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1YHQ|1 Chain 1, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|1 Chain 1, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|1 Chain 1, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|1 Chain 1, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|1 Chain 1, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|1 Chain 1, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|1 Chain 1, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|1 Chain 1, The Structure Of The Transition State Analogue "daa"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQ5|1 Chain 1, The Structure Of The Transition State Analogue "raa"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQ6|1 Chain 1, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|1 Chain 1, The Structure Of The Transition State Analogue "dca"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQ8|1 Chain 1, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|1 Chain 1, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|1 Chain 1, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|1 Chain 1, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|1 Chain 1, The Structure Of The Transition State Analogue "dan"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQN|1 Chain 1, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To
The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|1 Chain 1, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|1 Chain 1, The Structure Of The Transition State Analogue "rap"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|2OTJ|1 Chain 1, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|1 Chain 1, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|1 Chain 1, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|3CC2|1 Chain 1, 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|1 Chain 1, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|1 Chain 1, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|1 Chain 1, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|1 Chain 1, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|1 Chain 1, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|1 Chain 1, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|1 Chain 1, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|1 Chain 1, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|1 Chain 1, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|1 Chain 1, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|1 Chain 1, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|1 Chain 1, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|Z Chain Z, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|1 Chain 1, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|1 Chain 1, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2QEX|1 Chain 1, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3I55|1 Chain 1, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|1 Chain 1, Co-Crystal Structure Of Triacetyloleandomcyin Bound To
The Large Ribosomal Subunit
pdb|4ADX|1 Chain 1, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 57
Score = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/53 (47%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 2 GKGTGSFGKRRNKTHTLCVRCGRRSFHIQKSRCSACAY-PAARVRKYNWSVKA 53
G GT S GK+ THT C RCG +S+H +K CS+C + +A+ R Y W KA
Sbjct: 3 GAGTPSQGKKNTTTHTKCRRCGEKSYHTKKKVCSSCGFGKSAKRRDYEWQSKA 55
>pdb|1FFK|X Chain X, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1JJ2|Z Chain Z, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|Z Chain Z, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|2 Chain 2, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|2 Chain 2, Co-Crystal Structure Of Tylosin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1KD1|2 Chain 2, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|2 Chain 2, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|2 Chain 2, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1K73|2 Chain 2, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|2 Chain 2, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|2 Chain 2, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|2 Chain 2, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|2 Chain 2, Crystal Structure Of Ccdap-puromycin Bound At The
Peptidyl Transferase Center Of The 50s Ribosomal
Subunit
pdb|1Q81|2 Chain 2, Crystal Structure Of Minihelix With 3' Puromycin Bound
To A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|2 Chain 2, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|2 Chain 2, 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|Z Chain Z, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|Z Chain Z, Structure Of Cca Oligonucleotide Bound To The Trna
Binding Sites Of The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1W2B|Z Chain Z, Trigger Factor Ribosome Binding Domain In Complex With
50s
pdb|3CXC|Z Chain Z, The Structure Of An Enhanced Oxazolidinone Inhibitor
Bound To The 50s Ribosomal Subunit Of H. Marismortui
pdb|3G4S|1 Chain 1, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|1 Chain 1, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|1 Chain 1, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|3OW2|Z Chain Z, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 56
Score = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/54 (46%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 1 MGKGTGSFGKRRNKTHTLCVRCGRRSFHIQKSRCSACAY-PAARVRKYNWSVKA 53
G GT S GK+ THT C RCG +S+H +K CS+C + +A+ R Y W KA
Sbjct: 1 TGAGTPSQGKKNTTTHTKCRRCGEKSYHTKKKVCSSCGFGKSAKRRDYEWQSKA 54
>pdb|3J21|EE Chain e, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 62
Score = 49.3 bits (116), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 26/52 (50%), Positives = 36/52 (69%), Gaps = 2/52 (3%)
Query: 1 MGKGTGSFGKRRNK-THTLCVRCGRRSFHIQKSRCSACAYP-AARVRKYNWS 50
MG GT +FGKR + TH C RCGR S++++K C+AC + + R+RKY WS
Sbjct: 1 MGSGTATFGKRNSTPTHIRCRRCGRVSYNVKKGYCAACGFGRSRRLRKYRWS 52
>pdb|3FL2|A Chain A, Crystal Structure Of The Ring Domain Of The E3
Ubiquitin- Protein Ligase Uhrf1
Length = 124
Score = 25.8 bits (55), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 13/28 (46%)
Query: 16 HTLCVRCGRRSFHIQKSRCSACAYPAAR 43
H +C C RSF Q C AC Y R
Sbjct: 72 HNVCKDCLDRSFRAQVFSCPACRYDLGR 99
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
0.324 0.131 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,762,087
Number of Sequences: 62578
Number of extensions: 87076
Number of successful extensions: 175
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 160
Number of HSP's gapped (non-prelim): 14
length of query: 95
length of database: 14,973,337
effective HSP length: 62
effective length of query: 33
effective length of database: 11,093,501
effective search space: 366085533
effective search space used: 366085533
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)