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= psy6164
(64 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKR|KK Chain k, 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 = 140
Score = 85.1 bits (209), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 39/46 (84%), Positives = 45/46 (97%)
Query: 1 MSKRGRGGSAGAKFRISLALPVGAVINCADNTGAKNLFVIAVQGVK 46
MSKRGRGGS+GAKFRISL LPVGAVINCADNTGAKNL++I+V+G+K
Sbjct: 1 MSKRGRGGSSGAKFRISLGLPVGAVINCADNTGAKNLYIISVKGIK 46
>pdb|3IZR|M Chain M, Localization Of The Large Subunit Ribosomal Proteins
Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
Translating 80s Ribosome
Length = 140
Score = 78.2 bits (191), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 35/46 (76%), Positives = 42/46 (91%)
Query: 1 MSKRGRGGSAGAKFRISLALPVGAVINCADNTGAKNLFVIAVQGVK 46
MSKRGRGGSAG KFR+SL LPV A +NCADNTGAKNL++I+V+G+K
Sbjct: 1 MSKRGRGGSAGNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIK 46
>pdb|4A17|J Chain J, 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|J Chain J, 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|J Chain J, 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|J Chain J, 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 = 141
Score = 64.3 bits (155), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 29/43 (67%), Positives = 35/43 (81%)
Query: 4 RGRGGSAGAKFRISLALPVGAVINCADNTGAKNLFVIAVQGVK 46
RGRGG G K ++SL LPVGAV+NCADN+GAKNL+ IA G+K
Sbjct: 5 RGRGGQVGTKAKVSLGLPVGAVMNCADNSGAKNLYTIACFGIK 47
>pdb|3ZF7|W Chain W, High-resolution Cryo-electron Microscopy Structure Of
The Trypanosoma Brucei Ribosome
Length = 139
Score = 62.8 bits (151), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 26/34 (76%), Positives = 33/34 (97%)
Query: 11 GAKFRISLALPVGAVINCADNTGAKNLFVIAVQG 44
G +FR+SLALPVGAV+NCADNTGAKNL++I+V+G
Sbjct: 10 GCRFRVSLALPVGAVVNCADNTGAKNLYIISVKG 43
>pdb|1S1I|R Chain R, 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.
pdb|3IZS|M Chain M, Localization Of The Large Subunit Ribosomal Proteins
Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|U Chain U, Yeast 80s Ribosome. This Entry Consists Of The 60s
Subunit Of The First 80s In The Asymmetric Unit.
pdb|3O5H|U Chain U, Yeast 80s Ribosome. This Entry Consists Of The 60s
Subunit Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|V Chain V, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|V Chain V, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|3J16|I Chain I, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
pdb|4B6A|V Chain V, Cryo-Em Structure Of The 60s Ribosomal Subunit In
Complex With Arx1 And Rei1
Length = 137
Score = 62.0 bits (149), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 26/37 (70%), Positives = 34/37 (91%)
Query: 8 GSAGAKFRISLALPVGAVINCADNTGAKNLFVIAVQG 44
G+ G KFRISL LPVGA++NCADN+GA+NL++IAV+G
Sbjct: 5 GAQGTKFRISLGLPVGAIMNCADNSGARNLYIIAVKG 41
>pdb|2X7N|C Chain C, Mechanism Of Eif6s Anti-Association Activity
Length = 132
Score = 60.1 bits (144), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 25/34 (73%), Positives = 32/34 (94%)
Query: 11 GAKFRISLALPVGAVINCADNTGAKNLFVIAVQG 44
G KFRISL LPVGA++NCADN+GA+NL++IAV+G
Sbjct: 3 GTKFRISLGLPVGAIMNCADNSGARNLYIIAVKG 36
>pdb|3JYW|R Chain R, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus
Ribosome At 8.9a Resolution
Length = 131
Score = 60.1 bits (144), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 25/34 (73%), Positives = 32/34 (94%)
Query: 11 GAKFRISLALPVGAVINCADNTGAKNLFVIAVQG 44
G KFRISL LPVGA++NCADN+GA+NL++IAV+G
Sbjct: 2 GTKFRISLGLPVGAIMNCADNSGARNLYIIAVKG 35
>pdb|3J21|J Chain J, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 141
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/43 (46%), Positives = 29/43 (67%), Gaps = 1/43 (2%)
Query: 1 MSKRGRGGSAG-AKFRISLALPVGAVINCADNTGAKNLFVIAV 42
M+K+G G + G + R + ALPVGA + ADN+GAK + +I V
Sbjct: 1 MAKKGAGATRGVSAVRPTRALPVGAYLTVADNSGAKVIQIIGV 43
>pdb|1FFK|H Chain H, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1JJ2|J Chain J, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|J Chain J, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|L Chain L, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|L Chain L, Co-Crystal Structure Of Tylosin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1KD1|L Chain L, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|L Chain L, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|L Chain L, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1K73|L Chain L, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|L Chain L, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|L Chain L, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|L Chain L, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|L Chain L, Crystal Structure Of Ccdap-puromycin Bound At The
Peptidyl Transferase Center Of The 50s Ribosomal
Subunit
pdb|1Q81|L Chain L, Crystal Structure Of Minihelix With 3' Puromycin Bound
To A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|L Chain L, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|L Chain L, 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|J Chain J, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|J Chain J, Structure Of Cca Oligonucleotide Bound To The Trna
Binding Sites Of The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1W2B|J Chain J, Trigger Factor Ribosome Binding Domain In Complex With
50s
pdb|3CC2|K Chain K, 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|K Chain K, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|K Chain K, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|K Chain K, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|K Chain K, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|K Chain K, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|K Chain K, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|K Chain K, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|K Chain K, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|K Chain K, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|K Chain K, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|K Chain K, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|K Chain K, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|J Chain J, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|K Chain K, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|K Chain K, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CXC|J Chain J, The Structure Of An Enhanced Oxazolidinone Inhibitor
Bound To The 50s Ribosomal Subunit Of H. Marismortui
pdb|3G4S|K Chain K, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|K Chain K, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|K Chain K, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|3I55|K Chain K, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|K Chain K, Co-Crystal Structure Of Triacetyloleandomcyin Bound To
The Large Ribosomal Subunit
pdb|4ADX|K Chain K, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
pdb|3OW2|J Chain J, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 132
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 21/29 (72%)
Query: 16 ISLALPVGAVINCADNTGAKNLFVIAVQG 44
++ L G++I CADNTGA+ L VI+V G
Sbjct: 8 VTQGLEKGSLITCADNTGARELKVISVHG 36
>pdb|1S72|K Chain K, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1YHQ|K Chain K, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|K Chain K, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|K Chain K, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|K Chain K, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|K Chain K, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|K Chain K, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|K Chain K, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|K Chain K, The Structure Of The Transition State Analogue "daa"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQ5|K Chain K, The Structure Of The Transition State Analogue "raa"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQ6|K Chain K, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|K Chain K, The Structure Of The Transition State Analogue "dca"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQ8|K Chain K, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|K Chain K, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|K Chain K, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|K Chain K, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|K Chain K, The Structure Of The Transition State Analogue "dan"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQN|K Chain K, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To
The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|K Chain K, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|K Chain K, The Structure Of The Transition State Analogue "rap"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|2OTJ|K Chain K, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|K Chain K, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|K Chain K, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|2QEX|K Chain K, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
Length = 132
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 21/29 (72%)
Query: 16 ISLALPVGAVINCADNTGAKNLFVIAVQG 44
++ L G++I CADNTGA+ L VI+V G
Sbjct: 8 VTQGLEKGSLITCADNTGARELKVISVHG 36
>pdb|1SVX|A Chain A, Crystal Structure Of A Designed Selected Ankyrin Repeat
Protein In Complex With The Maltose Binding Protein
Length = 169
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 10 AGAKFRISLALPVGAVINCADNTGAKNLFVIAVQG 44
AG + + + GA +N ADNTG L + A G
Sbjct: 24 AGQDDEVRILMANGADVNAADNTGTTPLHLAAYSG 58
>pdb|3H0K|A Chain A, Crystal Structure Of An Adenylated Kinase Related
Protein From Sulfolobus Solfataricus To 3.25a
pdb|3H0K|B Chain B, Crystal Structure Of An Adenylated Kinase Related
Protein From Sulfolobus Solfataricus To 3.25a
Length = 178
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 28 CADNTGAKNLFVIAVQGVKDLTTFEEFERF 57
C + G N ++ GV+ L EEF+R
Sbjct: 68 CVEELGTSNHDLVVFDGVRSLAEVEEFKRL 97
>pdb|3LI0|A Chain A, Crystal Structure Of The Mutant R203a Of Orotidine
5'-Monoph Decarboxylase From Methanobacterium
Thermoautotrophicum Com With Inhibitor Bmp
pdb|3LI0|B Chain B, Crystal Structure Of The Mutant R203a Of Orotidine
5'-Monoph Decarboxylase From Methanobacterium
Thermoautotrophicum Com With Inhibitor Bmp
Length = 228
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 6 RGGSAGAKFRISLALPVGAVINCADNTGAKNLFVIAVQGVKDL 48
+GG G R + A+ VGA I ADN A +I + +KDL
Sbjct: 185 QGGDPGETLRFADAIIVGASIYLADNPAAAAAGII--ESIKDL 225
>pdb|2YGK|A Chain A, Crystal Structure Of The Nura Nuclease From Sulfolobus
Solfataricus
pdb|2YGK|B Chain B, Crystal Structure Of The Nura Nuclease From Sulfolobus
Solfataricus
Length = 339
Score = 26.2 bits (56), Expect = 5.6, Method: Composition-based stats.
Identities = 14/31 (45%), Positives = 15/31 (48%)
Query: 7 GGSAGAKFRISLALPVGAVINCADNTGAKNL 37
GGS G RI + VGA DN G K L
Sbjct: 59 GGSFGRPXRIGIVYAVGAESVIGDNKGVKTL 89
>pdb|3LW7|A Chain A, The Crystal Structure Of An Adenylate Kinase-Related
Protein Bound To Amp From Sulfolobus Solfataricus To
2.3a
pdb|3LW7|B Chain B, The Crystal Structure Of An Adenylate Kinase-Related
Protein Bound To Amp From Sulfolobus Solfataricus To
2.3a
Length = 179
Score = 26.2 bits (56), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 28 CADNTGAKNLFVIAVQGVKDLTTFEEFERF 57
C + G N ++ GV+ L EEF+R
Sbjct: 69 CVEELGTSNHDLVVFDGVRSLAEVEEFKRL 98
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 0.140 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,823,946
Number of Sequences: 62578
Number of extensions: 53716
Number of successful extensions: 179
Number of sequences better than 100.0: 68
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 54
Number of HSP's that attempted gapping in prelim test: 165
Number of HSP's gapped (non-prelim): 68
length of query: 64
length of database: 14,973,337
effective HSP length: 35
effective length of query: 29
effective length of database: 12,783,107
effective search space: 370710103
effective search space used: 370710103
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: 45 (21.9 bits)