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= 030949
(168 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKR|UU Chain u, 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 = 157
Score = 70.1 bits (170), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 29/65 (44%), Positives = 41/65 (63%)
Query: 1 MRLEKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKMKRNPRKVKWTKAYRRLHG 60
M++E C F +YPGHG ++ R D K+F+F +KC F KRNPR++ WT YRR H
Sbjct: 1 MKVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHK 60
Query: 61 KDMTQ 65
K ++
Sbjct: 61 KGQSE 65
>pdb|3IZS|Z Chain Z, Localization Of The Large Subunit Ribosomal Proteins
Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|V Chain V, Yeast 80s Ribosome. This Entry Consists Of The 60s
Subunit Of The First 80s In The Asymmetric Unit.
pdb|3O5H|V Chain V, Yeast 80s Ribosome. This Entry Consists Of The 60s
Subunit Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|W Chain W, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|W Chain W, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|W Chain W, Cryo-Em Structure Of The 60s Ribosomal Subunit In
Complex With Arx1 And Rei1
Length = 155
Score = 65.5 bits (158), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 29/65 (44%), Positives = 42/65 (64%)
Query: 1 MRLEKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKMKRNPRKVKWTKAYRRLHG 60
M++E F + +YPG G FVR D+KIFRF SK FK ++NPR++ WT +R+ H
Sbjct: 1 MKVEIDSFSGAKIYPGRGTLFVRGDSKIFRFQNSKSASLFKQRKNPRRIAWTVLFRKHHK 60
Query: 61 KDMTQ 65
K +T+
Sbjct: 61 KGITE 65
>pdb|3IZR|Z Chain Z, Localization Of The Large Subunit Ribosomal Proteins
Into A 5.5 A Cryo-Em Map Of Triticum Aestivum
Translating 80s Ribosome
Length = 162
Score = 62.0 bits (149), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 26/63 (41%), Positives = 39/63 (61%)
Query: 1 MRLEKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKMKRNPRKVKWTKAYRRLHG 60
++ E C F +YPG GI+F+R D+++F F SKC + F + P K+ WT YR+ H
Sbjct: 3 LKTELCRFSGQKIYPGKGIRFIRADSQVFLFANSKCKRYFHNRLKPAKLTWTAMYRKQHK 62
Query: 61 KDM 63
KD+
Sbjct: 63 KDI 65
>pdb|1S1I|S Chain S, 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|2X7N|D Chain D, Mechanism Of Eif6s Anti-Association Activity
Length = 56
Score = 59.7 bits (143), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 36/56 (64%)
Query: 1 MRLEKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKMKRNPRKVKWTKAYR 56
M++E F + +YPG G FVR D+KIFRF SK FK ++NPR++ WT +R
Sbjct: 1 MKVEIDSFSGAKIYPGRGTLFVRGDSKIFRFQNSKSASLFKQRKNPRRIAWTVLFR 56
>pdb|3J21|V Chain V, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 66
Score = 59.3 bits (142), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 34/55 (61%)
Query: 2 RLEKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKMKRNPRKVKWTKAYR 56
R C +C PG G +VRND ++ FC KC + + M RNPRK+KWTKAY+
Sbjct: 3 RWNVCSYCGKPFEPGTGKMYVRNDGRVLFFCSRKCERYYFMGRNPRKLKWTKAYQ 57
>pdb|3JYW|S Chain S, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus
Ribosome At 8.9a Resolution
Length = 45
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 23/45 (51%), Positives = 30/45 (66%)
Query: 8 FCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKMKRNPRKVKWT 52
F + +YPG G FVR D+KIFRF SK FK ++NPR++ WT
Sbjct: 1 FSGAKIYPGRGTLFVRGDSKIFRFQNSKSASLFKQRKNPRRIAWT 45
>pdb|2QA4|U Chain U, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|3CC2|U Chain U, 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|U Chain U, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|U Chain U, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|U Chain U, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|U Chain U, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|U Chain U, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|U Chain U, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|U Chain U, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|U Chain U, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|U Chain U, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|U Chain U, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|U Chain U, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|U Chain U, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|T Chain T, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|U Chain U, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|U Chain U, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2QEX|U Chain U, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|4ADX|U Chain U, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 67
Score = 53.9 bits (128), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 29/60 (48%)
Query: 2 RLEKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKMKRNPRKVKWTKAYRRLHGK 61
R +C +C + + PG G FV D FC SKC N + R R ++WT R G+
Sbjct: 3 RTRECDYCGTDIEPGTGTMFVHKDGATTHFCSSKCENNADLGREARNLEWTDTARGEAGE 62
>pdb|1FFK|R Chain R, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1GIY|R Chain R, 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|1JJ2|T Chain T, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|T Chain T, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|V Chain V, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|V Chain V, Co-Crystal Structure Of Tylosin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1KD1|V Chain V, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|V Chain V, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|V Chain V, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1ML5|RR Chain r, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
pdb|1K73|V Chain V, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|V Chain V, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|V Chain V, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|V Chain V, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|V Chain V, Crystal Structure Of Ccdap-puromycin Bound At The
Peptidyl Transferase Center Of The 50s Ribosomal
Subunit
pdb|1Q81|V Chain V, Crystal Structure Of Minihelix With 3' Puromycin Bound
To A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|V Chain V, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|V Chain V, 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|T Chain T, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|T Chain T, Structure Of Cca Oligonucleotide Bound To The Trna
Binding Sites Of The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1S72|U Chain U, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1W2B|T Chain T, Trigger Factor Ribosome Binding Domain In Complex With
50s
pdb|1YHQ|U Chain U, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|U Chain U, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|U Chain U, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|U Chain U, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|U Chain U, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|U Chain U, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|U Chain U, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YL3|R Chain R, 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|1VQ4|U Chain U, The Structure Of The Transition State Analogue "daa"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQ5|U Chain U, The Structure Of The Transition State Analogue "raa"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQ6|U Chain U, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|U Chain U, The Structure Of The Transition State Analogue "dca"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQ8|U Chain U, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|U Chain U, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|U Chain U, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|U Chain U, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|U Chain U, The Structure Of The Transition State Analogue "dan"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQN|U Chain U, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To
The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|U Chain U, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|U Chain U, The Structure Of The Transition State Analogue "rap"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|2B66|T Chain T, 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|T Chain T, 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|T Chain T, 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.
pdb|2OTJ|U Chain U, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|U Chain U, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|3CXC|T Chain T, The Structure Of An Enhanced Oxazolidinone Inhibitor
Bound To The 50s Ribosomal Subunit Of H. Marismortui
pdb|3I55|U Chain U, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|U Chain U, Co-Crystal Structure Of Triacetyloleandomcyin Bound To
The Large Ribosomal Subunit
Length = 66
Score = 53.9 bits (128), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 29/60 (48%)
Query: 2 RLEKCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKMKRNPRKVKWTKAYRRLHGK 61
R +C +C + + PG G FV D FC SKC N + R R ++WT R G+
Sbjct: 2 RTRECDYCGTDIEPGTGTMFVHKDGATTHFCSSKCENNADLGREARNLEWTDTARGEAGE 61
>pdb|3ZF7|Y Chain Y, High-resolution Cryo-electron Microscopy Structure Of
The Trypanosoma Brucei Ribosome
Length = 125
Score = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 36/69 (52%), Gaps = 4/69 (5%)
Query: 1 MRLEKCWFCSSTVYPGHGIQFVR----NDAKIFRFCRSKCHKNFKMKRNPRKVKWTKAYR 56
MR C F V+PGHG ++V + + F R KC + K+NPR + WT+ YR
Sbjct: 1 MRTIDCEFSHFAVHPGHGRRYVPFAFLSTKPVLTFARPKCFAMYMRKKNPRFIAWTRTYR 60
Query: 57 RLHGKDMTQ 65
R+H K T
Sbjct: 61 RIHRKTTTD 69
>pdb|3G4S|U Chain U, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|U Chain U, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|U Chain U, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|3OW2|T Chain T, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 53
Score = 49.3 bits (116), Expect = 9e-07, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 26/52 (50%)
Query: 5 KCWFCSSTVYPGHGIQFVRNDAKIFRFCRSKCHKNFKMKRNPRKVKWTKAYR 56
+C +C + + PG G FV D FC SKC N + R R ++WT R
Sbjct: 2 ECDYCGTDIEPGTGTMFVHKDGATTHFCSSKCENNADLGREARNLEWTDTAR 53
>pdb|4A17|T Chain T, 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|T Chain T, 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|T Chain T, 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|T Chain T, 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 = 158
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 33/60 (55%), Gaps = 4/60 (6%)
Query: 1 MRLEKCWFCSSTVYPGHGIQFVRNDAKIFRFC--RSKCHKNFKMKRNPRKVKWTKAYRRL 58
+R C FC +YPG G +F+ D + F F ++KC K+K +K+ WT A RRL
Sbjct: 3 VRTGTCSFCEYRIYPGRGQRFIAKDGRGFFFLTKKAKCLSLRKVK--AQKITWTIARRRL 60
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
0.334 0.144 0.465
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,852,497
Number of Sequences: 62578
Number of extensions: 175303
Number of successful extensions: 602
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 588
Number of HSP's gapped (non-prelim): 14
length of query: 168
length of database: 14,973,337
effective HSP length: 92
effective length of query: 76
effective length of database: 9,216,161
effective search space: 700428236
effective search space used: 700428236
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.6 bits)
S2: 48 (23.1 bits)