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= 006078
(662 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1FFK|A Chain A, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1JJ2|A Chain A, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|A Chain A, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|C Chain C, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|C Chain C, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|C Chain C, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|C Chain C, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|C Chain C, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1K73|C Chain C, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|C Chain C, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|C Chain C, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|C Chain C, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|C Chain C, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|C Chain C, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|C Chain C, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|C Chain C, 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|A Chain A, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|A Chain A, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1W2B|A Chain A, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|3CXC|A Chain A, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
Length = 239
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 32/63 (50%), Gaps = 8/63 (12%)
Query: 305 NPDDGGSFIQDIQISA-MFTHHQKIVVVDSP---MPNGDPERRRIMSFVGGIDLCDGRYD 360
+P DGG F + ++A + TH + + VV P M DP+ R + VGG GR D
Sbjct: 111 SPGDGGKFARASGVNAQLLTHDRNVAVVKLPSGEMKRLDPQCRATIGVVGG----GGRTD 166
Query: 361 TPF 363
PF
Sbjct: 167 KPF 169
>pdb|3OW2|A Chain A, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 237
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 32/63 (50%), Gaps = 8/63 (12%)
Query: 305 NPDDGGSFIQDIQISA-MFTHHQKIVVVDSP---MPNGDPERRRIMSFVGGIDLCDGRYD 360
+P DGG F + ++A + TH + + VV P M DP+ R + VGG GR D
Sbjct: 111 SPGDGGKFARASGVNAQLLTHDRNVAVVKLPSGEMKRLDPQCRATIGVVGG----GGRTD 166
Query: 361 TPF 363
PF
Sbjct: 167 KPF 169
>pdb|1S72|A Chain A, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1YHQ|A Chain A, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|A Chain A, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|A Chain A, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|A Chain A, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|A Chain A, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|A Chain A, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|A Chain A, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|A Chain A, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|A Chain A, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|A Chain A, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|A Chain A, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|A Chain A, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|A Chain A, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|A Chain A, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|A Chain A, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|A Chain A, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|A Chain A, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|A Chain A, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|A Chain A, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|A Chain A, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2QA4|A Chain A, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|3CC2|A Chain A, 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|A Chain A, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|A Chain A, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|A Chain A, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|A Chain A, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|A Chain A, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|A Chain A, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|A Chain A, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|A Chain A, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|A Chain A, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|A Chain A, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|A Chain A, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|A Chain A, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|A Chain A, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|A Chain A, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|A Chain A, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|2QEX|A Chain A, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3I55|A Chain A, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|A Chain A, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
pdb|4ADX|A Chain A, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 240
Score = 33.1 bits (74), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 8/63 (12%)
Query: 305 NPDDGGSFIQDIQISA-MFTHHQKIVVVDSP---MPNGDPERRRIMSFVGGIDLCDGRYD 360
+P DGG F + ++A + TH + + VV P M DP+ R + V G GR D
Sbjct: 112 SPGDGGKFARASGVNAQLLTHDRNVAVVKLPSGEMKRLDPQCRATIGVVAG----GGRTD 167
Query: 361 TPF 363
PF
Sbjct: 168 KPF 170
>pdb|3G4S|A Chain A, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|A Chain A, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|A Chain A, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
Length = 237
Score = 33.1 bits (74), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 8/63 (12%)
Query: 305 NPDDGGSFIQDIQISA-MFTHHQKIVVVDSP---MPNGDPERRRIMSFVGGIDLCDGRYD 360
+P DGG F + ++A + TH + + VV P M DP+ R + V G GR D
Sbjct: 111 SPGDGGKFARASGVNAQLLTHDRNVAVVKLPSGEMKRLDPQCRATIGVVAG----GGRTD 166
Query: 361 TPF 363
PF
Sbjct: 167 KPF 169
>pdb|2OTL|A Chain A, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
Length = 239
Score = 33.1 bits (74), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 8/63 (12%)
Query: 305 NPDDGGSFIQDIQISA-MFTHHQKIVVVDSP---MPNGDPERRRIMSFVGGIDLCDGRYD 360
+P DGG F + ++A + TH + + VV P M DP+ R + V G GR D
Sbjct: 111 SPGDGGKFARASGVNAQLLTHDRNVAVVKLPSGEMKRLDPQCRATIGVVAG----GGRTD 166
Query: 361 TPF 363
PF
Sbjct: 167 KPF 169
>pdb|1SRY|A Chain A, Refined Crystal Structure Of The Seryl-Trna Synthetase
From Thermus Thermophilus At 2.5 Angstroms Resolution
pdb|1SRY|B Chain B, Refined Crystal Structure Of The Seryl-Trna Synthetase
From Thermus Thermophilus At 2.5 Angstroms Resolution
pdb|1SER|A Chain A, The 2.9 Angstroms Crystal Structure Of T. Thermophilus
Seryl-Trna Synthetase Complexed With Trna Ser
pdb|1SER|B Chain B, The 2.9 Angstroms Crystal Structure Of T. Thermophilus
Seryl-Trna Synthetase Complexed With Trna Ser
pdb|1SES|A Chain A, Crystal Structures At 2.5 Angstroms Resolution Of
Seryl-Trna Synthetase Complexed With Two Different
Analogues Of Seryl-Adenylate
pdb|1SES|B Chain B, Crystal Structures At 2.5 Angstroms Resolution Of
Seryl-Trna Synthetase Complexed With Two Different
Analogues Of Seryl-Adenylate
pdb|1SET|A Chain A, Crystal Structures At 2.5 Angstroms Resolution Of
Seryl-Trna Synthetase Complexed With Two Different
Analogues Of Seryl-Adenylate
pdb|1SET|B Chain B, Crystal Structures At 2.5 Angstroms Resolution Of
Seryl-Trna Synthetase Complexed With Two Different
Analogues Of Seryl-Adenylate
Length = 421
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 45/102 (44%), Gaps = 8/102 (7%)
Query: 499 IHAIRRAKNFIYIENQYFLGSSFAWSADGI------KPEEINALHLIPKELSLKIVSKIE 552
+ + R F +E QY L + ++D EEI L +P L +
Sbjct: 266 VRGLMRVHQFHKVE-QYVLTEASLEASDRAFQELLENAEEILRLLELPYRLVEVATGDMG 324
Query: 553 AGERFTVYIVVPMWPEG-FPESGSVQAILDWQRRTMDMMYKD 593
G+ V I V + EG + E+ S A+LDWQ R ++ Y+D
Sbjct: 325 PGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRANLRYRD 366
>pdb|3ERR|A Chain A, Microtubule Binding Domain From Mouse Cytoplasmic Dynein
As A Fusion With Seryl-Trna Synthetase
pdb|3ERR|B Chain B, Microtubule Binding Domain From Mouse Cytoplasmic Dynein
As A Fusion With Seryl-Trna Synthetase
Length = 536
Score = 29.6 bits (65), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 45/102 (44%), Gaps = 8/102 (7%)
Query: 499 IHAIRRAKNFIYIENQYFLGSSFAWSADGI------KPEEINALHLIPKELSLKIVSKIE 552
+ + R F +E QY L + ++D EEI L +P L +
Sbjct: 375 VRGLMRVHQFHKVE-QYVLTEASLEASDRAFQELLENAEEILRLLELPYRLVEVATGDMG 433
Query: 553 AGERFTVYIVVPMWPEG-FPESGSVQAILDWQRRTMDMMYKD 593
G+ V I V + EG + E+ S A+LDWQ R ++ Y+D
Sbjct: 434 PGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRANLRYRD 475
>pdb|1EWD|A Chain A, Fructose 1,6-Bisphosphate Aldolase From Rabbit Muscle
pdb|1EWD|B Chain B, Fructose 1,6-Bisphosphate Aldolase From Rabbit Muscle
pdb|1EWD|C Chain C, Fructose 1,6-Bisphosphate Aldolase From Rabbit Muscle
pdb|1EWD|D Chain D, Fructose 1,6-Bisphosphate Aldolase From Rabbit Muscle
Length = 363
Score = 29.3 bits (64), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 36/89 (40%), Gaps = 1/89 (1%)
Query: 227 YTEISLVRDSR-RPKPGGDIMLGELLKKKASEGVRVCMLVWDDRTSVSLLKKDGLMATHD 285
Y ++ L D R P GG I+ E L +KA +G ++ V ++ G++
Sbjct: 58 YRQLLLTADDRVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIMVDKGVVPLAG 117
Query: 286 EETEKFFQGTDVHCILCPRNPDDGGSFIQ 314
E QG D C + DG F +
Sbjct: 118 TNGETTTQGLDGLSERCAQYKKDGADFAK 146
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 0.139 0.438
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,114,571
Number of Sequences: 62578
Number of extensions: 946049
Number of successful extensions: 1663
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1663
Number of HSP's gapped (non-prelim): 10
length of query: 662
length of database: 14,973,337
effective HSP length: 105
effective length of query: 557
effective length of database: 8,402,647
effective search space: 4680274379
effective search space used: 4680274379
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: 55 (25.8 bits)