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= 027713
(220 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1ZAW|A Chain A, Ribosomal Protein L10-L12(Ntd) Complex, Space Group
P212121, Form A
Length = 180
Score = 74.7 bits (182), Expect = 4e-14, Method: Compositional matrix adjust.
Identities = 48/156 (30%), Positives = 78/156 (50%), Gaps = 4/156 (2%)
Query: 62 CHLIAAIKYKGFTVKQFQDLRRSLPE----NTKLIVAKNTLVYKAIEGTQWEALKPCMSG 117
LI + GFTV +LR L E + V KNTL+ A++ ++E + + G
Sbjct: 22 TSLILFADFLGFTVADLTELRSRLREKYGDGARFRVVKNTLLNLALKNAEYEGYEEFLKG 81
Query: 118 MNAWLFVHTEEIPAAIKPYRNFQKEKKLEENDFAGAVFEGKFYAPGDFKALESMPTRAEI 177
A L+V + A+K NF K+KK + + G EGK + + + + +P++ E+
Sbjct: 82 PTAVLYVTEGDPVEAVKIIYNFYKDKKADLSRLKGGFLEGKKFTAEEVENIAKLPSKEEL 141
Query: 178 YAKLLGALQGSAIGLVGTLQAPARDLLMVLKAYAKK 213
YA L+G ++ GLV L R+L+ VL A +K
Sbjct: 142 YAXLVGRVKAPITGLVFALSGILRNLVYVLNAIKEK 177
>pdb|1ZAV|A Chain A, Ribosomal Protein L10-L12(Ntd) Complex, Space Group P21
pdb|1ZAX|A Chain A, Ribosomal Protein L10-L12(Ntd) Complex, Space Group
P212121, Form B
Length = 180
Score = 73.9 bits (180), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 48/156 (30%), Positives = 78/156 (50%), Gaps = 4/156 (2%)
Query: 62 CHLIAAIKYKGFTVKQFQDLRRSLPE----NTKLIVAKNTLVYKAIEGTQWEALKPCMSG 117
LI + GFTV +LR L E + V KNTL+ A++ ++E + + G
Sbjct: 22 TSLILFADFLGFTVADLTELRSRLREKYGDGARFRVVKNTLLNLALKNAEYEGYEEFLKG 81
Query: 118 MNAWLFVHTEEIPAAIKPYRNFQKEKKLEENDFAGAVFEGKFYAPGDFKALESMPTRAEI 177
A L+V + A+K NF K+KK + + G EGK + + + + +P++ E+
Sbjct: 82 PTAVLYVTEGDPVEAVKIIYNFYKDKKADLSRLKGGFLEGKKFTAEEVENIAKLPSKEEL 141
Query: 178 YAKLLGALQGSAIGLVGTLQAPARDLLMVLKAYAKK 213
YA L+G ++ GLV L R+L+ VL A +K
Sbjct: 142 YAMLVGRVKAPITGLVFALSGILRNLVYVLNAIKEK 177
>pdb|2J01|J Chain J, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 2 Of 4).
This File Contains The 50s Subunit From Molecule I.
pdb|2J03|J Chain J, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 4 Of 4).
This File Contains The 50s Subunit From Molecule Ii.
pdb|3D5B|J Chain J, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 50s Subunit Of One 70s
Ribosome. The Entire Crystal Structure Contains Two 70s
Ribosomes As Described In Remark 400.
pdb|3D5D|J Chain J, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 50s Subunit Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400.
pdb|3KIR|J Chain J, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Precleavage State; Part 2 Of 4)
pdb|3KIT|J Chain J, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Precleavage State; Part 4 Of 4)
pdb|3KIW|J Chain J, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Postcleavage State; Part 2 Of 4)
pdb|3KIY|J Chain J, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Postcleavage State; Part 4 Of 4)
pdb|3I8I|Y Chain Y, Elongation Complex Of The 70s Ribosome With Three Trnas
And Entry 3i8i Contains 50s Ribosomal Subnit. The 30s
Ribosomal Can Be Found In Pdb Entry 3i8h. Molecule A In
The Same Asym Unit Is Deposited As 3i8f (50s) And 3i8g
(30s).
pdb|3MRZ|I Chain I, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3mrz Contains 50s Ribosomal Subunit. The 30s
Ribosomal Subunit Can Be Found In Pdb Entry 3ms0.
Molecule A In The Same Asymmetric Unit Is Deposited As
3mr8 (50s) And 3ms1 (30s).
pdb|3MS1|I Chain I, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3ms1 Contains 50s Ribosomal Subunit. The 30s
Ribosomal Subunit Can Be Found In Pdb Entry 3mr8.
Molecule B In The Same Asymmetric Unit Is Deposited As
3mrz (50s) And 3ms0 (30s)
Length = 173
Score = 66.2 bits (160), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 49/148 (33%), Positives = 75/148 (50%), Gaps = 6/148 (4%)
Query: 68 IKYKGFTVKQFQDLRRSLPEN-TKLIVAKNTLVYKAIEGTQWEALKPCMSGMNA-WLFVH 125
+ Y+G K+ LR++L +N +L VAKNTL+ A++ E P + G+ V
Sbjct: 27 VNYQGLPAKETHALRQALKQNGARLFVAKNTLIRLALK----ELGLPELDGLQGPSAVVF 82
Query: 126 TEEIPAAIKPYRNFQKEKKLEENDFAGAVFEGKFYAPGDFKALESMPTRAEIYAKLLGAL 185
E+ AA K F K + +G+ D +AL +PT E+ A+L+G L
Sbjct: 83 YEDPVAAAKTLVQFAKSNPKGIPQVKSGLLQGQILTAKDVEALAELPTMDELRAELVGVL 142
Query: 186 QGSAIGLVGTLQAPARDLLMVLKAYAKK 213
Q LVG L AR+L+ +L+AYA+K
Sbjct: 143 QAPMAELVGVLGGVARELVGILEAYAEK 170
>pdb|3J0T|J Chain J, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class2 Of The Six
Classes)
pdb|3J0W|J Chain J, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 4a Of The Six
Classes)
pdb|3J0Y|J Chain J, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 4b Of The Six
Classes)
pdb|3J11|J Chain J, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 3 Of The Six
Classes)
pdb|3J12|J Chain J, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 5 Of The Six
Classes)
pdb|3J14|J Chain J, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 6 Of The Six
Classes)
Length = 164
Score = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 43/135 (31%), Positives = 70/135 (51%), Gaps = 8/135 (5%)
Query: 71 KGFTVKQFQDLRRSLPE-NTKLIVAKNTLVYKAIEGTQWEALKPCMSGMNAWLFVHTEEI 129
+G TV + +LR++ E + V +NTL+ +A+EGT +E LK G L ++ E
Sbjct: 30 RGVTVDKMTELRKAGREAGVYMRVVRNTLLRRAVEGTPFECLKDAFVGPT--LIAYSMEH 87
Query: 130 P-AAIKPYRNFQKEKKLEENDFAGAVFEGKFYAPGDFKALESMPTRAEIYAKLLGALQGS 188
P AA + ++ F K + + A FEG+ L ++PT E A+L+ ++ +
Sbjct: 88 PGAAARLFKEFAKANA--KFEVKAAAFEGELIPASQIDRLATLPTYEEAIARLMATMKEA 145
Query: 189 AIG-LVGTLQAPARD 202
+ G LV TL A RD
Sbjct: 146 SAGKLVRTL-AAVRD 159
>pdb|3SGF|H Chain H, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome
pdb|3UOS|H Chain H, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome (Without
Viomycin)
Length = 165
Score = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 43/135 (31%), Positives = 70/135 (51%), Gaps = 8/135 (5%)
Query: 71 KGFTVKQFQDLRRSLPE-NTKLIVAKNTLVYKAIEGTQWEALKPCMSGMNAWLFVHTEEI 129
+G TV + +LR++ E + V +NTL+ +A+EGT +E LK G L ++ E
Sbjct: 31 RGVTVDKMTELRKAGREAGVYMRVVRNTLLRRAVEGTPFECLKDAFVGPT--LIAYSMEH 88
Query: 130 P-AAIKPYRNFQKEKKLEENDFAGAVFEGKFYAPGDFKALESMPTRAEIYAKLLGALQGS 188
P AA + ++ F K + + A FEG+ L ++PT E A+L+ ++ +
Sbjct: 89 PGAAARLFKEFAKANA--KFEVKAAAFEGELIPASQIDRLATLPTYEEAIARLMATMKEA 146
Query: 189 AIG-LVGTLQAPARD 202
+ G LV TL A RD
Sbjct: 147 SAGKLVRTL-AAVRD 160
>pdb|3CC2|G Chain G, 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|G Chain G, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|G Chain G, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|G Chain G, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|G Chain G, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|G Chain G, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3G4S|G Chain G, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|G Chain G, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|G Chain G, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|3I55|G Chain G, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|G Chain G, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
Length = 348
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 5/83 (6%)
Query: 59 LENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGTQWEALKPCMSGM 118
+E+ + + G +Q QD+RR L +L V++NTL+ +A++ + + +
Sbjct: 27 IESYESVGVVNIAGIPSRQLQDMRRDLHGTAELRVSRNTLLERALDD-----VDDGLEDL 81
Query: 119 NAWLFVHTEEIPAAIKPYRNFQK 141
N ++ I P+ FQ+
Sbjct: 82 NGYITGQVGLIGTDDNPFSLFQE 104
>pdb|1JJ2|G Chain G, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|G Chain G, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|I Chain I, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|I Chain I, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|I Chain I, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|I Chain I, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|I Chain I, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1K73|I Chain I, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|I Chain I, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|I Chain I, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|I Chain I, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|I Chain I, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|I Chain I, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|I Chain I, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|I Chain I, 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|G Chain G, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|G Chain G, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1S72|G Chain G, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1W2B|G Chain G, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|1YHQ|G Chain G, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|G Chain G, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|G Chain G, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|G Chain G, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|G Chain G, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|G Chain G, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|G Chain G, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|G Chain G, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|G Chain G, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|G Chain G, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|G Chain G, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|G Chain G, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|G Chain G, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|G Chain G, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|G Chain G, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|G Chain G, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|G Chain G, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|G Chain G, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|G Chain G, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|G Chain G, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|G Chain G, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|G Chain G, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|3CME|G Chain G, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|2QEX|G Chain G, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3CXC|G Chain G, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
Length = 348
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 5/83 (6%)
Query: 59 LENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGTQWEALKPCMSGM 118
+E+ + + G +Q QD+RR L +L V++NTL+ +A++ + + +
Sbjct: 27 IESYESVGVVNIAGIPSRQLQDMRRDLHGTAELRVSRNTLLERALDD-----VDDGLEDL 81
Query: 119 NAWLFVHTEEIPAAIKPYRNFQK 141
N ++ I P+ FQ+
Sbjct: 82 NGYITGQVGLIGTDDNPFSLFQE 104
>pdb|3OW2|G Chain G, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 62
Score = 33.5 bits (75), Expect = 0.086, Method: Composition-based stats.
Identities = 14/46 (30%), Positives = 27/46 (58%)
Query: 59 LENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIE 104
+E+ + + G +Q QD+RR L +L V++NTL+ +A++
Sbjct: 16 IESYESVGVVNIAGIPSRQLQDMRRDLHGTAELRVSRNTLLERALD 61
>pdb|3O5H|M Chain M, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit
Length = 312
Score = 30.8 bits (68), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 58 HLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGT-----QWEALK 112
+LE + + + +Q ++R+ L +++ KNT+V +AI G +E L
Sbjct: 18 YLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIRGFLSDLPDFEKLL 77
Query: 113 PCMSGMNAWLFVH 125
P + G ++F +
Sbjct: 78 PFVKGYVGFVFTN 90
>pdb|3U5I|QQ Chain q, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|QQ Chain q, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 312
Score = 30.4 bits (67), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 58 HLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGT-----QWEALK 112
+LE + + + +Q ++R+ L +++ KNT+V +AI G +E L
Sbjct: 18 YLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIRGFLSDLPDFEKLL 77
Query: 113 PCMSGMNAWLFVH 125
P + G ++F +
Sbjct: 78 PFVKGNVGFVFTN 90
>pdb|3IZS|SS Chain s, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3J16|G Chain G, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
Length = 312
Score = 30.4 bits (67), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 58 HLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGT-----QWEALK 112
+LE + + + +Q ++R+ L +++ KNT+V +AI G +E L
Sbjct: 18 YLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIRGFLSDLPDFEKLL 77
Query: 113 PCMSGMNAWLFVH 125
P + G ++F +
Sbjct: 78 PFVKGNVGFVFTN 90
>pdb|3JYW|8 Chain 8, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 118
Score = 30.0 bits (66), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 58 HLENCHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEGT-----QWEALK 112
+LE + + + +Q ++R+ L +++ KNT+V +AI G +E L
Sbjct: 16 YLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIRGFLSDLPDFEKLL 75
Query: 113 PCMSGMNAWLFVH 125
P + G ++F +
Sbjct: 76 PFVKGYVGFVFTN 88
>pdb|3QED|A Chain A, The Structure And Function Of An Arabinan-Specific
Alpha-1,2- Arabinofuranosidase Identified From Screening
The Activities Of Bacterial Gh43 Glycoside Hydrolases
pdb|3QED|B Chain B, The Structure And Function Of An Arabinan-Specific
Alpha-1,2- Arabinofuranosidase Identified From Screening
The Activities Of Bacterial Gh43 Glycoside Hydrolases
pdb|3QED|C Chain C, The Structure And Function Of An Arabinan-Specific
Alpha-1,2- Arabinofuranosidase Identified From Screening
The Activities Of Bacterial Gh43 Glycoside Hydrolases
pdb|3QED|D Chain D, The Structure And Function Of An Arabinan-Specific
Alpha-1,2- Arabinofuranosidase Identified From Screening
The Activities Of Bacterial Gh43 Glycoside Hydrolases
Length = 314
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 82 RRSLPENTKLIVAKNTLVYKAIEGTQWEALKPCM 115
R P+NT V LVY + + WEA P +
Sbjct: 37 RDEAPDNTTFFVXNEWLVYSSDDXANWEAHGPGL 70
>pdb|2ZKR|GG Chain g, 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 = 317
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 8/67 (11%)
Query: 62 CHLIAAIKYKGFTVKQFQDLRRSLPENTKLIVAKNTLVYKAIEG-----TQWEALKPCMS 116
C ++ A KQ Q +R SL +++ KNT++ KAI G E L P +
Sbjct: 27 CFIVGA---DNVGSKQMQQIRMSLRGKAVVLMGKNTMMRKAIRGHLENNPALEKLLPHIR 83
Query: 117 GMNAWLF 123
G ++F
Sbjct: 84 GNVGFVF 90
>pdb|3T51|B Chain B, Crystal Structures Of The Pre-Extrusion And Extrusion
States Of The Cusba Adaptor-Transporter Complex
pdb|3T51|C Chain C, Crystal Structures Of The Pre-Extrusion And Extrusion
States Of The Cusba Adaptor-Transporter Complex
pdb|3T53|B Chain B, Crystal Structures Of The Extrusion State Of The Cusba
Adaptor- Transporter Complex
pdb|3T53|C Chain C, Crystal Structures Of The Extrusion State Of The Cusba
Adaptor- Transporter Complex
pdb|3T56|B Chain B, Crystal Structure Of The Pre-Extrusion State Of The Cusba
Adaptor- Transporter Complex
pdb|3T56|C Chain C, Crystal Structure Of The Pre-Extrusion State Of The Cusba
Adaptor- Transporter Complex
Length = 336
Score = 27.3 bits (59), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 17/27 (62%), Gaps = 3/27 (11%)
Query: 109 EALKPCMSGMNAWLFVHTEEIPAAIKP 135
EALKP GMNAWL ++T P + P
Sbjct: 228 EALKP---GMNAWLQLNTASEPMLLIP 251
>pdb|3OW7|A Chain A, Crystal Structure Of The Membrane Fusion Protein Cusb From
Escherichia Coli.
pdb|3OW7|B Chain B, Crystal Structure Of The Membrane Fusion Protein Cusb From
Escherichia Coli.
pdb|3OOC|A Chain A, Crystal Structure Of The Membrane Fusion Protein Cusb From
Escherichia Coli
pdb|3OOC|B Chain B, Crystal Structure Of The Membrane Fusion Protein Cusb From
Escherichia Coli
pdb|3NE5|B Chain B, Crystal Structure Of The Cusba Heavy-Metal Efflux Complex
From Escherichia Coli
pdb|3NE5|C Chain C, Crystal Structure Of The Cusba Heavy-Metal Efflux Complex
From Escherichia Coli
pdb|3OPO|A Chain A, Crystal Structure Of The Membrane Fusion Protein Cusb From
Escherichia Coli
pdb|3OPO|B Chain B, Crystal Structure Of The Membrane Fusion Protein Cusb From
Escherichia Coli
pdb|4DNT|B Chain B, Crystal Structure Of The Cusba Heavy-Metal Efflux Complex
From Escherichia Coli, Mutant
pdb|4DNT|C Chain C, Crystal Structure Of The Cusba Heavy-Metal Efflux Complex
From Escherichia Coli, Mutant
pdb|4DOP|B Chain B, Crystal Structure Of The Cusba Heavy-Metal Efflux Complex
From Escherichia Coli, R Mutant
pdb|4DOP|C Chain C, Crystal Structure Of The Cusba Heavy-Metal Efflux Complex
From Escherichia Coli, R Mutant
pdb|4DNR|B Chain B, Crystal Structure Of The Cusba Heavy-metal Efflux Complex
From Escherichia Coli, E716f Mutant
pdb|4DNR|C Chain C, Crystal Structure Of The Cusba Heavy-metal Efflux Complex
From Escherichia Coli, E716f Mutant
Length = 413
Score = 26.9 bits (58), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 17/27 (62%), Gaps = 3/27 (11%)
Query: 109 EALKPCMSGMNAWLFVHTEEIPAAIKP 135
EALKP GMNAWL ++T P + P
Sbjct: 305 EALKP---GMNAWLQLNTASEPMLLIP 328
>pdb|3H94|A Chain A, Crystal Structure Of The Membrane Fusion Protein Cusb From
Escherichia Coli
pdb|3H94|B Chain B, Crystal Structure Of The Membrane Fusion Protein Cusb From
Escherichia Coli
Length = 407
Score = 26.9 bits (58), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 17/27 (62%), Gaps = 3/27 (11%)
Query: 109 EALKPCMSGMNAWLFVHTEEIPAAIKP 135
EALKP GMNAWL ++T P + P
Sbjct: 305 EALKP---GMNAWLQLNTASEPMLLIP 328
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
0.318 0.134 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,031,912
Number of Sequences: 62578
Number of extensions: 228370
Number of successful extensions: 467
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 453
Number of HSP's gapped (non-prelim): 21
length of query: 220
length of database: 14,973,337
effective HSP length: 95
effective length of query: 125
effective length of database: 9,028,427
effective search space: 1128553375
effective search space used: 1128553375
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)