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= 029226
(197 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4A17|F Chain F, 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|F Chain F, 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|F Chain F, 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|F Chain F, 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 = 255
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 32/58 (55%), Gaps = 4/58 (6%)
Query: 106 QLQVILLAADCSPRWLIKHLPGLALSRNVPVIFVKDKKGGSLRLGELVKLKTAIAVGI 163
Q +++++A D P L+ LP L +VP FVK G LG+LV KTA AV +
Sbjct: 140 QAKLVVIAHDVDPIELVIFLPQLCRKNDVPFAFVK----GKAALGKLVNKKTATAVAL 193
>pdb|2JNB|A Chain A, Solution Structure Of Rna-Binding Protein 15.5k
Length = 144
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 40/91 (43%), Gaps = 26/91 (28%)
Query: 54 DSLPEKLWFKQRFSIGVNEVTRVLERMAPRANMGISPQQPHILCGNSKVPSVQLQVILLA 113
D + + +KQ G NE T+ L R GIS + I++A
Sbjct: 40 DLVQQSCNYKQ-LRKGANEATKTLNR-------GIS------------------EFIVMA 73
Query: 114 ADCSPRWLIKHLPGLALSRNVPVIFVKDKKG 144
AD P +I HLP L +NVP +FV+ K+
Sbjct: 74 ADAEPLEIILHLPLLCEDKNVPYVFVRSKQA 104
>pdb|2OZB|A Chain A, Structure Of A Human Prp31-15.5k-U4 Snrna Complex
pdb|2OZB|D Chain D, Structure Of A Human Prp31-15.5k-U4 Snrna Complex
pdb|3SIU|A Chain A, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Monomeric Form
pdb|3SIU|D Chain D, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Monomeric Form
pdb|3SIV|A Chain A, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Dimeric Form
pdb|3SIV|D Chain D, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Dimeric Form
pdb|3SIV|G Chain G, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Dimeric Form
pdb|3SIV|J Chain J, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Dimeric Form
Length = 130
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 34/76 (44%), Gaps = 25/76 (32%)
Query: 69 GVNEVTRVLERMAPRANMGISPQQPHILCGNSKVPSVQLQVILLAADCSPRWLIKHLPGL 128
G NE T+ L R GIS + I++AAD P +I HLP L
Sbjct: 40 GANEATKTLNR-------GIS------------------EFIVMAADAEPLEIILHLPLL 74
Query: 129 ALSRNVPVIFVKDKKG 144
+NVP +FV+ K+
Sbjct: 75 CEDKNVPYVFVRSKQA 90
>pdb|1E7K|A Chain A, Crystal Structure Of The Spliceosomal 15.5kd Protein Bound
To A U4 Snrna Fragment
pdb|1E7K|B Chain B, Crystal Structure Of The Spliceosomal 15.5kd Protein Bound
To A U4 Snrna Fragment
Length = 128
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 34/76 (44%), Gaps = 25/76 (32%)
Query: 69 GVNEVTRVLERMAPRANMGISPQQPHILCGNSKVPSVQLQVILLAADCSPRWLIKHLPGL 128
G NE T+ L R GIS + I++AAD P +I HLP L
Sbjct: 38 GANEATKTLNR-------GIS------------------EFIVMAADAEPLEIILHLPLL 72
Query: 129 ALSRNVPVIFVKDKKG 144
+NVP +FV+ K+
Sbjct: 73 CEDKNVPYVFVRSKQA 88
>pdb|1ZWZ|A Chain A, Structural Comparison Of Yeast Snornp And Splicesomal
Protein Snu13p With Its Homologs
pdb|1ZWZ|B Chain B, Structural Comparison Of Yeast Snornp And Splicesomal
Protein Snu13p With Its Homologs
Length = 126
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 32/71 (45%), Gaps = 25/71 (35%)
Query: 69 GVNEVTRVLERMAPRANMGISPQQPHILCGNSKVPSVQLQVILLAADCSPRWLIKHLPGL 128
G NE T+ L R GIS + I++AADC P ++ HLP L
Sbjct: 36 GANEATKTLNR-------GIS------------------EFIIMAADCEPIEILLHLPLL 70
Query: 129 ALSRNVPVIFV 139
+NVP +FV
Sbjct: 71 CEDKNVPYVFV 81
>pdb|2ALE|A Chain A, Crystal Structure Of Yeast Rna Splicing Factor Snu13p
Length = 134
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 32/71 (45%), Gaps = 25/71 (35%)
Query: 69 GVNEVTRVLERMAPRANMGISPQQPHILCGNSKVPSVQLQVILLAADCSPRWLIKHLPGL 128
G NE T+ L R GIS + I++AADC P ++ HLP L
Sbjct: 36 GANEATKTLNR-------GIS------------------EFIIMAADCEPIEILLHLPLL 70
Query: 129 ALSRNVPVIFV 139
+NVP +FV
Sbjct: 71 CEDKNVPYVFV 81
>pdb|1RLG|A Chain A, Molecular Basis Of Box CD RNA-Protein Interaction: Co-
Crystal Structure Of The Archaeal Srnp Intiation Complex
pdb|1RLG|B Chain B, Molecular Basis Of Box CD RNA-Protein Interaction: Co-
Crystal Structure Of The Archaeal Srnp Intiation Complex
Length = 119
Score = 36.6 bits (83), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 39/88 (44%), Gaps = 25/88 (28%)
Query: 55 SLPEKLWFKQRFSIGVNEVTRVLERMAPRANMGISPQQPHILCGNSKVPSVQLQVILLAA 114
SL EK+ + G NE T+ +ER G++ +++ +A
Sbjct: 17 SLLEKVRESGKVKKGTNETTKAVER-------GLA------------------KLVYIAE 51
Query: 115 DCSPRWLIKHLPGLALSRNVPVIFVKDK 142
D P ++ HLP L +NVP I+VK K
Sbjct: 52 DVDPPEIVAHLPLLCEEKNVPYIYVKSK 79
>pdb|2AIF|A Chain A, Crystal Structure Of High Mobility Like Protein, Nhp2,
Putative From Cryptosporidium Parvum
Length = 135
Score = 36.2 bits (82), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 23/35 (65%)
Query: 108 QVILLAADCSPRWLIKHLPGLALSRNVPVIFVKDK 142
+++LLAAD P ++ HLP + +N P +FV+ K
Sbjct: 59 EIVLLAADAEPLEILLHLPLVCEDKNTPYVFVRSK 93
>pdb|3HJW|C Chain C, Structure Of A Functional Ribonucleoprotein Pseudouridine
Synthase Bound To A Substrate Rna
Length = 120
Score = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 106 QLQVILLAADCSPRWLIKHLPGLALSRNVPVIFVKDKK 143
Q +++++A D P ++ HLP L + +P I+V KK
Sbjct: 45 QAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKK 82
>pdb|2CZW|A Chain A, Crystal Structure Analysis Of Protein Component Ph1496p Of
P.Horikoshii Ribonuclease P
Length = 124
Score = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 106 QLQVILLAADCSPRWLIKHLPGLALSRNVPVIFVKDKK 143
Q +++++A D P ++ HLP L + +P I+V KK
Sbjct: 48 QAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKK 85
>pdb|3LWO|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
5BRU
pdb|3LWP|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
5BRDU
pdb|3LWQ|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
3MU
pdb|3LWR|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
4SU
pdb|3LWV|C Chain C, Structure Of HACA RNP BOUND TO A SUBSTRATE RNA CONTAINING
2'- Deoxyuridine
pdb|3J20|3 Chain 3, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
pdb|3J21|G Chain G, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
pdb|3J21|4 Chain 4, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 123
Score = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 106 QLQVILLAADCSPRWLIKHLPGLALSRNVPVIFVKDKK 143
Q +++++A D P ++ HLP L + +P I+V KK
Sbjct: 47 QAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKK 84
>pdb|3NMU|C Chain C, Crystal Structure Of Substrate-Bound Halfmer Box CD RNP
pdb|3NMU|G Chain G, Crystal Structure Of Substrate-Bound Halfmer Box CD RNP
pdb|3NVI|B Chain B, Structure Of N-Terminal Truncated Nop5658 BOUND WITH L7AE
AND BOX CD Rna
pdb|3NVI|D Chain D, Structure Of N-Terminal Truncated Nop5658 BOUND WITH L7AE
AND BOX CD Rna
pdb|3NVK|E Chain E, Structural Basis For Substrate Placement By An Archaeal
Box CD Ribonucleoprotein Particle
pdb|3NVK|H Chain H, Structural Basis For Substrate Placement By An Archaeal
Box CD Ribonucleoprotein Particle
Length = 129
Score = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 106 QLQVILLAADCSPRWLIKHLPGLALSRNVPVIFVKDKK 143
Q +++++A D P ++ HLP L + +P I+V KK
Sbjct: 53 QAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKK 90
>pdb|2HVY|D Chain D, Crystal Structure Of An HACA BOX RNP FROM PYROCOCCUS
FURIOSUS
pdb|3HAX|D Chain D, Crystal Structure Of A Substrate-Bound Gar1-Minus HACA RNP
FROM Pyrococcus Furiosus
pdb|3HAY|D Chain D, Crystal Structure Of A Substrate-Bound Full HACA RNP FROM
Pyrococcus Furiosus
Length = 130
Score = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 106 QLQVILLAADCSPRWLIKHLPGLALSRNVPVIFVKDKK 143
Q +++++A D P ++ HLP L + +P I+V KK
Sbjct: 48 QAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKK 85
>pdb|1PXW|A Chain A, Crystal Structure Of L7ae Srnp Core Protein From
Pyrococcus Abyssii
pdb|1PXW|B Chain B, Crystal Structure Of L7ae Srnp Core Protein From
Pyrococcus Abyssii
Length = 128
Score = 35.0 bits (79), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 106 QLQVILLAADCSPRWLIKHLPGLALSRNVPVIFVKDKK 143
Q +++++A D P ++ HLP L + +P I+V KK
Sbjct: 52 QAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKK 89
>pdb|1S72|F Chain F, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1YHQ|F Chain F, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|F Chain F, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|F Chain F, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|F Chain F, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|F Chain F, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|F Chain F, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|F Chain F, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|F Chain F, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|F Chain F, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|F Chain F, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|F Chain F, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|F Chain F, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|F Chain F, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|F Chain F, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|F Chain F, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|F Chain F, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|F Chain F, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|F Chain F, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|F Chain F, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|F Chain F, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|F Chain F, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|F Chain F, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|3CC2|F Chain F, 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|F Chain F, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|F Chain F, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|F Chain F, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|F Chain F, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|F Chain F, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|F Chain F, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|2QEX|F Chain F, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3I55|F Chain F, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|F Chain F, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
pdb|4ADX|F Chain F, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 120
Score = 34.7 bits (78), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 21/33 (63%)
Query: 108 QVILLAADCSPRWLIKHLPGLALSRNVPVIFVK 140
+++ +A D P ++ H+P LA + VP IFV+
Sbjct: 47 ELVFVAEDVQPEEIVMHIPELADEKGVPFIFVE 79
>pdb|3G4S|F Chain F, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|F Chain F, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|F Chain F, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
Length = 119
Score = 34.7 bits (78), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 21/33 (63%)
Query: 108 QVILLAADCSPRWLIKHLPGLALSRNVPVIFVK 140
+++ +A D P ++ H+P LA + VP IFV+
Sbjct: 46 ELVFVAEDVQPEEIVMHIPELADEKGVPFIFVE 78
>pdb|1FFK|E Chain E, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1JJ2|F Chain F, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|F Chain F, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|H Chain H, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|H Chain H, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|H Chain H, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|H Chain H, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|H Chain H, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1K73|H Chain H, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|H Chain H, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|H Chain H, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|H Chain H, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|H Chain H, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|H Chain H, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|H Chain H, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|H Chain H, 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|F Chain F, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|F Chain F, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1W2B|F Chain F, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|3CXC|F Chain F, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
pdb|3OW2|F Chain F, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 119
Score = 34.7 bits (78), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 21/33 (63%)
Query: 108 QVILLAADCSPRWLIKHLPGLALSRNVPVIFVK 140
+++ +A D P ++ H+P LA + VP IFV+
Sbjct: 46 ELVFVAEDVQPEEIVMHIPELADEKGVPFIFVE 78
>pdb|2ZKR|FF Chain f, 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 = 266
Score = 33.9 bits (76), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 4/62 (6%)
Query: 102 VPSVQLQVILLAADCSPRWLIKHLPGLALSRNVPVIFVKDKKGGSLRLGELVKLKTAIAV 161
V + + Q++++A D P L+ LP L VP +K G RLG LV KT V
Sbjct: 147 VENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCIIK----GKARLGHLVHRKTCTTV 202
Query: 162 GI 163
Sbjct: 203 AF 204
>pdb|1RA4|A Chain A, Crystal Structure Of The Methanococcus Jannaschii L7ae
Protein
pdb|1XBI|A Chain A, High Resolution Structure Of Methanocaldococcus Jannaschii
L7ae
Length = 120
Score = 33.9 bits (76), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 25/80 (31%)
Query: 64 QRFSIGVNEVTRVLERMAPRANMGISPQQPHILCGNSKVPSVQLQVILLAADCSPRWLIK 123
Q+ G NEVT+ +ER GI+ +++++A D P ++
Sbjct: 28 QKIKKGANEVTKAVER-------GIA------------------KLVIIAEDVKPEEVVA 62
Query: 124 HLPGLALSRNVPVIFVKDKK 143
HLP L + +P +V K+
Sbjct: 63 HLPYLCEEKGIPYAYVASKQ 82
>pdb|1SDS|A Chain A, Structure Of Protein L7ae Bound To A K-Turn Derived From
An Archaeal Box HACA SRNA
pdb|1SDS|B Chain B, Structure Of Protein L7ae Bound To A K-Turn Derived From
An Archaeal Box HACA SRNA
pdb|1SDS|C Chain C, Structure Of Protein L7ae Bound To A K-Turn Derived From
An Archaeal Box HACA SRNA
Length = 117
Score = 33.9 bits (76), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 25/80 (31%)
Query: 64 QRFSIGVNEVTRVLERMAPRANMGISPQQPHILCGNSKVPSVQLQVILLAADCSPRWLIK 123
Q+ G NEVT+ +ER GI+ +++++A D P ++
Sbjct: 25 QKIKKGANEVTKAVER-------GIA------------------KLVIIAEDVKPEEVVA 59
Query: 124 HLPGLALSRNVPVIFVKDKK 143
HLP L + +P +V K+
Sbjct: 60 HLPYLCEEKGIPYAYVASKQ 79
>pdb|3IZS|H Chain H, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|H Chain H, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|H Chain H, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|G Chain G, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|G Chain G, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|G Chain G, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 256
Score = 33.5 bits (75), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 38/89 (42%), Gaps = 15/89 (16%)
Query: 106 QLQVILLAADCSPRWLIKHLPGLALSRNVPVIFVKDKKGGSLRLGELVKLKTAIAVGIKA 165
+ +++L+A D P L+ LP L VP VK G RLG LV KT+
Sbjct: 147 KAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVK----GKARLGTLVNQKTSAVAA--- 199
Query: 166 KGNIINQLMDKILHGDEVDLLKLSETPEA 194
+ ++ DE L KL T +A
Sbjct: 200 --------LTEVRAEDEAALAKLVSTIDA 220
>pdb|3PAF|A Chain A, M. Jannaschii L7ae Mutant
pdb|3PAF|B Chain B, M. Jannaschii L7ae Mutant
Length = 117
Score = 33.1 bits (74), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 25/80 (31%)
Query: 64 QRFSIGVNEVTRVLERMAPRANMGISPQQPHILCGNSKVPSVQLQVILLAADCSPRWLIK 123
Q+ G NEVT+ +ER GI+ +++++A D P ++
Sbjct: 25 QQIKKGANEVTKAVER-------GIA------------------KLVIIAEDVKPEEVVA 59
Query: 124 HLPGLALSRNVPVIFVKDKK 143
HLP L + +P +V K+
Sbjct: 60 HLPYLCEEKGIPYAYVASKQ 79
>pdb|1S1I|G Chain G, 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 = 119
Score = 32.7 bits (73), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 37/87 (42%), Gaps = 15/87 (17%)
Query: 108 QVILLAADCSPRWLIKHLPGLALSRNVPVIFVKDKKGGSLRLGELVKLKTAIAVGIKAKG 167
+++L+A D P L+ LP L VP VK G RLG LV KT+
Sbjct: 48 KLVLIANDVDPIELVVFLPALCKKMGVPYAIVK----GKARLGTLVNQKTSAVAA----- 98
Query: 168 NIINQLMDKILHGDEVDLLKLSETPEA 194
+ ++ DE L KL T +A
Sbjct: 99 ------LTEVRAEDEAALAKLVSTIDA 119
>pdb|3IZR|H Chain H, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 258
Score = 32.3 bits (72), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 34/78 (43%), Gaps = 4/78 (5%)
Query: 108 QVILLAADCSPRWLIKHLPGLALSRNVPVIFVKDKKGGSLRLGELVKLKTAIAVGIKAKG 167
Q++++A D P L+ LP L VP VK G RLG +V KTA + +
Sbjct: 145 QLVVIAHDVDPIELVVWLPALCRKMEVPYCIVK----GKARLGSIVHKKTASVLCLTTVK 200
Query: 168 NIINQLMDKILHGDEVDL 185
N KIL + +
Sbjct: 201 NEDKLEFSKILEAIKANF 218
>pdb|3JYW|G Chain G, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 113
Score = 32.3 bits (72), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 108 QVILLAADCSPRWLIKHLPGLALSRNVPVIFVKDKKGGSLRLGELVKLKTA 158
+++L+A D P L+ LP L VP VK G RLG LV KT+
Sbjct: 43 KLVLIANDVDPIELVVFLPALCKKMGVPYAIVK----GKARLGTLVNQKTS 89
>pdb|2LBX|A Chain A, Solution Structure Of The S. Cerevisiae HACA RNP PROTEIN
NHP2P
Length = 121
Score = 31.6 bits (70), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 109 VILLAADCSPRWLIKHLPGLALSRNVPVIFVKDK 142
++++A D SP +I H+P L +VP IF+ K
Sbjct: 39 LVVIAGDISPADVISHIPVLCEDHSVPYIFIPSK 72
>pdb|3O85|A Chain A, Giardia Lamblia 15.5kd Rna Binding Protein
pdb|3O85|B Chain B, Giardia Lamblia 15.5kd Rna Binding Protein
Length = 122
Score = 30.4 bits (67), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 108 QVILLAADCSPRWLIKHLPGLALSRNVPVIFVKDKKGGSLRLGELVKLKTAIAVGIKAK- 166
+++++AAD P ++ HLP + VP +F+ K LG + V K
Sbjct: 49 ELVIIAADADPIEIVLHLPLACEDKGVPYVFIGSKNA----LGRACNVSVPTIVASIGKH 104
Query: 167 ---GNIINQLMDKI 177
GN++ +++ K+
Sbjct: 105 DALGNVVAEIVGKV 118
>pdb|2LBW|A Chain A, Solution Structure Of The S. Cerevisiae HACA RNP PROTEIN
NHP2P-S82w Mutant
Length = 121
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 109 VILLAADCSPRWLIKHLPGLALSRNVPVIFVKDKK 143
++++A D P +I H+P L +VP IF+ K+
Sbjct: 39 LVVIAGDIWPADVISHIPVLCEDHSVPYIFIPSKQ 73
>pdb|4EAH|A Chain A, Crystal Structure Of The Formin Homology 2 Domain Of Fmnl3
Bound To Actin
pdb|4EAH|E Chain E, Crystal Structure Of The Formin Homology 2 Domain Of Fmnl3
Bound To Actin
pdb|4EAH|C Chain C, Crystal Structure Of The Formin Homology 2 Domain Of Fmnl3
Bound To Actin
pdb|4EAH|B Chain B, Crystal Structure Of The Formin Homology 2 Domain Of Fmnl3
Bound To Actin
Length = 402
Score = 27.7 bits (60), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 27/94 (28%), Positives = 46/94 (48%), Gaps = 15/94 (15%)
Query: 32 ESLVRLLKLIQREIVSARSLHGDSLP-EKLWFKQRFSIGVNEVTRVLERMAPRANMG--- 87
E L+R L + E+ R + P E+L + RF + ++V R+ +RMA A +G
Sbjct: 127 ECLMRFLP-TEAEVKLLRQYERERQPLEELAAEDRFMLLFSKVERLTQRMAGMAFLGNFQ 185
Query: 88 -----ISPQQPHILCGNSKVPSVQ-----LQVIL 111
++PQ I+ ++ V S Q L++IL
Sbjct: 186 DNLQMLTPQLNAIIAASASVKSSQKLKQMLEIIL 219
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 0.136 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,659,904
Number of Sequences: 62578
Number of extensions: 206665
Number of successful extensions: 443
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 416
Number of HSP's gapped (non-prelim): 30
length of query: 197
length of database: 14,973,337
effective HSP length: 94
effective length of query: 103
effective length of database: 9,091,005
effective search space: 936373515
effective search space used: 936373515
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)