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= 033552
(117 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2LBX|A Chain A, Solution Structure Of The S. Cerevisiae HACA RNP PROTEIN
NHP2P
Length = 121
Score = 89.0 bits (219), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 62/90 (68%)
Query: 23 LLFHECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVL 82
L E L VIAG+ISP DVI+H+P+LCE+ +PYI++ SK+DL AGATKRPT V ++
Sbjct: 32 LRKGEKGLVVIAGDISPADVISHIPVLCEDHSVPYIFIPSKQDLGAAGATKRPTSVVFIV 91
Query: 83 TKPTKGELGQEEQDKLKADYTLVVEDVKEL 112
K + G+ ++++ K + VV++V+ L
Sbjct: 92 PGSNKKKDGKNKEEEYKESFNEVVKEVQAL 121
>pdb|2LBW|A Chain A, Solution Structure Of The S. Cerevisiae HACA RNP PROTEIN
NHP2P-S82w Mutant
Length = 121
Score = 87.0 bits (214), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 39/86 (45%), Positives = 60/86 (69%)
Query: 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPT 86
E L VIAG+I P DVI+H+P+LCE+ +PYI++ SK+DL AGATKRPT V ++
Sbjct: 36 EKGLVVIAGDIWPADVISHIPVLCEDHSVPYIFIPSKQDLGAAGATKRPTSVVFIVPGSN 95
Query: 87 KGELGQEEQDKLKADYTLVVEDVKEL 112
K + G+ ++++ K + VV++V+ L
Sbjct: 96 KKKDGKNKEEEYKESFNEVVKEVQAL 121
>pdb|3PAF|A Chain A, M. Jannaschii L7ae Mutant
pdb|3PAF|B Chain B, M. Jannaschii L7ae Mutant
Length = 117
Score = 62.8 bits (151), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 27/63 (42%), Positives = 38/63 (60%)
Query: 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTK 87
+L +IA ++ P +V+ H+P LCEE IPY YVASK+DL A RP V ++ +
Sbjct: 43 AKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAGVSRPASSVAIINEGDA 102
Query: 88 GEL 90
EL
Sbjct: 103 EEL 105
>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 = 56.2 bits (134), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 37/63 (58%)
Query: 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTK 87
+L +IA ++ P +V+ H+P LCEE IPY YVASK+DL A + V ++ +
Sbjct: 46 AKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAGLEVAASSVAIINEGDA 105
Query: 88 GEL 90
EL
Sbjct: 106 EEL 108
>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 = 56.2 bits (134), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 37/63 (58%)
Query: 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTK 87
+L +IA ++ P +V+ H+P LCEE IPY YVASK+DL A + V ++ +
Sbjct: 43 AKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAGLEVAASSVAIINEGDA 102
Query: 88 GEL 90
EL
Sbjct: 103 EEL 105
>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 = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 40/66 (60%), Gaps = 3/66 (4%)
Query: 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTK 87
+L IA ++ P +++ H+P+LCEE ++PYIYV SK DL A + P ++ +
Sbjct: 44 AKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKSKNDLGRAVGIEVPCASAAII---NE 100
Query: 88 GELGQE 93
GEL +E
Sbjct: 101 GELRKE 106
>pdb|3ID5|C Chain C, Crystal Structure Of Sulfolobus Solfataricus CD RNP
ASSEMBLED WITH Nop5, Fibrillarin, L7ae And A Split Half
CD RNA
pdb|3ID5|G Chain G, Crystal Structure Of Sulfolobus Solfataricus CD RNP
ASSEMBLED WITH Nop5, Fibrillarin, L7ae And A Split Half
CD RNA
pdb|3PLA|C Chain C, Crystal Structure Of A Catalytically Active
Substrate-Bound Box CD Rnp From Sulfolobus Solfataricus
pdb|3PLA|D Chain D, Crystal Structure Of A Catalytically Active
Substrate-Bound Box CD Rnp From Sulfolobus Solfataricus
pdb|3PLA|L Chain L, Crystal Structure Of A Catalytically Active
Substrate-Bound Box CD Rnp From Sulfolobus Solfataricus
Length = 130
Score = 51.2 bits (121), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 36/56 (64%)
Query: 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVL 82
+ +L +IA ++ P +++ H+P+LC+E IPY+YV+SK+ L A + T +L
Sbjct: 50 QAKLVIIAEDVQPEEIVAHLPLLCDEKKIPYVYVSSKKALGEACGLQVATASAAIL 105
>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 = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 19/41 (46%), Positives = 31/41 (75%)
Query: 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67
+ +L +IA ++ P +++ H+P LCEE +IPYIYV SK++L
Sbjct: 52 QAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELG 92
>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 = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 19/41 (46%), Positives = 31/41 (75%)
Query: 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67
+ +L +IA ++ P +++ H+P LCEE +IPYIYV SK++L
Sbjct: 47 QAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELG 87
>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 = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 19/41 (46%), Positives = 31/41 (75%)
Query: 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67
+ +L +IA ++ P +++ H+P LCEE +IPYIYV SK++L
Sbjct: 53 QAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELG 93
>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 = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 19/41 (46%), Positives = 31/41 (75%)
Query: 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67
+ +L +IA ++ P +++ H+P LCEE +IPYIYV SK++L
Sbjct: 48 QAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELG 88
>pdb|2CZW|A Chain A, Crystal Structure Analysis Of Protein Component Ph1496p
Of P.Horikoshii Ribonuclease P
Length = 124
Score = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 19/41 (46%), Positives = 31/41 (75%)
Query: 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67
+ +L +IA ++ P +++ H+P LCEE +IPYIYV SK++L
Sbjct: 48 QAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELG 88
>pdb|2JNB|A Chain A, Solution Structure Of Rna-Binding Protein 15.5k
Length = 144
Score = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 33/53 (62%)
Query: 32 VIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTK 84
V+A + P+++I H+P+LCE+ ++PY++V SK+ L A RP V K
Sbjct: 71 VMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIK 123
>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 = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 31/44 (70%)
Query: 32 VIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRP 75
V+A + P+++I H+P+LCE+ ++PY++V SK+ L A RP
Sbjct: 55 VMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRP 98
>pdb|2FC3|A Chain A, Crystal Structure Of The Extremely Thermostable
Aeropyrum Pernix L7ae Multifunctional Protein
Length = 124
Score = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 34/55 (61%)
Query: 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVL 82
+L VIA ++ P +++ H+P+LC+E IPY+YV SK+ L A + V ++
Sbjct: 45 AKLVVIAEDVDPPEIVMHLPLLCDEKKIPYVYVPSKKRLGEAAGIEVAAASVAII 99
>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 = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 31/44 (70%)
Query: 32 VIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRP 75
V+A + P+++I H+P+LCE+ ++PY++V SK+ L A RP
Sbjct: 57 VMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRP 100
>pdb|3HJW|C Chain C, Structure Of A Functional Ribonucleoprotein
Pseudouridine Synthase Bound To A Substrate Rna
Length = 120
Score = 50.1 bits (118), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 19/41 (46%), Positives = 31/41 (75%)
Query: 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLA 67
+ +L +IA ++ P +++ H+P LCEE +IPYIYV SK++L
Sbjct: 45 QAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELG 85
>pdb|2ALE|A Chain A, Crystal Structure Of Yeast Rna Splicing Factor Snu13p
Length = 134
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 40/76 (52%)
Query: 32 VIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPTKGELG 91
++A + PI+++ H+P+LCE+ ++PY++V S+ L A RP + T
Sbjct: 53 IMAADCEPIEILLHLPLLCEDKNVPYVFVPSRVALGRACGVSRPVIAASITTNDASAIKT 112
Query: 92 QEEQDKLKADYTLVVE 107
Q K K + L++E
Sbjct: 113 QIYAVKDKIETLLILE 128
>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 = 45.8 bits (107), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 32/52 (61%)
Query: 32 VIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLT 83
++A + PI+++ H+P+LCE+ ++PY++V S+ L A RP + T
Sbjct: 53 IMAADCEPIEILLHLPLLCEDKNVPYVFVPSRVALGRACGVSRPVIAASITT 104
>pdb|3ZF7|XX Chain x, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 276
Score = 45.4 bits (106), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 28/54 (51%)
Query: 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLV 81
RL +IA N+ PI+++ +P LC + IPY V K L +A K TC
Sbjct: 161 ARLVLIANNVDPIELVLWMPTLCRANKIPYAIVKDKARLGDAIGRKTATCVAFT 214
>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 = 45.1 bits (105), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 38/74 (51%)
Query: 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTKPT 86
+ L +IA + PI+++ H+P+ CE+ +PY+++ SK L A PT +
Sbjct: 47 KAELVIIAADADPIEIVLHLPLACEDKGVPYVFIGSKNALGRACNVSVPTIVASIGKHDA 106
Query: 87 KGELGQEEQDKLKA 100
G + E K++A
Sbjct: 107 LGNVVAEIVGKVEA 120
>pdb|2AIF|A Chain A, Crystal Structure Of High Mobility Like Protein, Nhp2,
Putative From Cryptosporidium Parvum
Length = 135
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 33/57 (57%)
Query: 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTK 84
+ ++A + P++++ H+P++CE+ + PY++V SK L A RP + +K
Sbjct: 58 AEIVLLAADAEPLEILLHLPLVCEDKNTPYVFVRSKVALGRACGVSRPVIAAAITSK 114
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 30/55 (54%)
Query: 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLV 81
+ +L VIA ++ PI+++ +P LC ++D+P+ +V K L K T L
Sbjct: 140 QAKLVVIAHDVDPIELVIFLPQLCRKNDVPFAFVKGKAALGKLVNKKTATAVALT 194
>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 = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 30/54 (55%)
Query: 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLV 81
L +A ++ P +++ H+P L +E +P+I+V ++DL +A + + V
Sbjct: 46 AELVFVAEDVQPEEIVMHIPELADEKGVPFIFVEQQDDLGHAAGLEVGSAAAAV 99
>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 = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 30/54 (55%)
Query: 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLV 81
L +A ++ P +++ H+P L +E +P+I+V ++DL +A + + V
Sbjct: 45 AELVFVAEDVQPEEIVMHIPELADEKGVPFIFVEQQDDLGHAAGLEVGSAAAAV 98
>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 = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 27/44 (61%)
Query: 28 CRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGA 71
L +A ++ P +++ H+P L +E +P+I+V ++DL +A
Sbjct: 45 AELVFVAEDVQPEEIVMHIPELADEKGVPFIFVEQQDDLGHAAG 88
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLT 83
+ +L VIA ++ PI+++ +P LC + ++PY V K L + K T VL LT
Sbjct: 143 KAQLVVIAHDVDPIELVVWLPALCRKMEVPYCIVKGKARLGSIVHKK--TASVLCLT 197
>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 = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 27 ECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLTK 84
+ +L VIA ++ PI+++ +P LC + +PY + K L + R TC + T+
Sbjct: 151 KAQLVVIAHDVDPIELVVFLPALCRKMGVPYCIIKGKARLGH--LVHRKTCTTVAFTQ 206
>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 = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 26 HECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLT 83
+ +L +IA ++ PI+++ +P LC++ +PY V K L + T V LT
Sbjct: 146 KKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLGT--LVNQKTSAVAALT 201
>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 = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 26 HECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLT 83
+ +L +IA ++ PI+++ +P LC++ +PY V K L + T V LT
Sbjct: 40 KKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLGT--LVNQKTSAVAALT 95
>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 = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 26 HECRLCVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATKRPTCCVLVLT 83
+ +L +IA ++ PI+++ +P LC++ +PY V K L + T V LT
Sbjct: 45 KKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLGT--LVNQKTSAVAALT 100
>pdb|3TML|A Chain A, Crystal Structure Of 2-Dehydro-3-Deoxyphosphooctonate
Aldolase From Burkholderia Cenocepacia
pdb|3TML|B Chain B, Crystal Structure Of 2-Dehydro-3-Deoxyphosphooctonate
Aldolase From Burkholderia Cenocepacia
pdb|3TML|C Chain C, Crystal Structure Of 2-Dehydro-3-Deoxyphosphooctonate
Aldolase From Burkholderia Cenocepacia
pdb|3TML|D Chain D, Crystal Structure Of 2-Dehydro-3-Deoxyphosphooctonate
Aldolase From Burkholderia Cenocepacia
Length = 288
Score = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 31 CVIAGNISPIDVITHVPILCEESDIPYIYVASKEDLANAGATK 73
CV+ ID + +CE+ ++P+IY +S D AN + K
Sbjct: 25 CVVESEQMTIDTAGRLKEICEKLNVPFIYKSSY-DKANRSSGK 66
>pdb|2QND|A Chain A, Crystal Structure Of The Kh1-Kh2 Domains From Human
Fragile X Mental Retardation Protein
pdb|2QND|B Chain B, Crystal Structure Of The Kh1-Kh2 Domains From Human
Fragile X Mental Retardation Protein
Length = 144
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 8/19 (42%), Positives = 15/19 (78%)
Query: 51 EESDIPYIYVASKEDLANA 69
EE +P+++V +K+ +ANA
Sbjct: 114 EEGXVPFVFVGTKDSIANA 132
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
0.320 0.138 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,438,371
Number of Sequences: 62578
Number of extensions: 128024
Number of successful extensions: 254
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 33
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 221
Number of HSP's gapped (non-prelim): 35
length of query: 117
length of database: 14,973,337
effective HSP length: 80
effective length of query: 37
effective length of database: 9,967,097
effective search space: 368782589
effective search space used: 368782589
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)