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= 035100
(73 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 89.7 bits (221), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 44/73 (60%), Positives = 52/73 (71%)
Query: 1 MAADTXXXXXXXXXXXXAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQ 60
MAAD EDKNVPYVFVPS+ ALGRACGV+RPV+A S+T+N+AS +KTQ
Sbjct: 54 MAADCEPIEILLHLPLLCEDKNVPYVFVPSRVALGRACGVSRPVIAASITTNDASAIKTQ 113
Query: 61 IQQLKDAIEKLLI 73
I +KD IE LLI
Sbjct: 114 IYAVKDKIETLLI 126
>pdb|2ALE|A Chain A, Crystal Structure Of Yeast Rna Splicing Factor Snu13p
Length = 134
Score = 89.7 bits (221), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 44/73 (60%), Positives = 52/73 (71%)
Query: 1 MAADTXXXXXXXXXXXXAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQ 60
MAAD EDKNVPYVFVPS+ ALGRACGV+RPV+A S+T+N+AS +KTQ
Sbjct: 54 MAADCEPIEILLHLPLLCEDKNVPYVFVPSRVALGRACGVSRPVIAASITTNDASAIKTQ 113
Query: 61 IQQLKDAIEKLLI 73
I +KD IE LLI
Sbjct: 114 IYAVKDKIETLLI 126
>pdb|2JNB|A Chain A, Solution Structure Of Rna-Binding Protein 15.5k
Length = 144
Score = 80.5 bits (197), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 45/73 (61%), Positives = 52/73 (71%)
Query: 1 MAADTXXXXXXXXXXXXAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQ 60
MAAD EDKNVPYVFV SKQALGRACGV+RPV+ACSVT E SQLK Q
Sbjct: 72 MAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQ 131
Query: 61 IQQLKDAIEKLLI 73
IQ ++ +IE+LL+
Sbjct: 132 IQSIQQSIERLLV 144
>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 = 80.5 bits (197), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 45/73 (61%), Positives = 52/73 (71%)
Query: 1 MAADTXXXXXXXXXXXXAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQ 60
MAAD EDKNVPYVFV SKQALGRACGV+RPV+ACSVT E SQLK Q
Sbjct: 58 MAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQ 117
Query: 61 IQQLKDAIEKLLI 73
IQ ++ +IE+LL+
Sbjct: 118 IQSIQQSIERLLV 130
>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 = 80.1 bits (196), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 45/73 (61%), Positives = 52/73 (71%)
Query: 1 MAADTXXXXXXXXXXXXAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQ 60
MAAD EDKNVPYVFV SKQALGRACGV+RPV+ACSVT E SQLK Q
Sbjct: 56 MAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQ 115
Query: 61 IQQLKDAIEKLLI 73
IQ ++ +IE+LL+
Sbjct: 116 IQSIQQSIERLLV 128
>pdb|2AIF|A Chain A, Crystal Structure Of High Mobility Like Protein, Nhp2,
Putative From Cryptosporidium Parvum
Length = 135
Score = 79.0 bits (193), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 38/73 (52%), Positives = 49/73 (67%)
Query: 1 MAADTXXXXXXXXXXXXAEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQ 60
+AAD EDKN PYVFV SK ALGRACGV+RPV+A ++TS + S L +Q
Sbjct: 63 LAADAEPLEILLHLPLVCEDKNTPYVFVRSKVALGRACGVSRPVIAAAITSKDGSSLSSQ 122
Query: 61 IQQLKDAIEKLLI 73
I +LKD IE++L+
Sbjct: 123 ITELKDQIEQILV 135
>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 = 48.9 bits (115), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 34/54 (62%), Gaps = 2/54 (3%)
Query: 19 EDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQIQQLKDAIEKLL 72
EDK VPYVF+ SK ALGRAC V+ P + S+ ++A L + ++ +E L+
Sbjct: 71 EDKGVPYVFIGSKNALGRACNVSVPTIVASIGKHDA--LGNVVAEIVGKVEALV 122
>pdb|3PAF|A Chain A, M. Jannaschii L7ae Mutant
pdb|3PAF|B Chain B, M. Jannaschii L7ae Mutant
Length = 117
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 33/47 (70%), Gaps = 1/47 (2%)
Query: 19 EDKNVPYVFVPSKQALGRACGVTRPVVACSVTS-NEASQLKTQIQQL 64
E+K +PY +V SKQ LG+A GV+RP + ++ + +A +LK I+++
Sbjct: 66 EEKGIPYAYVASKQDLGKAAGVSRPASSVAIINEGDAEELKVLIEKV 112
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 33/53 (62%), Gaps = 2/53 (3%)
Query: 19 EDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQIQQLKDAIEKL 71
E+KNVPY++V SK LGRA G+ P + ++ + +L+ ++ L + I+ L
Sbjct: 67 EEKNVPYIYVKSKNDLGRAVGIEVPCASAAIINE--GELRKELGSLVEKIKGL 117
>pdb|2LBW|A Chain A, Solution Structure Of The S. Cerevisiae HACA RNP PROTEIN
NHP2P-S82w Mutant
Length = 121
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 19 EDKNVPYVFVPSKQALGRACGVTRP--VVACSVTSNEASQLKTQIQQLKDAIEKLL 72
ED +VPY+F+PSKQ LG A RP VV SN+ K + ++ K++ +++
Sbjct: 60 EDHSVPYIFIPSKQDLGAAGATKRPTSVVFIVPGSNKKKDGKNKEEEYKESFNEVV 115
>pdb|2LBX|A Chain A, Solution Structure Of The S. Cerevisiae HACA RNP PROTEIN
NHP2P
Length = 121
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 19 EDKNVPYVFVPSKQALGRACGVTRP--VVACSVTSNEASQLKTQIQQLKDAIEKLL 72
ED +VPY+F+PSKQ LG A RP VV SN+ K + ++ K++ +++
Sbjct: 60 EDHSVPYIFIPSKQDLGAAGATKRPTSVVFIVPGSNKKKDGKNKEEEYKESFNEVV 115
>pdb|2FC3|A Chain A, Crystal Structure Of The Extremely Thermostable Aeropyrum
Pernix L7ae Multifunctional Protein
Length = 124
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 34/53 (64%), Gaps = 2/53 (3%)
Query: 19 EDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQIQQLKDAIEKL 71
++K +PYV+VPSK+ LG A G+ V A SV E +T ++++ + +++L
Sbjct: 68 DEKKIPYVYVPSKKRLGEAAGIE--VAAASVAIIEPGDAETLVREIVEKVKEL 118
>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 = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 18 AEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQIQQLKDAIEKL 71
A++K VP++FV + LG A G+ A +VT +A + ++ + D +E+L
Sbjct: 68 ADEKGVPFIFVEQQDDLGHAAGLEVGSAAAAVT--DAGEADADVEDIADKVEEL 119
>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 = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 18 AEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQIQQLKDAIEKL 71
A++K VP++FV + LG A G+ A +VT +A + ++ + D +E+L
Sbjct: 67 ADEKGVPFIFVEQQDDLGHAAGLEVGSAAAAVT--DAGEADADVEDIADKVEEL 118
>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 = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 5/49 (10%)
Query: 19 EDKNVPYVFVPSKQALGRACGVTRPVVACSV---TSNEASQLKTQIQQL 64
E+K +PY +V SKQ LG+A G+ V A SV +A +LK I+++
Sbjct: 69 EEKGIPYAYVASKQDLGKAAGLE--VAASSVAIINEGDAEELKVLIEKV 115
>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 = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 13/22 (59%), Positives = 19/22 (86%)
Query: 19 EDKNVPYVFVPSKQALGRACGV 40
++K +PYV+V SK+ALG ACG+
Sbjct: 74 DEKKIPYVYVSSKKALGEACGL 95
>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 = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 30/49 (61%), Gaps = 5/49 (10%)
Query: 19 EDKNVPYVFVPSKQALGRACGVTRPVVACSV---TSNEASQLKTQIQQL 64
E+K +PY +V SKQ LG+A G+ V A SV +A +LK I+++
Sbjct: 66 EEKGIPYAYVASKQDLGKAAGLE--VAASSVAIINEGDAEELKVLIEKV 112
>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 = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 15/17 (88%)
Query: 19 EDKNVPYVFVPSKQALG 35
E+K +PY++VPSK+ LG
Sbjct: 76 EEKEIPYIYVPSKKELG 92
>pdb|2CZW|A Chain A, Crystal Structure Analysis Of Protein Component Ph1496p
Of P.Horikoshii Ribonuclease P
Length = 124
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 15/17 (88%)
Query: 19 EDKNVPYVFVPSKQALG 35
E+K +PY++VPSK+ LG
Sbjct: 72 EEKEIPYIYVPSKKELG 88
>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 = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 15/17 (88%)
Query: 19 EDKNVPYVFVPSKQALG 35
E+K +PY++VPSK+ LG
Sbjct: 71 EEKEIPYIYVPSKKELG 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 = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 15/17 (88%)
Query: 19 EDKNVPYVFVPSKQALG 35
E+K +PY++VPSK+ LG
Sbjct: 77 EEKEIPYIYVPSKKELG 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 = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 15/17 (88%)
Query: 19 EDKNVPYVFVPSKQALG 35
E+K +PY++VPSK+ LG
Sbjct: 72 EEKEIPYIYVPSKKELG 88
>pdb|3HJW|C Chain C, Structure Of A Functional Ribonucleoprotein
Pseudouridine Synthase Bound To A Substrate Rna
Length = 120
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 10/17 (58%), Positives = 15/17 (88%)
Query: 19 EDKNVPYVFVPSKQALG 35
E+K +PY++VPSK+ LG
Sbjct: 69 EEKEIPYIYVPSKKELG 85
>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 = 30.4 bits (67), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 18 AEDKNVPYVFVPSKQALGRACGVTRPVVACSVTSNEASQLKTQIQQLKDAIEKL 71
A++K VP++FV + LG A G+ V + + +A T ++++ D +E+L
Sbjct: 67 ADEKGVPFIFVEQQDDLGHAAGLE--VGSAAAAVTDAGAAATVLEEIADKVEEL 118
>pdb|3V7E|A Chain A, Crystal Structure Of Ybxf Bound To The Sam-I Riboswitch
Aptamer
pdb|3V7E|B Chain B, Crystal Structure Of Ybxf Bound To The Sam-I Riboswitch
Aptamer
Length = 82
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 18 AEDKNVPYVFVPSKQALGRACGV 40
AED+ + V S + LG+ACG+
Sbjct: 49 AEDQGISVSMVESMKKLGKACGI 71
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
0.315 0.127 0.347
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,365,071
Number of Sequences: 62578
Number of extensions: 32276
Number of successful extensions: 107
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 82
Number of HSP's gapped (non-prelim): 25
length of query: 73
length of database: 14,973,337
effective HSP length: 43
effective length of query: 30
effective length of database: 12,282,483
effective search space: 368474490
effective search space used: 368474490
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)