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= psy6265
(91 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 = 63.5 bits (153), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 49/90 (54%), Gaps = 11/90 (12%)
Query: 9 LQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKPCICVIV- 67
L++ L + AGD++P +++ H+P +CED +PY ++PSK+D+G A K+P V +
Sbjct: 32 LRKGEKGLVVIAGDISPADVISHIPVLCEDHSVPYIFIPSKQDLGAAGATKRPTSVVFIV 91
Query: 68 ----------KSTESVAELYEEVKQEIGAL 87
E E + EV +E+ AL
Sbjct: 92 PGSNKKKDGKNKEEEYKESFNEVVKEVQAL 121
>pdb|3PAF|A Chain A, M. Jannaschii L7ae Mutant
pdb|3PAF|B Chain B, M. Jannaschii L7ae Mutant
Length = 117
Score = 62.4 bits (150), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 43/74 (58%)
Query: 3 STVQGPLQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKPC 62
+ V ++R L I A DV P E++ HLP +CE+K IPY YV SK+D+G+A G +P
Sbjct: 32 NEVTKAVERGIAKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAGVSRPA 91
Query: 63 ICVIVKSTESVAEL 76
V + + EL
Sbjct: 92 SSVAIINEGDAEEL 105
>pdb|2ALE|A Chain A, Crystal Structure Of Yeast Rna Splicing Factor Snu13p
Length = 134
Score = 62.0 bits (149), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 27/66 (40%), Positives = 39/66 (59%)
Query: 9 LQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKPCICVIVK 68
L R I A D PIEI+ HLP +CEDK++PY +VPS+ +G A G +P I +
Sbjct: 44 LNRGISEFIIMAADCEPIEILLHLPLLCEDKNVPYVFVPSRVALGRACGVSRPVIAASIT 103
Query: 69 STESVA 74
+ ++ A
Sbjct: 104 TNDASA 109
>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 = 61.6 bits (148), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 27/66 (40%), Positives = 39/66 (59%)
Query: 9 LQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKPCICVIVK 68
L R I A D PIEI+ HLP +CEDK++PY +VPS+ +G A G +P I +
Sbjct: 44 LNRGISEFIIMAADCEPIEILLHLPLLCEDKNVPYVFVPSRVALGRACGVSRPVIAASIT 103
Query: 69 STESVA 74
+ ++ A
Sbjct: 104 TNDASA 109
>pdb|2LBW|A Chain A, Solution Structure Of The S. Cerevisiae HACA RNP PROTEIN
NHP2P-S82w Mutant
Length = 121
Score = 61.6 bits (148), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 48/90 (53%), Gaps = 11/90 (12%)
Query: 9 LQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKPCICVIV- 67
L++ L + AGD+ P +++ H+P +CED +PY ++PSK+D+G A K+P V +
Sbjct: 32 LRKGEKGLVVIAGDIWPADVISHIPVLCEDHSVPYIFIPSKQDLGAAGATKRPTSVVFIV 91
Query: 68 ----------KSTESVAELYEEVKQEIGAL 87
E E + EV +E+ AL
Sbjct: 92 PGSNKKKDGKNKEEEYKESFNEVVKEVQAL 121
>pdb|2AIF|A Chain A, Crystal Structure Of High Mobility Like Protein, Nhp2,
Putative From Cryptosporidium Parvum
Length = 135
Score = 61.2 bits (147), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 9 LQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKPCICVIVK 68
L R + + A D P+EI+ HLP VCEDK+ PY +V SK +G A G +P I +
Sbjct: 53 LNRGIAEIVLLAADAEPLEILLHLPLVCEDKNTPYVFVRSKVALGRACGVSRPVIAAAIT 112
Query: 69 S------TESVAELYEEVKQ 82
S + + EL ++++Q
Sbjct: 113 SKDGSSLSSQITELKDQIEQ 132
>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 = 60.5 bits (145), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 32/86 (37%), Positives = 50/86 (58%), Gaps = 8/86 (9%)
Query: 2 NSTVQGPLQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKP 61
N T + ++R L A DV P EI+ HLP +CE+K++PY YV SK D+G A+G + P
Sbjct: 33 NETTKA-VERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKSKNDLGRAVGIEVP 91
Query: 62 CICVIVKSTESVAELYEEVKQEIGAL 87
C + + E+++E+G+L
Sbjct: 92 CASAAIINE-------GELRKELGSL 110
>pdb|2FC3|A Chain A, Crystal Structure Of The Extremely Thermostable
Aeropyrum Pernix L7ae Multifunctional Protein
Length = 124
Score = 59.3 bits (142), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 28/56 (50%), Positives = 37/56 (66%), Gaps = 1/56 (1%)
Query: 2 NSTVQGPLQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALG 57
N T + ++R L + A DV P EI+ HLP +C++K IPY YVPSKK +GEA G
Sbjct: 34 NETTKA-VERGLAKLVVIAEDVDPPEIVMHLPLLCDEKKIPYVYVPSKKRLGEAAG 88
>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 = 58.9 bits (141), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 27/52 (51%), Positives = 36/52 (69%), Gaps = 1/52 (1%)
Query: 2 NSTVQGPLQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIG 53
N T + ++R L I A DV P EI+ HLP +CE+K+IPY YVPSKK++G
Sbjct: 38 NETTKA-VERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELG 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 = 58.9 bits (141), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 27/52 (51%), Positives = 36/52 (69%), Gaps = 1/52 (1%)
Query: 2 NSTVQGPLQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIG 53
N T + ++R L I A DV P EI+ HLP +CE+K+IPY YVPSKK++G
Sbjct: 37 NETTKA-VERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELG 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 = 58.9 bits (141), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 27/52 (51%), Positives = 36/52 (69%), Gaps = 1/52 (1%)
Query: 2 NSTVQGPLQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIG 53
N T + ++R L I A DV P EI+ HLP +CE+K+IPY YVPSKK++G
Sbjct: 43 NETTKA-VERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELG 93
>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 = 58.9 bits (141), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 36/55 (65%)
Query: 3 STVQGPLQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALG 57
+ V ++R L I A DV P E++ HLP +CE+K IPY YV SK+D+G+A G
Sbjct: 32 NEVTKAVERGIAKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAG 86
>pdb|2CZW|A Chain A, Crystal Structure Analysis Of Protein Component Ph1496p
Of P.Horikoshii Ribonuclease P
Length = 124
Score = 58.9 bits (141), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 27/52 (51%), Positives = 36/52 (69%), Gaps = 1/52 (1%)
Query: 2 NSTVQGPLQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIG 53
N T + ++R L I A DV P EI+ HLP +CE+K+IPY YVPSKK++G
Sbjct: 38 NETTKA-VERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELG 88
>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 = 58.9 bits (141), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 36/55 (65%)
Query: 3 STVQGPLQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALG 57
+ V ++R L I A DV P E++ HLP +CE+K IPY YV SK+D+G+A G
Sbjct: 35 NEVTKAVERGIAKLVIIAEDVKPEEVVAHLPYLCEEKGIPYAYVASKQDLGKAAG 89
>pdb|3HJW|C Chain C, Structure Of A Functional Ribonucleoprotein
Pseudouridine Synthase Bound To A Substrate Rna
Length = 120
Score = 58.5 bits (140), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 27/52 (51%), Positives = 36/52 (69%), Gaps = 1/52 (1%)
Query: 2 NSTVQGPLQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIG 53
N T + ++R L I A DV P EI+ HLP +CE+K+IPY YVPSKK++G
Sbjct: 35 NETTKA-VERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELG 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 = 58.5 bits (140), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 34/86 (39%), Positives = 49/86 (56%), Gaps = 1/86 (1%)
Query: 2 NSTVQGPLQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKP 61
N T + ++R L I A DV P EI+ HLP +CE+K+IPY YVPSKK++G A G +
Sbjct: 42 NETTKA-VERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELGAAAGIEVA 100
Query: 62 CICVIVKSTESVAELYEEVKQEIGAL 87
V + +L EE+ ++ L
Sbjct: 101 AASVAIIEPGKARDLVEEIAMKVREL 126
>pdb|2JNB|A Chain A, Solution Structure Of Rna-Binding Protein 15.5k
Length = 144
Score = 57.0 bits (136), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 34/56 (60%)
Query: 9 LQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKPCIC 64
L R + A D P+EI+ HLP +CEDK++PY +V SK+ +G A G +P I
Sbjct: 62 LNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIA 117
>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 = 57.0 bits (136), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 41/79 (51%)
Query: 9 LQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKPCICVIVK 68
+ R L I A D PIEI+ HLP CEDK +PY ++ SK +G A P I +
Sbjct: 43 VNRGKAELVIIAADADPIEIVLHLPLACEDKGVPYVFIGSKNALGRACNVSVPTIVASIG 102
Query: 69 STESVAELYEEVKQEIGAL 87
+++ + E+ ++ AL
Sbjct: 103 KHDALGNVVAEIVGKVEAL 121
>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 = 57.0 bits (136), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 34/56 (60%)
Query: 9 LQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKPCIC 64
L R + A D P+EI+ HLP +CEDK++PY +V SK+ +G A G +P I
Sbjct: 48 LNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIA 103
>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 = 56.6 bits (135), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 34/56 (60%)
Query: 9 LQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKPCIC 64
L R + A D P+EI+ HLP +CEDK++PY +V SK+ +G A G +P I
Sbjct: 46 LNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIA 101
>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 = 56.6 bits (135), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 28/56 (50%), Positives = 36/56 (64%), Gaps = 1/56 (1%)
Query: 2 NSTVQGPLQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALG 57
N T + ++R L I A DV P EI+ HLP +C++K IPY YV SKK +GEA G
Sbjct: 40 NETTKA-VERGQAKLVIIAEDVQPEEIVAHLPLLCDEKKIPYVYVSSKKALGEACG 94
>pdb|3ZF7|XX Chain x, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 276
Score = 48.1 bits (113), Expect = 1e-06, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 9 LQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKP-CICVIV 67
+++KT L + A +V PIE++ +P +C IPY V K +G+A+GRK C+
Sbjct: 156 IEKKTARLVLIANNVDPIELVLWMPTLCRANKIPYAIVKDKARLGDAIGRKTATCVAFTD 215
Query: 68 KSTESVAEL 76
+ E A L
Sbjct: 216 VNAEDQAAL 224
>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 = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 3 STVQGPLQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKPC 62
+TV ++ K L + A DV PIE++ LPA+C +PYC + K +G + RK
Sbjct: 141 NTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCIIKGKARLGHLVHRK--- 197
Query: 63 ICVIVKSTESVAE 75
C V T+ +E
Sbjct: 198 TCTTVAFTQVNSE 210
>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 = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 2 NSTVQGPLQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALG 57
N T + ++R + L A DV P EI+ H+P + ++K +P+ +V + D+G A G
Sbjct: 34 NETTKS-IERGSAELVFVAEDVQPEEIVMHIPELADEKGVPFIFVEQQDDLGHAAG 88
>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 = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 41/90 (45%), Gaps = 7/90 (7%)
Query: 9 LQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKPCICVIVK 68
++ K L + A DV PIE++ LP +C D+P+ +V K +G+ + +K + +
Sbjct: 136 IENKQAKLVVIAHDVDPIELVIFLPQLCRKNDVPFAFVKGKAALGKLVNKKTATAVALTE 195
Query: 69 -------STESVAELYEEVKQEIGALPVTW 91
+ +EL++ L TW
Sbjct: 196 VRNEDKAKLQQFSELFKTNYNANDELRKTW 225
>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 = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 43/87 (49%), Gaps = 8/87 (9%)
Query: 2 NSTVQGPLQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKP 61
N T + ++R + L A DV P EI+ H+P + ++K +P+ +V + D+G A G +
Sbjct: 35 NETTK-SIERGSAELVFVAEDVQPEEIVMHIPELADEKGVPFIFVEQQDDLGHAAGLEVG 93
Query: 62 CICVIVKST-------ESVAELYEEVK 81
V E +A+ EE++
Sbjct: 94 SAAAAVTDAGEADADVEDIADKVEELR 120
>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 = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 2 NSTVQGPLQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALG 57
N T + ++R + L A DV P EI+ H+P + ++K +P+ +V + D+G A G
Sbjct: 34 NETTK-SIERGSAELVFVAEDVQPEEIVMHIPELADEKGVPFIFVEQQDDLGHAAG 88
>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 = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 44/92 (47%), Gaps = 15/92 (16%)
Query: 9 LQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKPCICVIVK 68
++ K L + A DV PIE++ LPA+C+ +PY V K +G + +K + + +
Sbjct: 143 IENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLGTLVNQKTSAVAALTE 202
Query: 69 -------------ST--ESVAELYEEVKQEIG 85
ST + A+ Y+EVK+ G
Sbjct: 203 VRAEDEAALAKLVSTIDANFADKYDEVKKHWG 234
>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 = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 31/58 (53%)
Query: 9 LQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKPCICVI 66
++ K L + A DV PIE++ LPA+C+ +PY V K +G + +K + +
Sbjct: 42 IENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLGTLVNQKTSAVAAL 99
>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 = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 31/58 (53%)
Query: 9 LQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKPCICVI 66
++ K L + A DV PIE++ LPA+C+ +PY V K +G + +K + +
Sbjct: 37 IENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLGTLVNQKTSAVAAL 94
>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 = 42.4 bits (98), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 16 LCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKPCI-CVIVKSTESVA 74
L + A DV PIE++ LPA+C ++PYC V K +G + +K + C+ E
Sbjct: 146 LVVIAHDVDPIELVVWLPALCRKMEVPYCIVKGKARLGSIVHKKTASVLCLTTVKNEDKL 205
Query: 75 EL 76
E
Sbjct: 206 EF 207
>pdb|2DBJ|A Chain A, Solution Structures Of The Fn3 Domain Of Human Proto-
Oncogene Tyrosine-Protein Kinase Mer Precursor
Length = 124
Score = 29.3 bits (64), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 3/62 (4%)
Query: 22 DVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALGRKKPCICVIVKSTESVAELYEEVK 81
V P+ + L ++ DI + P+K+ GE +G + I + +S EL EEV
Sbjct: 19 SVAPLNVTVFLNESSDNVDIRWMKPPTKQQDGELVGYR---ISHVWQSAGISKELLEEVG 75
Query: 82 QE 83
Q
Sbjct: 76 QN 77
>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 = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 8 PLQRKTIMLCIFAGDVTPIEIMCHLPAVCEDKDIPYCYVPSKKDIGEALG 57
L+R ++ + A D PI + + ++ ED+ I V S K +G+A G
Sbjct: 22 ALKRGSVKEVVVAKDADPI-LTSSVVSLAEDQGISVSMVESMKKLGKACG 70
>pdb|2XZM|U Chain U, Crystal Structure Of The Eukaryotic 40s Ribosomal
Subunit In Complex With Initiation Factor 1. This File
Contains The 40s Subunit And Initiation Factor For
Molecule 1
pdb|2XZN|U Chain U, Crystal Structure Of The Eukaryotic 40s Ribosomal
Subunit In Complex With Initiation Factor 1. This File
Contains The 40s Subunit And Initiation Factor For
Molecule 2
Length = 126
Score = 25.8 bits (55), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 32 LPAVCEDKDIPYCYVPSKKDIGEALGR 58
+ A+C +I Y VP + +GE LG
Sbjct: 59 VKALCAKNEIKYVSVPKRASLGEYLGH 85
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
0.321 0.138 0.433
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,537,034
Number of Sequences: 62578
Number of extensions: 88836
Number of successful extensions: 205
Number of sequences better than 100.0: 34
Number of HSP's better than 100.0 without gapping: 32
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 173
Number of HSP's gapped (non-prelim): 34
length of query: 91
length of database: 14,973,337
effective HSP length: 58
effective length of query: 33
effective length of database: 11,343,813
effective search space: 374345829
effective search space used: 374345829
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)