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= psy9436
(188 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKR|JJ Chain j, 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 = 203
Score = 88.2 bits (217), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 36/67 (53%), Positives = 49/67 (73%)
Query: 64 SMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHEV 123
M PHK RG AL RLKV++GIPP Y +++R+ VP AL+ V LKP R + +GR++HEV
Sbjct: 86 GMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPAALKVVRLKPTRKFAYLGRLAHEV 145
Query: 124 GWKYKTI 130
GWKY+ +
Sbjct: 146 GWKYQAV 152
>pdb|3IZS|K Chain K, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|P Chain P, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|P Chain P, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit
Length = 199
Score = 87.8 bits (216), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 38/71 (53%), Positives = 51/71 (71%)
Query: 64 SMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHEV 123
M HK RG AL+RLKV+EGIPP Y +++R+ VP ALR + LKPGR Y ++G++S V
Sbjct: 86 GMVSHKTARGKAALERLKVFEGIPPPYDKKKRVVVPQALRVLRLKPGRKYTTLGKLSTSV 145
Query: 124 GWKYKTIVRHL 134
GWKY+ +V L
Sbjct: 146 GWKYEDVVAKL 156
>pdb|3IZR|K Chain K, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 206
Score = 85.1 bits (209), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 36/71 (50%), Positives = 47/71 (66%)
Query: 64 SMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHEV 123
M PHK RG AL RLK YEG+PP Y R +R+ +P AL+ + L+PG YC +G++S EV
Sbjct: 91 GMIPHKTARGEAALARLKAYEGVPPPYDRTKRMVIPDALKVLRLQPGHRYCLLGQLSKEV 150
Query: 124 GWKYKTIVRHL 134
GW Y +R L
Sbjct: 151 GWNYADTIREL 161
>pdb|4B6A|O Chain O, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 217
Score = 82.8 bits (203), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 38/72 (52%), Positives = 51/72 (70%), Gaps = 1/72 (1%)
Query: 64 SMTPHKLDRGAKALKRLK-VYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHE 122
M HK RG AL+RLK V+EGIPP Y +++R+ VP ALR + LKPGR Y ++G++S
Sbjct: 95 GMVSHKTARGKAALERLKIVFEGIPPPYDKKKRVVVPQALRVLRLKPGRKYTTLGKLSTS 154
Query: 123 VGWKYKTIVRHL 134
VGWKY+ +V L
Sbjct: 155 VGWKYEDVVAKL 166
>pdb|3U5E|O Chain O, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|O Chain O, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
Length = 217
Score = 82.8 bits (203), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 38/72 (52%), Positives = 51/72 (70%), Gaps = 1/72 (1%)
Query: 64 SMTPHKLDRGAKALKRLKV-YEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHE 122
M HK RG AL+RLKV +EGIPP Y +++R+ VP ALR + LKPGR Y ++G++S
Sbjct: 95 GMVSHKTARGKAALERLKVIFEGIPPPYDKKKRVVVPQALRVLRLKPGRKYTTLGKLSTS 154
Query: 123 VGWKYKTIVRHL 134
VGWKY+ +V L
Sbjct: 155 VGWKYEDVVAKL 166
>pdb|3JYW|M Chain M, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 178
Score = 80.5 bits (197), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 35/63 (55%), Positives = 46/63 (73%)
Query: 64 SMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHEV 123
M HK RG AL+RLKV+EGIPP Y +++R+ VP ALR + LKPGR Y ++G++S V
Sbjct: 80 GMVSHKTARGKAALERLKVFEGIPPPYDKKKRVVVPQALRVLRLKPGRKYTTLGKLSTSV 139
Query: 124 GWK 126
GWK
Sbjct: 140 GWK 142
>pdb|1S1I|M Chain M, 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 = 146
Score = 79.0 bits (193), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 34/62 (54%), Positives = 45/62 (72%)
Query: 64 SMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHEV 123
M HK RG AL+RLKV+EGIPP Y +++R+ VP ALR + LKPGR Y ++G++S V
Sbjct: 85 GMVSHKTARGKAALERLKVFEGIPPPYDKKKRVVVPQALRVLRLKPGRKYTTLGKLSTSV 144
Query: 124 GW 125
GW
Sbjct: 145 GW 146
>pdb|4A17|I Chain I, 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|I Chain I, 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|I Chain I, 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|I Chain I, 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 = 198
Score = 63.5 bits (153), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 30/71 (42%), Positives = 43/71 (60%)
Query: 64 SMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHEV 123
M PHK +GA AL+RLK++EGIP Y R ++ V AL+ L+ R C +G +S V
Sbjct: 85 GMLPHKTPKGAAALERLKIFEGIPTPYDRVKKQVVVDALKVQRLRNSRPVCKLGDLSASV 144
Query: 124 GWKYKTIVRHL 134
GW +T++ L
Sbjct: 145 GWGKQTLIEKL 155
>pdb|3ZF7|O Chain O, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 222
Score = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 64 SMTPHKLDRGAKALKRLKVYEGIPPKYARRQ-RLCVPTALRTVCLKPGRSYCSVGRISHE 122
SM P RG +AL++L YEG+P R R+ +P A R C + R + +G +
Sbjct: 104 SMLPRYTKRGQRALRQLVAYEGVPVNVVRTGGRVVIPKAQRHNCYRNERRFTVLGNMCKH 163
Query: 123 VGWKYKTIVRHL 134
VGWKY +V L
Sbjct: 164 VGWKYSDVVEKL 175
>pdb|1J3A|A Chain A, Crystal Structure Of Ribosomal Protein L13 From Pyrococcus
Horikoshii
Length = 142
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 54 SIENARNQSESMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSY 113
S E R M P K DRG KA +RLKVY GIP ++ +Q + A + +P Y
Sbjct: 71 SDEIVRRTIRGMLPWKTDRGRKAFRRLKVYVGIPKEFQDKQLETIVEAHVSRLSRP--KY 128
Query: 114 CSVGRISHEVGWKY 127
+VG ++ +G K+
Sbjct: 129 VTVGEVAKFLGGKF 142
>pdb|3J21|I Chain I, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 142
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 54 SIENARNQSESMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSY 113
S E R M P K DRG KA KRLKVY GIP ++ ++ + A + +P Y
Sbjct: 71 SDEIVRRTIRGMLPWKTDRGRKAFKRLKVYVGIPKEFQGKELETIIEAHVSRLSRP--KY 128
Query: 114 CSVGRISHEVGWKY 127
+VG ++ +G K+
Sbjct: 129 VTVGEVAKFLGGKF 142
>pdb|3VGJ|A Chain A, Crystal Of Plasmodium Falciparum Tyrosyl-Trna Synthetase
(Pftyrrs)in Complex With Adenylate Analog
pdb|3VGJ|B Chain B, Crystal Of Plasmodium Falciparum Tyrosyl-Trna Synthetase
(Pftyrrs)in Complex With Adenylate Analog
Length = 373
Score = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 38/72 (52%), Gaps = 11/72 (15%)
Query: 20 KTTSTKRNIGHFDRKRKQARHESKIRAVEKL--ELFSIENARNQSESMTPHKLDRGAKAL 77
+TT TKR + K+ A+ ESKI V+K+ ++ SI SE + P +L R L
Sbjct: 2 ETTDTKREEQEIEEKK--AQEESKIEDVDKILNDILSI-----SSECIQPDEL-RVKLLL 53
Query: 78 KR-LKVYEGIPP 88
KR L Y+G P
Sbjct: 54 KRKLICYDGFEP 65
>pdb|3G4S|J Chain J, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|J Chain J, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|J Chain J, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|3OW2|I Chain I, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 142
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 7/62 (11%)
Query: 64 SMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTAL-RTVCLKPGRSYCSVGRISHE 122
M PHK RG +A + ++VY G P Y + T+L R +K + ++G IS
Sbjct: 82 GMLPHKKQRGREAFESVRVYLGNP--YDEDGEVLDGTSLDRLSNIK----FVTLGEISET 135
Query: 123 VG 124
+G
Sbjct: 136 LG 137
>pdb|1FFK|G Chain G, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1GIY|M Chain M, Crystal Structure Of The Ribosome At 5.5 A Resolution.
This File, 1giy, Contains The 50s Ribosome Subunit. The
30s Ribosome Subunit, Three Trna, And Mrna Molecules Are
In The File 1gix
pdb|1JJ2|I Chain I, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|I Chain I, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|K Chain K, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|K Chain K, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|K Chain K, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|K Chain K, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|K Chain K, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1ML5|MM Chain m, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
pdb|1K73|K Chain K, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|K Chain K, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|K Chain K, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|K Chain K, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|K Chain K, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|K Chain K, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|K Chain K, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|K Chain K, 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|I Chain I, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|I Chain I, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1S72|J Chain J, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1W2B|I Chain I, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|1YHQ|J Chain J, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|J Chain J, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|J Chain J, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|J Chain J, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|J Chain J, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|J Chain J, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|J Chain J, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YL3|M Chain M, Crystal Structure Of 70s Ribosome With Thrs Operator And
Trnas. Large Subunit. The Coordinates For The Small
Subunit Are In The Pdb Entry 1yl4.
pdb|1VQ4|J Chain J, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|J Chain J, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|J Chain J, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|J Chain J, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|J Chain J, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|J Chain J, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|J Chain J, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|J Chain J, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|J Chain J, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|J Chain J, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|J Chain J, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|J Chain J, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2B66|N Chain N, 50s Ribosomal Subunit From A Crystal Structure Of Release
Factor Rf1, Trnas And Mrna Bound To The Ribosome. This
File Contains The 50s Subunit From A Crystal Structure
Of Release Factor Rf1, Trnas And Mrna Bound To The
Ribosome And Is Described In Remark 400
pdb|2B9N|N Chain N, 50s Ribosomal Subunit From A Crystal Structure Of Release
Factor Rf2, Trnas And Mrna Bound To The Ribosome. This
File Contains The 50s Subunit From A Crystal Structure
Of Release Factor Rf1, Trnas And Mrna Bound To The
Ribosome And Is Described In Remark 400.
pdb|2B9P|N Chain N, 50s Ribosomal Subunit From A Crystal Structure Of The
Ribosome In Complex With Trnas And Mrna With A Stop
Codon In The A-Site. This File Contains The 50s Subunit
From A Crystal Structure Of The Ribosome In Complex With
Trnas And Mrna With A Stop Codon In The A-Site And Is
Described In Remark 400.
pdb|2OTJ|J Chain J, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|J Chain J, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|J Chain J, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|3CC2|J Chain J, 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|J Chain J, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|J Chain J, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|J Chain J, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|J Chain J, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|J Chain J, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|J Chain J, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|J Chain J, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|J Chain J, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|J Chain J, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|J Chain J, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|J Chain J, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|J Chain J, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|I Chain I, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|J Chain J, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|J Chain J, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|2QEX|J Chain J, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3CXC|I Chain I, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
pdb|3I55|J Chain J, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|J Chain J, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
pdb|4ADX|J Chain J, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 145
Score = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 7/62 (11%)
Query: 64 SMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTAL-RTVCLKPGRSYCSVGRISHE 122
M PHK RG +A + ++VY G P Y + T+L R +K + ++G IS
Sbjct: 85 GMLPHKKQRGREAFESVRVYLGNP--YDEDGEVLDGTSLDRLSNIK----FVTLGEISET 138
Query: 123 VG 124
+G
Sbjct: 139 LG 140
>pdb|1DFO|A Chain A, Crystal Structure At 2.4 Angstrom Resolution Of E. Coli
Serine Hydroxymethyltransferase In Complex With Glycine
And 5-Formyl Tetrahydrofolate
pdb|1DFO|B Chain B, Crystal Structure At 2.4 Angstrom Resolution Of E. Coli
Serine Hydroxymethyltransferase In Complex With Glycine
And 5-Formyl Tetrahydrofolate
pdb|1DFO|C Chain C, Crystal Structure At 2.4 Angstrom Resolution Of E. Coli
Serine Hydroxymethyltransferase In Complex With Glycine
And 5-Formyl Tetrahydrofolate
pdb|1DFO|D Chain D, Crystal Structure At 2.4 Angstrom Resolution Of E. Coli
Serine Hydroxymethyltransferase In Complex With Glycine
And 5-Formyl Tetrahydrofolate
Length = 417
Score = 27.7 bits (60), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 27 NIGHFDRKRKQARHESKIRAVEKLELFSIEN 57
NI +D + QA + K+R E +EL + EN
Sbjct: 7 NIADYDAELWQAMEQEKVRQEEHIELIASEN 37
>pdb|1EQB|A Chain A, X-Ray Crystal Structure At 2.7 Angstroms Resolution Of
Ternary Complex Between The Y65f Mutant Of E-Coli
Serine Hydroxymethyltransferase, Glycine And 5-Formyl
Tetrahydrofolate
pdb|1EQB|B Chain B, X-Ray Crystal Structure At 2.7 Angstroms Resolution Of
Ternary Complex Between The Y65f Mutant Of E-Coli
Serine Hydroxymethyltransferase, Glycine And 5-Formyl
Tetrahydrofolate
pdb|1EQB|C Chain C, X-Ray Crystal Structure At 2.7 Angstroms Resolution Of
Ternary Complex Between The Y65f Mutant Of E-Coli
Serine Hydroxymethyltransferase, Glycine And 5-Formyl
Tetrahydrofolate
pdb|1EQB|D Chain D, X-Ray Crystal Structure At 2.7 Angstroms Resolution Of
Ternary Complex Between The Y65f Mutant Of E-Coli
Serine Hydroxymethyltransferase, Glycine And 5-Formyl
Tetrahydrofolate
Length = 417
Score = 27.7 bits (60), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 27 NIGHFDRKRKQARHESKIRAVEKLELFSIEN 57
NI +D + QA + K+R E +EL + EN
Sbjct: 7 NIADYDAELWQAMEQEKVRQEEHIELIASEN 37
>pdb|3G8M|A Chain A, Serine Hydroxymethyltransferase Y55f Mutant
Length = 417
Score = 27.7 bits (60), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 27 NIGHFDRKRKQARHESKIRAVEKLELFSIEN 57
NI +D + QA + K+R E +EL + EN
Sbjct: 7 NIADYDAELWQAMEQEKVRQEEHIELIASEN 37
>pdb|3GBX|A Chain A, Serine Hydroxymethyltransferase From Salmonella
Typhimurium
pdb|3GBX|B Chain B, Serine Hydroxymethyltransferase From Salmonella
Typhimurium
Length = 420
Score = 27.3 bits (59), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 25 KRNIGHFDRKRKQARHESKIRAVEKLELFSIEN 57
+ NI +D + QA + K+R E +EL + EN
Sbjct: 8 EXNIADYDAELWQAXEQEKVRQEEHIELIASEN 40
>pdb|2VID|A Chain A, Serine Protease Splb From Staphylococcus Aureus At 1.8a
Resolution
pdb|2VID|B Chain B, Serine Protease Splb From Staphylococcus Aureus At 1.8a
Resolution
Length = 204
Score = 26.9 bits (58), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 24/93 (25%), Positives = 41/93 (44%), Gaps = 4/93 (4%)
Query: 12 RLATLVTEKTTSTKRNIGHFDRKR---KQARHESKIRAVEKLELFSIENARNQSESMTPH 68
++ +T S K N G + K+ + + + VE+ + N ++++TP
Sbjct: 45 KVGDRITAHPNSDKGNGGIYSIKKIINYPGKEDVSVIQVEERAIERGPKGFNFNDNVTPF 104
Query: 69 KLDRGAKALKRLKVYEGIPPKYARRQRLCVPTA 101
K GAKA +R+KV G P Y + L T
Sbjct: 105 KYAAGAKAGERIKVI-GYPHPYKNKYVLYESTG 136
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 0.133 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,519,776
Number of Sequences: 62578
Number of extensions: 144608
Number of successful extensions: 317
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 297
Number of HSP's gapped (non-prelim): 22
length of query: 188
length of database: 14,973,337
effective HSP length: 93
effective length of query: 95
effective length of database: 9,153,583
effective search space: 869590385
effective search space used: 869590385
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: 48 (23.1 bits)