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= psy1816
(122 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2PA2|A Chain A, Crystal Structure Of Human Ribosomal Protein L10 Core
Domain
pdb|2PA2|B Chain B, Crystal Structure Of Human Ribosomal Protein L10 Core
Domain
Length = 151
Score = 110 bits (274), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 50/68 (73%), Positives = 61/68 (89%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MRGA+GKPQGTVARV+IGQ IMS+R+ + K VIEALRRAKFKFPGRQKI++SKKWGFT
Sbjct: 84 MRGAFGKPQGTVARVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFT 143
Query: 61 KYDREEYE 68
K++ +E+E
Sbjct: 144 KFNADEFE 151
>pdb|2ZKR|HH Chain h, 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 = 214
Score = 108 bits (270), Expect = 7e-25, Method: Compositional matrix adjust.
Identities = 50/75 (66%), Positives = 64/75 (85%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MRGA+GKPQGTVA+V+IGQ IMS+R+ + K VIEALRRAKFKFPGRQKI++SKKWGFT
Sbjct: 115 MRGAFGKPQGTVAKVHIGQVIMSIRTKLQNKEHVIEALRRAKFKFPGRQKIHISKKWGFT 174
Query: 61 KYDREEYETLRDQNR 75
K++ +E+E + + R
Sbjct: 175 KFNADEFENMVAEKR 189
>pdb|3IZR|I Chain I, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 224
Score = 101 bits (251), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 48/75 (64%), Positives = 57/75 (76%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MRGA+GKPQGT ARV+IGQ ++SVR + EALRRAKFKFPGRQKI S+KWGFT
Sbjct: 115 MRGAFGKPQGTCARVDIGQVLLSVRCKESNAKHAEEALRRAKFKFPGRQKIIHSRKWGFT 174
Query: 61 KYDREEYETLRDQNR 75
K+ REEY L+ + R
Sbjct: 175 KFTREEYVKLKAEGR 189
>pdb|3ZF7|K Chain K, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 213
Score = 96.3 bits (238), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 44/72 (61%), Positives = 53/72 (73%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MR +YGKP GT ARV IGQ ++S+R+ D + P +E+LRRAK KFPGRQ I +SK WGFT
Sbjct: 115 MRQSYGKPNGTCARVRIGQILLSMRTKDTYVPQALESLRRAKMKFPGRQIIVISKYWGFT 174
Query: 61 KYDREEYETLRD 72
R EYE LRD
Sbjct: 175 NILRNEYEELRD 186
>pdb|3IZS|I Chain I, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|J Chain J, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|J Chain J, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|I Chain I, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|I Chain I, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|I Chain I, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 221
Score = 95.9 bits (237), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 45/72 (62%), Positives = 54/72 (75%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MRGA+GKP G ARV+IGQ I SVR+ D K V+E LRRA++KFPG+QKI +SKKWGFT
Sbjct: 115 MRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILSKKWGFT 174
Query: 61 KYDREEYETLRD 72
DR EY R+
Sbjct: 175 NLDRPEYLKKRE 186
>pdb|3J0L|J Chain J, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
Fitted To A 9.8a Cryo-Em Map: Classic Pre State 1
pdb|3J0Q|J Chain J, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
Fitted To A 10.6a Cryo-Em Map: Rotated Pre State 2
Length = 219
Score = 95.9 bits (237), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 45/72 (62%), Positives = 54/72 (75%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MRGA+GKP G ARV+IGQ I SVR+ D K V+E LRRA++KFPG+QKI +SKKWGFT
Sbjct: 113 MRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILSKKWGFT 172
Query: 61 KYDREEYETLRD 72
DR EY R+
Sbjct: 173 NLDRPEYLKKRE 184
>pdb|4A17|H Chain H, 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|H Chain H, 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|H Chain H, 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|H Chain H, 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 = 215
Score = 80.9 bits (198), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 40/75 (53%), Positives = 50/75 (66%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MRGA+GK G ARV+IG + SVR + I+AL RAK KFPGRQK+ S+KWGFT
Sbjct: 115 MRGAFGKALGKAARVDIGSILFSVRVKEPHVKYAIDALTRAKAKFPGRQKVVTSQKWGFT 174
Query: 61 KYDREEYETLRDQNR 75
K R +Y LR+Q +
Sbjct: 175 KLTRAQYSRLRNQKK 189
>pdb|3JYW|I Chain I, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 165
Score = 73.6 bits (179), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 34/54 (62%), Positives = 42/54 (77%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVS 54
MRGA+GKP G ARV+IGQ I SVR+ D K V+E LRRA++KFPG+QKI +S
Sbjct: 112 MRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILS 165
>pdb|1S1I|I Chain I, 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 = 168
Score = 73.6 bits (179), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 34/54 (62%), Positives = 42/54 (77%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVS 54
MRGA+GKP G ARV+IGQ I SVR+ D K V+E LRRA++KFPG+QKI +S
Sbjct: 115 MRGAWGKPHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILS 168
>pdb|3J21|N Chain N, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 181
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 30/58 (51%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWG 58
MR +GKP G AR+ Q I+S+R + + IE RRA KFP + + K G
Sbjct: 112 MRRPFGKPIGLAARLKKDQKILSIRVNRQHLKFAIEGARRAAMKFPCKCYYRIYDKEG 169
>pdb|1YHQ|H Chain H, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|H Chain H, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|H Chain H, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|H Chain H, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|H Chain H, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|H Chain H, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|H Chain H, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CC2|H Chain H, 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|H Chain H, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|H Chain H, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|H Chain H, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|H Chain H, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|H Chain H, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|H Chain H, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|3G4S|H Chain H, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|H Chain H, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|H Chain H, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|4ADX|H Chain H, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 177
Score = 32.3 bits (72), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 28/55 (50%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSK 55
MR A+GK GT ARV G+ + + + + V EA RRA K +I V +
Sbjct: 116 MRAAFGKIVGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRAYNKITPSCRIKVER 170
>pdb|3I55|H Chain H, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|H Chain H, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
Length = 174
Score = 32.3 bits (72), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 28/55 (50%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSK 55
MR A+GK GT ARV G+ + + + + V EA RRA K +I V +
Sbjct: 116 MRAAFGKIVGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRAYNKITPSCRIKVER 170
>pdb|1S72|H Chain H, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1VQ4|H Chain H, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|H Chain H, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|H Chain H, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|H Chain H, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|H Chain H, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|H Chain H, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|H Chain H, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|H Chain H, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|H Chain H, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|H Chain H, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|H Chain H, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|H Chain H, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|H Chain H, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|H Chain H, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|H Chain H, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
Length = 171
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 24/45 (53%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKF 45
MR A+GK GT ARV G+ + + + + V EA RRA K
Sbjct: 113 MRAAFGKIVGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRAYNKI 157
>pdb|2QEX|H Chain H, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
Length = 174
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 24/45 (53%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKF 45
MR A+GK GT ARV G+ + + + + V EA RRA K
Sbjct: 116 MRAAFGKIVGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRAYNKI 160
>pdb|1JJ2|H Chain H, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|H Chain H, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|J Chain J, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|J Chain J, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|J Chain J, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|J Chain J, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|J Chain J, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1K73|J Chain J, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|J Chain J, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|J Chain J, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|J Chain J, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|J Chain J, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|J Chain J, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|J Chain J, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|J Chain J, 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|H Chain H, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|H Chain H, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1W2B|H Chain H, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|3CXC|H Chain H, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
pdb|3OW2|H Chain H, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 167
Score = 30.4 bits (67), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 21/45 (46%), Positives = 26/45 (57%), Gaps = 4/45 (8%)
Query: 1 MRGAYGKPQGTVARVNIGQPI-MSVRSSDKFKPAVIEALRRAKFK 44
MR +GKP GT ARV+ I ++ + D P V EA RRAK K
Sbjct: 111 MRAPFGKPVGTAARVHGANHIFIAWVNPD---PNVEEAWRRAKMK 152
>pdb|2GJP|A Chain A, Structure Of Bacillus Halmapalus Alpha-Amylase,
Crystallized With The Substrate Analogue Acarbose And
Maltose
pdb|2GJR|A Chain A, Structure Of Bacillus Halmapalus Alpha-Amylase Without Any
Substrate Analogues
Length = 485
Score = 30.4 bits (67), Expect = 0.28, Method: Composition-based stats.
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 42 KFKFPGRQKIYVSKKWGFTKYDREEYETLRD-QNR 75
KF FPGR Y KW + +D +++ R QNR
Sbjct: 142 KFDFPGRGNTYSDFKWRWYHFDGVDWDQSRQFQNR 176
>pdb|1W9X|A Chain A, Bacillus Halmapalus Alpha Amylase
Length = 481
Score = 30.0 bits (66), Expect = 0.30, Method: Composition-based stats.
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 42 KFKFPGRQKIYVSKKWGFTKYDREEYETLRD-QNR 75
KF FPGR Y KW + +D +++ R QNR
Sbjct: 138 KFDFPGRGNTYSDFKWRWYHFDGVDWDQSRQFQNR 172
>pdb|1VJS|A Chain A, Structure Of Alpha-Amylase Precursor
Length = 483
Score = 30.0 bits (66), Expect = 0.32, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 43 FKFPGRQKIYVSKKWGFTKYDREEYETLRDQNR 75
F FPGR Y KW + +D +++ R NR
Sbjct: 141 FHFPGRGSTYSDFKWHWYHFDGTDWDESRKLNR 173
>pdb|1BLI|A Chain A, Bacillus Licheniformis Alpha-Amylase
Length = 483
Score = 30.0 bits (66), Expect = 0.33, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 43 FKFPGRQKIYVSKKWGFTKYDREEYETLRDQNR 75
F FPGR Y KW + +D +++ R NR
Sbjct: 141 FHFPGRGSTYSDFKWHWYHFDGTDWDESRKLNR 173
>pdb|1OB0|A Chain A, Kinetic Stabilization Of Bacillus Licheniformis-Amylase
Through Introduction Of Hydrophobic Residues At The
Surface
Length = 483
Score = 30.0 bits (66), Expect = 0.34, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 43 FKFPGRQKIYVSKKWGFTKYDREEYETLRDQNR 75
F FPGR Y KW + +D +++ R NR
Sbjct: 141 FHFPGRGSTYSDFKWHWYHFDGTDWDESRKLNR 173
>pdb|1BPL|A Chain A, Glycosyltransferase
Length = 189
Score = 29.3 bits (64), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 22 MSVRSSDKFKPAVIEALRRA--KFKFPGRQKIYVSKKWGFTKYDREEYETLRDQNR 75
+ V +D+ + E L +A F FPGR Y KW + +D +++ R NR
Sbjct: 118 VEVDPADRNRVISGEHLIKAWTHFHFPGRGSTYSDFKWHWYHFDGTDWDESRKLNR 173
>pdb|1HVX|A Chain A, Bacillus Stearothermophilus Alpha-Amylase
Length = 515
Score = 28.9 bits (63), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 42 KFKFPGRQKIYVSKKWGFTKYDREEYETLRDQNR 75
KF FPGR Y S KW + +D +++ R +R
Sbjct: 141 KFDFPGRGNTYSSFKWRWYHFDGVDWDESRKLSR 174
>pdb|1E3X|A Chain A, Native Structure Of Chimaeric Amylase From B.
Amyloliquefaciens And B. Licheniformis At 1.92a
pdb|1E3Z|A Chain A, Acarbose Complex Of Chimaeric Amylase From B.
Amyloliquefaciens And B. Licheniformis At 1.93a
pdb|1E40|A Chain A, TrisMALTOTRIOSE COMPLEX OF CHIMAERIC AMYLASE FROM B.
Amyloliquefaciens And B. Licheniformis At 2.2a
pdb|1E43|A Chain A, Native Structure Of Chimaeric Amylase From B.
Amyloliquefaciens And B. Licheniformis At 1.7a
Length = 483
Score = 28.5 bits (62), Expect = 0.93, Method: Composition-based stats.
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 43 FKFPGRQKIYVSKKWGFTKYDREEYETLRDQNR 75
F+FPGR Y KW + +D +++ R +R
Sbjct: 139 FRFPGRGNTYSDFKWHWYHFDGADWDESRKISR 171
>pdb|1WP6|A Chain A, Crystal Structure Of Maltohexaose-producing Amylase From
Alkalophilic Bacillus Sp.707.
pdb|1WPC|A Chain A, Crystal Structure Of Maltohexaose-Producing Amylase
Complexed With Pseudo-Maltononaose
pdb|2D3L|A Chain A, Crystal Structure Of Maltohexaose-Producing Amylase From
Bacillus Sp.707 Complexed With Maltopentaose.
pdb|2D3N|A Chain A, Crystal Structure Of Maltohexaose-Producing Amylase From
Bacillus Sp.707 Complexed With Maltohexaose
Length = 485
Score = 28.1 bits (61), Expect = 1.3, Method: Composition-based stats.
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 35 IEALRRAKFKFPGRQKIYVSKKWGFTKYDREEYETLRDQN 74
IEA R F FPGR + S KW + +D +++ R N
Sbjct: 137 IEAWTR--FDFPGRGNTHSSFKWRWYHFDGVDWDQSRRLN 174
>pdb|2DIE|A Chain A, Alkaline Alpha-Amylase Amyk From Bacillus Sp. Ksm-1378
Length = 485
Score = 27.7 bits (60), Expect = 1.6, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 42 KFKFPGRQKIYVSKKWGFTKYDREEYETLRD-QNR 75
KF FPGR + + KW + +D +++ R QN+
Sbjct: 142 KFDFPGRGNTHSNFKWRWYHFDGTDWDQSRQLQNK 176
>pdb|3BH4|A Chain A, High Resolution Crystal Structure Of Bacillus
Amyloliquefaciens Alpha-Amylase
pdb|3BH4|B Chain B, High Resolution Crystal Structure Of Bacillus
Amyloliquefaciens Alpha-Amylase
Length = 483
Score = 26.9 bits (58), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 43 FKFPGRQKIYVSKKWGFTKYDREEYETLR 71
F+FPGR Y KW + +D +++ R
Sbjct: 139 FRFPGRGNTYSDFKWHWYHFDGADWDESR 167
>pdb|2F2F|C Chain C, Crystal Structure Of Cytolethal Distending Toxin (Cdt)
From Actinobacillus Actinomycetemcomitans
pdb|2F2F|F Chain F, Crystal Structure Of Cytolethal Distending Toxin (Cdt)
From Actinobacillus Actinomycetemcomitans
Length = 186
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 52 YVSKKWGFTKYDREEYETLRD 72
Y+S W Y +EYE LRD
Sbjct: 61 YLSTHWELIDYKGKEYEKLRD 81
>pdb|3OM5|A Chain A, Crystal Structure Of B. Megaterium Levansucrase Mutant
N252a
pdb|3OM5|B Chain B, Crystal Structure Of B. Megaterium Levansucrase Mutant
N252a
pdb|3OM5|C Chain C, Crystal Structure Of B. Megaterium Levansucrase Mutant
N252a
pdb|3OM5|D Chain D, Crystal Structure Of B. Megaterium Levansucrase Mutant
N252a
Length = 456
Score = 26.2 bits (56), Expect = 5.2, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 10/70 (14%)
Query: 5 YGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTK--Y 62
YGK T A+VN+ QP + + K ++ + K F G KIY + + + Y
Sbjct: 168 YGKQTLTTAQVNMSQP-----NDNTLK---VDGVEDYKSIFDGDGKIYQTVQQFIDEGGY 219
Query: 63 DREEYETLRD 72
D + TLRD
Sbjct: 220 DTGDAHTLRD 229
>pdb|3OM4|A Chain A, Crystal Structure Of B. Megaterium Levansucrase Mutant
K373a
pdb|3OM4|B Chain B, Crystal Structure Of B. Megaterium Levansucrase Mutant
K373a
pdb|3OM4|C Chain C, Crystal Structure Of B. Megaterium Levansucrase Mutant
K373a
pdb|3OM4|D Chain D, Crystal Structure Of B. Megaterium Levansucrase Mutant
K373a
Length = 456
Score = 26.2 bits (56), Expect = 5.6, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 10/70 (14%)
Query: 5 YGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTK--Y 62
YGK T A+VN+ QP + + K ++ + K F G KIY + + + Y
Sbjct: 168 YGKQTLTTAQVNMSQP-----NDNTLK---VDGVEDYKSIFDGDGKIYQTVQQFIDEGGY 219
Query: 63 DREEYETLRD 72
D + TLRD
Sbjct: 220 DTGDNHTLRD 229
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
0.322 0.137 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,802,508
Number of Sequences: 62578
Number of extensions: 95636
Number of successful extensions: 208
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 183
Number of HSP's gapped (non-prelim): 29
length of query: 122
length of database: 14,973,337
effective HSP length: 84
effective length of query: 38
effective length of database: 9,716,785
effective search space: 369237830
effective search space used: 369237830
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)