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= psy9094
(185 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3J2K|6 Chain 6, Cryo-Em Structure Of The Mammalian Erf1-Erf3-Associated
Termination Complex
Length = 411
Score = 280 bits (715), Expect = 4e-76, Method: Compositional matrix adjust.
Identities = 141/218 (64%), Positives = 160/218 (73%), Gaps = 35/218 (16%)
Query: 1 MEKRHNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDP---------- 50
MEKRHNYVRKVAE A LFI+ DK N+AGL+LAGSADFKTELSQSDMFD
Sbjct: 186 MEKRHNYVRKVAETAVQLFISGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLV 245
Query: 51 -----------------------VRFSPLKNKNKMGKYFDEISQDTGKYCFGVEDTLRAL 87
V+F ++ K +G+YFDEISQDTGKYCFGVEDTL+AL
Sbjct: 246 DISYGGENGFNQAIELSTEVLSNVKF--IQEKKLIGRYFDEISQDTGKYCFGVEDTLKAL 303
Query: 88 ELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQ 147
E+G+VE LI +ENLDI RYVL T E+++L+LTPEQEKDKSHFTDKETG E EL+E
Sbjct: 304 EMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTPEQEKDKSHFTDKETGQEHELIESM 363
Query: 148 PLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFGGIG 185
PLLEW ANNYK FGATLEI+TDKSQEGSQFV+GFGGIG
Sbjct: 364 PLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIG 401
>pdb|3E1Y|A Chain A, Crystal Structure Of Human Erf1ERF3 COMPLEX
pdb|3E1Y|B Chain B, Crystal Structure Of Human Erf1ERF3 COMPLEX
pdb|3E1Y|C Chain C, Crystal Structure Of Human Erf1ERF3 COMPLEX
pdb|3E1Y|D Chain D, Crystal Structure Of Human Erf1ERF3 COMPLEX
Length = 451
Score = 279 bits (714), Expect = 5e-76, Method: Compositional matrix adjust.
Identities = 141/218 (64%), Positives = 160/218 (73%), Gaps = 35/218 (16%)
Query: 1 MEKRHNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDP---------- 50
MEKRHNYVRKVAE A LFI+ DK N+AGL+LAGSADFKTELSQSDMFD
Sbjct: 209 MEKRHNYVRKVAETAVQLFISGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLV 268
Query: 51 -----------------------VRFSPLKNKNKMGKYFDEISQDTGKYCFGVEDTLRAL 87
V+F ++ K +G+YFDEISQDTGKYCFGVEDTL+AL
Sbjct: 269 DISYGGENGFNQAIELSTEVLSNVKF--IQEKKLIGRYFDEISQDTGKYCFGVEDTLKAL 326
Query: 88 ELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQ 147
E+G+VE LI +ENLDI RYVL T E+++L+LTPEQEKDKSHFTDKETG E EL+E
Sbjct: 327 EMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTPEQEKDKSHFTDKETGQEHELIESM 386
Query: 148 PLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFGGIG 185
PLLEW ANNYK FGATLEI+TDKSQEGSQFV+GFGGIG
Sbjct: 387 PLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIG 424
>pdb|1DT9|A Chain A, The Crystal Structure Of Human Eukaryotic Release Factor
Erf1-Mechanism Of Stop Codon Recognition And
Peptidyl-Trna Hydrolysis
Length = 437
Score = 279 bits (714), Expect = 6e-76, Method: Compositional matrix adjust.
Identities = 141/218 (64%), Positives = 160/218 (73%), Gaps = 35/218 (16%)
Query: 1 MEKRHNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDP---------- 50
MEKRHNYVRKVAE A LFI+ DK N+AGL+LAGSADFKTELSQSDMFD
Sbjct: 195 MEKRHNYVRKVAETAVQLFISGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLV 254
Query: 51 -----------------------VRFSPLKNKNKMGKYFDEISQDTGKYCFGVEDTLRAL 87
V+F ++ K +G+YFDEISQDTGKYCFGVEDTL+AL
Sbjct: 255 DISYGGENGFNQAIELSTEVLSNVKF--IQEKKLIGRYFDEISQDTGKYCFGVEDTLKAL 312
Query: 88 ELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDKSHFTDKETGVELELVECQ 147
E+G+VE LI +ENLDI RYVL T E+++L+LTPEQEKDKSHFTDKETG E EL+E
Sbjct: 313 EMGAVEILIVYENLDIMRYVLHCQGTEEEKILYLTPEQEKDKSHFTDKETGQEHELIESM 372
Query: 148 PLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFGGIG 185
PLLEW ANNYK FGATLEI+TDKSQEGSQFV+GFGGIG
Sbjct: 373 PLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIG 410
>pdb|2KTU|A Chain A, Human Erf1 C-Domain, "closed" Conformer
pdb|2KTV|A Chain A, Human Erf1 C-Domain, "open" Conformer
Length = 170
Score = 210 bits (535), Expect = 3e-55, Method: Compositional matrix adjust.
Identities = 98/130 (75%), Positives = 113/130 (86%)
Query: 56 LKNKNKMGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSE 115
++ K +G+YFDEISQDTGKYCFGVEDTL+ALE+G+VE LI +ENLDI RYVL T E
Sbjct: 6 IQEKKLIGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYENLDIMRYVLHCQGTEE 65
Query: 116 DRVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNYKSFGATLEIITDKSQEGS 175
+++L+LTPEQEKDKSHFTDKETG E EL+E PLLEW ANNYK FGATLEI+TDKSQEGS
Sbjct: 66 EKILYLTPEQEKDKSHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGS 125
Query: 176 QFVRGFGGIG 185
QFV+GFGGIG
Sbjct: 126 QFVKGFGGIG 135
>pdb|3E20|C Chain C, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
pdb|3E20|B Chain B, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
pdb|3E20|H Chain H, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
pdb|3E20|K Chain K, Crystal Structure Of S.Pombe Erf1ERF3 COMPLEX
Length = 441
Score = 201 bits (510), Expect = 3e-52, Method: Compositional matrix adjust.
Identities = 110/218 (50%), Positives = 139/218 (63%), Gaps = 35/218 (16%)
Query: 2 EKRHNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDPVRFSPL----- 56
EKRHNYVRKVAE A FIT+DKPN+AG++LAGSADFKTEL QSD+FD S +
Sbjct: 201 EKRHNYVRKVAEGAVQHFITDDKPNVAGIVLAGSADFKTELGQSDLFDQRLQSRIIKTVD 260
Query: 57 --------------------------KNKNKMGKYFDEISQDTGKYCFGVEDTLRALELG 90
+ K + ++FDEIS D+GKYCFGV DT+ AL+ G
Sbjct: 261 VSYGGDAGFNQAIELAADTLSNVKYVQEKKLIQRFFDEISLDSGKYCFGVVDTMNALQEG 320
Query: 91 SVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQE-KDK--SHFTDKETGVELELVECQ 147
+VETL+C+ +LD+ RY KN S + ++T EQE KD S DK+TG E+ELV
Sbjct: 321 AVETLLCFADLDMIRYEFKN-SEGNPVITYMTKEQEEKDSTNSFLLDKDTGAEMELVSSM 379
Query: 148 PLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFGGIG 185
L EWLA +YK +GA LE ++D+SQEG QFV+GFGGIG
Sbjct: 380 LLSEWLAEHYKDYGANLEFVSDRSQEGMQFVKGFGGIG 417
>pdb|2HST|A Chain A, Solution Structure Of The Middle Domain Of Human
Eukaryotic Translation Termination Factor Erf1
Length = 143
Score = 89.7 bits (221), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 41/49 (83%), Positives = 44/49 (89%)
Query: 1 MEKRHNYVRKVAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFD 49
MEKRHNYVRKVAE A LFI+ DK N+AGL+LAGSADFKTELSQSDMFD
Sbjct: 56 MEKRHNYVRKVAETAVQLFISGDKVNVAGLVLAGSADFKTELSQSDMFD 104
>pdb|3IR9|A Chain A, C-Terminal Domain Of Peptide Chain Release Factor From
Methanosarcina Mazei.
pdb|3IR9|B Chain B, C-Terminal Domain Of Peptide Chain Release Factor From
Methanosarcina Mazei
Length = 166
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 34/129 (26%), Positives = 58/129 (44%), Gaps = 3/129 (2%)
Query: 59 KNKMGKYFDEISQDTGKYCFGVEDTLRA-LELGSVETLICWENLDIQRYVLKNHSTS-ED 116
KN + +F E+ D+GK +G E +RA LE+ SV+ L+ E+L +R K E+
Sbjct: 30 KNAVRDFFKELIADSGKVAYG-ESQVRANLEINSVDVLLLSEDLRAERVTTKCSVCGYEN 88
Query: 117 RVLHLTPEQEKDKSHFTDKETGVELELVECQPLLEWLANNYKSFGATLEIITDKSQEGSQ 176
+ E + + G LE+ + +++ + A + ++ EGSQ
Sbjct: 89 KWTRRWKPGEPAPAAGNCPKCGSSLEVTDVTDIVDEFSELADKSNAKVVFVSTDFDEGSQ 148
Query: 177 FVRGFGGIG 185
FGGI
Sbjct: 149 LXNAFGGIA 157
>pdb|3AGK|A Chain A, Crystal Structure Of Archaeal Translation Termination
Factor, Arf1
pdb|3VMF|B Chain B, Archaeal Protein
Length = 373
Score = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 60 NKMGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENL-DIQRYVLKNHSTSEDRV 118
N M ++ +++ TG +G +D ALE+G+V+TL+ E+ D++ +V K S+ +
Sbjct: 284 NAMEEFKLHLAKGTGMIVYGEKDVEAALEMGAVKTLLIHESREDLEEWVEKAKSSGAQVI 343
Query: 119 LHLTPEQEKDKSHF 132
+ PE + F
Sbjct: 344 --VVPESLAEAEWF 355
>pdb|3OBW|A Chain A, Crystal Structure Of Two Archaeal Pelotas Reveal
Inter-Domain Structural Plasticity
Length = 364
Score = 29.6 bits (65), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 41 ELSQSDMFDPVR--FSPLKNKNKMGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICW 98
E+ + D+ D + + KM K + +++ +G+E A+E+G+VET++
Sbjct: 249 EVLKRDIIDKIMTDYEIAIGAKKMEKAMELLAKQPELVTYGLEQVKNAIEMGAVETVLVI 308
Query: 99 ENL 101
E+L
Sbjct: 309 EDL 311
>pdb|3MCA|B Chain B, Structure Of The Dom34-Hbs1 Complex And Implications For
Its Role In No-Go Decay
Length = 390
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 25/40 (62%)
Query: 62 MGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENL 101
+ K++D +++D K +G L+A ELG++ L+ ++L
Sbjct: 278 LNKFYDVMNEDDRKAWYGPNHVLKAFELGAIGELLISDSL 317
>pdb|3J15|A Chain A, Model Of Ribosome-Bound Archaeal Pelota And Abce1
Length = 357
Score = 28.1 bits (61), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 23/38 (60%)
Query: 64 KYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENL 101
K + I+++ G +G+++ A+ G+VETL+ + L
Sbjct: 269 KVLENIARNNGLVAYGLKEVEEAVNYGAVETLLVLDEL 306
>pdb|3CC2|C Chain C, 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|C Chain C, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|C Chain C, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|C Chain C, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|C Chain C, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|C Chain C, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|C Chain C, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|3G4S|C Chain C, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|C Chain C, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|C Chain C, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|3I55|C Chain C, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|C Chain C, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
pdb|4ADX|C Chain C, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 246
Score = 28.1 bits (61), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 9 RKVAEVATTLFITNDKPNIAGLILAGSADFKT 40
RK A+ LF+T+D+P+ A LAG AD T
Sbjct: 184 RKYRRPASILFVTSDEPSTAARNLAG-ADVAT 214
>pdb|2D6F|A Chain A, Crystal Structure Of Glu-Trna(Gln) Amidotransferase In The
Complex With Trna(Gln)
pdb|2D6F|B Chain B, Crystal Structure Of Glu-Trna(Gln) Amidotransferase In The
Complex With Trna(Gln)
Length = 435
Score = 28.1 bits (61), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 4/78 (5%)
Query: 111 HSTSEDRVLHLTPEQEKDKSHFTDKETGVE---LELVECQP-LLEWLANNYKSFGATLEI 166
H+T +D HL + K H + ++T L L E P ++ L NY+ G+
Sbjct: 236 HATMDDLSCHLHRGVKVRKMHTSRRDTFRSMNALPLAEVTPDGIKILEENYRKRGSDELE 295
Query: 167 ITDKSQEGSQFVRGFGGI 184
++D+ +E F++ + GI
Sbjct: 296 LSDRVEERVAFIKSYPGI 313
>pdb|1JJ2|C Chain C, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|C Chain C, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|E Chain E, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|E Chain E, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|E Chain E, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|E Chain E, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|E Chain E, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1K73|E Chain E, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|E Chain E, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|E Chain E, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|E Chain E, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|E Chain E, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|E Chain E, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|E Chain E, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|E Chain E, 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|C Chain C, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|C Chain C, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1S72|C Chain C, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1W2B|C Chain C, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|1YHQ|C Chain C, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|C Chain C, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|C Chain C, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|C Chain C, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJ9|C Chain C, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
pdb|1YJN|C Chain C, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|C Chain C, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|C Chain C, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|C Chain C, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|C Chain C, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|C Chain C, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|C Chain C, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|C Chain C, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|C Chain C, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|C Chain C, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|C Chain C, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|C Chain C, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|C Chain C, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|C Chain C, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|C Chain C, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|C Chain C, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|C Chain C, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|2QEX|C Chain C, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3CXC|C Chain C, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
pdb|3OW2|C Chain C, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 246
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 9 RKVAEVATTLFITNDKPNIAGLILAGSADFKT 40
RK A+ LF+T+D+P+ A LAG AD T
Sbjct: 184 RKYRRPASILFVTSDEPSTAARNLAG-ADVAT 214
>pdb|1FFK|C Chain C, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1GIY|F Chain F, 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|1ML5|FF Chain f, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
pdb|1YL3|F Chain F, 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|2B66|F Chain F, 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|F Chain F, 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|F Chain F, 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
Length = 246
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 9 RKVAEVATTLFITNDKPNIAGLILAGSADFKT 40
RK A+ LF+T+D+P+ A LAG AD T
Sbjct: 184 RKYRRPASILFVTSDEPSTAARNLAG-ADVAT 214
>pdb|3OAM|A Chain A, Crystal Structure Of Cytidylyltransferase From Vibrio
Cholerae
pdb|3OAM|B Chain B, Crystal Structure Of Cytidylyltransferase From Vibrio
Cholerae
pdb|3OAM|C Chain C, Crystal Structure Of Cytidylyltransferase From Vibrio
Cholerae
pdb|3OAM|D Chain D, Crystal Structure Of Cytidylyltransferase From Vibrio
Cholerae
Length = 252
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 19/38 (50%)
Query: 147 QPLLEWLANNYKSFGATLEIITDKSQEGSQFVRGFGGI 184
+P+++W+ GA II + Q V+ FGG+
Sbjct: 27 KPMIQWVYEQAMQAGADRVIIATDDERVEQAVQAFGGV 64
>pdb|3H5A|A Chain A, Crystal Structure Of E. Coli Mccb
pdb|3H5A|B Chain B, Crystal Structure Of E. Coli Mccb
pdb|3H5A|C Chain C, Crystal Structure Of E. Coli Mccb
pdb|3H5A|D Chain D, Crystal Structure Of E. Coli Mccb
Length = 358
Score = 27.7 bits (60), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 157 YKSFGATLEIITDKSQEGSQFVRGFGGIG 185
Y+S+GA ++ DK + + G GGIG
Sbjct: 99 YQSYGANPVLVQDKLKNAKVVILGCGGIG 127
>pdb|3H5N|A Chain A, Crystal Structure Of E. Coli Mccb + Atp
pdb|3H5N|B Chain B, Crystal Structure Of E. Coli Mccb + Atp
pdb|3H5N|C Chain C, Crystal Structure Of E. Coli Mccb + Atp
pdb|3H5N|D Chain D, Crystal Structure Of E. Coli Mccb + Atp
pdb|3H5R|A Chain A, Crystal Structure Of E. Coli Mccb + Succinimide
pdb|3H5R|B Chain B, Crystal Structure Of E. Coli Mccb + Succinimide
pdb|3H5R|C Chain C, Crystal Structure Of E. Coli Mccb + Succinimide
pdb|3H5R|D Chain D, Crystal Structure Of E. Coli Mccb + Succinimide
pdb|3H9G|A Chain A, Crystal Structure Of E. Coli Mccb + Mcca-N7isoasn
pdb|3H9G|B Chain B, Crystal Structure Of E. Coli Mccb + Mcca-N7isoasn
pdb|3H9G|C Chain C, Crystal Structure Of E. Coli Mccb + Mcca-N7isoasn
pdb|3H9G|D Chain D, Crystal Structure Of E. Coli Mccb + Mcca-N7isoasn
pdb|3H9J|A Chain A, Crystal Structure Of E. Coli Mccb + Ampcpp + Semet Mcca
pdb|3H9J|B Chain B, Crystal Structure Of E. Coli Mccb + Ampcpp + Semet Mcca
pdb|3H9J|C Chain C, Crystal Structure Of E. Coli Mccb + Ampcpp + Semet Mcca
pdb|3H9J|D Chain D, Crystal Structure Of E. Coli Mccb + Ampcpp + Semet Mcca
pdb|3H9Q|A Chain A, Crystal Structure Of E. Coli Mccb + Semet Mcca
pdb|3H9Q|B Chain B, Crystal Structure Of E. Coli Mccb + Semet Mcca
pdb|3H9Q|C Chain C, Crystal Structure Of E. Coli Mccb + Semet Mcca
pdb|3H9Q|D Chain D, Crystal Structure Of E. Coli Mccb + Semet Mcca
Length = 353
Score = 27.7 bits (60), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 157 YKSFGATLEIITDKSQEGSQFVRGFGGIG 185
Y+S+GA ++ DK + + G GGIG
Sbjct: 102 YQSYGANPVLVQDKLKNAKVVILGCGGIG 130
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
0.316 0.134 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,597,649
Number of Sequences: 62578
Number of extensions: 220175
Number of successful extensions: 541
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 515
Number of HSP's gapped (non-prelim): 29
length of query: 185
length of database: 14,973,337
effective HSP length: 93
effective length of query: 92
effective length of database: 9,153,583
effective search space: 842129636
effective search space used: 842129636
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: 48 (23.1 bits)