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= 024326
(269 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4F3L|A Chain A, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 361
Score = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 68 EDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPG-ATKMDKATLLTEVISQLKE 121
+D+ A + ++E+ RR + N + L S++PG A KMDK+T+L + I L++
Sbjct: 6 DDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRK 60
>pdb|4H10|B Chain B, Intermolecular Recognition Revealed By The Complex
Structure Of Human Clock-bmal1 Basic Helix-loop-helix
Domains With E-box Dna
Length = 71
Score = 31.6 bits (70), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 68 EDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPG-ATKMDKATLLTEVISQLKE 121
+D+ A + ++E+ RR + N + L S++PG A KMDK+T+L + I L++
Sbjct: 2 DDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRK 56
>pdb|2C77|A Chain A, Ef-Tu Complexed With A Gtp Analog And The Antibiotic
Ge2270 A
Length = 405
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 70 RSVAALKNHIEAERNRRKRIN----GHLDTLRSLIPGATKMDKATLL 112
R + H+E E +R + GH D ++++I GA +MD A L+
Sbjct: 59 RGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILV 105
>pdb|1EFT|A Chain A, The Crystal Structure Of Elongation Factor Ef-Tu From
Thermus Aquaticus In The Gtp Conformation
Length = 405
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 70 RSVAALKNHIEAERNRRKRIN----GHLDTLRSLIPGATKMDKATLL 112
R + H+E E +R + GH D ++++I GA +MD A L+
Sbjct: 59 RGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILV 105
>pdb|2WRN|Z Chain Z, The Crystal Structure Of The 70s Ribosome Bound To Ef-Tu
And Trna (Part 1 Of 4).
pdb|2WRQ|Z Chain Z, The Crystal Structure Of The 70s Ribosome Bound To Ef-Tu
And Trna (Part 3 Of 4)
Length = 406
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 70 RSVAALKNHIEAERNRRKRIN----GHLDTLRSLIPGATKMDKATLL 112
R + H+E E +R + GH D ++++I GA +MD A L+
Sbjct: 60 RGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILV 106
>pdb|4ABR|Z Chain Z, Complex Of Smpb, A Tmrna Fragment And Ef-Tu-Gdp-Kirromycin
With The 70s Ribosome
Length = 405
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 70 RSVAALKNHIEAERNRRKRIN----GHLDTLRSLIPGATKMDKATLL 112
R + H+E E +R + GH D ++++I GA +MD A L+
Sbjct: 59 RGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILV 105
>pdb|1EXM|A Chain A, Crystal Structure Of Thermus Thermophilus Elongation
Factor Tu (Ef-Tu) In Complex With The Gtp Analogue
Gppnhp.
pdb|1HA3|A Chain A, Elongation Factor Tu In Complex With Aurodox
pdb|1HA3|B Chain B, Elongation Factor Tu In Complex With Aurodox
pdb|3FIC|Z Chain Z, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas
And Ef- Tu.Gdp.Kirromycin Ternary Complex, Fitted To A
6.4 A Cryo-Em Map. This File Contains The 30s Subunit
And The Ligands
pdb|2XQD|Z Chain Z, The Structure Of Ef-Tu And Aminoacyl-Trna Bound To The 70s
Ribosome With A Gtp Analog
Length = 405
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 70 RSVAALKNHIEAERNRRKRIN----GHLDTLRSLIPGATKMDKATLL 112
R + H+E E +R + GH D ++++I GA +MD A L+
Sbjct: 59 RGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILV 105
>pdb|1AIP|A Chain A, Ef-Tu Ef-Ts Complex From Thermus Thermophilus
pdb|1AIP|B Chain B, Ef-Tu Ef-Ts Complex From Thermus Thermophilus
pdb|1AIP|E Chain E, Ef-Tu Ef-Ts Complex From Thermus Thermophilus
pdb|1AIP|F Chain F, Ef-Tu Ef-Ts Complex From Thermus Thermophilus
Length = 405
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 70 RSVAALKNHIEAERNRRKRIN----GHLDTLRSLIPGATKMDKATLL 112
R + H+E E +R + GH D ++++I GA +MD A L+
Sbjct: 59 RGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILV 105
>pdb|2C78|A Chain A, Ef-Tu Complexed With A Gtp Analog And The Antibiotic
Pulvomycin
Length = 405
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 70 RSVAALKNHIEAERNRRKRIN----GHLDTLRSLIPGATKMDKATLL 112
R + H+E E +R + GH D ++++I GA +MD A L+
Sbjct: 59 RGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILV 105
>pdb|1TTT|A Chain A, Phe-Trna, Elongation Factor Ef-Tu:gdpnp Ternary Complex
pdb|1TTT|B Chain B, Phe-Trna, Elongation Factor Ef-Tu:gdpnp Ternary Complex
pdb|1TTT|C Chain C, Phe-Trna, Elongation Factor Ef-Tu:gdpnp Ternary Complex
pdb|1TUI|A Chain A, Intact Elongation Factor Tu In Complex With Gdp
pdb|1TUI|B Chain B, Intact Elongation Factor Tu In Complex With Gdp
pdb|1TUI|C Chain C, Intact Elongation Factor Tu In Complex With Gdp
pdb|1B23|P Chain P, E. Coli Cysteinyl-Trna And T. Aquaticus Elongation Factor
Ef-Tu:gtp Ternary Complex
pdb|1ZC8|Y Chain Y, Coordinates Of Tmrna, Smpb, Ef-tu And H44 Fitted Into
Cryo- Em Map Of The 70s Ribosome And Tmrna Complex
pdb|1OB5|A Chain A, T. Aquaticus Elongation Factor Ef-Tu Complexed With The
Antibiotic Enacyloxin Iia, A Gtp Analog, And Phe-Trna
pdb|1OB5|C Chain C, T. Aquaticus Elongation Factor Ef-Tu Complexed With The
Antibiotic Enacyloxin Iia, A Gtp Analog, And Phe-Trna
pdb|1OB5|E Chain E, T. Aquaticus Elongation Factor Ef-Tu Complexed With The
Antibiotic Enacyloxin Iia, A Gtp Analog, And Phe-Trna
Length = 405
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 70 RSVAALKNHIEAERNRRKRIN----GHLDTLRSLIPGATKMDKATLL 112
R + H+E E +R + GH D ++++I GA +MD A L+
Sbjct: 59 RGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILV 105
>pdb|2Y0Y|Z Chain Z, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Near-Cognate Codon On The 70s Ribosome
pdb|2Y10|Z Chain Z, The Crystal Structure Of Ef-Tu And Trp-Trna-Trp Bound To A
Cognate Codon On The 70s Ribosome.
pdb|2Y12|Z Chain Z, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Near-Cognate Codon On The 70s Ribosome
pdb|2Y14|Z Chain Z, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Cognate Codon On The 70s Ribosome.
pdb|2Y16|Z Chain Z, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Cognate Codon On The 70s Ribosome.
pdb|2Y18|Z Chain Z, The Crystal Structure Of Ef-Tu And Trp-Trna-Trp Bound To A
Cognate Codon On The 70s Ribosome
Length = 405
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 70 RSVAALKNHIEAERNRRKRIN----GHLDTLRSLIPGATKMDKATLL 112
R + H+E E +R + GH D ++++I GA +MD A L+
Sbjct: 59 RGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILV 105
>pdb|2Y0U|Z Chain Z, The Crystal Structure Of Ef-Tu And A9c-Trna-Trp Bound To A
Near-Cognate Codon On The 70s Ribosome
pdb|2Y0W|Z Chain Z, The Crystal Structure Of Ef-Tu And A9c-Trna-Trp Bound To A
Near-Cognate Codon On The 70s Ribosome
Length = 405
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 70 RSVAALKNHIEAERNRRKRIN----GHLDTLRSLIPGATKMDKATLL 112
R + H+E E +R + GH D ++++I GA +MD A L+
Sbjct: 59 RGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILV 105
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 29/129 (22%), Positives = 51/129 (39%), Gaps = 21/129 (16%)
Query: 51 RGELVEANVKLQRKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKAT 110
R ++ + +LQ KG+S A L+N++ A+ + + D
Sbjct: 246 RAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEK-----------------FQRDDLQ 288
Query: 111 LLTEVISQLKELDKNAMEATEGFLIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGL 170
++ ++ ++K + F IP +I+ E G DG P A Y P
Sbjct: 289 IVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLP----AEAMLFYDPAD 344
Query: 171 LSDLRRVLE 179
++ LRR LE
Sbjct: 345 MAWLRRCLE 353
>pdb|1MJ1|A Chain A, Fitting The Ternary Complex Of Ef-TuTRNAGTP AND RIBOSOMAL
PROTEINS Into A 13 A Cryo-Em Map Of The Coli 70s
Ribosome
Length = 405
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 70 RSVAALKNHIEAERNRRKRIN----GHLDTLRSLIPGATKMDKATLL 112
R + H+E E +R + GH D ++++I GA +MD A L+
Sbjct: 59 RGITINTAHVEYETAKRHYSHVDCRGHADYIKNMITGAAQMDGAILV 105
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 27.7 bits (60), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 29/129 (22%), Positives = 50/129 (38%), Gaps = 21/129 (16%)
Query: 51 RGELVEANVKLQRKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKAT 110
R ++ + +LQ KG+S A L+N++ A+ + + D
Sbjct: 246 RAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEK-----------------FQRDDLQ 288
Query: 111 LLTEVISQLKELDKNAMEATEGFLIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGL 170
++ ++ ++K + F IP +I+ E G DG P A Y P
Sbjct: 289 IVVATVAFGXGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLP----AEAXLFYDPAD 344
Query: 171 LSDLRRVLE 179
+ LRR LE
Sbjct: 345 XAWLRRCLE 353
>pdb|1WX0|A Chain A, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
pdb|1WX0|B Chain B, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
pdb|1WX0|C Chain C, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
pdb|1WX0|D Chain D, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
pdb|1WX0|E Chain E, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
pdb|1WX0|F Chain F, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
pdb|1WX0|G Chain G, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
pdb|1WX0|H Chain H, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
pdb|1WX0|I Chain I, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
pdb|1WX0|J Chain J, Crystal Structure Of Transaldolase From Thermus
Thermophilus Hb8
Length = 223
Score = 27.3 bits (59), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 26/90 (28%), Positives = 42/90 (46%), Gaps = 10/90 (11%)
Query: 153 GAPYSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFE 212
G P S A + ++++ RR L A+H +IV T EG + +CK L+ E
Sbjct: 60 GGPVS--AEVTALEAEAMVAEGRR-LAAIHPNIVVKLPTTEEG-------LKACKRLSAE 109
Query: 213 NTEVCQSLVSSVHQAIRSVLDKFSATEEFL 242
+V +L+ S +QA+ + S FL
Sbjct: 110 GIKVNMTLIFSANQALLAARAGASYVSPFL 139
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
0.317 0.133 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,258,849
Number of Sequences: 62578
Number of extensions: 211233
Number of successful extensions: 588
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 586
Number of HSP's gapped (non-prelim): 23
length of query: 269
length of database: 14,973,337
effective HSP length: 97
effective length of query: 172
effective length of database: 8,903,271
effective search space: 1531362612
effective search space used: 1531362612
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)