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= psy2291
(96 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JNJ|A Chain A, Solution Structure Of The P8 Tfiih Subunit
pdb|2JNJ|B Chain B, Solution Structure Of The P8 Tfiih Subunit
Length = 74
Score = 72.0 bits (175), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 31/68 (45%), Positives = 51/68 (75%), Gaps = 2/68 (2%)
Query: 28 RRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQ 87
+ +I C D MKQFLL+LDE+N LG++FIIQD+D+TH+F+ ++++ +L RV +L+DQ
Sbjct: 9 KGVLIEC--DPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQ 66
Query: 88 ISFPINDR 95
+F + +
Sbjct: 67 NAFSLTQK 74
>pdb|1YDL|A Chain A, Crystal Structure Of The Human Tfiih, Northeast
Structural Genomics Target Hr2045
Length = 79
Score = 68.2 bits (165), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 30/68 (44%), Positives = 49/68 (72%), Gaps = 2/68 (2%)
Query: 28 RRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQ 87
+ +I C D KQFLL+LDE+N LG++FIIQD+D+TH+F+ ++++ +L RV +L DQ
Sbjct: 14 KGXLIEC--DPAXKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELXDQ 71
Query: 88 ISFPINDR 95
+F + +
Sbjct: 72 NAFSLTQK 79
>pdb|1EFT|A Chain A, The Crystal Structure Of Elongation Factor Ef-Tu From
Thermus Aquaticus In The Gtp Conformation
Length = 405
Score = 31.2 bits (69), Expect = 0.14, Method: Composition-based stats.
Identities = 15/56 (26%), Positives = 30/56 (53%)
Query: 36 SDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFP 91
+D PM Q H+ +G +I+ +++ + ++++L+ V DLL+Q FP
Sbjct: 109 ADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFP 164
>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 = 31.2 bits (69), Expect = 0.14, Method: Composition-based stats.
Identities = 15/56 (26%), Positives = 30/56 (53%)
Query: 36 SDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFP 91
+D PM Q H+ +G +I+ +++ + ++++L+ V DLL+Q FP
Sbjct: 110 ADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFP 165
>pdb|4ABR|Z Chain Z, Complex Of Smpb, A Tmrna Fragment And Ef-Tu-Gdp-Kirromycin
With The 70s Ribosome
Length = 405
Score = 31.2 bits (69), Expect = 0.14, Method: Composition-based stats.
Identities = 15/56 (26%), Positives = 30/56 (53%)
Query: 36 SDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFP 91
+D PM Q H+ +G +I+ +++ + ++++L+ V DLL+Q FP
Sbjct: 109 ADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFP 164
>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 = 31.2 bits (69), Expect = 0.14, Method: Composition-based stats.
Identities = 15/56 (26%), Positives = 30/56 (53%)
Query: 36 SDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFP 91
+D PM Q H+ +G +I+ +++ + ++++L+ V DLL+Q FP
Sbjct: 109 ADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFP 164
>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 = 31.2 bits (69), Expect = 0.14, Method: Composition-based stats.
Identities = 15/56 (26%), Positives = 30/56 (53%)
Query: 36 SDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFP 91
+D PM Q H+ +G +I+ +++ + ++++L+ V DLL+Q FP
Sbjct: 109 ADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFP 164
>pdb|2C77|A Chain A, Ef-Tu Complexed With A Gtp Analog And The Antibiotic
Ge2270 A
Length = 405
Score = 31.2 bits (69), Expect = 0.14, Method: Composition-based stats.
Identities = 15/56 (26%), Positives = 30/56 (53%)
Query: 36 SDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFP 91
+D PM Q H+ +G +I+ +++ + ++++L+ V DLL+Q FP
Sbjct: 109 ADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFP 164
>pdb|2C78|A Chain A, Ef-Tu Complexed With A Gtp Analog And The Antibiotic
Pulvomycin
Length = 405
Score = 31.2 bits (69), Expect = 0.14, Method: Composition-based stats.
Identities = 15/56 (26%), Positives = 30/56 (53%)
Query: 36 SDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFP 91
+D PM Q H+ +G +I+ +++ + ++++L+ V DLL+Q FP
Sbjct: 109 ADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFP 164
>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 = 31.2 bits (69), Expect = 0.14, Method: Composition-based stats.
Identities = 15/56 (26%), Positives = 30/56 (53%)
Query: 36 SDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFP 91
+D PM Q H+ +G +I+ +++ + ++++L+ V DLL+Q FP
Sbjct: 109 ADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFP 164
>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 = 31.2 bits (69), Expect = 0.14, Method: Composition-based stats.
Identities = 15/56 (26%), Positives = 30/56 (53%)
Query: 36 SDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFP 91
+D PM Q H+ +G +I+ +++ + ++++L+ V DLL+Q FP
Sbjct: 109 ADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFP 164
>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 = 31.2 bits (69), Expect = 0.14, Method: Composition-based stats.
Identities = 15/56 (26%), Positives = 30/56 (53%)
Query: 36 SDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFP 91
+D PM Q H+ +G +I+ +++ + ++++L+ V DLL+Q FP
Sbjct: 109 ADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFP 164
>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 = 28.5 bits (62), Expect = 1.0, Method: Composition-based stats.
Identities = 14/55 (25%), Positives = 30/55 (54%)
Query: 36 SDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISF 90
+D M+Q H+ +G R+I+ +++ + ++++L+ V DLL+Q F
Sbjct: 109 ADGRMRQTREHILLARQVGVRYIVVFMNKVDMVDDRELLDLVEMEVRDLLNQYEF 163
>pdb|1N2T|A Chain A, C-Des Mutant K223a With Gly Covalenty Linked To The
Plp-Cofactor
pdb|1N2T|B Chain B, C-Des Mutant K223a With Gly Covalenty Linked To The
Plp-Cofactor
pdb|1N31|A Chain A, Structure Of A Catalytically Inactive Mutant (K223a) Of
C-Des With A Substrate (Cystine) Linked To The Co-Factor
pdb|1N31|B Chain B, Structure Of A Catalytically Inactive Mutant (K223a) Of
C-Des With A Substrate (Cystine) Linked To The Co-Factor
Length = 386
Score = 26.2 bits (56), Expect = 4.7, Method: Composition-based stats.
Identities = 10/40 (25%), Positives = 21/40 (52%)
Query: 32 IHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISS 71
+HC + + L+ + LG R I+Q L+E +++ +
Sbjct: 315 VHCLATSAPQAGLVSFTVDSPLGHRAIVQKLEEQRIYLRT 354
>pdb|1ELQ|A Chain A, Crystal Structure Of The Cystine C-S Lyase C-Des
pdb|1ELQ|B Chain B, Crystal Structure Of The Cystine C-S Lyase C-Des
pdb|1ELU|A Chain A, Complex Between The Cystine C-S Lyase C-Des And Its
Reaction Product Cysteine Persulfide.
pdb|1ELU|B Chain B, Complex Between The Cystine C-S Lyase C-Des And Its
Reaction Product Cysteine Persulfide
Length = 390
Score = 26.2 bits (56), Expect = 4.7, Method: Composition-based stats.
Identities = 10/40 (25%), Positives = 21/40 (52%)
Query: 32 IHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISS 71
+HC + + L+ + LG R I+Q L+E +++ +
Sbjct: 319 VHCLATSAPQAGLVSFTVDSPLGHRAIVQKLEEQRIYLRT 358
>pdb|2VEQ|A Chain A, Insights Into Kinetochore-Dna Interactions From The
Structure Of Cep3p
Length = 565
Score = 25.8 bits (55), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 31/70 (44%), Gaps = 7/70 (10%)
Query: 25 TLGRRFIIHCFSD----KPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTR 80
TLGR F C D P K LH + ++ L +QDL ++ + E+L +
Sbjct: 245 TLGRIFYRLCGCDYLQSGPRKPIALHTEVSSLLQHAAYLQDLPNVDVYREENSTEVLYWK 304
Query: 81 VDDL---LDQ 87
+ L LDQ
Sbjct: 305 IISLDRDLDQ 314
>pdb|2QUQ|A Chain A, Crystal Structure Of The Essential Inner Kinetochore
Protein Cep3p
Length = 562
Score = 25.8 bits (55), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 31/70 (44%), Gaps = 7/70 (10%)
Query: 25 TLGRRFIIHCFSD----KPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTR 80
TLGR F C D P K LH + ++ L +QDL ++ + E+L +
Sbjct: 242 TLGRIFYRLCGCDYLQSGPRKPIALHTEVSSLLQHAAYLQDLPNVDVYREENSTEVLYWK 301
Query: 81 VDDL---LDQ 87
+ L LDQ
Sbjct: 302 IISLDRDLDQ 311
>pdb|3LUN|A Chain A, Structure Of Ulilysin Mutant M290c
pdb|3LUN|B Chain B, Structure Of Ulilysin Mutant M290c
Length = 262
Score = 25.8 bits (55), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 8/42 (19%)
Query: 4 YCNYVDDKPMKQFLLHLDETNTLGRRFIIHCFSDKPMKQFLL 45
YC+YVDDK M F T G+ ++ D P FL
Sbjct: 229 YCDYVDDKCMVMF--------TQGQATRVNACLDGPRSSFLA 262
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
0.328 0.146 0.435
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,678,407
Number of Sequences: 62578
Number of extensions: 94268
Number of successful extensions: 325
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 27
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 294
Number of HSP's gapped (non-prelim): 35
length of query: 96
length of database: 14,973,337
effective HSP length: 62
effective length of query: 34
effective length of database: 11,093,501
effective search space: 377179034
effective search space used: 377179034
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)