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= 028617
(206 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2OKV|A Chain A, C-Myc Dna Unwinding Element Binding Protein
pdb|2OKV|B Chain B, C-Myc Dna Unwinding Element Binding Protein
pdb|2OKV|C Chain C, C-Myc Dna Unwinding Element Binding Protein
pdb|2OKV|D Chain D, C-Myc Dna Unwinding Element Binding Protein
Length = 209
Score = 117 bits (294), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 57/120 (47%), Positives = 86/120 (71%), Gaps = 4/120 (3%)
Query: 53 GRLVSEIGPGLLVLVGLHEFDTDADADYVCRKVLNMRLFPNENTGKGWDLNVMQKKYGVL 112
G +S IG G+ VL+G+ DT + +++ RK+LN+R+F +E +GK W +VM K+Y +L
Sbjct: 17 GEQISAIGRGICVLLGISLEDTQKELEHMVRKILNLRVFEDE-SGKHWSKSVMDKQYEIL 75
Query: 113 LVSQFTLYGILKGNKPDFHVAMPPQKAKPFYDSLVDKFRKSYNPDAIK-GK--CAFQLHL 169
VSQFTL +LKGNKPDFH+AMP ++A+ FY+S +++ RK+Y P+ IK GK Q+H+
Sbjct: 76 CVSQFTLQCVLKGNKPDFHLAMPTEQAEGFYNSFLEQLRKTYRPELIKDGKFGAYMQVHI 135
>pdb|3KNF|A Chain A, Crystal Structure Of D-Tyr-Trna(Tyr) Deacylase From
Plasmodium Falciparum
pdb|3KNF|B Chain B, Crystal Structure Of D-Tyr-Trna(Tyr) Deacylase From
Plasmodium Falciparum
pdb|3KNF|C Chain C, Crystal Structure Of D-Tyr-Trna(Tyr) Deacylase From
Plasmodium Falciparum
pdb|3KNF|D Chain D, Crystal Structure Of D-Tyr-Trna(Tyr) Deacylase From
Plasmodium Falciparum
pdb|3KNF|E Chain E, Crystal Structure Of D-Tyr-Trna(Tyr) Deacylase From
Plasmodium Falciparum
pdb|3KNF|F Chain F, Crystal Structure Of D-Tyr-Trna(Tyr) Deacylase From
Plasmodium Falciparum
pdb|3KO4|A Chain A, Crystal Structure Of D-Tyr-Trna(Tyr) Deacylase From
Plasmodium Falciparum In Complex With Adp
pdb|3KO4|B Chain B, Crystal Structure Of D-Tyr-Trna(Tyr) Deacylase From
Plasmodium Falciparum In Complex With Adp
pdb|3KO4|C Chain C, Crystal Structure Of D-Tyr-Trna(Tyr) Deacylase From
Plasmodium Falciparum In Complex With Adp
pdb|3KO4|D Chain D, Crystal Structure Of D-Tyr-Trna(Tyr) Deacylase From
Plasmodium Falciparum In Complex With Adp
pdb|3KO4|E Chain E, Crystal Structure Of D-Tyr-Trna(Tyr) Deacylase From
Plasmodium Falciparum In Complex With Adp
pdb|3KO4|F Chain F, Crystal Structure Of D-Tyr-Trna(Tyr) Deacylase From
Plasmodium Falciparum In Complex With Adp
pdb|3KO5|A Chain A, D-Tyr-Trna(Tyr) Deacylase From Plasmodium Falciparum In
Complex With Adp
pdb|3KO5|B Chain B, D-Tyr-Trna(Tyr) Deacylase From Plasmodium Falciparum In
Complex With Adp
pdb|3KO5|C Chain C, D-Tyr-Trna(Tyr) Deacylase From Plasmodium Falciparum In
Complex With Adp
pdb|3KO5|D Chain D, D-Tyr-Trna(Tyr) Deacylase From Plasmodium Falciparum In
Complex With Adp
pdb|3KO5|E Chain E, D-Tyr-Trna(Tyr) Deacylase From Plasmodium Falciparum In
Complex With Adp
pdb|3KO5|F Chain F, D-Tyr-Trna(Tyr) Deacylase From Plasmodium Falciparum In
Complex With Adp
pdb|3KO7|A Chain A, Dtd From Plasmodium Falciparum In Complex With D-Lysine
pdb|3KO7|B Chain B, Dtd From Plasmodium Falciparum In Complex With D-Lysine
pdb|3KO7|C Chain C, Dtd From Plasmodium Falciparum In Complex With D-Lysine
pdb|3KO7|D Chain D, Dtd From Plasmodium Falciparum In Complex With D-Lysine
pdb|3KO7|E Chain E, Dtd From Plasmodium Falciparum In Complex With D-Lysine
pdb|3KO7|F Chain F, Dtd From Plasmodium Falciparum In Complex With D-Lysine
pdb|3KO9|A Chain A, Dtd From Plasmodium Falciparum In Complex With D-Arginine
pdb|3KO9|B Chain B, Dtd From Plasmodium Falciparum In Complex With D-Arginine
pdb|3KO9|C Chain C, Dtd From Plasmodium Falciparum In Complex With D-Arginine
pdb|3KO9|D Chain D, Dtd From Plasmodium Falciparum In Complex With D-Arginine
pdb|3KO9|E Chain E, Dtd From Plasmodium Falciparum In Complex With D-Arginine
pdb|3KO9|F Chain F, Dtd From Plasmodium Falciparum In Complex With D-Arginine
pdb|3KNP|A Chain A, Crystal Structure Of Dtd From Plasmodium Falciparum
pdb|3KNP|B Chain B, Crystal Structure Of Dtd From Plasmodium Falciparum
pdb|3KNP|C Chain C, Crystal Structure Of Dtd From Plasmodium Falciparum
pdb|3KNP|D Chain D, Crystal Structure Of Dtd From Plasmodium Falciparum
pdb|3KNP|E Chain E, Crystal Structure Of Dtd From Plasmodium Falciparum
pdb|3KNP|F Chain F, Crystal Structure Of Dtd From Plasmodium Falciparum
pdb|3KO3|A Chain A, D-Tyrosyl-Trna(Tyr) Deacylase From Plasmodium Falciparum
Incomplex With Adp, Obtained Through Soaking Native
Enzyme Crystal With The Atp
pdb|3KO3|B Chain B, D-Tyrosyl-Trna(Tyr) Deacylase From Plasmodium Falciparum
Incomplex With Adp, Obtained Through Soaking Native
Enzyme Crystal With The Atp
pdb|3KO3|C Chain C, D-Tyrosyl-Trna(Tyr) Deacylase From Plasmodium Falciparum
Incomplex With Adp, Obtained Through Soaking Native
Enzyme Crystal With The Atp
pdb|3KO3|D Chain D, D-Tyrosyl-Trna(Tyr) Deacylase From Plasmodium Falciparum
Incomplex With Adp, Obtained Through Soaking Native
Enzyme Crystal With The Atp
pdb|3KO3|E Chain E, D-Tyrosyl-Trna(Tyr) Deacylase From Plasmodium Falciparum
Incomplex With Adp, Obtained Through Soaking Native
Enzyme Crystal With The Atp
pdb|3KO3|F Chain F, D-Tyrosyl-Trna(Tyr) Deacylase From Plasmodium Falciparum
Incomplex With Adp, Obtained Through Soaking Native
Enzyme Crystal With The Atp
pdb|3KOB|A Chain A, Dtd From Plasmodium Falciparum In Complex With D-Glutamic
Acid
pdb|3KOB|B Chain B, Dtd From Plasmodium Falciparum In Complex With D-Glutamic
Acid
pdb|3KOB|C Chain C, Dtd From Plasmodium Falciparum In Complex With D-Glutamic
Acid
pdb|3KOB|D Chain D, Dtd From Plasmodium Falciparum In Complex With D-Glutamic
Acid
pdb|3KOB|E Chain E, Dtd From Plasmodium Falciparum In Complex With D-Glutamic
Acid
pdb|3KOB|F Chain F, Dtd From Plasmodium Falciparum In Complex With D-Glutamic
Acid
pdb|3KOC|A Chain A, Dtd From Plasmodium Falciparum In Complex With D-Histidine
pdb|3KOC|B Chain B, Dtd From Plasmodium Falciparum In Complex With D-Histidine
pdb|3KOC|C Chain C, Dtd From Plasmodium Falciparum In Complex With D-Histidine
pdb|3KOC|D Chain D, Dtd From Plasmodium Falciparum In Complex With D-Histidine
pdb|3KOC|E Chain E, Dtd From Plasmodium Falciparum In Complex With D-Histidine
pdb|3KOC|F Chain F, Dtd From Plasmodium Falciparum In Complex With D-Histidine
pdb|3KOD|A Chain A, Dtd From Plasmodium Falciparum In Complex With D-Serine
pdb|3KOD|B Chain B, Dtd From Plasmodium Falciparum In Complex With D-Serine
pdb|3KOD|C Chain C, Dtd From Plasmodium Falciparum In Complex With D-Serine
pdb|3KOD|D Chain D, Dtd From Plasmodium Falciparum In Complex With D-Serine
pdb|3KOD|E Chain E, Dtd From Plasmodium Falciparum In Complex With D-Serine
pdb|3KOD|F Chain F, Dtd From Plasmodium Falciparum In Complex With D-Serine
pdb|3LMT|A Chain A, Crystal Strucutre Of Dtd From Plasmodium Falciparum
pdb|3LMT|B Chain B, Crystal Strucutre Of Dtd From Plasmodium Falciparum
pdb|3LMT|C Chain C, Crystal Strucutre Of Dtd From Plasmodium Falciparum
pdb|3LMT|D Chain D, Crystal Strucutre Of Dtd From Plasmodium Falciparum
pdb|3LMT|E Chain E, Crystal Strucutre Of Dtd From Plasmodium Falciparum
pdb|3LMT|F Chain F, Crystal Strucutre Of Dtd From Plasmodium Falciparum
pdb|3LMU|A Chain A, Crystal Strucutre Of Dtd From Plasmodium Falciparum
pdb|3LMU|B Chain B, Crystal Strucutre Of Dtd From Plasmodium Falciparum
pdb|3LMU|C Chain C, Crystal Strucutre Of Dtd From Plasmodium Falciparum
pdb|3LMU|D Chain D, Crystal Strucutre Of Dtd From Plasmodium Falciparum
pdb|3LMU|E Chain E, Crystal Strucutre Of Dtd From Plasmodium Falciparum
pdb|3LMU|F Chain F, Crystal Strucutre Of Dtd From Plasmodium Falciparum
pdb|3LMU|G Chain G, Crystal Strucutre Of Dtd From Plasmodium Falciparum
pdb|3LMU|H Chain H, Crystal Strucutre Of Dtd From Plasmodium Falciparum
pdb|3LMV|A Chain A, D-Tyr-Trna(Tyr) Deacylase From Plasmodium Falciparum In
Complex With Hepes
pdb|3LMV|B Chain B, D-Tyr-Trna(Tyr) Deacylase From Plasmodium Falciparum In
Complex With Hepes
pdb|3LMV|C Chain C, D-Tyr-Trna(Tyr) Deacylase From Plasmodium Falciparum In
Complex With Hepes
pdb|3LMV|D Chain D, D-Tyr-Trna(Tyr) Deacylase From Plasmodium Falciparum In
Complex With Hepes
pdb|3LMV|E Chain E, D-Tyr-Trna(Tyr) Deacylase From Plasmodium Falciparum In
Complex With Hepes
pdb|3LMV|F Chain F, D-Tyr-Trna(Tyr) Deacylase From Plasmodium Falciparum In
Complex With Hepes
Length = 164
Score = 110 bits (275), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 55/108 (50%), Positives = 75/108 (69%), Gaps = 3/108 (2%)
Query: 54 RLVSEIGPGLLVLVGLHEFDTDADADYVCRKVLNMRLFPNENTGKGWDLNVMQKKYGVLL 113
++SEI GL+ +G+H+ DT DA Y+ RK LN+RL+ N+N K WD NV Y +L+
Sbjct: 28 EIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDN--KTWDKNVKDLNYELLI 85
Query: 114 VSQFTLYG-ILKGNKPDFHVAMPPQKAKPFYDSLVDKFRKSYNPDAIK 160
VSQFTL+G KGNKPDFH+A P +A FY+ ++D+F+K YN D IK
Sbjct: 86 VSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIK 133
>pdb|2DBO|A Chain A, Crystal Structure Of D-Tyr-Trna(Tyr) Deacylase From
Aquifex Aeolicus
Length = 148
Score = 77.0 bits (188), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 41/102 (40%), Positives = 65/102 (63%), Gaps = 3/102 (2%)
Query: 53 GRLVSEIGPGLLVLVGLHEFDTDADADYVCRKVLNMRLFPNENTGKGWDLNVMQKKYGVL 112
G++V I GL V +G+ + DT+ D + + K+LN+R+F +E GK + +V+ K +L
Sbjct: 17 GKVVGSINEGLNVFLGVRKGDTEEDIEKLVNKILNLRIFEDER-GK-FQYSVLDIKGEIL 74
Query: 113 LVSQFTLYG-ILKGNKPDFHVAMPPQKAKPFYDSLVDKFRKS 153
+VSQFTLY + KG +P F A P++AK Y+ VDK ++S
Sbjct: 75 VVSQFTLYANVKKGRRPSFEEAEEPKRAKELYEKFVDKIKES 116
>pdb|1JKE|A Chain A, D-Tyr Trnatyr Deacylase From Escherichia Coli
pdb|1JKE|B Chain B, D-Tyr Trnatyr Deacylase From Escherichia Coli
pdb|1JKE|C Chain C, D-Tyr Trnatyr Deacylase From Escherichia Coli
pdb|1JKE|D Chain D, D-Tyr Trnatyr Deacylase From Escherichia Coli
Length = 145
Score = 72.8 bits (177), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 40/101 (39%), Positives = 59/101 (58%), Gaps = 3/101 (2%)
Query: 53 GRLVSEIGPGLLVLVGLHEFDTDADADYVCRKVLNMRLFPNENTGKGWDLNVMQKKYGVL 112
G + EIG GLLVL+G+ + D + A+ +C +VL R+F + GK +LNV Q VL
Sbjct: 17 GEVTGEIGAGLLVLLGVEKDDDEQKANRLCERVLGYRIFSDAE-GK-MNLNVQQAGGSVL 74
Query: 113 LVSQFTLYG-ILKGNKPDFHVAMPPQKAKPFYDSLVDKFRK 152
+VSQFTL +G +P F P +A+ YD V++ R+
Sbjct: 75 VVSQFTLAADTERGMRPSFSKGASPDRAEALYDYFVERCRQ 115
>pdb|1J7G|A Chain A, Structure Of Yihz From Haemophilus Influenzae (Hi0670), A
D-Tyr- Trna(Tyr) Deacylase
Length = 144
Score = 67.0 bits (162), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 39/98 (39%), Positives = 54/98 (55%), Gaps = 3/98 (3%)
Query: 53 GRLVSEIGPGLLVLVGLHEFDTDADADYVCRKVLNMRLFPNENTGKGWDLNVMQKKYGVL 112
G + +IG GLLVL+G+ + D AD + KVLN R+F +EN +LNV Q + +L
Sbjct: 17 GETIGKIGKGLLVLLGVEKEDNREKADKLAEKVLNYRIFSDEN--DKMNLNVQQAQGELL 74
Query: 113 LVSQFTLYG-ILKGNKPDFHVAMPPQKAKPFYDSLVDK 149
+VSQFTL KG +P F P A Y+ + K
Sbjct: 75 IVSQFTLAADTQKGLRPSFSKGASPALANELYEYFIQK 112
>pdb|3BBO|Q Chain Q, Homology Model For The Spinach Chloroplast 50s Subunit
Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
Length = 161
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 20/27 (74%)
Query: 7 LPSFPINLARSRSRKLNKTQLHNRKRQ 33
LPSFPI A++++R+ ++T H R R+
Sbjct: 31 LPSFPIIEAKAKTRREDRTARHVRIRK 57
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
0.325 0.141 0.433
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,589,422
Number of Sequences: 62578
Number of extensions: 211587
Number of successful extensions: 537
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 522
Number of HSP's gapped (non-prelim): 7
length of query: 206
length of database: 14,973,337
effective HSP length: 94
effective length of query: 112
effective length of database: 9,091,005
effective search space: 1018192560
effective search space used: 1018192560
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)