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= 006580
(640 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1LFP|A Chain A, Crystal Structure Of A Conserved Hypothetical Protein
Aq1575 From Aquifex Aeolicus
Length = 249
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 213 SWNSLISGCFNSGYGELALDQFYSMRYSGYSPDEYTISIVINACTKLRNLDKGKQVF 269
W + I G GEL +QF + Y GY+P + ++ + R + + VF
Sbjct: 62 PWEN-IERAIKKGAGELEGEQFEEVIYEGYAPGGVAVXVLATTDNRNRTTSEVRHVF 117
>pdb|4BCA|A Chain A, Mammalian Alkyldihydroxyacetonephosphate Synthase:
Tyr578phe Mutant
pdb|4BCA|B Chain B, Mammalian Alkyldihydroxyacetonephosphate Synthase:
Tyr578phe Mutant
pdb|4BCA|C Chain C, Mammalian Alkyldihydroxyacetonephosphate Synthase:
Tyr578phe Mutant
pdb|4BCA|D Chain D, Mammalian Alkyldihydroxyacetonephosphate Synthase:
Tyr578phe Mutant
Length = 658
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 29/50 (58%)
Query: 230 ALDQFYSMRYSGYSPDEYTISIVINACTKLRNLDKGKQVFALSVKVGFLS 279
L +FY ++ G+ P++ +++ ++ + + L KQV+ ++ K G L+
Sbjct: 446 GLKKFYITKFKGFDPNQLSVATLLFEGDREKVLQHEKQVYDIAAKFGGLA 495
>pdb|4BC7|A Chain A, Mammalian Alkyldihydroxyacetonephosphate Synthase:
Arg419his Mutant
pdb|4BC7|B Chain B, Mammalian Alkyldihydroxyacetonephosphate Synthase:
Arg419his Mutant
pdb|4BC7|C Chain C, Mammalian Alkyldihydroxyacetonephosphate Synthase:
Arg419his Mutant
pdb|4BC7|D Chain D, Mammalian Alkyldihydroxyacetonephosphate Synthase:
Arg419his Mutant
Length = 658
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 29/50 (58%)
Query: 230 ALDQFYSMRYSGYSPDEYTISIVINACTKLRNLDKGKQVFALSVKVGFLS 279
L +FY ++ G+ P++ +++ ++ + + L KQV+ ++ K G L+
Sbjct: 446 GLKKFYITKFKGFDPNQLSVATLLFEGDREKVLQHEKQVYDIAAKFGGLA 495
>pdb|4BBY|A Chain A, Mammalian Alkyldihydroxyacetonephosphate Synthase:
Wild-Type
pdb|4BBY|B Chain B, Mammalian Alkyldihydroxyacetonephosphate Synthase:
Wild-Type
pdb|4BBY|C Chain C, Mammalian Alkyldihydroxyacetonephosphate Synthase:
Wild-Type
pdb|4BBY|D Chain D, Mammalian Alkyldihydroxyacetonephosphate Synthase:
Wild-Type
pdb|4BC9|A Chain A, Mammalian Alkyldihydroxyacetonephosphate Synthase: Wild-
Type, Adduct With Cyanoethyl
pdb|4BC9|B Chain B, Mammalian Alkyldihydroxyacetonephosphate Synthase: Wild-
Type, Adduct With Cyanoethyl
pdb|4BC9|C Chain C, Mammalian Alkyldihydroxyacetonephosphate Synthase: Wild-
Type, Adduct With Cyanoethyl
pdb|4BC9|D Chain D, Mammalian Alkyldihydroxyacetonephosphate Synthase: Wild-
Type, Adduct With Cyanoethyl
Length = 658
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/50 (24%), Positives = 29/50 (58%)
Query: 230 ALDQFYSMRYSGYSPDEYTISIVINACTKLRNLDKGKQVFALSVKVGFLS 279
L +FY ++ G+ P++ +++ ++ + + L KQV+ ++ K G L+
Sbjct: 446 GLKKFYITKFKGFDPNQLSVATLLFEGDREKVLQHEKQVYDIAAKFGGLA 495
>pdb|3SFK|A Chain A, Crystal Structure Of Plasmodium Falciparum Dihydroorotate
Dehydrogenase Bound With Inhibitor Dsm267
Length = 400
Score = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 28/130 (21%), Positives = 59/130 (45%), Gaps = 19/130 (14%)
Query: 324 RYGFGEVALELFQLMLREDIRPTEFTLSCVLSSIPIPPVEHGSQFHSMAIKSGFDSNAVV 383
+Y GE+ +LF L+ + +I P + + + + I +H + + +GFD N V
Sbjct: 38 KYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNI---KHLDFINPFGVAAGFDKNGVC 94
Query: 384 ASSLMEM---YAKTGSI-------DSSTEIFVKLDKRDLVSWNTIMMGLTQNG--RAAET 431
S++++ + + G+I ++ IF ++ R +++ G G + E
Sbjct: 95 IDSILKLGFSFIEIGTITPRGQTGNAKPRIFRDVESRSIINS----CGFNNMGCDKVTEN 150
Query: 432 LDVFEELLEE 441
L +F + EE
Sbjct: 151 LILFRKRQEE 160
>pdb|3I65|A Chain A, Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound
With Triazolopyrimidine-Based Inhibitor Dsm1
pdb|3I68|A Chain A, Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound
With Triazolopyrimidine-Based Inhibitor Dsm2
pdb|3I6R|A Chain A, Plasmodium Falciparum Dihydroorotate Dehydrogenase Bound
With Triazolopyrimidine-Based Inhibitor Dsm74
pdb|3O8A|A Chain A, Crystal Structure Of Plasmodium Falciparum Dihydroorotate
Dehydrogenase Bound With Novel Inhibitor Genz667348
Length = 415
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 28/130 (21%), Positives = 59/130 (45%), Gaps = 19/130 (14%)
Query: 324 RYGFGEVALELFQLMLREDIRPTEFTLSCVLSSIPIPPVEHGSQFHSMAIKSGFDSNAVV 383
+Y GE+ +LF L+ + +I P + + + + I +H + + +GFD N V
Sbjct: 53 KYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNI---KHLDFINPFGVAAGFDKNGVC 109
Query: 384 ASSLMEM---YAKTGSI-------DSSTEIFVKLDKRDLVSWNTIMMGLTQNG--RAAET 431
S++++ + + G+I ++ IF ++ R +++ G G + E
Sbjct: 110 IDSILKLGFSFIEIGTITPRGQTGNAKPRIFRDVESRSIINS----CGFNNMGCDKVTEN 165
Query: 432 LDVFEELLEE 441
L +F + EE
Sbjct: 166 LILFRKRQEE 175
>pdb|1TV5|A Chain A, Plasmodium Falciparum Dihydroorotate Dehydrogenase With A
Bound Inhibitor
Length = 443
Score = 30.0 bits (66), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 28/130 (21%), Positives = 59/130 (45%), Gaps = 19/130 (14%)
Query: 324 RYGFGEVALELFQLMLREDIRPTEFTLSCVLSSIPIPPVEHGSQFHSMAIKSGFDSNAVV 383
+Y GE+ +LF L+ + +I P + + + + I +H + + +GFD N V
Sbjct: 51 KYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNI---KHLDFINPFGVAAGFDKNGVC 107
Query: 384 ASSLMEM---YAKTGSI-------DSSTEIFVKLDKRDLVSWNTIMMGLTQNG--RAAET 431
S++++ + + G+I ++ IF ++ R +++ G G + E
Sbjct: 108 IDSILKLGFSFIEIGTITPRGQTGNAKPRIFRDVESRSIINS----CGFNNMGCDKVTEN 163
Query: 432 LDVFEELLEE 441
L +F + EE
Sbjct: 164 LILFRKRQEE 173
>pdb|1YRL|A Chain A, Escherichia Coli Ketol-Acid Reductoisomerase
pdb|1YRL|B Chain B, Escherichia Coli Ketol-Acid Reductoisomerase
pdb|1YRL|C Chain C, Escherichia Coli Ketol-Acid Reductoisomerase
pdb|1YRL|D Chain D, Escherichia Coli Ketol-Acid Reductoisomerase
Length = 491
Score = 29.3 bits (64), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 393 KTGSIDSSTEIFVKLDKRDLVSWNTIMMGLTQNGRAAETLDVFEELLEEGLPP 445
+ G ++SS FV K DL+ TI+ G+ Q G +L F++L+EEG P
Sbjct: 202 RAGVLESS---FVAEVKSDLMGEQTILCGMLQAG----SLLCFDKLVEEGTDP 247
>pdb|3ULK|A Chain A, E. Coli Ketol-Acid Reductoisomerase In Complex With Nadph
And Mg2+
pdb|3ULK|B Chain B, E. Coli Ketol-Acid Reductoisomerase In Complex With Nadph
And Mg2+
Length = 491
Score = 29.3 bits (64), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 7/53 (13%)
Query: 393 KTGSIDSSTEIFVKLDKRDLVSWNTIMMGLTQNGRAAETLDVFEELLEEGLPP 445
+ G ++SS FV K DL+ TI+ G+ Q G +L F++L+EEG P
Sbjct: 202 RAGVLESS---FVAEVKSDLMGEQTILCGMLQAG----SLLCFDKLVEEGTDP 247
>pdb|1J8Y|F Chain F, Signal Recognition Particle Conserved Gtpase Domain From
A. Ambivalens T112a Mutant
Length = 297
Score = 28.9 bits (63), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 317 VMISTYGRYGFGEVALELFQLM-LREDIRPTEFTL 350
+++ T GR+G+GE A L ++ + E I+P E TL
Sbjct: 184 IIVDTAGRHGYGEEAALLEEMKNIYEAIKPDEVTL 218
>pdb|1J8M|F Chain F, Signal Recognition Particle Conserved Gtpase Domain From
A. Ambivalens
Length = 297
Score = 28.9 bits (63), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 317 VMISTYGRYGFGEVALELFQLM-LREDIRPTEFTL 350
+++ T GR+G+GE A L ++ + E I+P E TL
Sbjct: 184 IIVDTAGRHGYGEEAALLEEMKNIYEAIKPDEVTL 218
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 0.138 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,284,843
Number of Sequences: 62578
Number of extensions: 721599
Number of successful extensions: 1846
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1842
Number of HSP's gapped (non-prelim): 13
length of query: 640
length of database: 14,973,337
effective HSP length: 105
effective length of query: 535
effective length of database: 8,402,647
effective search space: 4495416145
effective search space used: 4495416145
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: 55 (25.8 bits)