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= 020428
(326 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1VHN|A Chain A, Crystal Structure Of A Putative Flavin Oxidoreductase With
Flavin
Length = 318
Score = 82.4 bits (202), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 63/237 (26%), Positives = 101/237 (42%), Gaps = 19/237 (8%)
Query: 6 KLVLAPMVRVGTLPFRLLAAQYGADITYGEEIIDHKLLKCERRVNEYIGSTDFVEKGTDS 65
K+ LAP FR LA ++GAD + E + L ++ E +
Sbjct: 6 KVGLAPXAGYTDSAFRTLAFEWGADFAFSEXVSAKGFLXNSQKTEELLPQP--------- 56
Query: 66 VVFRTCHQERNHVVFQMGTSDAVRALTAAKMVCKDVAAIDINMGCPKSFSVSGGMGAALL 125
ERN V Q+ S+ AA+++ + ID+N GCP V G G ALL
Sbjct: 57 -------HERN-VAVQIFGSEPNELSEAARILSEKYKWIDLNAGCPVRKVVKEGAGGALL 108
Query: 126 SKPELIHDILTMLKRNLDVPVTCKIRLLKSSQDTVELARRIEKTGVSALAVHGRKVADRP 185
I+ L++++ + K RL + E+ R + + GV + +H R V
Sbjct: 109 KDLRHFRYIVRELRKSVSGKFSVKTRLGWEKNEVEEIYRILVEEGVDEVFIHTRTVVQSF 168
Query: 186 RDPAKWGEIADIVAALSIPVIANGDVFEYDDFQRIKTAAGASSVMAARGALWNASIF 242
A+W ++ V IP +GD+F +D +R +G ++ ARGA+ IF
Sbjct: 169 TGRAEWKALS--VLEKRIPTFVSGDIFTPEDAKRALEESGCDGLLVARGAIGRPWIF 223
>pdb|3B0P|A Chain A, Trna-Dihydrouridine Synthase From Thermus Thermophilus
pdb|3B0P|B Chain B, Trna-Dihydrouridine Synthase From Thermus Thermophilus
pdb|3B0U|X Chain X, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
Complex With Trna Fragment
pdb|3B0U|Y Chain Y, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
Complex With Trna Fragment
Length = 350
Score = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 51/181 (28%), Positives = 79/181 (43%), Gaps = 26/181 (14%)
Query: 6 KLVLAPMVRVGTLPFRLLAAQYGADIT-YGEEIIDHKLLKCERRVNEYIGSTDFVEKGTD 64
+L +APMV FR L Q + Y E +D +L+ R
Sbjct: 5 RLSVAPMVDRTDRHFRFLVRQVSLGVRLYTEMTVDQAVLRGNR---------------ER 49
Query: 65 SVVFRTCHQERNHVVFQMGTSDAVRALTAAKMVCKDVA--AIDINMGCPKSFSVSGGMGA 122
+ FR E + + Q+ SD ++L A + + I++N+GCP + GG GA
Sbjct: 50 LLAFRP---EEHPIALQLAGSDP-KSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGA 105
Query: 123 ALLSKPELIHDILTMLKRNLDVPVTCKIRLLKSSQDTVE-LARRIE---KTGVSALAVHG 178
LL + +IL + + VPVT K+RL ++T LA+ +E + GV VH
Sbjct: 106 CLLLDLARVREILKAMGEAVRVPVTVKMRLGLEGKETYRGLAQSVEAMAEAGVKVFVVHA 165
Query: 179 R 179
R
Sbjct: 166 R 166
>pdb|3B0V|C Chain C, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
Complex With Trna
pdb|3B0V|D Chain D, Trna-Dihydrouridine Synthase From Thermus Thermophilus In
Complex With Trna
Length = 363
Score = 50.8 bits (120), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 50/181 (27%), Positives = 76/181 (41%), Gaps = 26/181 (14%)
Query: 6 KLVLAPMVRVGTLPFRLLAAQYGADIT-YGEEIIDHKLLKCERRVNEYIGSTDFVEKGTD 64
+L +AP V FR L Q + Y E +D +L+ R
Sbjct: 26 RLSVAPXVDRTDRHFRFLVRQVSLGVRLYTEXTVDQAVLRGNR---------------ER 70
Query: 65 SVVFRTCHQERNHVVFQMGTSDAVRALTAAKMVCKDVA--AIDINMGCPKSFSVSGGMGA 122
+ FR E + + Q+ SD ++L A + + I++N+GCP + GG GA
Sbjct: 71 LLAFRP---EEHPIALQLAGSDP-KSLAEAARIGEAFGYDEINLNLGCPSEKAQEGGYGA 126
Query: 123 ALLSKPELIHDILTMLKRNLDVPVTCKIRLLKSSQDTVE-LARRIE---KTGVSALAVHG 178
LL + +IL + VPVT K RL ++T LA+ +E + GV VH
Sbjct: 127 CLLLDLARVREILKAXGEAVRVPVTVKXRLGLEGKETYRGLAQSVEAXAEAGVKVFVVHA 186
Query: 179 R 179
R
Sbjct: 187 R 187
>pdb|1H7W|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig
pdb|1H7W|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig
pdb|1H7W|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig
pdb|1H7W|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig
pdb|1GT8|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And Uracil-4-Acetic Acid
pdb|1GT8|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And Uracil-4-Acetic Acid
pdb|1GT8|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And Uracil-4-Acetic Acid
pdb|1GT8|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And Uracil-4-Acetic Acid
pdb|1GTE|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary
Complex With 5-Iodouracil
pdb|1GTE|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary
Complex With 5-Iodouracil
pdb|1GTE|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary
Complex With 5-Iodouracil
pdb|1GTE|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Binary
Complex With 5-Iodouracil
pdb|1GTH|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And 5-Iodouracil
pdb|1GTH|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And 5-Iodouracil
pdb|1GTH|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And 5-Iodouracil
pdb|1GTH|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex With Nadph And 5-Iodouracil
Length = 1025
Score = 35.4 bits (80), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 103 AIDINMGCPKSFSVSGGMGAALLSKPELIHDILTMLKRNLDVPVTCKIRLLKSSQDTVEL 162
A+++N+ CP GMG A PEL+ +I +++ + +P K L + D V +
Sbjct: 664 ALELNLSCPHGMG-ERGMGLACGQDPELVRNICRWVRQAVQIPFFAK--LTPNVTDIVSI 720
Query: 163 ARRIEKTGVSAL 174
AR ++ G +
Sbjct: 721 ARAAKEGGADGV 732
>pdb|1H7X|A Chain A, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex Of A Mutant Enzyme (C671a), Nadph And 5-
Fluorouracil
pdb|1H7X|B Chain B, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex Of A Mutant Enzyme (C671a), Nadph And 5-
Fluorouracil
pdb|1H7X|C Chain C, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex Of A Mutant Enzyme (C671a), Nadph And 5-
Fluorouracil
pdb|1H7X|D Chain D, Dihydropyrimidine Dehydrogenase (Dpd) From Pig, Ternary
Complex Of A Mutant Enzyme (C671a), Nadph And 5-
Fluorouracil
Length = 1025
Score = 31.6 bits (70), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 103 AIDINMGCPKSFSVSGGMGAALLSKPELIHDILTMLKRNLDVPVTCKIRLLKSSQDTVEL 162
A+++N+ P GMG A PEL+ +I +++ + +P K L + D V +
Sbjct: 664 ALELNLSAPHGMG-ERGMGLACGQDPELVRNICRWVRQAVQIPFFAK--LTPNVTDIVSI 720
Query: 163 ARRIEKTGVSAL 174
AR ++ G +
Sbjct: 721 ARAAKEGGADGV 732
>pdb|2Z6J|A Chain A, Crystal Structure Of S. Pneumoniae Enoyl-acyl Carrier
Protein Reductase (fabk) In Complex With An Inhibitor
pdb|2Z6J|B Chain B, Crystal Structure Of S. Pneumoniae Enoyl-acyl Carrier
Protein Reductase (fabk) In Complex With An Inhibitor
Length = 332
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 26/53 (49%)
Query: 159 TVELARRIEKTGVSALAVHGRKVADRPRDPAKWGEIADIVAALSIPVIANGDV 211
+V LA+R+EK G A+ G + + + A+SIPVIA G +
Sbjct: 119 SVALAKRMEKIGADAVIAEGMEAGGHIGKLTTMTLVRQVATAISIPVIAAGGI 171
>pdb|2Z6I|A Chain A, Crystal Structure Of S. Pneumoniae Enoyl-acyl Carrier
Protein Reductase (fabk)
pdb|2Z6I|B Chain B, Crystal Structure Of S. Pneumoniae Enoyl-acyl Carrier
Protein Reductase (fabk)
Length = 332
Score = 28.5 bits (62), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 25/53 (47%)
Query: 159 TVELARRIEKTGVSALAVHGRKVADRPRDPAKWGEIADIVAALSIPVIANGDV 211
+V LA+R EK G A+ G + + + A+SIPVIA G +
Sbjct: 119 SVALAKRXEKIGADAVIAEGXEAGGHIGKLTTXTLVRQVATAISIPVIAAGGI 171
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
0.319 0.134 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,194,357
Number of Sequences: 62578
Number of extensions: 360993
Number of successful extensions: 1017
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1010
Number of HSP's gapped (non-prelim): 16
length of query: 326
length of database: 14,973,337
effective HSP length: 99
effective length of query: 227
effective length of database: 8,778,115
effective search space: 1992632105
effective search space used: 1992632105
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)