Score = 57.8 bits (138), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 42/83 (50%)
Query: 9 KLVSLAAVSSGSFALFSGINIYQNNENYYNNVLLPILFKFDAETAHNIAIWTAKYKLLPK 68
+L SL V+ G AL +GI Y+N + + ++P + AE +H +A+ KY+L P
Sbjct: 18 RLRSLGIVTVGGAALVAGITAYKNQDQLFRTFVMPAVRLLPAEASHQLAVLACKYRLCPV 77
Query: 69 SVYEDPPQLASQVWNLKFPNPLA 91
S Y D L + + NP+
Sbjct: 78 SQYHDDQNLHTSFFGRMLSNPIG 100
Catalyzes the conversion of dihydroorotate to orotate with quinone as electron acceptor. Drosophila melanogaster (taxid: 7227) EC: 1EC: .EC: 3EC: .EC: 5EC: .EC: 2
In the de novo pyrimidine biosynthesic pathway, catalyzes the stereospecific oxidation of (S)-dihydroorotate to orotate with reduction of flavin and the transfer of electrons to ubiquinone, which is part of the repiratory chain. Does not use fumarate and NAD as electron acceptors.
Score = 87 (35.7 bits), Expect = 3.7e-05, Sum P(2) = 3.7e-05
Identities = 24/84 (28%), Positives = 35/84 (41%)
Query: 7 LKKLVSLAAVSSGSFALFSGXXXXXXXXXXXXXVLLPILFKFDAETAHNIAIWTAKYKLL 66
+++ + L A + G L G ++P L E AH +A+ A LL
Sbjct: 1 MRRRLRLLAAALGGCGLLLGSALAAGDERLYTAAVMPALRVVTPEAAHGLALRAAALGLL 60
Query: 67 PKSVYEDPPQLASQVWNLKFPNPL 90
P + D P L V L+F NPL
Sbjct: 61 PPA-RPDSPSLEVHVLGLRFRNPL 83
Score = 94 (38.1 bits), Expect = 0.00076, P = 0.00076
Identities = 19/50 (38%), Positives = 27/50 (54%)
Query: 42 LPILFKFDA-ETAHNIAIWTAKYKLLPKSVYEDPPQLASQVWNLKFPNPL 90
+P+ F E +H +AI A + + PK D P LA +VW KF NP+
Sbjct: 69 MPLFHAFTTPEFSHRVAILAASWGITPKDRVADDPSLAVEVWGKKFCNPI 118
Parameters:
V=100
filter=SEG
E=0.001
ctxfactor=1.00
Query ----- As Used ----- ----- Computed ----
Frame MatID Matrix name Lambda K H Lambda K H
+0 0 BLOSUM62 0.315 0.132 0.389 same same same
Q=9,R=2 0.244 0.0300 0.180 n/a n/a n/a
Query
Frame MatID Length Eff.Length E S W T X E2 S2
+0 0 122 109 0.00091 102 3 11 22 0.48 30
29 0.41 32
Statistics:
Database: /share/blast/go-seqdb.fasta
Title: go_20130330-seqdb.fasta
Posted: 5:47:42 AM PDT Apr 1, 2013
Created: 5:47:42 AM PDT Apr 1, 2013
Format: XDF-1
# of letters in database: 169,044,731
# of sequences in database: 368,745
# of database sequences satisfying E: 9
No. of states in DFA: 538 (57 KB)
Total size of DFA: 112 KB (2075 KB)
Time to generate neighborhood: 0.00u 0.00s 0.00t Elapsed: 00:00:02
No. of threads or processors used: 24
Search cpu time: 12.26u 0.07s 12.33t Elapsed: 00:00:04
Total cpu time: 12.27u 0.07s 12.34t Elapsed: 00:00:06
Start: Thu Aug 15 11:18:50 2013 End: Thu Aug 15 11:18:56 2013
Score = 53.7 bits (130), Expect = 1e-09
Identities = 22/51 (43%), Positives = 29/51 (56%), Gaps = 3/51 (5%)
Query: 43 PILFKFDAETAHNIAIWTAKYKLLPKSVYE---DPPQLASQVWNLKFPNPL 90
P+LF D ETAH +AI K L P + D P+L +V+ L FPNP+
Sbjct: 2 PLLFLLDPETAHRLAIRALKLGLGPPLLLLLVYDDPRLEVEVFGLTFPNPV 52
DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences, their cellular location and their natural electron acceptor used to reoxidize the flavin group. Members of class 1 are cytosolic enzymes and multimers, while class 2 enzymes are membrane associated, monomeric and use respiratory quinones as their physiological electron acceptors. Length = 327
Score = 36.7 bits (85), Expect = 0.001
Identities = 16/52 (30%), Positives = 22/52 (42%), Gaps = 6/52 (11%)
Query: 45 LFKFDAETAHNIAIWTAK------YKLLPKSVYEDPPQLASQVWNLKFPNPL 90
LF+ D E AH + + L +S+ +L V L FPNPL
Sbjct: 8 LFQLDPERAHEFTFQQLRLITGTPFLALLRSLVGAKDKLPVTVLGLTFPNPL 59
This model describes enzyme protein dihydroorotate dehydrogenase exclusively for subfamily 2. It includes members from bacteria, yeast, plants etc. The subfamilies 1 and 2 share extensive homology, particularly toward the C-terminus. This subfamily has a longer N-terminal region [Purines, pyrimidines, nucleosides, and nucleotides, Pyrimidine ribonucleotide biosynthesis]. Length = 336
DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences, their cellular location and their natural electron acceptor used to reoxidize the flavin group. Members of class 1 are cytosolic enzymes and multimers, while class 2 enzymes are membrane associated, monomeric and use respiratory quinones as their physiological electron acceptors.
>COG0167 PyrD Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]
>PF01180 DHO_dh: Dihydroorotate dehydrogenase; InterPro: IPR012135 Dihydroorotate dehydrogenase (DHOD), also known as dihydroorotate oxidase, catalyses the fourth step in de novo pyrimidine biosynthesis, the stereospecific oxidation of (S)-dihydroorotate to orotate, which is the only redox reaction in this pathway
DHODs can be divided into two mains classes: class 1 cytosolic enzymes found primarily in Gram-positive bacteria, and class 2 membrane-associated enzymes found primarily in eukaryotic mitochondria and Gram-negative bacteria []. The class 1 DHODs can be further divided into subclasses 1A and 1B, which differ in their structural organisation and use of electron acceptors. The 1A enzyme is a homodimer of two PyrD subunits where each subunit forms a TIM barrel fold with a bound FMN cofactor located near the top of the barrel []. Fumarate is the natural electron acceptor for this enzyme. The 1B enzyme, in contrast is a heterotetramer composed of a central, FMN-containing, PyrD homodimer resembling the 1A homodimer, and two additional PyrK subunits which contain FAD and a 2Fe-2S cluster []. These additional groups allow the enzyme to use NAD(+) as its natural electron acceptor. The class 2 membrane-associated enzymes are monomers which have the FMN-containing TIM barrel domain found in the class 1 PyrD subunit, and an additional N-terminal alpha helical domain [, ]. These enzymes use respiratory quinones as the physiological electron acceptor. This entry represents the FMN-binding subunit common to all classes of dihydroorotate dehydrogenase.; GO: 0004152 dihydroorotate dehydrogenase activity, 0006222 UMP biosynthetic process, 0055114 oxidation-reduction process; PDB: 3GYE_A 3GZ3_A 3MHU_B 3MJY_A 3TQ0_A 2B4G_C 1EP3_A 1EP2_A 1EP1_A 3I6R_A ....
DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively.
DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN, and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass the dimer interface twice. Two of the Fe-S clusters show a hitherto unobserved coordination involving a glutamine residue.
>cd04740 DHOD_1B_like Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain
DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively.
>cd04739 DHOD_like Dihydroorotate dehydrogenase (DHOD) like proteins
DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. This subgroup has the conserved FMN binding site, but lacks some catalytic residues and may therefore be inactive.
DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass its homodimeric interface twice. Two of
This family includes subfamily 1 dihydroorotate dehydrogenases while excluding the closely related subfamily 2 (TIGR01036). This family also includes a number of uncharacterized proteins and a domain of dihydropyrimidine dehydrogenase. The uncharacterized proteins might all be dihydroorotate dehydrogenase.
Score = 71.1 bits (173), Expect = 3e-16
Identities = 16/61 (26%), Positives = 24/61 (39%)
Query: 30 YQNNENYYNNVLLPILFKFDAETAHNIAIWTAKYKLLPKSVYEDPPQLASQVWNLKFPNP 89
Y Y+ L L D E H++ + KY +LP D + + +L F NP
Sbjct: 4 YNPEFFLYDIFLKFCLKYIDGEICHDLFLLLGKYNILPYDTSNDSIYACTNIKHLDFINP 63
Query: 90 L 90
Sbjct: 64 F 64
