Align D-2-hydroxyglutarate--pyruvate transhydrogenase DLD2; D-2HG--pyruvate transhydrogenase DLD2; Actin-interacting protein 2; D-lactate dehydrogenase [cytochrome] 2, mitochondrial; D-lactate ferricytochrome C oxidoreductase; D-LCR; EC 1.1.99.40; EC 1.1.2.4 (characterized)
to candidate WP_086509740.1 BZY95_RS09535 FAD-binding oxidoreductase
Query= SwissProt::P46681 (530 letters) >NCBI__GCF_002151265.1:WP_086509740.1 Length = 463 Score = 291 bits (746), Expect = 3e-83 Identities = 158/460 (34%), Positives = 253/460 (55%), Gaps = 10/460 (2%) Query: 71 SILSEQEILRASESEDLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVP 130 +I+ E +L +D++ DWM ++ ++RP ++++ ++ C+ VV Sbjct: 10 AIVGEGNVLTG---DDVAQRRVDWMSGASCRAGAIVRPADTDELARVMRLCHAVAQPVVT 66 Query: 131 QGGNTGLVGGSVPIFDELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMF 190 GG TGLV G DEL +SL + I DP+ G + AG+ L+ E + F Sbjct: 67 HGGLTGLVHGGEASPDELAISLERMTAIEAIDPIGGSMTVQAGIALQTVQEAAAEHDLQF 126 Query: 191 PLDLGAKGSCHVGGVVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTG 250 LDLGA+GSC +GG +ATNAGG+R++RYG + VLGLE V+ +G +V+SM+ M K+N G Sbjct: 127 ALDLGARGSCTIGGNIATNAGGVRVIRYGMMRQQVLGLEAVLADGSVVSSMNRMLKNNAG 186 Query: 251 YDLKQLFIGSEGTIGIITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILS 310 YDLKQLFIGSEGT+GI+T + P+ + + ++ F+ V + + L L Sbjct: 187 YDLKQLFIGSEGTLGIVTRAVLRLQPRMTSERTALVACPDFDGVTGLLRHLGRTLGGSLG 246 Query: 311 AFEFMDAKSQVLAKSQLKDAAFPLEDEHPFYILIETSGSNKDHDDSKLETFLENVMEEGI 370 FE M L + PL PFY ++E+ GS+ + ++ LE+ +E G+ Sbjct: 247 TFEVMWRNHYALLTEESGRNTPPLPARWPFYAIVESLGSDDAANVAQFSAALESALEAGL 306 Query: 371 VTDGVVAQDETELQNLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAE 430 + D V+AQ + + Q +W RE I ++ +DVSLP+ D+ +A R+ E Sbjct: 307 IEDAVLAQSDAQRQGIWDIREDIEGLIDNLSPLFTFDVSLPIPDMADYADALERRIGER- 365 Query: 431 LVGDSPKPVVGAIGYGHVGDGNLHLNVAVREYNKNIEKTLEPFVYEFVSSKHGSVSAEHG 490 P + +GH+GDGNLH++V V + + +E VY ++ GS+SAEHG Sbjct: 366 ------WPEGRMVIFGHLGDGNLHVSVGVGSGDPQTRRDVEQIVYGPLAELGGSISAEHG 419 Query: 491 LGFQKKNYIGYSKSPEEVKMMKDLKVHYDPNGILNPYKYI 530 +G +K++Y+ S++P E+ +M+ LK DP G+LN +K + Sbjct: 420 IGLEKRDYLPLSRTPGEIALMRTLKQALDPKGLLNRHKIL 459 Lambda K H 0.316 0.135 0.385 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 520 Number of extensions: 22 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 530 Length of database: 463 Length adjustment: 34 Effective length of query: 496 Effective length of database: 429 Effective search space: 212784 Effective search space used: 212784 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory