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_084199888.1 C0029_RS05565 FAD-binding oxidoreductase
Query= SwissProt::P46681 (530 letters) >NCBI__GCF_002869505.1:WP_084199888.1 Length = 456 Score = 298 bits (764), Expect = 2e-85 Identities = 161/440 (36%), Positives = 255/440 (57%), Gaps = 12/440 (2%) Query: 91 NEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGSVPIFDELIL 150 N W R + + ++RP++ E+VS I+ C+ ++ VVP GG TGLV G +L+L Sbjct: 27 NHSWGRG-ECPAMAIVRPRTTEEVSRIMALCHAQEQRVVPWGGLTGLVDGITCEAGDLVL 85 Query: 151 SLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCHVGGVVATNA 210 S+ + I +P +G L+ AG +L++ + E + F +DLG +GS +GG+VATNA Sbjct: 86 SMERMQNIEHCEPDAGTLRVQAGAVLQSVQDAAAEAGWQFAVDLGGRGSAQIGGLVATNA 145 Query: 211 GGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSEGTIGIITGV 270 GG ++RYG + VLGLEVV+ +G++++S++ + K+N GYD+KQLFIGSEGT+GI+T Sbjct: 146 GGNAVVRYGMMREQVLGLEVVLADGRVMSSLNEVLKNNAGYDMKQLFIGSEGTLGIVTRA 205 Query: 271 SILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDAKSQVLAKSQLKDA 330 + P A ++L + SF+DV + + L LS+FE M A +L Sbjct: 206 VLRLRPAANARQTAFLGMNSFDDVAALLRHLQSHLEGKLSSFEVMWANHYRFMVEELATH 265 Query: 331 AFPLEDEHPFYILIETSGSNKDHDDSKLETFLENVMEEGIVTDGVVAQDETELQNLWKWR 390 L ++P+Y+L+E+ G D +++ + L +MEEG + D V+AQ + + LW R Sbjct: 266 QTFLPVDYPYYVLVESEGQFPDREEALFTSVLGELMEEGTIADAVIAQSGQQAEQLWAMR 325 Query: 391 EMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPVVGAIGYGHVGD 450 + + +A + +D+SLPL+D+ + V A L++ P + +GH+GD Sbjct: 326 DDVASLIEAMAPMAAFDISLPLRDMQTYVAAMEQGLAKR-------LPEARVVVFGHLGD 378 Query: 451 GNLHLNVAVREYNKNIEKTLEPFVYEFVSSKHGSVSAEHGLGFQKKNYIGYSKSPEEVKM 510 GN+HL V N K +E VY + + GS+SAEHG+G +K++Y+ YSK E+ + Sbjct: 379 GNIHLVVG----NIPDHKAVEEVVYGELRNLGGSISAEHGIGLEKRDYLAYSKGEIEIDL 434 Query: 511 MKDLKVHYDPNGILNPYKYI 530 M+ LK DP GILNP K I Sbjct: 435 MRTLKHALDPKGILNPGKVI 454 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: 540 Number of extensions: 21 Number of successful extensions: 3 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: 456 Length adjustment: 34 Effective length of query: 496 Effective length of database: 422 Effective search space: 209312 Effective search space used: 209312 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