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 H281DRAFT_02585 H281DRAFT_02585 FAD/FMN-containing dehydrogenase
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__Burk376:H281DRAFT_02585 Length = 461 Score = 295 bits (755), Expect = 2e-84 Identities = 163/439 (37%), Positives = 249/439 (56%), Gaps = 12/439 (2%) Query: 92 EDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGSVPIFDELILS 151 +DW ++RP+S E V+ L C+ VV QGG TGLVGG+ + E+ LS Sbjct: 31 QDWSGLPGAVPTALIRPRSTEDVARALRVCHAFSQPVVTQGGLTGLVGGANALGGEVALS 90 Query: 152 LANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCHVGGVVATNAG 211 L +N+I + D S + +AGV L+ ++ + FPLDLGA+GSC +GG +ATNAG Sbjct: 91 LERMNRIVEVDRTSATMTVEAGVPLQVVQEAALDAGFYFPLDLGARGSCTIGGNLATNAG 150 Query: 212 GLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSEGTIGIITGVS 271 G R+++YG + VLG+E V+ NG++ + MH M K+N+GYDL+ L IGSEGT+ +IT Sbjct: 151 GNRVIKYGMMRDQVLGIEAVLANGEVTSGMHKMIKNNSGYDLRHLLIGSEGTLAVITRAV 210 Query: 272 ILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDA--KSQVLAKSQLKD 329 + P+P A ++ ++ ++ V K+ ++ +LS +SAFE M A VLA L+ Sbjct: 211 LRLRPRPTAVATAWCALPDYDAVTKLLACSQAQLSAGVSAFEVMWAGYYDAVLANLPLR- 269 Query: 330 AAFPLEDEHPFYILIETSGSNKDHDDSKLETFLENVMEEGIVTDGVVAQDETELQNLWKW 389 PL+ +P+Y+L+E+ GS+ D E FL +++E G+V+D +AQ E + Q W Sbjct: 270 --APLDKHYPYYVLLESVGSDPDRHAEAFEAFLGDMLEAGVVSDAALAQSEADAQAFWTI 327 Query: 390 REMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPVVGAIGYGHVG 449 R+ E + YDVS + D+ + RL E P + YGH+G Sbjct: 328 RDAPGEYPKFIPHHSAYDVSFSISDVGQVAAHCEQRLQER-------WPDALVMIYGHLG 380 Query: 450 DGNLHLNVAVREYNKNIEKTLEPFVYEFVSSKHGSVSAEHGLGFQKKNYIGYSKSPEEVK 509 DGNLH+ V + + ++ +Y+ HGSVSAEHG+G +KK Y+G+++S E+ Sbjct: 381 DGNLHIVVDIPGSEGRLHDEIDRVIYDVTREFHGSVSAEHGIGVKKKAYLGHTRSDAEIT 440 Query: 510 MMKDLKVHYDPNGILNPYK 528 M+ +K DP ILNP K Sbjct: 441 AMRLIKTALDPRSILNPGK 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: 508 Number of extensions: 18 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: 461 Length adjustment: 34 Effective length of query: 496 Effective length of database: 427 Effective search space: 211792 Effective search space used: 211792 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 17 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