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_011781626.1 MVAN_RS22475 FAD-binding oxidoreductase
Query= SwissProt::P46681 (530 letters) >NCBI__GCF_000015305.1:WP_011781626.1 Length = 450 Score = 232 bits (592), Expect = 2e-65 Identities = 142/435 (32%), Positives = 230/435 (52%), Gaps = 23/435 (5%) Query: 93 DWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGSVPIFDELILSL 152 D +Y+G + ++RP S ++V+ +L C D + V QGG T LV G+VP D+++LS Sbjct: 31 DHTGRYRGHASALVRPGSADEVAAVLRVCRDAGVNVTVQGGRTSLVAGTVPEHDDVLLST 90 Query: 153 ANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCHVGGVVATNAGG 212 L + + D V ++ AG L +F +DL A+ S VGG+ +TNAGG Sbjct: 91 ERLRDVGEVDVVERRIRVGAGATLAEVQRAAAAAGLVFGVDLAARDSATVGGMASTNAGG 150 Query: 213 LRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSEGTIGIITGVSI 272 LR + YG++ V+GL+VV+P+G +V+ +R DNTGYDL LF+G+EGT+G+IT + + Sbjct: 151 LRTVCYGNMGEQVIGLDVVLPDGSVVHRHSQVRSDNTGYDLASLFVGAEGTLGVITALDL 210 Query: 273 LTVPKPKAFNVSYLSVESFEDVQKVFVRARQ-ELSEILSAFEFMDAKSQVLAKSQLKDAA 331 P P+ ++ F D+ + R E ++A E +DA++ L AA Sbjct: 211 RLHPTPRQ---RVTAICGFADLDALIETGRVFRDMEGIAALELIDARASALTAEHAGVAA 267 Query: 332 FPLEDEHPFYILIETSGSNKDHDDSKLETFLENVMEEGIVTD-GVVAQDETELQNLWKWR 390 P++ + +LIE +G ++ L L +E +TD V D Q LW+ R Sbjct: 268 -PVQG--AWQLLIELAG------ETDLTDRLAEALESAELTDEPAVGVDANAQQRLWQVR 318 Query: 391 EMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPVVGAIGYGHVGD 450 E + E G K+DVSLPL + E A ++E P + +GHVG+ Sbjct: 319 EAVAEVLGVYGPPLKFDVSLPLSAIRGFAEDAAALVAE-------HAPDAIPVLFGHVGE 371 Query: 451 GNLHLNVAVREYNKNIEKTLEPFVYEFVSSKHGSVSAEHGLGFQKKNYIGYSKSPEEVKM 510 GNLHLN+ + E+ L + ++ G+VS+EHG+G +K++Y+ +++ ++ Sbjct: 372 GNLHLNIL--RCDLTGERGLYSAMMALIARHGGNVSSEHGVGTRKRDYLSMARTEADIAA 429 Query: 511 MKDLKVHYDPNGILN 525 M+ +K +DP G LN Sbjct: 430 MRTVKAAFDPTGYLN 444 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: 447 Number of extensions: 15 Number of successful extensions: 4 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: 450 Length adjustment: 34 Effective length of query: 496 Effective length of database: 416 Effective search space: 206336 Effective search space used: 206336 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