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_043745229.1 AMB_RS18795 FAD-binding oxidoreductase
Query= SwissProt::P46681 (530 letters) >NCBI__GCF_000009985.1:WP_043745229.1 Length = 469 Score = 279 bits (713), Expect = 2e-79 Identities = 156/456 (34%), Positives = 244/456 (53%), Gaps = 14/456 (3%) Query: 82 SESEDLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGS 141 +E+ DL+ Y + Y+G + V+RP S +V+ ++ C I +VPQGGNTGL GG Sbjct: 18 TEASDLAPYLVEERGLYQGAALGVVRPGSTAEVAEVVRLCAAAGIPMVPQGGNTGLCGGG 77 Query: 142 VPIFD--ELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGS 199 VP D +++S L +IR DPV L +AG +L N E +FPL LGA+GS Sbjct: 78 VPSEDGQSVVISTERLTRIRAVDPVDFTLTAEAGCVLANLQQAAEEAGCLFPLSLGAEGS 137 Query: 200 CHVGGVVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIG 259 C +GG ++TNAGG +LRYG+ VLGLEVV+P+G++ N + +RKDNTGY L+ LFIG Sbjct: 138 CRIGGNISTNAGGTNVLRYGNTRDLVLGLEVVLPDGRVWNGLKRLRKDNTGYALQHLFIG 197 Query: 260 SEGTIGIITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDAKS 319 +EGT+GI+T + P+P+ +++++ E +F RAR + ++A E + + Sbjct: 198 AEGTLGIVTACVLKLFPRPREIATAFVALADLEAALPLFSRARTASGDSVTACELVPRRG 257 Query: 320 QVLAKSQLKDAAFPLEDEHPFYILIETSGSNKDHDDSKLETFLENVMEEGIVTDGVVAQD 379 L + P H + +L+E S S LE L E+G+ D V+A+ Sbjct: 258 LELGMRHVPGVRAPFAAFHDWMLLLELSSSRPGGLREALEEMLGQAFEDGLAVDAVIAES 317 Query: 380 ETELQNLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPV 439 + + + W+ RE IPEA + GG K+DV++ + ++ + A P Sbjct: 318 DAQRADFWRIREAIPEAQKKEGGSIKHDVAVATSRVPEMIRRCTRAVEAA-------MPG 370 Query: 440 VGAIGYGHVGDGNLHLNVAVREYNKNIE-----KTLEPFVYEFVSSKHGSVSAEHGLGFQ 494 V + +GH+GDGN H N+ E + + V++ V GS+SAEHG+G Sbjct: 371 VRVVPFGHLGDGNTHFNLTQPEGADKAAFLARWEEMNRIVHDIVVEMEGSISAEHGIGRL 430 Query: 495 KKNYIGYSKSPEEVKMMKDLKVHYDPNGILNPYKYI 530 K + + + K ++ +M +K DP G +NP K + Sbjct: 431 KVDELAHYKPGVDLDLMARIKGALDPLGQMNPGKIL 466 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: 497 Number of extensions: 19 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: 469 Length adjustment: 34 Effective length of query: 496 Effective length of database: 435 Effective search space: 215760 Effective search space used: 215760 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