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 AZOBR_RS05770 AZOBR_RS05770 2-hydroxyacid dehydrogenase
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__azobra:AZOBR_RS05770 Length = 462 Score = 320 bits (821), Expect = 5e-92 Identities = 172/455 (37%), Positives = 269/455 (59%), Gaps = 17/455 (3%) Query: 85 EDLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGSVPI 144 ED++ Y +W ++KG S V+RP S E+V+ ++ C + I VVPQGGNT LVGGS+P Sbjct: 15 EDMAPYLSEWRGRFKGNSPAVVRPASTEEVAAVVTICAEAGIPVVPQGGNTSLVGGSIPY 74 Query: 145 FD--ELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCHV 202 + E+++SL+ +NKIR D ++ + +AGV+L+ A +++ + P+ LGA+G+C + Sbjct: 75 EEGREIVISLSRMNKIRGIDTLNYTMTVEAGVVLKTAQEAAKDKDRLLPMSLGAEGTCQI 134 Query: 203 GGVVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSEG 262 GG+++TNAGG+ +LRYG++ VLGLEVV+ +G++ N + S+RK+NTGYDLK LFIG+EG Sbjct: 135 GGLISTNAGGINVLRYGNMRDLVLGLEVVLADGRVWNGLRSLRKNNTGYDLKHLFIGAEG 194 Query: 263 TIGIITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDAKSQVL 322 T+GI+T + P+P+ ++++V S ++ R R+ + ++AFE M + Sbjct: 195 TLGIVTAAVLKLYPRPRQAETAFIAVPSPAAAIELLARLREASGDAVAAFELMSRRCLEF 254 Query: 323 AKSQLKDAAFPLEDEHPFYILIE-TSGSNKDHDDSKLETFLENVMEEGIVTDGVVAQDET 381 A + PL + P+Y+L E T+G+ D +E L E + TD +AQ ET Sbjct: 255 ALKHVAGTIDPLSEPSPWYVLTELTAGTQSDAFRETVEAALGEAFEAELATDATIAQSET 314 Query: 382 ELQNLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPVVG 441 + LW RE I EA + GG K DVS+P+ + +E A + A G P P Sbjct: 315 QANQLWFIREAIVEAQKFEGGSIKNDVSVPVSRVAEFIERAEAAV-VAACPGIRPTP--- 370 Query: 442 AIGYGHVGDGNLHLNVAVRE------YNKNIEKTLEPFVYEFVSSKHGSVSAEHGLGFQK 495 +GHVGDGN+H N++ E Y ++ V E + + GS+SAEHG+G K Sbjct: 371 ---FGHVGDGNIHFNLSQPEGADTAAYLARWDEICH-VVNEVIFALDGSISAEHGVGRFK 426 Query: 496 KNYIGYSKSPEEVKMMKDLKVHYDPNGILNPYKYI 530 K+ + KSP E +++ +K DP G+LNP K + Sbjct: 427 KDEMPVIKSPVEFDLLRAMKAALDPKGLLNPGKML 461 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: 522 Number of extensions: 21 Number of successful extensions: 5 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: 462 Length adjustment: 34 Effective length of query: 496 Effective length of database: 428 Effective search space: 212288 Effective search space used: 212288 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