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 Ga0059261_1572 Ga0059261_1572 FAD/FMN-containing dehydrogenases
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__Korea:Ga0059261_1572 Length = 480 Score = 280 bits (717), Expect = 7e-80 Identities = 154/458 (33%), Positives = 260/458 (56%), Gaps = 17/458 (3%) Query: 82 SESEDLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGS 141 ++++ ++ + DW +Y G + +L+P S E V+ ++ +A+VPQGGNT +VGG+ Sbjct: 22 TDADVIAPWLNDWRGRYHGAAAAILQPDSTEAVAAMVTLAGQHGVALVPQGGNTSMVGGA 81 Query: 142 VPIFD--ELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGS 199 P D LILSL LN++R D + + + +AGVIL + ++ + Q FPL LGAKGS Sbjct: 82 TPPADGSALILSLRRLNRVRRIDAAANLAEVEAGVILADLHDAALAQGRRFPLTLGAKGS 141 Query: 200 CHVGGVVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIG 259 VGG+V+TNAGG ++LR+G++ G VLGLE V+ +G I + +++KDN GYDL QL IG Sbjct: 142 ATVGGLVSTNAGGTQVLRFGTMRGLVLGLEAVLADGSIHGGLAALKKDNRGYDLNQLLIG 201 Query: 260 SEGTIGIITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDAKS 319 +EGT+G++T S+ V A V+++ + S ++ R + ++ + +FE + A+S Sbjct: 202 AEGTLGVVTAASLKLVAAVHARAVAWIGLASPHAGLELLQRL-EAATDTIESFEIIPARS 260 Query: 320 QVLAKSQLKDAAFPLEDEHPFYILIETSGSNKDHD--DSKLETFLENVMEEGIVTDGVVA 377 + PL +H +++LIE + + + +E L +E G+ D +A Sbjct: 261 LGAVLRHIPGTRAPLSGDHGWHVLIEAVAVSAEQEAPAQLIERLLGPALESGLAQDATIA 320 Query: 378 QDETELQNLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPK 437 +E + + WK RE I EA +A+G ++D+S+P V A + + ++ Sbjct: 321 ANEAQAEAFWKLRESISEAERASGPALQHDISVP-------VAAMPDFMIDGAKAVETRF 373 Query: 438 PVVGAIGYGHVGDGNLHLNV-----AVREYNKNIEKTLEPFVYEFVSSKHGSVSAEHGLG 492 P V A +GH+GDGN+H +V + ++ K + PFV++ V + GS+SAEHG+G Sbjct: 374 PGVSAGAFGHLGDGNVHFHVRAPAGSAADWAKTHSDIISPFVHDLVVAAGGSISAEHGIG 433 Query: 493 FQKKNYIGYSKSPEEVKMMKDLKVHYDPNGILNPYKYI 530 K++ + SP + + +K +DP +LNP K + Sbjct: 434 QMKRDELARLSSPARMHALAAIKRAFDPRNLLNPGKLV 471 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: 493 Number of extensions: 19 Number of successful extensions: 6 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: 480 Length adjustment: 34 Effective length of query: 496 Effective length of database: 446 Effective search space: 221216 Effective search space used: 221216 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