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_057508924.1 ABB28_RS12370 FAD-binding oxidoreductase
Query= SwissProt::P46681 (530 letters) >NCBI__GCF_001431535.1:WP_057508924.1 Length = 462 Score = 288 bits (737), Expect = 3e-82 Identities = 162/452 (35%), Positives = 255/452 (56%), Gaps = 18/452 (3%) Query: 82 SESEDLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGS 141 +++ DL Y DW R++ + P SV++V ++ + E +AVVP GG TGL GG+ Sbjct: 20 TDAADLEHYGRDWTRRWTPAPLAIALPASVDEVQAVMRWSAAEGVAVVPSGGRTGLSGGA 79 Query: 142 VPIFDELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCH 201 V EL+LSL +NK +D V L AG+ LE +N +E ++P+D A+GSC Sbjct: 80 VAANGELVLSLERMNKALGYDAVDRTLVVQAGMPLEALHNAALEHGLIYPVDFAARGSCS 139 Query: 202 VGGVVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSE 261 +GG +ATNAGG+R++RYG+ + GL+VV +G+++ + K+++GYD +QL IGSE Sbjct: 140 IGGNIATNAGGIRVIRYGNTREWIAGLKVVTADGELLELNKGLIKNSSGYDFRQLLIGSE 199 Query: 262 GTIGIITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDAKSQV 321 GT+G+I ++ P A NV L+V SFE + +VF R L L AFEF A Q Sbjct: 200 GTLGVIVEATVKLTDPPPASNVMLLAVPSFEVLMQVFAAFRARLQ--LQAFEFFTA--QA 255 Query: 322 LAKSQLKDAAFPLEDEHPFYILIETSGSNKDHDDSKLETFLENVMEEGIVTDGVVAQDET 381 L A P ++ HPFY++ E + ++ + + + F E+ M G V+DGV++ + Sbjct: 256 LTHVLAHGAQAPFDEVHPFYVVTEFAAGDEAQEAAAMAAF-EDCMGNGWVSDGVISASDA 314 Query: 382 ELQNLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPVVG 441 + LW+ RE I EA A YK DVS+ + + + + T A +++A P Sbjct: 315 QAAQLWRLREGITEA-VARYKPYKNDVSVRISAMPAFLAETQALITQA-------YPQFE 366 Query: 442 AIGYGHVGDGNLHLNVAVREYNKNIE-----KTLEPFVYEFVSSKHGSVSAEHGLGFQKK 496 + +GH+GDGNLH+NV + + E + + + + ++ GS+SAEHG+G KK Sbjct: 367 VVWFGHIGDGNLHINVLKPDDTGDAEFLQQCEQVTKLLAQVLARFDGSISAEHGIGLVKK 426 Query: 497 NYIGYSKSPEEVKMMKDLKVHYDPNGILNPYK 528 Y+ ++ P E+ +MK +K +DP LNP K Sbjct: 427 AYLDSTRGPAEIALMKAVKRAFDPQARLNPGK 458 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: 528 Number of extensions: 20 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 Apr 09 2024. 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