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 BPHYT_RS13750 BPHYT_RS13750 D-2-hydroxyacid dehydrogenase
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__BFirm:BPHYT_RS13750 Length = 472 Score = 289 bits (740), Expect = 1e-82 Identities = 161/458 (35%), Positives = 252/458 (55%), Gaps = 16/458 (3%) Query: 82 SESEDLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGS 141 ++ D + Y DW R+Y G + VL P + ++V+ ++ + +IA+VPQGGNTGL GG+ Sbjct: 21 TDPHDTALYLTDWRRRYAGAACAVLCPATPDEVAALVKLAVEHRIALVPQGGNTGLAGGA 80 Query: 142 VPIFD--ELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGS 199 P + ++SL LN++RD DP + + +AGVIL + E +FPL L A+GS Sbjct: 81 TPDASGAQAVISLRRLNRVRDIDPHNNTITVEAGVILAEVQKHADEAGRLFPLSLAAEGS 140 Query: 200 CHVGGVVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIG 259 C +GG +ATNAGG +LRYG+ LGLEVV P G++ + + +RKDNTGYDL+ LFIG Sbjct: 141 CTIGGNLATNAGGTGVLRYGNARELCLGLEVVTPQGELWDGLRGLRKDNTGYDLRDLFIG 200 Query: 260 SEGTIGIITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDAKS 319 +EGT+GIIT + P+P A + ++ S ++ +L+ FE M Sbjct: 201 AEGTLGIITAAVLKLHPRPAARVTALAALASPHAALDFLSLTQRVAGPLLTGFELMSDFC 260 Query: 320 QVLAKSQLKDAAFPLEDEHPFYILIETSGS-NKDHDDSKLETFLENVMEEGIVTDGVVAQ 378 L + +P + H +L+E S S +++H E +E +E G+V D VVA+ Sbjct: 261 LRLVGRHFEQMRYPFAEPHAQVVLLELSDSESEEHARELFERLMETALESGLVQDAVVAE 320 Query: 379 DETELQNLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKP 438 + ++ + W RE IP A G K+D+++P+ + +E T+A +++A P Sbjct: 321 NLSQSRAFWNLREHIPLAQAEEGLNIKHDIAVPISRVGHFIEETDAAIAQA-------VP 373 Query: 439 VVGAIGYGHVGDGNLHLNVAVRE------YNKNIEKTLEPFVYEFVSSKHGSVSAEHGLG 492 + +GH+GDGNLH NV E + + + VY+ V GS+SAEHGLG Sbjct: 374 GARMVTFGHLGDGNLHYNVQAPEGVDAKAFLTQYQSPINQIVYDSVHRHRGSISAEHGLG 433 Query: 493 FQKKNYIGYSKSPEEVKMMKDLKVHYDPNGILNPYKYI 530 K + + K EV++M+ +K DP ++NP K + Sbjct: 434 QLKIDEAMHYKQDVEVQLMRAVKRALDPLNLMNPGKVL 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: 548 Number of extensions: 20 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: 472 Length adjustment: 34 Effective length of query: 496 Effective length of database: 438 Effective search space: 217248 Effective search space used: 217248 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