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_RS32905 BPHYT_RS32905 FAD-linked oxidase
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__BFirm:BPHYT_RS32905 Length = 463 Score = 296 bits (757), Expect = 1e-84 Identities = 169/435 (38%), Positives = 249/435 (57%), Gaps = 14/435 (3%) Query: 93 DWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGSVPIFDELILSL 152 DW + + ++ L P++ E V+ L + + AVV QGG TGL GG+ P E+ LSL Sbjct: 35 DWSDAPRMRPRMTLLPRNPEDVARALRVLGEHRQAVVVQGGLTGLAGGATPQAGEVALSL 94 Query: 153 ANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCHVGGVVATNAGG 212 A +N I FD + G L AGV LE +V + + FPLDLGA+G+C +GG ATNAGG Sbjct: 95 ARVNAIESFDRIGGTLTVQAGVPLEQLQTFVEAEGWFFPLDLGARGTCQIGGNAATNAGG 154 Query: 213 LRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSEGTIGIITGVSI 272 R++R+G++ +LGLEV +P+G +++ M+ + K+ TG DLKQLFIGSEGT+G+IT + + Sbjct: 155 NRVIRFGTMRDLILGLEVALPDGTMLSMMNRVTKNTTGIDLKQLFIGSEGTLGVITRIVL 214 Query: 273 LTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFM--DAKSQVLAKSQLKDA 330 PKP A N + +V SF+D ++ R L+ LS+FE M D S + + LK Sbjct: 215 KLEPKPSAVNTALCAVASFDDATRLLKYLRARLAN-LSSFELMWQDFMSAAMDIAHLK-- 271 Query: 331 AFPLEDEHPFYILIETSGSNKDHDDSKLETFLENVMEEGIVTDGVVAQDETELQNLWKWR 390 P D +P Y+LIET G + D D LE LE ++++GIV D ++AQ + LW +R Sbjct: 272 -APFGDTYPVYVLIETLGESDDDDRRALEHSLERMLDDGIVQDVIIAQSIEHAKQLWAYR 330 Query: 391 EMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPVVGAIGYGHVGD 450 E + E +D+ +P+ + VE A L+E + +GH+GD Sbjct: 331 ETVGELLSKLKPHAAFDIGIPMDRMNGFVEDARAALNER-------FSQQAHLFFGHLGD 383 Query: 451 GNLHLNVAVREYNKNIEKTLEPFVYEFVSSKHGSVSAEHGLGFQKKNYIGYSKSPEEVKM 510 GNLHL ++ K +E +Y V+ G +SAEHG+G K+ ++ YS+S E+ + Sbjct: 384 GNLHLLSGPYADAADLLK-VEELIYAAVNDVQGCISAEHGIGVIKQPFLHYSRSAPELDL 442 Query: 511 MKDLKVHYDPNGILN 525 M LK DP GILN Sbjct: 443 MGKLKALLDPAGILN 457 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: 516 Number of extensions: 23 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: 463 Length adjustment: 34 Effective length of query: 496 Effective length of database: 429 Effective search space: 212784 Effective search space used: 212784 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