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 GFF620 PGA1_c06340 putative FAD linked oxidase
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__Phaeo:GFF620 Length = 474 Score = 265 bits (678), Expect = 2e-75 Identities = 155/447 (34%), Positives = 237/447 (53%), Gaps = 20/447 (4%) Query: 90 YNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGSV-----PI 144 Y E+ +Y+GQ+ ++ P+S E+V+ +L + ++ VVP GG TGLVGG + P Sbjct: 30 YLEEPRGRYQGQAGVIALPRSTEEVATLLRAAHTARVPVVPYGGGTGLVGGQIMGAAGPA 89 Query: 145 FDELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGSCHVGG 204 L++SL + +R P ++ +AG+IL E +FPL L A+G+ +GG Sbjct: 90 --PLVISLERMTALRGVYPQENVIAVEAGMILAEVQRAATEAGRLFPLSLAAEGTARIGG 147 Query: 205 VVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIGSEGTI 264 +ATNAGG+ +LRYG+ LGLE V+PNG+I + +RKDNTGYDL+ L IG+EGT+ Sbjct: 148 TLATNAGGVNVLRYGNARDLCLGLEAVLPNGEIWQGLSRLRKDNTGYDLRNLLIGAEGTL 207 Query: 265 GIITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDAKSQVLAK 324 GIIT S+ P P + L+V S + AR +L E +SAFE + + + Sbjct: 208 GIITAASLKLSPIPAEQGTAMLTVASPVAAIDLLAMARDQLGETISAFELIHRQGLEFLR 267 Query: 325 SQLKDAAFPLEDEHPFYILIETSGSNKDHDDSKLETFLENVMEEGIVTDGVVAQDETELQ 384 L D P D + +LI+ L E ++ G+ DGV+AQ E + Q Sbjct: 268 ETLPDLRLPFADLPDWCVLIDLGLPKGRSPADALAALFETALDAGLCADGVIAQSEAQRQ 327 Query: 385 NLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKPVVGAIG 444 LW RE IPE ++ G V +D+S+P+ + + RL+ +GD + Sbjct: 328 ALWSAREHIPEGNRRIGSVSSHDISIPISRIPDFIFEGGKRLA---ALGD-----MRINC 379 Query: 445 YGHVGDGNLHLNV-----AVREYNKNIEKTLEPFVYEFVSSKHGSVSAEHGLGFQKKNYI 499 +GH+GDGNLH NV R +++ ++ V++ GSVSAEHG+G K + Sbjct: 380 FGHLGDGNLHYNVFPAQGKDRRAYEHLRDDVKRCVHDLTHEYDGSVSAEHGIGRLKVADL 439 Query: 500 GYSKSPEEVKMMKDLKVHYDPNGILNP 526 P ++ M+ +K DP+GI+NP Sbjct: 440 RRYGDPVKLAAMQAIKQALDPHGIMNP 466 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: 585 Number of extensions: 22 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: 474 Length adjustment: 34 Effective length of query: 496 Effective length of database: 440 Effective search space: 218240 Effective search space used: 218240 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