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 RR42_RS26635 RR42_RS26635 2-hydroxyacid dehydrogenase
Query= SwissProt::P46681 (530 letters) >FitnessBrowser__Cup4G11:RR42_RS26635 Length = 466 Score = 300 bits (768), Expect = 8e-86 Identities = 165/458 (36%), Positives = 266/458 (58%), Gaps = 16/458 (3%) Query: 82 SESEDLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGS 141 S D Y D+ R Y+G++++V+ P + E+VS ++ +C+ + VVPQGGNT L+GG+ Sbjct: 12 SGDADTESYVTDYRRIYRGKAQVVVMPSTTEQVSQVMAWCHAHDVPVVPQGGNTSLMGGA 71 Query: 142 VPIFD--ELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGS 199 VP ++LSL +N++ D ++ + AGV L A ++ +F L +G++GS Sbjct: 72 VPDDSGTAVLLSLGRMNRVLAVDTINDTMTVQAGVTLNAARTAAEQEQRLFALRIGSEGS 131 Query: 200 CHVGGVVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIG 259 C +GG +ATNAGG +LRYG++ VLG+E V+P+G+I +S+ +RKDNTGYDLKQLF+G Sbjct: 132 CQIGGNLATNAGGTAVLRYGNMRDLVLGIEAVLPDGRIYSSLRGLRKDNTGYDLKQLFVG 191 Query: 260 SEGTIGIITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDAKS 319 SEGT+GIIT + +P+P+A V++++V+S E ++ A+Q + ++AFE + A + Sbjct: 192 SEGTLGIITAAVLKLMPQPRANAVAFVAVQSPEAAVRLLGVAKQHGGQAVTAFELISAPA 251 Query: 320 QVLAKSQLKDAAFPLEDEHPFYILIE-TSGSNKDHDDSKLETFLENVMEEGIVTDGVVAQ 378 L L D PL H + +LIE TSG + + ++ L LE + + +V D VA Sbjct: 252 LELVLEYLGDVTSPLPARHDWMVLIELTSGGSDESLNATLMEILEAGLAQELVLDAAVAA 311 Query: 379 DETELQNLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSPKP 438 + Q W+ RE I +A GG K DVS+PL + + + +A++ E P Sbjct: 312 SLADAQRFWRIREEISDAQTRTGGSIKCDVSVPLSRIAAFIGDASAKVLALE-------P 364 Query: 439 VVGAIGYGHVGDGNLHLNV------AVREYNKNIEKTLEPFVYEFVSSKHGSVSAEHGLG 492 + YGH+GDGN+H N + ++ + V +++GS+SAEHG+G Sbjct: 365 AARMVIYGHMGDGNVHFNPLRPKDRSAADFLGQWYAPISEAVDTLAHAENGSISAEHGIG 424 Query: 493 FQKKNYIGYSKSPEEVKMMKDLKVHYDPNGILNPYKYI 530 K++ + KSP E+++M +K DP +LNP K + Sbjct: 425 VAKRDDLKRYKSPVELELMWQVKRALDPKNLLNPAKML 462 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: 544 Number of extensions: 25 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: 466 Length adjustment: 34 Effective length of query: 496 Effective length of database: 432 Effective search space: 214272 Effective search space used: 214272 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