Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate WP_106718831.1 CU100_RS22305 tartrate dehydrogenase
Query= BRENDA::P76251 (361 letters) >NCBI__GCF_003010935.1:WP_106718831.1 Length = 367 Score = 508 bits (1309), Expect = e-149 Identities = 243/357 (68%), Positives = 295/357 (82%), Gaps = 6/357 (1%) Query: 4 TMRIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPDDWH 63 +++IA I GDGIGKEV+PEG+RVL+ AAE +G FE ++ASC+YY+ HG+MMP+DW Sbjct: 5 SLKIAVIAGDGIGKEVVPEGLRVLETAAEIFGIDTRFETFDFASCDYYAKHGRMMPEDWK 64 Query: 64 EQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLAGKQ 123 Q+ DAI+FGAVGWP+TVPDHISLWGSLL+FRREFDQYVNLRPVRL PGVP PLAG++ Sbjct: 65 AQIGGHDAIFFGAVGWPETVPDHISLWGSLLQFRREFDQYVNLRPVRLMPGVPSPLAGRK 124 Query: 124 PGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQSRPR 183 PGDIDF+VVRENTEGEYSS+GG++ GT+ E+V+QE+V +R GVDRILR+AF+LA+SR + Sbjct: 125 PGDIDFFVVRENTEGEYSSIGGKMYPGTDREIVVQETVMSRVGVDRILRFAFDLARSRGK 184 Query: 184 KTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVVVAS 243 K LTSATKSNG++I+MPYWDERVE MA++Y ++RWDK HIDILCA FV+ P+RFDVVVAS Sbjct: 185 KHLTSATKSNGISITMPYWDERVEEMAQSYADVRWDKYHIDILCAHFVLNPDRFDVVVAS 244 Query: 244 NLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIATIWA 303 NLFGDILSDLGPACTGTIGIAPS N+NPER FPSLFEPVHGSAPDI GK IANPI IWA Sbjct: 245 NLFGDILSDLGPACTGTIGIAPSGNINPERDFPSLFEPVHGSAPDIAGKGIANPIGQIWA 304 Query: 304 GAMMLDFLGNGDERFQQAHNGILAAIEEVIAH-GPKTPDMKGNATTPQVADAICKII 359 GAMMLD LG+ QA I+ AIE+++A +T D+ G A T A+ + + Sbjct: 305 GAMMLDHLGHA-----QAAAAIVKAIEKILADPSSRTRDLGGTANTAACGRAVAEAL 356 Lambda K H 0.321 0.138 0.432 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: 501 Number of extensions: 11 Number of successful extensions: 1 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: 361 Length of database: 367 Length adjustment: 29 Effective length of query: 332 Effective length of database: 338 Effective search space: 112216 Effective search space used: 112216 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
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