Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate WP_038209403.1 Q392_RS15265 tartrate dehydrogenase
Query= BRENDA::P76251 (361 letters) >NCBI__GCF_000745855.1:WP_038209403.1 Length = 362 Score = 489 bits (1258), Expect = e-143 Identities = 236/367 (64%), Positives = 291/367 (79%), Gaps = 13/367 (3%) Query: 1 MMKTMRIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPD 60 M RIA I GDGIGKE +PEG+RV+ AAA ++G L+F+ +++S +Y HGKM+PD Sbjct: 1 MSSKKRIAVIAGDGIGKETMPEGLRVVDAAARKFGVDLAFDHFDFSSWDYCEKHGKMLPD 60 Query: 61 DWHEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPL- 119 DW Q+ DAI+FGAVGWP+ +PDH+SLWGSLL FRREFDQY+NLRP RL PG+ P+ Sbjct: 61 DWKAQIGGHDAIFFGAVGWPEKIPDHVSLWGSLLLFRREFDQYINLRPARLMPGITAPVV 120 Query: 120 ----AGKQPGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAF 175 + ++PG+ID Y+VRENTEGEYSS+GGR+ EGT E+V+QE+V +R GVDR+L++AF Sbjct: 121 RRDGSPREPGEIDMYIVRENTEGEYSSIGGRMYEGTPREIVVQETVMSRHGVDRVLKFAF 180 Query: 176 ELAQSRPRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPE 235 +LAQSRP+K LTSATKSNG++I+MPYWDERV MA+ YP++R DK HIDIL A FV +P+ Sbjct: 181 DLAQSRPKKHLTSATKSNGISITMPYWDERVAQMAKTYPDVRLDKFHIDILTAHFVQRPD 240 Query: 236 RFDVVVASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIA 295 FDVVVASNLFGDILSDLGPACTGTIGIAPSANLNPERT PSLFEPVHGSAPDI GK IA Sbjct: 241 FFDVVVASNLFGDILSDLGPACTGTIGIAPSANLNPERTTPSLFEPVHGSAPDIAGKGIA 300 Query: 296 NPIATIWAGAMMLDFLGNGDERFQQAHNGILAAIEEVIAHG---PKTPDMKGNATTPQVA 352 NPI IW GAMML+FLG+ D AH+ ILAAIE+V+ G P+TPD+ G+A T + Sbjct: 301 NPIGQIWCGAMMLEFLGHKD-----AHDAILAAIEKVLTPGSGAPRTPDIGGSARTQDLG 355 Query: 353 DAICKII 359 AI + + Sbjct: 356 RAIAEAL 362 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: 497 Number of extensions: 17 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: 361 Length of database: 362 Length adjustment: 29 Effective length of query: 332 Effective length of database: 333 Effective search space: 110556 Effective search space used: 110556 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 25 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