Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate WP_041750617.1 BBTA_RS13420 tartrate dehydrogenase
Query= BRENDA::P76251 (361 letters) >NCBI__GCF_000015165.1:WP_041750617.1 Length = 357 Score = 497 bits (1279), Expect = e-145 Identities = 238/358 (66%), Positives = 288/358 (80%), Gaps = 6/358 (1%) Query: 3 KTMRIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPDDW 62 K RIA IPGDGIGKEV+PEG+RV++AAA++ G A+ F+ +++S +YY HG+MMPDDW Sbjct: 4 KPYRIAVIPGDGIGKEVMPEGLRVIEAAAKKHGVAVQFDHFDFSSYDYYEKHGQMMPDDW 63 Query: 63 HEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLAGK 122 Q+ DAIYFGAVGWP + DH+SLWGSL+KFRREFDQYVNLRPVRL PGVP PLAG+ Sbjct: 64 KAQIGSHDAIYFGAVGWPAKIADHVSLWGSLIKFRREFDQYVNLRPVRLMPGVPSPLAGR 123 Query: 123 QPGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQSRP 182 +PGDIDF+VVRENTEGEYSS+GGR+ T+ E V Q++V TR GVDRIL++AFELAQSRP Sbjct: 124 KPGDIDFWVVRENTEGEYSSVGGRMFPDTDREFVTQQTVMTRTGVDRILKFAFELAQSRP 183 Query: 183 RKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVVVA 242 +K LTSATKSNG++I+MPYWDERVEAMA+NYP ++WDK HIDIL A FV+ P+ FDVVV Sbjct: 184 KKHLTSATKSNGISITMPYWDERVEAMAKNYPGVKWDKYHIDILTANFVLHPDWFDVVVG 243 Query: 243 SNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIATIW 302 SNLFGDILSDLGPACTGTIGIAPS N+NPER FPS+FEPVHGSAPDI G+ IANPI IW Sbjct: 244 SNLFGDILSDLGPACTGTIGIAPSGNINPERNFPSVFEPVHGSAPDIAGQGIANPIGMIW 303 Query: 303 AGAMMLDFLGNGDERFQQAHNGILAAIEEVIAHGP-KTPDMKGNATTPQVADAICKII 359 +GAMML+ LG + A I+ AIE +A +T D+ GNA T A+ +++ Sbjct: 304 SGAMMLEHLGE-----KTAAQAIVGAIERTLAERTLRTRDLGGNADTEACGKAVAEMV 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: 477 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: 357 Length adjustment: 29 Effective length of query: 332 Effective length of database: 328 Effective search space: 108896 Effective search space used: 108896 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 Apr 10 2024. The underlying query database was built on Apr 09 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