Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate WP_011767582.1 AZO_RS19370 tartrate dehydrogenase
Query= BRENDA::P76251 (361 letters) >NCBI__GCF_000061505.1:WP_011767582.1 Length = 359 Score = 569 bits (1466), Expect = e-167 Identities = 266/354 (75%), Positives = 303/354 (85%) Query: 6 RIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPDDWHEQ 65 RIA I GDGIG+EV+PEG+R +QAAA ++ AL F +WA C+YY HGKMMPDDW EQ Sbjct: 6 RIAVIAGDGIGQEVMPEGLRAVQAAAAKFDIALEFTHFDWAHCDYYLQHGKMMPDDWFEQ 65 Query: 66 LSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLAGKQPG 125 L FDAI+FGAVGWPD VPDHISLWGSLLKFRR+FDQYVNLRPVRL PGVPCPLA K+ G Sbjct: 66 LKGFDAIFFGAVGWPDKVPDHISLWGSLLKFRRDFDQYVNLRPVRLMPGVPCPLANKKVG 125 Query: 126 DIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQSRPRKT 185 DIDFYVVRENTEGEYSS+GG++ EGTE E V+QES+FTR+GVDRIL+YAFELAQ RP+K Sbjct: 126 DIDFYVVRENTEGEYSSVGGKMYEGTERETVLQESIFTRKGVDRILKYAFELAQKRPKKH 185 Query: 186 LTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVVVASNL 245 LTSATKSNG+AISMPYWD RV+ M + YPE++WD+ HIDIL ARFV+ PERFDVVVASNL Sbjct: 186 LTSATKSNGIAISMPYWDGRVKEMGKAYPEVKWDQYHIDILTARFVLSPERFDVVVASNL 245 Query: 246 FGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIATIWAGA 305 FGDILSDLGPAC GTIGIAPSANLNP+RTFPSLFEPVHGSAPDIYG+NIANP+A IW+GA Sbjct: 246 FGDILSDLGPACAGTIGIAPSANLNPDRTFPSLFEPVHGSAPDIYGRNIANPVAMIWSGA 305 Query: 306 MMLDFLGNGDERFQQAHNGILAAIEEVIAHGPKTPDMKGNATTPQVADAICKII 359 MMLDFLGNGD R+ AH+ I+ AIE V+ GP+TPDM G A T +V A+ I Sbjct: 306 MMLDFLGNGDARYTAAHDAIVKAIETVLVEGPRTPDMGGTANTTEVGKAVAAAI 359 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: 541 Number of extensions: 18 Number of successful extensions: 2 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: 359 Length adjustment: 29 Effective length of query: 332 Effective length of database: 330 Effective search space: 109560 Effective search space used: 109560 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