Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate WP_073038275.1 BUB04_RS07005 tartrate dehydrogenase
Query= BRENDA::P76251 (361 letters) >NCBI__GCF_900129305.1:WP_073038275.1 Length = 352 Score = 442 bits (1138), Expect = e-129 Identities = 225/350 (64%), Positives = 264/350 (75%), Gaps = 7/350 (2%) Query: 6 RIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPDDWHEQ 65 RIA IPGDGIGKEV+PEG+R L+A ++GF +SF + + SC+YY HG+MMP D EQ Sbjct: 4 RIAVIPGDGIGKEVVPEGVRTLEALGRKFGFEVSFAEFPY-SCQYYLDHGEMMPPDGLEQ 62 Query: 66 LSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLAGKQPG 125 L FDAI GAVG P VPDH+SLWG LL RR FD YVNLRPVRL PGV PLAG+ Sbjct: 63 LKAFDAILLGAVGDP-RVPDHVSLWGLLLPIRRGFDLYVNLRPVRLLPGVRSPLAGRGRD 121 Query: 126 DIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQSRPRKT 185 DIDF VVRENTEGEYS +GGR+ GT+ EVVIQE+VFTR+GVDR+LRYAFELA+ RP + Sbjct: 122 DIDFVVVRENTEGEYSEIGGRLFPGTDREVVIQETVFTRKGVDRVLRYAFELARRRPDRH 181 Query: 186 LTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVVVASNL 245 +TSATKSNG+ +MP+WDER +A+A YP++R D+ HIDIL A FV+ P+ FDVVV SNL Sbjct: 182 VTSATKSNGILHTMPFWDERFKAIAREYPDVRADQYHIDILTAHFVLHPDWFDVVVGSNL 241 Query: 246 FGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIATIWAGA 305 GDILSDLGPA G IGIAPSANLNPER FPS+FEPVHGSAPDI GK IANPIAT+W Sbjct: 242 LGDILSDLGPAVAGGIGIAPSANLNPERRFPSMFEPVHGSAPDIAGKGIANPIATLWCVQ 301 Query: 306 MMLDFLGNGDERFQQAHNGILAAIEEVIAHGPKTPDMKGNATTPQVADAI 355 MMLDFLG +A ++ AIE V A G TPD+ G A T + D + Sbjct: 302 MMLDFLGE-----PRAAEALMRAIEAVTAEGVLTPDLGGTAKTVEFTDRV 346 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: 475 Number of extensions: 14 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: 361 Length of database: 352 Length adjustment: 29 Effective length of query: 332 Effective length of database: 323 Effective search space: 107236 Effective search space used: 107236 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 09 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