Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate RR42_RS02600 RR42_RS02600 tartrate dehydrogenase
Query= BRENDA::P76251 (361 letters) >FitnessBrowser__Cup4G11:RR42_RS02600 Length = 362 Score = 494 bits (1272), Expect = e-144 Identities = 240/367 (65%), Positives = 288/367 (78%), Gaps = 14/367 (3%) Query: 2 MKTMRIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPDD 61 M +IA IPGDGIG EV+PEG+RV+ AAA R+G + F+ +++SC+YY+ HGKM+PDD Sbjct: 1 MSKYKIAVIPGDGIGTEVMPEGLRVMDAAARRFGIDMQFDHFDFSSCDYYARHGKMLPDD 60 Query: 62 WHEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLA- 120 W + L ++DAIYFGAVGWPD VPDHISLWGSLL+FRR FDQYVNLRPVRL PG+ PL Sbjct: 61 WFDTLVKYDAIYFGAVGWPDAVPDHISLWGSLLQFRRSFDQYVNLRPVRLMPGIRSPLVD 120 Query: 121 ----GKQPGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFE 176 ++PGDIDFYVVRENTEGEYSS+GGR+ GT+ EVVIQE+V TR GVDRIL++AFE Sbjct: 121 RDGHARKPGDIDFYVVRENTEGEYSSIGGRMFPGTDREVVIQETVMTRTGVDRILKFAFE 180 Query: 177 LAQSRPRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPER 236 LAQ RP + LTSATKSNG++I+MPYWDERVEAMA +YP ++ DK HIDIL A FV P+ Sbjct: 181 LAQKRPARHLTSATKSNGISITMPYWDERVEAMATHYPGVKVDKYHIDILTAHFVQHPDW 240 Query: 237 FDVVVASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIAN 296 FDVVVASNLFGDILSDLGPACTGTIGIAPS N+NP+RTFPSLFEPVHGSAPDI G+ +AN Sbjct: 241 FDVVVASNLFGDILSDLGPACTGTIGIAPSGNINPDRTFPSLFEPVHGSAPDIAGRGVAN 300 Query: 297 PIATIWAGAMMLDFLGNGDERFQQAHNGILAAIEEVIA----HGPKTPDMKGNATTPQVA 352 PI IW GAMML+ LG +A +L AIE+V++ H P T D+ G A T + Sbjct: 301 PIGQIWCGAMMLEHLGQ-----PEAGAAVLGAIEKVLSAGPEHAPLTRDIGGKAGTADLG 355 Query: 353 DAICKII 359 AI + + Sbjct: 356 QAIAQAL 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: 510 Number of extensions: 18 Number of successful extensions: 3 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 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