Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate WP_011649387.1 RL_RS36060 tartrate dehydrogenase
Query= BRENDA::P76251 (361 letters) >NCBI__GCF_000009265.1:WP_011649387.1 Length = 347 Score = 332 bits (850), Expect = 1e-95 Identities = 176/335 (52%), Positives = 221/335 (65%), Gaps = 10/335 (2%) Query: 2 MKTMRIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPDD 61 MKT +IA +PGDGIG++V VL+ AA GF+L W SC+YY +G MMP D Sbjct: 1 MKTYKIALLPGDGIGRDVTAAAWAVLEKAARLNGFSLDATSYPW-SCDYYLENGSMMPAD 59 Query: 62 WHEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLAG 121 E L FDAI GAVGWP VPD +SL G LL R+ F QY N+RP RL PGV PL Sbjct: 60 GIEILRSFDAILLGAVGWPRKVPDSVSLHGLLLPIRKAFVQYANIRPHRLLPGVQGPL-- 117 Query: 122 KQPGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQSR 181 + + +RENTEGEYS GGRV++GT++EV ++ S+FTR+GV+RILR+ FE A++R Sbjct: 118 -RSDGFNILCIRENTEGEYSGAGGRVHQGTDNEVAVETSIFTRKGVERILRFGFEQARAR 176 Query: 182 PRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVVV 241 R L S TKSN SM +WDE + ++ YP++ HID + AR VM P+ DVVV Sbjct: 177 -RGKLASVTKSNAQKYSMVFWDEITQRLSAEYPDVEVTSYHIDAMAARMVMAPDSLDVVV 235 Query: 242 ASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIATI 301 ASNLFGDIL+DLG A G +G A SAN+NP+R+ PS+FEPVHGSAPDI IANPIA I Sbjct: 236 ASNLFGDILTDLGAAIQGGLGFAASANINPDRSAPSMFEPVHGSAPDIADLGIANPIAAI 295 Query: 302 WAGAMMLDFLGNGDERFQQAHNGILAAIEEVIAHG 336 W+GAMML+ LG A ++A+IE A G Sbjct: 296 WSGAMMLEHLGE-----PAAAARVMASIEATTARG 325 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: 380 Number of extensions: 16 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: 347 Length adjustment: 29 Effective length of query: 332 Effective length of database: 318 Effective search space: 105576 Effective search space used: 105576 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