Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate WP_013076957.1 BTUS_RS15235 tartrate dehydrogenase
Query= BRENDA::P76251 (361 letters) >NCBI__GCF_000092905.1:WP_013076957.1 Length = 363 Score = 378 bits (971), Expect = e-109 Identities = 193/360 (53%), Positives = 255/360 (70%), Gaps = 10/360 (2%) Query: 2 MKTMRIAAIPGDGIGKEVLPEGIRVLQAAAERWG-FALSFEQMEWASCEYYSHHGKMMPD 60 M+T RIA IPGDGIG EV+ EG++VL+AAA R G F L F+ + W +C YY HG+MMP Sbjct: 1 MRTHRIAVIPGDGIGPEVVREGVKVLEAAAVRAGMFRLEFDWLPW-NCSYYRRHGRMMPA 59 Query: 61 DWHEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLA 120 D EQL +D IY GAVG P +VPDH+S+W +L R+ F QYVNLRP +L G+ PL Sbjct: 60 DGIEQLRTYDGIYLGAVGDP-SVPDHVSVWQLILPIRKAFQQYVNLRPAKLLAGLESPLR 118 Query: 121 GKQPGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQS 180 K+ D+DF +VRENTEGEYS +GGR++ GT E+ +Q SVFTR G++R+ RYA LA+ Sbjct: 119 HKEARDLDFVIVRENTEGEYSDIGGRLHPGTPVEMAVQTSVFTRYGIERVARYALSLARR 178 Query: 181 RPRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVV 240 R R + ATKSNGLA +MPYWDE + + +P++ H+D L FV++PE DVV Sbjct: 179 R-RGHVAVATKSNGLAHTMPYWDEVIRSCRVEFPDVDVSFYHVDALSTLFVLRPETLDVV 237 Query: 241 VASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIAT 300 +A+NLFGDILSDLG A G +G+AP+ N+NPE+ FPS+FEPVHGSAPDI GK IANPIA Sbjct: 238 LATNLFGDILSDLGAAVVGGLGVAPAGNINPEKRFPSMFEPVHGSAPDIAGKGIANPIAA 297 Query: 301 IWAGAMMLDFLGNGDERFQQAHNGILAAIEEVIAHGPK-TPDMKGNATTPQVADAICKII 359 IW+GAMML+ LG+ + + ++ AIE+V+A G T D+ G A+T +V DA+ + + Sbjct: 298 IWSGAMMLEHLGHPEPAAE-----VVRAIEQVLAEGRVWTRDLGGTASTEEVGDAVVRAL 352 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: 445 Number of extensions: 11 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: 363 Length adjustment: 29 Effective length of query: 332 Effective length of database: 334 Effective search space: 110888 Effective search space used: 110888 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