Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate GFF1775 PGA1_c17990 D-malate dehydrogenase
Query= BRENDA::P76251 (361 letters) >FitnessBrowser__Phaeo:GFF1775 Length = 354 Score = 405 bits (1040), Expect = e-117 Identities = 206/349 (59%), Positives = 252/349 (72%), Gaps = 8/349 (2%) Query: 1 MMKTMRIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPD 60 M KT RIAAIPGDGIGKEVLP G RV+ A++ F + + + +W SCE Y G+MMP+ Sbjct: 1 MTKTYRIAAIPGDGIGKEVLPVGRRVIDLVAQKHNFTVDWTEFDW-SCERYHDTGRMMPE 59 Query: 61 DWHEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLA 120 D EQ+ FD+IY GAVG+P VPDH+SLWG L+ RRE DQY N+RPVRL G+ PLA Sbjct: 60 DGIEQMKAFDSIYLGAVGFPG-VPDHVSLWGLLIPLRRELDQYANVRPVRLLKGISSPLA 118 Query: 121 GKQPGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQS 180 G+ DID +VREN EGEYS +GGRV +GTEHE IQES+ TRRG DRI+ YAF +A++ Sbjct: 119 GRGADDIDMIIVRENVEGEYSEIGGRVYQGTEHEAAIQESILTRRGTDRIMDYAFNVAKT 178 Query: 181 RPRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVV 240 R RK ++SATKSNG+ +MP+WDER A AE +P I + HIDI+ A FV+ P+ FDVV Sbjct: 179 RKRKHVSSATKSNGIIHTMPFWDERFAAAAERHPAIGTAQFHIDIMTANFVLHPDWFDVV 238 Query: 241 VASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIAT 300 VASNLFGDILSDLGPA G+IGIAPSAN+NPE +PS+FEPVHGSAPDI GK +ANP+A Sbjct: 239 VASNLFGDILSDLGPAVAGSIGIAPSANINPEGKYPSMFEPVHGSAPDIAGKGVANPVAA 298 Query: 301 IWAGAMMLDFLGNGDERFQQAHNGILAAIEEVIAH-GPKTPDMKGNATT 348 +W AMML+ LG + A I AIE +A KT D+ G A T Sbjct: 299 VWTAAMMLEHLGEAN-----AAADIEQAIETSLASPDTKTRDLGGTADT 342 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: 435 Number of extensions: 7 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: 354 Length adjustment: 29 Effective length of query: 332 Effective length of database: 325 Effective search space: 107900 Effective search space used: 107900 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