Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate Ac3H11_375 Tartrate dehydrogenase (EC 1.1.1.93) @ Tartrate decarboxylase (EC 4.1.1.73) @ D-malic enzyme (EC 1.1.1.83)
Query= BRENDA::P76251 (361 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_375 Length = 364 Score = 481 bits (1238), Expect = e-140 Identities = 232/362 (64%), Positives = 286/362 (79%), Gaps = 13/362 (3%) Query: 6 RIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPDDWHEQ 65 RIA + GDGIGKEV+PEG+RVL AA ++G L F+ +++S +YY HGKM+PD+W EQ Sbjct: 5 RIAVVAGDGIGKEVMPEGLRVLDVAARKFGIDLHFDHFDFSSWDYYEKHGKMLPDNWKEQ 64 Query: 66 LSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLAGKQ-- 123 + +AIYFGAVGWP+ + DH+SLWGSLL FRREFDQY+NLRP RL PGV P+ + Sbjct: 65 IGSHEAIYFGAVGWPEKIADHVSLWGSLLLFRREFDQYINLRPARLMPGVIAPVVRRDGS 124 Query: 124 ---PGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQS 180 PG+ID +VRENTEGEYSS+GGR+ EGT E+V+QE+V +R GVDR+L++AF+LAQS Sbjct: 125 PRLPGEIDMLIVRENTEGEYSSIGGRMYEGTPREIVMQETVMSRHGVDRVLKFAFDLAQS 184 Query: 181 RPRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVV 240 RP+K LTSATKSNG+AI+MPYWDERV MA++YP+++ DK HIDIL A FV +P+ FDVV Sbjct: 185 RPKKHLTSATKSNGIAITMPYWDERVAEMAKSYPDVKVDKFHIDILTAHFVQRPDFFDVV 244 Query: 241 VASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIAT 300 VASNLFGDILSDLGPACTGTIGIAPSANLNP RT PSLFEPVHGSAPDI G+ IANPI Sbjct: 245 VASNLFGDILSDLGPACTGTIGIAPSANLNPTRTMPSLFEPVHGSAPDIAGQGIANPIGQ 304 Query: 301 IWAGAMMLDFLGNGDERFQQAHNGILAAIEEVI---AHGPKTPDMKGNATTPQVADAICK 357 IW GAMMLDFLG ++ AH+ +LAAIE V+ + GP+TPD+ G + T V AI + Sbjct: 305 IWCGAMMLDFLG-----YRAAHDAVLAAIEAVLDPQSGGPRTPDLGGKSGTQDVGKAIAE 359 Query: 358 II 359 + Sbjct: 360 AL 361 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: 495 Number of extensions: 20 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: 364 Length adjustment: 29 Effective length of query: 332 Effective length of database: 335 Effective search space: 111220 Effective search space used: 111220 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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