Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate Ac3H11_3259 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_3259 Length = 366 Score = 540 bits (1391), Expect = e-158 Identities = 256/350 (73%), Positives = 300/350 (85%) Query: 6 RIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPDDWHEQ 65 RIA I GDGIGKEVLPEG+RV+QAAA R+G AL ++WASC+YY+ HGKMMPDDW Q Sbjct: 10 RIALIAGDGIGKEVLPEGLRVVQAAAARFGIALETTTIDWASCDYYAAHGKMMPDDWKAQ 69 Query: 66 LSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLAGKQPG 125 LS DAI+FGAVGWP VPDH+SLWGSLLKFRREFDQY+NLRPVRLF GVPCPLAG+QPG Sbjct: 70 LSGMDAIFFGAVGWPSAVPDHVSLWGSLLKFRREFDQYINLRPVRLFEGVPCPLAGRQPG 129 Query: 126 DIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQSRPRKT 185 DID+YVVRENTEGEY+SLGG + EGT+ E+ IQESV++R G +R+L++AF+LAQSR +K Sbjct: 130 DIDYYVVRENTEGEYTSLGGLMYEGTDREICIQESVYSRHGANRLLKFAFDLAQSRAKKH 189 Query: 186 LTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVVVASNL 245 +T ATKSNG+AISMP+WD+R + +A+ YPE+ DKQHIDIL ARFV+QP RFDVV A+NL Sbjct: 190 VTLATKSNGIAISMPWWDQRADDVAQGYPEVTLDKQHIDILTARFVLQPGRFDVVAATNL 249 Query: 246 FGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIATIWAGA 305 FGDILSDLGPA TGTIG+APSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIA IW+GA Sbjct: 250 FGDILSDLGPATTGTIGLAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIAMIWSGA 309 Query: 306 MMLDFLGNGDERFQQAHNGILAAIEEVIAHGPKTPDMKGNATTPQVADAI 355 +MLDFL G + AH+ I+ AIEEVI GP+TPD+ G A+T QV +AI Sbjct: 310 LMLDFLTQGQGAGRAAHDAIVNAIEEVIKSGPRTPDLGGAASTTQVGEAI 359 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: 512 Number of extensions: 10 Number of successful extensions: 2 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: 366 Length adjustment: 29 Effective length of query: 332 Effective length of database: 337 Effective search space: 111884 Effective search space used: 111884 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