Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate WP_057508507.1 ABB28_RS10115 tartrate dehydrogenase
Query= BRENDA::P76251 (361 letters) >NCBI__GCF_001431535.1:WP_057508507.1 Length = 356 Score = 536 bits (1382), Expect = e-157 Identities = 253/359 (70%), Positives = 302/359 (84%), Gaps = 5/359 (1%) Query: 1 MMKTMRIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPD 60 M +T +IA IPGDGIG+EV+PEG+RVL+AAA R+ L F ++WASC+YY HG+MMPD Sbjct: 1 MTQTFKIAVIPGDGIGQEVMPEGLRVLEAAARRFQLDLQFTHIDWASCDYYQQHGQMMPD 60 Query: 61 DWHEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLA 120 DW QL DAI+FGAVGWPDTVPDH+SLWGSLLKFRREFDQY+NLRPVRLF GVPCPLA Sbjct: 61 DWKVQLQDMDAIFFGAVGWPDTVPDHVSLWGSLLKFRREFDQYINLRPVRLFEGVPCPLA 120 Query: 121 GKQPGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQS 180 G++PGDIDF VVRENTEGEY++LGG + GTE E+VIQE+V +R G DR+L+YA+ELAQS Sbjct: 121 GRKPGDIDFLVVRENTEGEYTNLGGIMYAGTEREIVIQETVMSRHGADRVLKYAYELAQS 180 Query: 181 RPRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVV 240 R R+ LT ATKSNG+AISMP+WD R +A+ YPE+ DKQHIDIL ARFV+QP+RFDVV Sbjct: 181 RTRRHLTVATKSNGIAISMPWWDGRADAVGAAYPEVTVDKQHIDILTARFVLQPQRFDVV 240 Query: 241 VASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIAT 300 VASNLFGDILSDLGPACTGTIG+APSANLNPER FPSLFEPVHGSAPDI+G+ IANPIA Sbjct: 241 VASNLFGDILSDLGPACTGTIGLAPSANLNPERDFPSLFEPVHGSAPDIFGQGIANPIAM 300 Query: 301 IWAGAMMLDFLGNGDERFQQAHNGILAAIEEVIAHGPKTPDMKGNATTPQVADAICKII 359 IW+GA+ML FLG+ ++AH+ I+AAIE V+A GP TPD+ G ATT Q+ +A+ + Sbjct: 301 IWSGALMLKFLGS-----EEAHDAIMAAIEGVLAQGPLTPDLGGKATTAQLGEAVAAAV 354 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: 509 Number of extensions: 14 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: 356 Length adjustment: 29 Effective length of query: 332 Effective length of database: 327 Effective search space: 108564 Effective search space used: 108564 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 10 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