Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate WP_234803296.1 TX73_RS08890 tartrate dehydrogenase
Query= BRENDA::P76251 (361 letters) >NCBI__GCF_000195775.1:WP_234803296.1 Length = 337 Score = 463 bits (1191), Expect = e-135 Identities = 223/341 (65%), Positives = 273/341 (80%), Gaps = 6/341 (1%) Query: 20 LPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPDDWHEQLSRFDAIYFGAVGW 79 +PEG+RVL+AAA++ L F+ ++AS +YY HG+MMPDDW E++ DAI+FGAVGW Sbjct: 1 MPEGLRVLEAAAKKHRVKLVFDHFDFASYDYYEKHGQMMPDDWKEKIGGHDAIFFGAVGW 60 Query: 80 PDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLAGKQPGDIDFYVVRENTEGE 139 P +PDHISLWGSL+KFRREFDQYVNLRPVRL PGVP PLAG++PGDIDF+VVRENTEGE Sbjct: 61 PAKIPDHISLWGSLIKFRREFDQYVNLRPVRLMPGVPSPLAGRKPGDIDFWVVRENTEGE 120 Query: 140 YSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQSRPRKTLTSATKSNGLAISM 199 YSS+GGR+ TE E V Q+SV TR GVDRIL++AFELAQSRP++ LTSATKSNG++I+M Sbjct: 121 YSSVGGRMFPDTEREFVTQQSVMTRVGVDRILKFAFELAQSRPKRHLTSATKSNGISITM 180 Query: 200 PYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVVVASNLFGDILSDLGPACTG 259 PYWDERVEA+A++YPE++WDK HIDIL A FV+ P+ FDVVV SNLFGDILSDLGPACTG Sbjct: 181 PYWDERVEAVAKSYPEVKWDKYHIDILTAHFVLHPDWFDVVVGSNLFGDILSDLGPACTG 240 Query: 260 TIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIATIWAGAMMLDFLGNGDERFQ 319 TIGIAPS N+NPE FPS+FEPVHGSAPDI G+ IANPI IW+GAMML+ LG + Sbjct: 241 TIGIAPSGNINPEGDFPSVFEPVHGSAPDIAGQGIANPIGMIWSGAMMLEHLGE-----K 295 Query: 320 QAHNGILAAIEEVIAHGP-KTPDMKGNATTPQVADAICKII 359 QA + I+ AIE + +T D+ G A T + +++ Sbjct: 296 QAADSIVKAIERTLEERTLRTRDLGGQADTSACGKGVAEMV 336 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: 465 Number of extensions: 15 Number of successful extensions: 1 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: 337 Length adjustment: 29 Effective length of query: 332 Effective length of database: 308 Effective search space: 102256 Effective search space used: 102256 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