Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate H281DRAFT_01534 H281DRAFT_01534 tartrate dehydrogenase/decarboxylase / D-malate dehydrogenase
Query= BRENDA::P76251 (361 letters) >FitnessBrowser__Burk376:H281DRAFT_01534 Length = 364 Score = 343 bits (881), Expect = 3e-99 Identities = 178/362 (49%), Positives = 236/362 (65%), Gaps = 9/362 (2%) Query: 2 MKTMRIAAIPGDGIGKEVLPEGIRVLQAAAERW-GFALSFEQMEWASCEYYSHHGKMMPD 60 M+T RIA IPGDGIGKEV+P G +VL+A A FA FE +W +YY HG MMP Sbjct: 1 MQTYRIATIPGDGIGKEVVPAGAQVLEALARTTKSFAFEFENFDWGG-DYYRKHGVMMPA 59 Query: 61 DWHEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLA 120 D + + DAI FG+ G PD + DHI+LWG LK + FDQY N+RP R+ PG+ PL Sbjct: 60 DGLDAIRGKDAILFGSAGDPD-IADHITLWGLRLKICQGFDQYANVRPTRILPGIDAPLK 118 Query: 121 GKQPGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQS 180 +P D+++ +VREN+EGEYS +GGRV++G E S+ TR GV+RI+R+AF LAQS Sbjct: 119 RCKPEDLNWVIVRENSEGEYSGVGGRVHQGHPIEAATDVSIMTRAGVERIMRFAFRLAQS 178 Query: 181 RPRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVV 240 RPRK LT TKSN +M WDE +++ +P++ WDK+ +D AR + +P D + Sbjct: 179 RPRKLLTVITKSNAQRHAMVMWDEIALQVSKEFPDVTWDKELVDASTARMINRPASLDTI 238 Query: 241 VASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIAT 300 VA+NL DILSDL A G++GIAP+ N++PER FPS+FEP+HGSA DI GK +ANP+ T Sbjct: 239 VATNLHADILSDLAAALAGSLGIAPTGNIDPERRFPSMFEPIHGSAFDIMGKGLANPVGT 298 Query: 301 IWAGAMMLDFLGNGDERFQQAHNGILAAIEEVIA-HGPKTPDMKGNATTPQVADAICKII 359 W+ M+L+ LG D A N ++ A+E V A T D+ G ATT QV A+C I Sbjct: 299 FWSVVMLLEHLGELD-----AANRVMQAVEAVTADKSLHTGDLGGTATTAQVTAAVCAFI 353 Query: 360 LR 361 R Sbjct: 354 ER 355 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: 391 Number of extensions: 17 Number of successful extensions: 5 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 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