Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate Pf1N1B4_4412 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__pseudo1_N1B4:Pf1N1B4_4412 Length = 351 Score = 353 bits (907), Expect = e-102 Identities = 189/361 (52%), Positives = 245/361 (67%), Gaps = 11/361 (3%) Query: 2 MKTMRIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPDD 61 M +IAA+PGDGIG EV+ G+ VLQA +++ GF L+F+ +W S + Y +G +P+ Sbjct: 1 MSAYKIAAVPGDGIGVEVIAAGVEVLQALSKKSGFDLTFKHYDWNS-DNYLKNGYYIPEG 59 Query: 62 WHEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLAG 121 E+L FDAI+FGAVG + VPDHISLWG L + FDQY N+RP R+ PGV PL Sbjct: 60 GLEELKTFDAIFFGAVGALN-VPDHISLWGLRLPICQGFDQYANVRPARVLPGVKSPLLN 118 Query: 122 KQPGD-IDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQS 180 GD ID+ VVREN+EGEYS GGRV+ G EV + SVFTR GV+RI R+AFELA+S Sbjct: 119 ---GDQIDWVVVRENSEGEYSGNGGRVHRGLPEEVATEVSVFTRAGVERIHRFAFELARS 175 Query: 181 RPRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVV 240 RPRK LT TKSN M WDE +A+++P+++ DK+ +D + R V++P DV+ Sbjct: 176 RPRKHLTMVTKSNAQRHGMVLWDEIFYEVAKDFPDVKIDKELVDAVTTRMVLKPSTLDVI 235 Query: 241 VASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIAT 300 VA+NL DILSDL A +G++GIAP+ANLNP R FPS+FEP+HGSA DI GK +ANPIAT Sbjct: 236 VATNLHADILSDLAAALSGSLGIAPTANLNPSRKFPSMFEPIHGSAFDITGKGVANPIAT 295 Query: 301 IWAGAMMLDFLGNGDERFQQAHNGILAAIEEVIAHGPKTPDMKGNATTPQVADAICKIIL 360 W AMML+ LG A +++AIE V G TPD+ GNATT Q+ DA+ +I Sbjct: 296 FWTAAMMLEHLGE-----TTAAKQLMSAIEAVTESGLHTPDLGGNATTRQITDAVIALIN 350 Query: 361 R 361 R Sbjct: 351 R 351 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: 400 Number of extensions: 15 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: 351 Length adjustment: 29 Effective length of query: 332 Effective length of database: 322 Effective search space: 106904 Effective search space used: 106904 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