Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate AO353_28225 AO353_28225 tartrate dehydrogenase
Query= BRENDA::P76251 (361 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28225 Length = 359 Score = 594 bits (1532), Expect = e-174 Identities = 279/355 (78%), Positives = 314/355 (88%) Query: 1 MMKTMRIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPD 60 M KT RIAAI GDGIGKEVLPEG+RVL+ AA++W LS E ++WA C+YY HG+MMPD Sbjct: 1 MSKTFRIAAIAGDGIGKEVLPEGLRVLEQAAKKWQLELSIEVLDWAHCDYYLEHGQMMPD 60 Query: 61 DWHEQLSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLA 120 DW EQL FDAIYFGAVGWPD VPDHISLWGSLLKFRR+FDQYVN+RPVRLFPGVPCPLA Sbjct: 61 DWFEQLKGFDAIYFGAVGWPDKVPDHISLWGSLLKFRRDFDQYVNIRPVRLFPGVPCPLA 120 Query: 121 GKQPGDIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQS 180 G++PGDIDF V+RENTEGEYSS+GG++ EGTEHE V+QESVFTRRGVDRIL++AF+LAQ+ Sbjct: 121 GRKPGDIDFVVIRENTEGEYSSVGGKMFEGTEHEFVLQESVFTRRGVDRILKFAFDLAQT 180 Query: 181 RPRKTLTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVV 240 RPRK LT+ATKSNG++ISMPYWDER MA YPEI WDKQHIDILCARFV+QP+RFDVV Sbjct: 181 RPRKRLTAATKSNGISISMPYWDERTALMAAQYPEITWDKQHIDILCARFVLQPDRFDVV 240 Query: 241 VASNLFGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIAT 300 VASNLFGDILSDLGPAC GTIGIAPSANL+PER FPSLFEPVHGSAPDIYG+NIANPIA Sbjct: 241 VASNLFGDILSDLGPACAGTIGIAPSANLDPERRFPSLFEPVHGSAPDIYGQNIANPIAM 300 Query: 301 IWAGAMMLDFLGNGDERFQQAHNGILAAIEEVIAHGPKTPDMKGNATTPQVADAI 355 IW+GA+MLDFLGNGDER++ AH+GIL AIE VIA GP TPD+ G +T V AI Sbjct: 301 IWSGALMLDFLGNGDERYRAAHDGILQAIERVIAEGPITPDLGGKGSTQDVGKAI 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: 548 Number of extensions: 13 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: 359 Length adjustment: 29 Effective length of query: 332 Effective length of database: 330 Effective search space: 109560 Effective search space used: 109560 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