Align D-malate dehydrogenase (decarboxylating) (EC 1.1.1.83) (characterized)
to candidate 3607360 Dshi_0775 tartrate dehydrogenase (RefSeq)
Query= BRENDA::P76251 (361 letters) >FitnessBrowser__Dino:3607360 Length = 359 Score = 498 bits (1283), Expect = e-146 Identities = 246/357 (68%), Positives = 285/357 (79%), Gaps = 6/357 (1%) Query: 6 RIAAIPGDGIGKEVLPEGIRVLQAAAERWGFALSFEQMEWASCEYYSHHGKMMPDDWHEQ 65 RIA IPGDGIG EV+PEG++VL AAA ++ L FE ++AS YY HG+MMPDDW + Sbjct: 7 RIAVIPGDGIGTEVVPEGLKVLTAAARKFDIGLEFETHDFASAAYYQAHGQMMPDDWKSR 66 Query: 66 LSRFDAIYFGAVGWPDTVPDHISLWGSLLKFRREFDQYVNLRPVRLFPGVPCPLAGKQPG 125 + DA+YFGAVGWPD VPDH+SLWGSLLKFRREFDQYVNLRPVRL PGV PLAG+ PG Sbjct: 67 IGDSDALYFGAVGWPDMVPDHVSLWGSLLKFRREFDQYVNLRPVRLMPGVTSPLAGRAPG 126 Query: 126 DIDFYVVRENTEGEYSSLGGRVNEGTEHEVVIQESVFTRRGVDRILRYAFELAQSRPRKT 185 +IDF+VVRENTEGEYSS+GGR+ EGTE E V+QE+V TR GVDR+LR+AFELAQSRP+K Sbjct: 127 EIDFWVVRENTEGEYSSIGGRIFEGTERETVMQETVMTRVGVDRVLRFAFELAQSRPKKH 186 Query: 186 LTSATKSNGLAISMPYWDERVEAMAENYPEIRWDKQHIDILCARFVMQPERFDVVVASNL 245 LTSATKSNG++I+MPYWDERV MA+ YPE+ DK HIDIL A FV+ P+ FDVVVASNL Sbjct: 187 LTSATKSNGISITMPYWDERVVEMAKGYPEVAVDKYHIDILTAHFVLHPDWFDVVVASNL 246 Query: 246 FGDILSDLGPACTGTIGIAPSANLNPERTFPSLFEPVHGSAPDIYGKNIANPIATIWAGA 305 FGDILSDLGPACTGTIGIAPS N+NPER FPSLFEPVHGSAPDI GK IANP+ +WAGA Sbjct: 247 FGDILSDLGPACTGTIGIAPSGNINPERDFPSLFEPVHGSAPDIAGKGIANPVGQVWAGA 306 Query: 306 MMLDFLGNGDERFQQAHNGILAAIEEVIAHG-PKTPDMKGNATTPQVADAICKIILR 361 MMLD LG G +A I+AA+EEV+A +T D+ G A T DAI + R Sbjct: 307 MMLDHLGQG-----EAAAAIVAALEEVLADPVRRTADLGGQAGTVACGDAIVAALER 358 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: 484 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