Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate WP_011384506.1 AMB_RS10625 3-oxoacyl-[acyl-carrier-protein] reductase
Query= SwissProt::Q92EU6 (254 letters) >NCBI__GCF_000009985.1:WP_011384506.1 Length = 245 Score = 121 bits (304), Expect = 1e-32 Identities = 71/241 (29%), Positives = 126/241 (52%), Gaps = 1/241 (0%) Query: 10 FNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQINPSRTLALQVDI 69 F++T K A+VTGA+ GIG A+A+ +GA V L + + D A R L ++ Sbjct: 2 FDLTGKTALVTGASGGIGGAIAKALHARGATVGLHGTRREALDALAAELGERVHVLPANL 61 Query: 70 TKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMAQI 129 + +E++ + + +DIL N+AG+ + +E W +++NL +F +++ Sbjct: 62 SDAAAVEQLAKDAEAAMGSVDILVNNAGLTKDGLVLRMKDEDWQTVLDVNLTAAFRLSRA 121 Query: 130 IGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNAIS 189 + + G+I+N+ S V V Y ASKA ++ M++ LA E A NI VN ++ Sbjct: 122 AVKGQMKRRWGRIINITSIVGVTGNPGQVNYAASKAGMIGMSKALAQEVASRNITVNCVA 181 Query: 190 PTVILTELGKKAWAGQVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGENLIIDG 249 P + + + + + + IPAGR G +E+AA ++L S A+ +TG+ L ++G Sbjct: 182 PGFVSSAM-TDVLSDEQKTKLNAGIPAGRMGTADEIAAAVVYLASAEAAYVTGQTLHVNG 240 Query: 250 G 250 G Sbjct: 241 G 241 Lambda K H 0.316 0.133 0.369 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: 148 Number of extensions: 9 Number of successful extensions: 2 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: 254 Length of database: 245 Length adjustment: 24 Effective length of query: 230 Effective length of database: 221 Effective search space: 50830 Effective search space used: 50830 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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