Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate Dsui_2448 Dsui_2448 3-oxoacyl-(acyl-carrier-protein) reductase
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__PS:Dsui_2448 Length = 246 Score = 126 bits (316), Expect = 5e-34 Identities = 77/240 (32%), Positives = 128/240 (53%), Gaps = 6/240 (2%) Query: 15 KVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKED----VKDVAAQINPSRTLALQVDIT 70 ++A+VTGA+ GIGKA+A + GA VV +D + A+ AL +++ Sbjct: 5 QIALVTGASRGIGKAVALELARLGATVVGTATSDDGAGKISAYLAEAGAKGRGAL-LEVR 63 Query: 71 KKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMAQII 130 + ++ ++A ++K + + IL N+AG+ A + ++ WD ++ NLK F +++ + Sbjct: 64 DQAQVDALIAALEKEFGAVSILVNNAGITRDNLAMRMKDDEWDAVIDTNLKAVFRLSKAV 123 Query: 131 GREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNAISP 190 R M+ G+I+N+ S YCA+KA + MT+ LA E NI VN ++P Sbjct: 124 MRGMMKARAGRIINITSVVGHAGNPGQANYCAAKAGVSGMTRSLARELGSRNITVNCVAP 183 Query: 191 TVILTELGKKAWAGQVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGENLIIDGG 250 I T++ KA + E + IP GR G PE++AA FL S AA +TG + ++GG Sbjct: 184 GFIDTDM-TKALDDKQKEGLLGNIPLGRLGSPEDIAAAVAFLASPAAGYVTGSTIHVNGG 242 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: 153 Number of extensions: 10 Number of successful extensions: 3 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: 246 Length adjustment: 24 Effective length of query: 230 Effective length of database: 222 Effective search space: 51060 Effective search space used: 51060 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