Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate CA265_RS00760 CA265_RS00760 2-deoxy-D-gluconate 3-dehydrogenase
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__Pedo557:CA265_RS00760 Length = 254 Score = 153 bits (386), Expect = 4e-42 Identities = 93/247 (37%), Positives = 132/247 (53%), Gaps = 5/247 (2%) Query: 10 FNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQIN----PSRTLAL 65 FN+ K A+VTG GIGKAMA +E GA ++ + +++ A + + A Sbjct: 5 FNLAGKTALVTGCKRGIGKAMALALAEAGADIIGVSASLELQGSAVEKEILALGRKFYAY 64 Query: 66 QVDITKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFL 125 Q D K+EN A++K +P IDIL N+AG L + + +EYWD+ + +N F+ Sbjct: 65 QCDFGKRENTLAFAAQVKADHPVIDILVNNAGTILRQPIAEHSDEYWDEVIAVNQTAPFI 124 Query: 126 MAQIIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINV 185 + + IGREMIA G GK++ AS S Y ASK AI S+T+ A EWA +NV Sbjct: 125 LTREIGREMIARGSGKVIFTASLLSFQGGITVPGYAASKGAIASLTKAFANEWASKGVNV 184 Query: 186 NAISPTVILTELGKKAWAGQ-VGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGEN 244 NAI+P I T+ Q + IPAGR+G PE+ LFL S A+ + G Sbjct: 185 NAIAPGYIATDNTSALREDQDRSTSILSRIPAGRWGTPEDFKGPTLFLASPASDYVHGTI 244 Query: 245 LIIDGGY 251 L +DGG+ Sbjct: 245 LTVDGGW 251 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: 163 Number of extensions: 8 Number of successful extensions: 4 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: 254 Length adjustment: 24 Effective length of query: 230 Effective length of database: 230 Effective search space: 52900 Effective search space used: 52900 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: 47 (22.7 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