Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate WP_025272126.1 HALAL_RS0100575 SDR family NAD(P)-dependent oxidoreductase
Query= SwissProt::Q92EU6 (254 letters) >NCBI__GCF_000527155.1:WP_025272126.1 Length = 290 Score = 106 bits (265), Expect = 5e-28 Identities = 75/253 (29%), Positives = 132/253 (52%), Gaps = 17/253 (6%) Query: 11 NITDKVAVVTGAAS--GIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQINPSRTLALQVD 68 ++ K A+VTGA + GIG A+A GA + L+ + + + A +++ + D Sbjct: 45 SLIGKTALVTGAGADDGIGMAIATRLRLAGARLALVSTTKRIHERANELD---AVGFVAD 101 Query: 69 ITKKENIEKVVAEIKKVYPKIDILANSAGV------ALLEKAEDLPEEYWDKTMELNLKG 122 +T + + + + + ++DI+ N+AG+ A+ + L + W+ + NL Sbjct: 102 LTDEAEVAGLGDAVTEGLGEVDIVVNNAGMTSKTAPAVTKPVAQLGFDDWEAEITRNLHS 161 Query: 123 SFLMAQIIGREMIATGGGKIVNMASQASVIA-LDKHVAYCASKAAIVSMTQVLAMEWAPY 181 +FL+++ + M +G G+IVN+++ A V + + AY ++KA + +T+ LA E Sbjct: 162 TFLVSRYFVQSMAESGWGRIVNVSATAGVSSVMPAEAAYASAKAGVAGLTRALATEVVAD 221 Query: 182 NINVNAISPTVILTELGKKAWAGQVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLIT 241 + VNA++P +I T Q G D P GR G PEEVAA F S +AS +T Sbjct: 222 GVTVNAVAPGLIHTGSSTVPEL-QRGVDS----PLGRPGTPEEVAAAVAFFCSPSASYVT 276 Query: 242 GENLIIDGGYTIK 254 G+ L++DGG I+ Sbjct: 277 GQTLVVDGGNGIR 289 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: 156 Number of extensions: 11 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: 290 Length adjustment: 25 Effective length of query: 229 Effective length of database: 265 Effective search space: 60685 Effective search space used: 60685 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 Apr 09 2024. 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