Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate WP_011384971.1 AMB_RS13035 NAD(P)-dependent oxidoreductase
Query= SwissProt::Q92EU6 (254 letters) >NCBI__GCF_000009985.1:WP_011384971.1 Length = 248 Score = 131 bits (330), Expect = 1e-35 Identities = 87/243 (35%), Positives = 131/243 (53%), Gaps = 4/243 (1%) Query: 14 DKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQINPSRTLA---LQVDIT 70 DKVA++TG ASGIG + +E GA V++ DI + + AA ++ +++D+T Sbjct: 5 DKVALITGGASGIGYCTVKSMAELGADVLIADINVEAGEKAAAELTAKGFKAEFVRLDVT 64 Query: 71 KKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMAQII 130 K NI +V + ++DIL N AG ++ D + + K M LNL G + + Sbjct: 65 DKANIARVKEHVVATRGRLDILCNVAGWGHIQPFVDNDDAFIAKVMSLNLTGPIELIRAF 124 Query: 131 GREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNAISP 190 MI GKIVN+AS A + Y A+K +++ ++ LA E A +NINVNAI P Sbjct: 125 FPLMIEKKTGKIVNVASDAGRVGSLGESVYSAAKGGLIAFSKALAREGARFNINVNAICP 184 Query: 191 TVILTELGKKAWAGQVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGENLIIDGG 250 T L K+ + E K+IP RFG P+EVA +F+ S+ A ITG+ L ++GG Sbjct: 185 GPTDTPL-LKSEPEKFLEAFLKVIPMRRFGQPQEVADSIVFMASNRADYITGQVLSVNGG 243 Query: 251 YTI 253 T+ Sbjct: 244 ITM 246 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: 158 Number of extensions: 11 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: 248 Length adjustment: 24 Effective length of query: 230 Effective length of database: 224 Effective search space: 51520 Effective search space used: 51520 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