Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate WP_057508989.1 ABB28_RS12825 2-deoxy-D-gluconate 3-dehydrogenase
Query= SwissProt::Q92EU6 (254 letters) >NCBI__GCF_001431535.1:WP_057508989.1 Length = 251 Score = 149 bits (376), Expect = 5e-41 Identities = 91/245 (37%), Positives = 139/245 (56%), Gaps = 4/245 (1%) Query: 10 FNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQINP--SRTLALQV 67 F++ KVA+VTG +G+G+ +A + GA V + I D A+I R LA++ Sbjct: 5 FSLEGKVALVTGGNTGLGQGIAVALAAAGADVAVAGIAPPT-DTVAKITGLGRRCLAIEA 63 Query: 68 DITKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMA 127 ++ E +E+VV E + +DIL N+AG+ A D E+ WD M +N+K +F ++ Sbjct: 64 NLVSIEPVERVVRETIEGLGGLDILVNNAGLIRRADAVDFTEQDWDDVMNVNIKSAFFIS 123 Query: 128 QIIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNA 187 Q GR IA G GKI+N+AS S + +Y ASK+ I +T++LA EWA INVNA Sbjct: 124 QAAGRHFIAQGHGKIINIASMLSFQGGVRVPSYTASKSGIAGITRLLANEWAGKGINVNA 183 Query: 188 ISPTVILTELGKKAWA-GQVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGENLI 246 I+P + T+ A + + + IPA R+G PE++A A+FL S A+ + G L Sbjct: 184 IAPGYMATDNTAALRADADRNKSILERIPAARWGNPEDLAGAAVFLASSASDYVNGAVLP 243 Query: 247 IDGGY 251 +DGG+ Sbjct: 244 VDGGW 248 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: 154 Number of extensions: 6 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: 251 Length adjustment: 24 Effective length of query: 230 Effective length of database: 227 Effective search space: 52210 Effective search space used: 52210 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 24 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