Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate RR42_RS31670 RR42_RS31670 NAD-dependent dehydratase
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__Cup4G11:RR42_RS31670 Length = 254 Score = 155 bits (393), Expect = 6e-43 Identities = 91/244 (37%), Positives = 139/244 (56%), Gaps = 2/244 (0%) Query: 9 DFNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQINPSRTLALQVD 68 DF +T +V VVTG SGIGKA+A F+ GA VV+LD + A S D Sbjct: 7 DFRLTGQVTVVTGGGSGIGKALAHTFAGAGARVVVLDTNGAAAEQVANEIGSMAQHAVAD 66 Query: 69 ITKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMAQ 128 ++ ++ IE V+ ++ + + +ID+L N+AGV + DL W+ + +N+ G FL A+ Sbjct: 67 VSNEDAIESVMEDVARQHGRIDVLFNNAGVNRRNTSFDLTIADWNAVVAVNMTGMFLCAR 126 Query: 129 IIGREMIATGGGKIVNMASQASVI-ALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNA 187 R M GGG+IVN AS + ++ Y A+K A+V+MT+ A+EWAPYNI VNA Sbjct: 127 AAARHMRDGGGGRIVNTASILGISGGWYPNIVYQATKGAVVNMTRSWAVEWAPYNIRVNA 186 Query: 188 ISPTVILTELGKKAWA-GQVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGENLI 246 ++P++I T + + + V + L P GR P ++ LFL + A+S++TG L Sbjct: 187 VAPSIIRTPMTEALTSQPDVVAKFEALTPLGRLCEPADMTGPVLFLATAASSMVTGHILP 246 Query: 247 IDGG 250 +DGG Sbjct: 247 VDGG 250 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: 180 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: 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