Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate RR42_RS21790 RR42_RS21790 short-chain dehydrogenase
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__Cup4G11:RR42_RS21790 Length = 252 Score = 165 bits (417), Expect = 1e-45 Identities = 93/245 (37%), Positives = 146/245 (59%), Gaps = 7/245 (2%) Query: 15 KVAVVTGAASGIGKAMAELFSEKGAYVVLLDIK-EDVKDVAAQINPS----RTLALQVDI 69 KV + TG ASGIG+AMA F+ GA ++LLD+ + + A++ + + ++ I Sbjct: 4 KVVLNTGGASGIGRAMAHGFARHGARLMLLDLDAQGLASAKAELEAAYPEVQVEIVKASI 63 Query: 70 TKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMAQI 129 T + +E+ A + + +IDIL N+AG+++ + + +L + W + ++++L G F Q Sbjct: 64 TDPDAVEQACAATEARFGRIDILLNNAGISMNKPSLELTPDDWRRAIDIDLSGVFFCTQA 123 Query: 130 IGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNAIS 189 R M+ GGG I++ AS + + + +AYCA+KA +VS+T+ LA EWA YNI VNA+ Sbjct: 124 AARRMVRQGGGSILSTASMWGLASSARRLAYCAAKAGVVSLTKSLAAEWAEYNIRVNAVC 183 Query: 190 PTVILTELGKKAWAGQV--GEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGENLII 247 P T L + A + GE + P RFG PEE+A ALFL SD+A+ ITG L+ Sbjct: 184 PGYTSTALMETLLASKAIDGEALLARTPLRRFGAPEEMAEVALFLASDSAAFITGHALVS 243 Query: 248 DGGYT 252 DGG+T Sbjct: 244 DGGWT 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: 155 Number of extensions: 10 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: 252 Length adjustment: 24 Effective length of query: 230 Effective length of database: 228 Effective search space: 52440 Effective search space used: 52440 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