Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate 3608642 Dshi_2035 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__Dino:3608642 Length = 254 Score = 140 bits (354), Expect = 2e-38 Identities = 83/246 (33%), Positives = 131/246 (53%), Gaps = 1/246 (0%) Query: 10 FNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQINPSRTLALQVDI 69 F++T +VA VTGA+SG+G+ A + + GA VV + + D P RT + D+ Sbjct: 9 FDLTGRVACVTGASSGLGRRAATVLARAGASVVGVARRADALAAWEAETPGRTASAAWDV 68 Query: 70 TKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMAQI 129 ++++ +V I + DIL +AG+ E+A+ + WD T+ LNL F +AQ Sbjct: 69 ADRDSLPDMVEAISAPFGAPDILVLAAGINNRERADAVTAAGWDATLALNLTAPFFLAQA 128 Query: 130 IGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNAIS 189 + M G G+IVN AS + A VAY A+K I +T+ +A W+ IN NA+ Sbjct: 129 LVPAMSEKGWGRIVNFASLQTTRAFPGGVAYGATKGGIAQLTRAMAEAWSAQGINANAVG 188 Query: 190 PTVILTELGKKAWAG-QVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGENLIID 248 P TEL + + +++ GR G P ++ LFL SDA++ +TG+ L++D Sbjct: 189 PGFFKTELTAPVFDNPALAQELADKTCIGRNGVPGDIDGPLLFLCSDASAYVTGQILMVD 248 Query: 249 GGYTIK 254 GG+T K Sbjct: 249 GGFTAK 254 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: 153 Number of extensions: 5 Number of successful extensions: 2 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