Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate 5210421 Shew_2862 short chain dehydrogenase (RefSeq)
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__PV4:5210421 Length = 255 Score = 140 bits (352), Expect = 3e-38 Identities = 91/249 (36%), Positives = 137/249 (55%), Gaps = 5/249 (2%) Query: 10 FNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIK-EDVKDVAAQI--NPSRTLALQ 66 F+++ ++A+VTGA+ GIG A+AEL + GA+V++ K E + VA QI N A+ Sbjct: 7 FDLSGRIALVTGASRGIGAAIAELLAAYGAHVIVASRKAEGCQTVAEQIIDNGGSAEAMA 66 Query: 67 VDITKKENIEKVVAEIKKVYPKIDILANSAGV-ALLEKAEDLPEEYWDKTMELNLKGSFL 125 + E I+ +I+ + ++DIL N+A D ++KTME+NL+G F Sbjct: 67 CHVGDLEAIQATFEQIQAKHGRLDILVNNAATNPYFGHILDTDLNAFNKTMEVNLRGYFF 126 Query: 126 MAQIIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINV 185 M+ GR M G G I+N AS ++ + Y SKAA+VSMT+ A E AP I Sbjct: 127 MSVTAGRMMREQGHGVILNTASVNALQPGEMQGIYSISKAAVVSMTKAFAKECAPLGIRC 186 Query: 186 NAISPTVILTELGKKAWAG-QVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGEN 244 NA+ P T+ + ++ + + IP GR P E+A L+LVSDA+S TGE Sbjct: 187 NALLPGFTKTQFAGALFNNDKIYQQLIARIPMGRHAVPSEMAGAVLYLVSDASSYTTGET 246 Query: 245 LIIDGGYTI 253 L++DGG T+ Sbjct: 247 LVVDGGLTL 255 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: 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: 255 Length adjustment: 24 Effective length of query: 230 Effective length of database: 231 Effective search space: 53130 Effective search space used: 53130 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