Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate H281DRAFT_04145 H281DRAFT_04145 NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__Burk376:H281DRAFT_04145 Length = 245 Score = 167 bits (422), Expect = 2e-46 Identities = 97/247 (39%), Positives = 151/247 (61%), Gaps = 8/247 (3%) Query: 10 FNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQINPSRTLALQVDI 69 F+ + + +VTGA+SGIG+A E+ GA VV V ++A + L +D+ Sbjct: 5 FDFSGRSILVTGASSGIGRATVEMLCACGANVVAA--ARSVSELARLAEETGCEPLMLDV 62 Query: 70 TKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMAQI 129 + + I+ A + D L N AG+ALLE+A D +D+ M +N +G+ L+A+ Sbjct: 63 SDEAAIDDAFASLGP----FDGLVNCAGIALLERAVDTTAASFDRVMAVNTRGAVLVAKH 118 Query: 130 IGREMI-ATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNAI 188 + R MI A G IVN++SQA+++ALD H++Y ASKAA+ ++T+ L +E P+ I N++ Sbjct: 119 VARGMIEAKRAGSIVNVSSQAALVALDDHLSYSASKAAMDAVTRALCIELGPFGIRANSV 178 Query: 189 SPTVILTELGKKAWAGQV-GEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGENLII 247 +PTV LT + +AW+ V E K IP GRF P EVA+ FL+SDAAS+++G +L + Sbjct: 179 NPTVTLTPMAVQAWSDPVKREPALKAIPLGRFAEPVEVASVVAFLLSDAASMVSGVSLAV 238 Query: 248 DGGYTIK 254 DGG+T + Sbjct: 239 DGGFTAR 245 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: 139 Number of extensions: 5 Number of successful extensions: 4 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: 245 Length adjustment: 24 Effective length of query: 230 Effective length of database: 221 Effective search space: 50830 Effective search space used: 50830 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