Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate GFF1748 HP15_1707 short-chain dehydrogenase/reductase SDR
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__Marino:GFF1748 Length = 256 Score = 130 bits (327), Expect = 3e-35 Identities = 83/250 (33%), Positives = 133/250 (53%), Gaps = 10/250 (4%) Query: 15 KVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQINPSRTLAL---QVDITK 71 KVAV+TG + GIG A A +E+GA V +LD ++ + A+ R L D++K Sbjct: 7 KVAVITGGSVGIGAATALRMAEEGAAVAILDCQDSEGEALAKQLEGRGLKAGYWHCDVSK 66 Query: 72 KENIEKVVAEIKKVYPKIDILANSAGVALLEK-AEDLPEEYWDKTMELNLKGSFLMAQII 130 ++ +++V+ + + +L N+AG+A K +L EE WD ++N+KG F + Sbjct: 67 EQEVKQVLDAVANTFGTPTVLVNNAGIAGANKPTHELTEEEWDHVQDVNVKGVFFCTKHA 126 Query: 131 GREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNAISP 190 M G G I+N++S +++ Y ASK A+ M++ A+ +A NI N+I P Sbjct: 127 IPHMKKAGVGSIINLSSIYGLVSAPDIPPYHASKGAVRLMSKTDALLYATENIRCNSIHP 186 Query: 191 TVILTEL--GKKAWAGQVGEDMKK----LIPAGRFGYPEEVAACALFLVSDAASLITGEN 244 I T L GQ E+ KK + P G G P+++A A++L SD + +TG Sbjct: 187 GFIWTPLVEAHLKTTGQDPEEAKKATAAMHPVGHMGEPDDIAWGAVYLASDESKFVTGSE 246 Query: 245 LIIDGGYTIK 254 L+IDGGYT + Sbjct: 247 LVIDGGYTAR 256 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: 146 Number of extensions: 6 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: 256 Length adjustment: 24 Effective length of query: 230 Effective length of database: 232 Effective search space: 53360 Effective search space used: 53360 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