Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate AO353_01660 AO353_01660 short-chain dehydrogenase
Query= SwissProt::Q92EU6 (254 letters) >FitnessBrowser__pseudo3_N2E3:AO353_01660 Length = 253 Score = 139 bits (349), Expect = 7e-38 Identities = 91/260 (35%), Positives = 150/260 (57%), Gaps = 19/260 (7%) Query: 1 MTFKGFDKDFNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQINPS 60 MTF G +VA+VTGAA+GIG+A A+ F+ +G VV+ D+ + A++ + Sbjct: 3 MTFSG---------QVALVTGAAAGIGRATAQAFAAEGLKVVVADLDVAGGEGTAELIRA 53 Query: 61 ---RTLALQVDITKKENIEKVVAEIKKVYPKIDILANSAGVALLEK---AEDLPEEYWDK 114 + +Q ++T++ +++ ++A+ Y ++D N+AG+ + EK AE +E+ D Sbjct: 54 AGGEAVFVQCNVTQESDVQNLMAKAVSTYGRLDYAFNNAGIEI-EKGKLAEGTLDEF-DA 111 Query: 115 TMELNLKGSFLMAQIIGREMIATGGGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVL 174 M +N+KG +L + M+A GGG IVN AS A + A K Y ASK A++ +T+ Sbjct: 112 IMGVNVKGVWLCMKYQLPLMLAQGGGAIVNTASVAGLGAAPKMSIYAASKHAVIGLTKSA 171 Query: 175 AMEWAPYNINVNAISPTVILTELGKKAWAG--QVGEDMKKLIPAGRFGYPEEVAACALFL 232 A+E+A I VNA+ P VI T++ ++A+ + + + P GR G EE+A+ L+L Sbjct: 172 AIEYAKKKIRVNAVCPAVIDTDMFRRAYEADPKKADFAAAMHPVGRIGKVEEIASAVLYL 231 Query: 233 VSDAASLITGENLIIDGGYT 252 SD A+ TG +L +DGG T Sbjct: 232 CSDGAAFTTGHSLAVDGGVT 251 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: 142 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: 253 Length adjustment: 24 Effective length of query: 230 Effective length of database: 229 Effective search space: 52670 Effective search space used: 52670 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