Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate SMc02849 SMc02849 2-hydroxyacid dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Smeli:SMc02849 Length = 334 Score = 175 bits (443), Expect = 2e-48 Identities = 118/281 (41%), Positives = 160/281 (56%), Gaps = 11/281 (3%) Query: 36 VAALKDADGGIGSSV-KITPAMLEGA-TRLKALSTISVGFDQFDVADLTRRGIVLANTPD 93 VAA+K AD + + +I A++E A +LK ++ S G D DV R+GI + NTP+ Sbjct: 44 VAAVKRADVLVPTVTDRIDAALIEQAGPQLKLIAAFSNGVDNIDVDAAARKGITVTNTPN 103 Query: 94 VLTESTADTVFSLILASARRVVELAEWV--KAGHWQHSIGPALFGVDVQGKTLGIVGLGR 151 VLTE TAD +LILA RR+ E A+ + + G W + G + GK +GIVG+GR Sbjct: 104 VLTEDTADMTMALILAVPRRLAEGAQVLTDRKGEWAGWSPTWMLGRRIAGKRIGIVGMGR 163 Query: 152 IGGAVARRAALGFNMKVLYTNRS-ANPQAEEAYGARRVE-LAELLATADFVCLQVPLTPE 209 IG AVARRA F + + Y NR P+ EE A + L ++LA D V + P TP Sbjct: 164 IGTAVARRAK-AFGLSIHYHNRHRVKPETEEMLEATYWDSLDQMLARVDIVSVNCPSTPA 222 Query: 210 TKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSP 269 T HL+ A L M+ + ++N +RG +DE ALI++L+ G I GAGLDVFE EP + Sbjct: 223 TYHLLSARRLALMRPDSYIVNTARGGIIDEAALIKSLREGKIAGAGLDVFENEPCVNPK- 281 Query: 270 LLKLA---NVVALPHIGSATHETRHAMARNAAENLVAALDG 307 L+KLA VV LPH+ SAT E R M N+ DG Sbjct: 282 LIKLAGEGKVVLLPHMSSATLEGRIDMGEKVVINIRTFFDG 322 Lambda K H 0.317 0.131 0.366 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: 234 Number of extensions: 8 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: 321 Length of database: 334 Length adjustment: 28 Effective length of query: 293 Effective length of database: 306 Effective search space: 89658 Effective search space used: 89658 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 (21.7 bits) S2: 48 (23.1 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