Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate GFF2436 PGA1_c24680 glyoxylate reductase GyaR
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Phaeo:GFF2436 Length = 318 Score = 181 bits (458), Expect = 3e-50 Identities = 108/248 (43%), Positives = 141/248 (56%), Gaps = 3/248 (1%) Query: 60 ATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAE 119 A R + L+ VG++ DV GI ++NTP +T++TADT +L+L +ARR E Sbjct: 67 APRCRLLANFGVGYNHIDVDAAKTAGIAVSNTPGAVTDATADTALTLMLMTARRAGEGER 126 Query: 120 WVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQA 179 V++G WQ + G+ + GK +GIVG GRIG A+ARR GF M V Y RS Sbjct: 127 LVRSGQWQGWHPTQMLGLHLTGKHVGIVGFGRIGEAIARRCHFGFGMSVSYLARSEKSPG 186 Query: 180 EEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDE 239 A R L L A+ D + L VP ET+HLI A L +M+ A+LIN +RG VDE Sbjct: 187 FPA--VRADSLTALAASVDVLVLAVPGGAETRHLINAEVLAAMRPEALLINIARGEVVDE 244 Query: 240 KALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAE 299 ALI ALQ G I GAGLDV+E EP L ++ V LPH+G+AT E R M A + Sbjct: 245 AALISALQTGQIAGAGLDVYEFEP-EVPLALQQMEQVTLLPHLGTATEEVRSDMGHLALD 303 Query: 300 NLVAALDG 307 N+ A L G Sbjct: 304 NVAAFLAG 311 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: 179 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: 318 Length adjustment: 28 Effective length of query: 293 Effective length of database: 290 Effective search space: 84970 Effective search space used: 84970 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