Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate GFF932 PS417_04730 bifunctional glyoxylate/hydroxypyruvate reductase B
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__WCS417:GFF932 Length = 324 Score = 322 bits (824), Expect = 1e-92 Identities = 175/320 (54%), Positives = 221/320 (69%), Gaps = 4/320 (1%) Query: 2 KKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDA---FVAALKDADGGIGSSVKITPAMLE 58 K ++A+ + +++ LQQ +V+ + D F AL A G IG K+ L+ Sbjct: 3 KTVLAFSRVTPEMIERLQQDFEVIAPNPKLGDISAQFNEALPHAHGLIGVGRKLGREQLQ 62 Query: 59 GATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELA 118 GA++L+ +S++SVG+D +DVA RGI+L NTPDVLTESTAD F+L+++SARRV EL Sbjct: 63 GASKLEVVSSVSVGYDNYDVAYFNERGIMLTNTPDVLTESTADLAFALLMSSARRVAELD 122 Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQ 178 W KAG W+ S+G LFG DV GKTLGIVG+G IG AVARR LGFNM +LY+ S P Sbjct: 123 AWTKAGQWKASVGAPLFGCDVHGKTLGIVGMGNIGAAVARRGRLGFNMPILYSGNSRKPA 182 Query: 179 AEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVD 238 E+ GA+ L ELLA ADFVCL VPL+ +T+HLI EL MK SAILIN SRG VD Sbjct: 183 LEQELGAQFRSLDELLAEADFVCLVVPLSDKTRHLISTRELGLMKSSAILINISRGPVVD 242 Query: 239 EKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAA 298 E ALI+ALQN TI GAGLDV+E EPL ++SPL +L+N V LPHIGSATHETR AMA A Sbjct: 243 EPALIDALQNQTIRGAGLDVYEQEPL-AESPLFQLSNAVTLPHIGSATHETREAMANRAL 301 Query: 299 ENLVAALDGTLTSNIVNREV 318 +NL +AL G ++VN +V Sbjct: 302 DNLRSALLGQRPQDLVNPQV 321 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: 258 Number of extensions: 8 Number of successful extensions: 2 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: 324 Length adjustment: 28 Effective length of query: 293 Effective length of database: 296 Effective search space: 86728 Effective search space used: 86728 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