Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate BWI76_RS26960 BWI76_RS26960 bifunctional glyoxylate/hydroxypyruvate reductase B
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Koxy:BWI76_RS26960 Length = 323 Score = 330 bits (847), Expect = 2e-95 Identities = 179/318 (56%), Positives = 222/318 (69%), Gaps = 3/318 (0%) Query: 4 IVAWKSLPEDVLAYLQQHAQVVQVDATQHDAF---VAALKDADGGIGSSVKITPAMLEGA 60 ++ +K+LP+D+ L+QH V QV + + AA +A G +GSS K+ A+LE Sbjct: 5 VILYKTLPDDLQQRLEQHFTVTQVKNLRPETVSQHAAAFAEAVGLLGSSEKVDTALLEKM 64 Query: 61 TRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEW 120 +L+A STISVG+D FDV L R ++L +TP VLTE+ ADTV +L+L++ARRVVE+A Sbjct: 65 PKLRATSTISVGYDNFDVDALNARKVLLMHTPTVLTETVADTVMALVLSTARRVVEVANR 124 Query: 121 VKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAE 180 VKAG W SIGP FG DV KTLGIVG+GRIG A+A+RA GF M +LY R +PQAE Sbjct: 125 VKAGEWTKSIGPDWFGNDVHHKTLGIVGMGRIGMALAQRAHAGFGMPILYNARRQHPQAE 184 Query: 181 EAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEK 240 E + AR +L LL ADFVCL +PLT ET HL G A+ MK SAI INA RG VDEK Sbjct: 185 ERFNARYCDLDTLLQEADFVCLILPLTEETHHLFGKAQFAKMKSSAIFINAGRGPVVDEK 244 Query: 241 ALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAEN 300 ALI ALQ G I+ AGLDVFE EPL DSPLL + NVVALPHIGSATHETR+ MA A +N Sbjct: 245 ALIAALQEGEIYAAGLDVFEQEPLAKDSPLLSMPNVVALPHIGSATHETRYNMAACAVDN 304 Query: 301 LVAALDGTLTSNIVNREV 318 L+ AL+G++ N VN +V Sbjct: 305 LIDALNGSVEKNCVNPQV 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: 241 Number of extensions: 5 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: 323 Length adjustment: 28 Effective length of query: 293 Effective length of database: 295 Effective search space: 86435 Effective search space used: 86435 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