Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate PP_1261 PP_1261 2-ketoaldonate reductase / hydroxypyruvate/glyoxylate reductase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Putida:PP_1261 Length = 324 Score = 303 bits (775), Expect = 5e-87 Identities = 172/320 (53%), Positives = 209/320 (65%), Gaps = 4/320 (1%) Query: 2 KKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDA---FVAALKDADGGIGSSVKITPAMLE 58 K ++A+ + + LQQ V+ + D F AL +A G IG K+ A LE Sbjct: 3 KTVLAFSRITPAMAERLQQDFNVILPNPKLGDISAQFNEALPEAHGLIGVGRKLGRAQLE 62 Query: 59 GATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELA 118 GA RL+ +S++SVG+D +D+ RGI L NTPDVLTESTAD FSLI+ ARR EL Sbjct: 63 GAARLEVVSSVSVGYDNYDLDYFNERGIALTNTPDVLTESTADLGFSLIMGCARRTAELD 122 Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQ 178 W KAG+WQ ++GPA FG DV GKTLGIVG+G IG AVARR GFNM +LY+ S Sbjct: 123 AWTKAGNWQATVGPAHFGSDVHGKTLGIVGMGNIGAAVARRGRFGFNMPILYSGNSRKTA 182 Query: 179 AEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVD 238 E+ GA+ L +LLA ADFV + VPL+ T+ LI + ELK MK SA LIN +RG VD Sbjct: 183 LEKELGAQFRSLDQLLAEADFVVIVVPLSDATRKLISSRELKLMKPSAFLINIARGPVVD 242 Query: 239 EKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAA 298 E ALIEALQ GTI G GLDV+E EPL SDSPL KL N + LPHIGSAT ETR AMA A Sbjct: 243 EAALIEALQAGTIRGTGLDVYEKEPL-SDSPLFKLPNALTLPHIGSATAETREAMANRAI 301 Query: 299 ENLVAALDGTLTSNIVNREV 318 +NL AAL G ++VN +V Sbjct: 302 DNLRAALLGERPRDLVNPQV 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: 249 Number of extensions: 9 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