Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_011973284.1 MAEO_RS02815 phosphoglycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_000017185.1:WP_011973284.1 Length = 523 Score = 202 bits (514), Expect = 1e-56 Identities = 117/316 (37%), Positives = 176/316 (55%), Gaps = 6/316 (1%) Query: 1 MKKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVAALKDADG-GIGSSVKITPAMLEG 59 M KI+ S+ +D + L+Q V + +KDAD I S K T +++ Sbjct: 1 MPKILITDSIHDDAVELLKQAGTVEVATDLTVEELKEKIKDADALVIRSGTKATKEIIDA 60 Query: 60 ATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAE 119 A LK ++ VG D D+ T +GI++ N+PD + S A+ L+L+SAR + + Sbjct: 61 ADNLKVIARAGVGVDNVDLTAATEKGIIVVNSPDASSISVAELALGLMLSSARNIPQATA 120 Query: 120 WVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQA 179 +K G W + G+++ GKTLGI+GLGRIG +A+RA F M V+ + + Sbjct: 121 SLKRGEWDRK---SFKGMELYGKTLGIIGLGRIGQQIAKRAE-AFGMTVVAYDPYIPVEV 176 Query: 180 EEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDE 239 + G +E+ +L +DF+ L VPLTP+TKH+IG ++ MK + I++N +RG +DE Sbjct: 177 AKNMGIELMEVNDLCKVSDFITLHVPLTPKTKHMIGKEQISLMKPNTIIVNCARGGLIDE 236 Query: 240 KALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAE 299 +AL +A+ N I GAGLDVFE EP P D+PLL L + PH G++T E + + AE Sbjct: 237 EALYDAINNKKIGGAGLDVFEEEP-PKDNPLLTLDKFIGTPHQGASTVEAQKSAGTVVAE 295 Query: 300 NLVAALDGTLTSNIVN 315 +V L G NIVN Sbjct: 296 QVVKILAGKPADNIVN 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: 328 Number of extensions: 12 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: 523 Length adjustment: 31 Effective length of query: 290 Effective length of database: 492 Effective search space: 142680 Effective search space used: 142680 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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