Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_092487414.1 BM299_RS17355 phosphoglycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_900115975.1:WP_092487414.1 Length = 529 Score = 192 bits (488), Expect = 2e-53 Identities = 115/316 (36%), Positives = 177/316 (56%), Gaps = 8/316 (2%) Query: 3 KIVAWKSLPEDVLAYLQQHAQVVQVDATQ--HDAFVAALKDADGGI-GSSVKITPAMLEG 59 K++A ++ E L L++ + V + D V + D D I S+ K+TP +LE Sbjct: 5 KVLAMDNVSEKGLEPLRKEPDIEVVIGKKMTEDELVEIIGDYDAMIVRSATKVTPRVLEN 64 Query: 60 ATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAE 119 A +LK + VG D D+ T+ G+++ N PD T + + +++LA AR + + Sbjct: 65 APKLKVVGRAGVGVDNIDLNAATQHGVLVVNAPDGNTIAATEHTIAMMLALARNIPQAVA 124 Query: 120 WVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQA 179 +K G W A GV+++GK LG++GLGRIG AVARRA M ++ + + Sbjct: 125 KMKNGVWDKK---AFLGVELRGKVLGVIGLGRIGSAVARRAQ-ALEMDIVAYDPYITSEK 180 Query: 180 EEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDE 239 E+ G + V + ELL ADF+ + +P T ET H++ MK +IN +RG VDE Sbjct: 181 AESLGIKLVTMDELLPVADFITMHMPKTKETYHMLDEQAFAKMKDGVRVINCARGGIVDE 240 Query: 240 KALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAE 299 +AL + +Q+G + GA LDVFE EP ++SPLL L N +A PH+G++T E + +A + AE Sbjct: 241 EALYKYMQSGKVAGAALDVFEKEP-NTESPLLALDNFIATPHLGASTAEAQLNVAIDVAE 299 Query: 300 NLVAALDGTLTSNIVN 315 +V AL G + N VN Sbjct: 300 EIVEALQGKVVRNTVN 315 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: 342 Number of extensions: 18 Number of successful extensions: 4 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: 529 Length adjustment: 31 Effective length of query: 290 Effective length of database: 498 Effective search space: 144420 Effective search space used: 144420 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