Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_017559746.1 C892_RS0126925 phosphoglycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_000341205.1:WP_017559746.1 Length = 529 Score = 171 bits (432), Expect = 5e-47 Identities = 106/302 (35%), Positives = 156/302 (51%), Gaps = 6/302 (1%) Query: 15 LAYLQQHAQVVQVDATQHDAFVAALKDADGGI-GSSVKITPAMLEGATRLKALSTISVGF 73 LA L+ +V + AL D D I S+ ++ L A +LK ++ VG Sbjct: 17 LALLEGDFEVRHTTGADRSQLLPALADVDALIVRSATQVDAEALAAAPKLKVVARAGVGL 76 Query: 74 DQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPA 133 D DV T+ G+++ N P S A+ +L+LASAR + G W+ S Sbjct: 77 DNVDVDAATKAGVLVVNAPTSNIISAAEQAVNLLLASARNTAPAHNALVNGEWKRS---K 133 Query: 134 LFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAEL 193 GV+V KT+G+VGLGRIG VA+R A F K++ + P G V L EL Sbjct: 134 YTGVEVYDKTVGVVGLGRIGALVAQRLA-AFGTKLIAYDPFVQPARAAQMGVEMVSLDEL 192 Query: 194 LATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHG 253 L +DF+ + +P + +T LIG L +K S +INA+RG +DE AL A++ G + G Sbjct: 193 LQRSDFITVHLPKSKDTLGLIGDEALHKVKPSVRVINAARGGILDEDALYRAIKEGRVAG 252 Query: 254 AGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAENLVAALDGTLTSNI 313 AG+DV+ +EP +DSPL + NVV PH+G++THE + ++ AL G + Sbjct: 253 AGIDVWASEPC-TDSPLFEFENVVVAPHLGASTHEAQEKAGTQVVRSVKLALAGEFVPDA 311 Query: 314 VN 315 VN Sbjct: 312 VN 313 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: 343 Number of extensions: 13 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: 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 Sep 24 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