Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_037452955.1 N825_RS14670 D-glycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_000576635.1:WP_037452955.1 Length = 326 Score = 191 bits (485), Expect = 2e-53 Identities = 112/277 (40%), Positives = 158/277 (57%), Gaps = 4/277 (1%) Query: 33 DAFVAALKDADGGIGSSVKITPA-MLEGAT-RLKALSTISVGFDQFDVADLTRRGIVLAN 90 D + + AD + +V PA ++ G ++ ++T SVG D D+A RG+ +AN Sbjct: 44 DEMIRLAQGADAMLVCAVDQVPADLIRGLPDSVRMIATFSVGTDHIDLAAAKERGVTVAN 103 Query: 91 TPDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLG 150 TP VLT++TAD F L+L +ARR E ++ W L GV V GK L I+G+G Sbjct: 104 TPGVLTDATADIAFLLLLGAARRAAEGERLIREHRWDGWAPTQLVGVHVTGKRLAILGMG 163 Query: 151 RIGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPET 210 RIG A+ARRA GF+M++ Y NR P +EA + E+L ADF+ + P TPET Sbjct: 164 RIGQAMARRAQ-GFDMEIHYHNRRRLPADQEAGAIYHADADEMLGIADFLSIHSPATPET 222 Query: 211 KHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPL 270 +H + A + + A+++N +RG VD++ALI AL++G + AGLDVFE EP Sbjct: 223 RHWLNAGRIARLPDGAVVVNTARGTLVDDEALIAALRSGKLAAAGLDVFENEP-KLHPGY 281 Query: 271 LKLANVVALPHIGSATHETRHAMARNAAENLVAALDG 307 L N LPH+GSAT +TR AM A +NL A G Sbjct: 282 AGLPNTFLLPHLGSATDQTRDAMGFKALDNLDAFFAG 318 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: 228 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: 326 Length adjustment: 28 Effective length of query: 293 Effective length of database: 298 Effective search space: 87314 Effective search space used: 87314 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 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