Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_086509103.1 BZY95_RS06210 D-glycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_002151265.1:WP_086509103.1 Length = 328 Score = 324 bits (830), Expect = 2e-93 Identities = 179/317 (56%), Positives = 217/317 (68%), Gaps = 3/317 (0%) Query: 2 KKIVAWKSLPEDVLAYLQQHAQVVQVDA---TQHDAFVAALKDADGGIGSSVKITPAMLE 58 K+IVA+ L L L+Q V +A T F AL A G +GSS+ I P +++ Sbjct: 3 KRIVAYTRLKPIHLDQLRQRFHVDYFEALKSTDDPGFRQALGQAHGLVGSSLVIAPELID 62 Query: 59 GATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELA 118 A +L+A++TISVG+D + V LTRRGI+L NTPDVLTE+TADT F LI+A+ARR +ELA Sbjct: 63 LAPQLEAVATISVGYDNYPVEALTRRGILLCNTPDVLTETTADTGFLLIMATARRAIELA 122 Query: 119 EWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQ 178 + VK G W SIG FG DV GKTLG+VG GRIG VARR ALGF M+VLY S P Sbjct: 123 DLVKRGDWTASIGEPHFGTDVHGKTLGMVGFGRIGAGVARRGALGFGMRVLYACSSPKPA 182 Query: 179 AEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVD 238 E+ GA R EL ELL+ ADFVC+ VPLT ET HLIG E MK SAI +N +RG VD Sbjct: 183 LEQELGAVRCELDELLSQADFVCVTVPLTAETTHLIGRREFGLMKPSAIFVNIARGKVVD 242 Query: 239 EKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAA 298 E ALI AL+ G IH AGLDVFE EPL +SPL +ANVVALPH+GSATHETR AMA+ A Sbjct: 243 EAALIAALETGEIHAAGLDVFEQEPLSPESPLPHMANVVALPHVGSATHETRDAMAQRAV 302 Query: 299 ENLVAALDGTLTSNIVN 315 +N+ AL+G ++VN Sbjct: 303 DNITLALEGKRPLSLVN 319 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: 247 Number of extensions: 8 Number of successful extensions: 1 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: 328 Length adjustment: 28 Effective length of query: 293 Effective length of database: 300 Effective search space: 87900 Effective search space used: 87900 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