Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate CA265_RS17230 CA265_RS17230 D-glycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Pedo557:CA265_RS17230 Length = 319 Score = 212 bits (539), Expect = 1e-59 Identities = 119/276 (43%), Positives = 168/276 (60%), Gaps = 1/276 (0%) Query: 33 DAFVAALKDADGGIGSSV-KITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANT 91 + +AA +D D I KI A L+ + LK ++ SVG+DQ DVA + I + NT Sbjct: 36 EELIAACQDQDALISVGPNKINAAFLKACSHLKVIALHSVGYDQVDVAAAKKLNIPIGNT 95 Query: 92 PDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGR 151 P VL+++TADT F L+LA +R+ + + G W++ G++V GKTLGI GLG+ Sbjct: 96 PGVLSKATADTAFLLMLAVSRKAFFAHKKIIKGEWKNYEPTPELGIEVNGKTLGIFGLGK 155 Query: 152 IGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETK 211 IG +A++ + M V+Y NRS N +AE+ GA+ V LLA +D + + LTPETK Sbjct: 156 IGLEMAKKCIGAYQMPVIYHNRSRNEEAEKEIGAKYVSFETLLAQSDVLSVHTALTPETK 215 Query: 212 HLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLL 271 K MK ++I IN +RGA +EK LI+AL+ I GAGLDV EP+ ++PLL Sbjct: 216 DKFTLDVFKQMKANSIFINTARGAIHNEKDLIKALEKKIIWGAGLDVTNPEPMDKNNPLL 275 Query: 272 KLANVVALPHIGSATHETRHAMARNAAENLVAALDG 307 + NV LPHIGSAT ETR AMA+ +N++A L+G Sbjct: 276 SMENVAVLPHIGSATEETRAAMAQIIVKNIIAGLNG 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: 222 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: 319 Length adjustment: 28 Effective length of query: 293 Effective length of database: 291 Effective search space: 85263 Effective search space used: 85263 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 17 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