Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_009141108.1 HMPREF9452_RS05340 phosphoglycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_000225705.1:WP_009141108.1 Length = 326 Score = 173 bits (439), Expect = 4e-48 Identities = 110/275 (40%), Positives = 153/275 (55%), Gaps = 8/275 (2%) Query: 40 KDADGGIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTEST 99 KDAD I + ++ A + + LK + G D D ++L +R I +ANTP E T Sbjct: 51 KDADVIILGNDRLDSATIGKLSNLKLVVRHGAGLDNIDFSELGKRDITVANTPGANKEET 110 Query: 100 ADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARR 159 AD F+LIL AR V + +K G W G L+G KT+GI+G+G IG AVA R Sbjct: 111 ADLTFALILDLARMVTQSINQLKGGVWNKIPGRTLYG-----KTIGIIGVGAIGMAVASR 165 Query: 160 AALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAEL 219 A +GF M +L + +A +G L ELL+ +D V + VPLT TK+LIGA EL Sbjct: 166 A-MGFGMDILGNDIVQRDEAAR-FGLLYTSLNELLSASDVVTIHVPLTSATKNLIGAREL 223 Query: 220 KSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVAL 279 K MK A+LIN +R V E AL +AL +G + G +DV+ EP P + + L NV+ Sbjct: 224 KRMKPDALLINTARAGVVREAALEKALMSGHLGGYAVDVYVKEP-PDPTSYMSLPNVLTT 282 Query: 280 PHIGSATHETRHAMARNAAENLVAALDGTLTSNIV 314 PHIGS+T E M A +N++A ++G + N V Sbjct: 283 PHIGSSTMEANLRMGDMAVDNILAFMNGAVLPNKV 317 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: 217 Number of extensions: 5 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