Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_066330061.1 BLR17_RS12115 3-phosphoglycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_900100165.1:WP_066330061.1 Length = 316 Score = 124 bits (312), Expect = 2e-33 Identities = 89/276 (32%), Positives = 142/276 (51%), Gaps = 24/276 (8%) Query: 46 IGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFS 105 + S+ K+ +++ LK + VG D DV +GI + NTP +ES A+ VF+ Sbjct: 48 VRSATKVRKDIIDACPGLKIIGRGGVGMDNIDVDYAKSKGIHVINTPASSSESVAELVFA 107 Query: 106 LILASAR------RVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARR 159 +L R R + L K + + GV+++GKTLGIVG+GRIG A A+ Sbjct: 108 HLLTGVRFLHDSNRNMPLEGDTKFNDLKKAYAN---GVELRGKTLGIVGIGRIGQATAKM 164 Query: 160 AALGFNMKVLYTNRSANPQAE---EAYGARRV-------ELAELLATADFVCLQVPLTPE 209 A LG MKV+ + S PQ + E + + + L + A +DF+ L VP + Sbjct: 165 A-LGLGMKVIAAD-SFIPQVDVKVEFFDGQSITTTIKTQSLESVFAESDFITLHVPA--Q 220 Query: 210 TKHLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSP 269 +++ E +MK ++N +RG ++E L++AL +G + AGLDVFE EP P+ + Sbjct: 221 NGYIVTEKEFATMKNGVGIVNCARGGVINEVDLVKALDSGKVAFAGLDVFENEPTPA-TQ 279 Query: 270 LLKLANVVALPHIGSATHETRHAMARNAAENLVAAL 305 LL + PHIG+AT E + + A +++ L Sbjct: 280 LLMHPKISLTPHIGAATGEAQDRIGTELASQIISIL 315 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: 203 Number of extensions: 10 Number of successful extensions: 4 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: 316 Length adjustment: 27 Effective length of query: 294 Effective length of database: 289 Effective search space: 84966 Effective search space used: 84966 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