Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate WP_004688676.1 BIBO1_RS11805 phosphoglycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >NCBI__GCF_000182725.1:WP_004688676.1 Length = 533 Score = 181 bits (459), Expect = 4e-50 Identities = 104/284 (36%), Positives = 162/284 (57%), Gaps = 6/284 (2%) Query: 33 DAFVAALKDADG-GIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANT 91 + + + + DG I S+ K+T ++ A +LK + +G D D+ +RRGI++ NT Sbjct: 37 EKLLEVIGEYDGLAIRSATKVTEKLIAAAKKLKVVGRAGIGVDNVDIPAASRRGIIVMNT 96 Query: 92 PDVLTESTADTVFSLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGR 151 P + +TA+ +L+ A AR++ E +AG W+ + GV++ GKTLG+VG G Sbjct: 97 PFGNSITTAEHAIALMFAVARQLPEADTSTRAGKWEKN---RFMGVEITGKTLGVVGCGN 153 Query: 152 IGGAVARRAALGFNMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETK 211 IG VA R +G M V+ + + + G +VEL ELLA ADF+ L PLT +T+ Sbjct: 154 IGSIVATRG-IGLKMHVVAFDPFLSDARAQELGVEKVELDELLARADFITLHTPLTDKTR 212 Query: 212 HLIGAAELKSMKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLL 271 ++I A L MK ++N +RG + EK LI AL++G + GAG+DV+ETEP +++ L Sbjct: 213 NIINAQTLAKMKPGVRIVNCARGGLIVEKDLIAALKSGHVAGAGIDVYETEP-ATENELF 271 Query: 272 KLANVVALPHIGSATHETRHAMARNAAENLVAALDGTLTSNIVN 315 L NVV PH+G++T E + +A AE + L SN +N Sbjct: 272 SLPNVVCTPHLGASTSEAQENVALQVAEQMSDYLVKGAVSNAIN 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: 337 Number of extensions: 19 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: 533 Length adjustment: 31 Effective length of query: 290 Effective length of database: 502 Effective search space: 145580 Effective search space used: 145580 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: 50 (23.9 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