Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate HSERO_RS07550 HSERO_RS07550 bifunctional glyoxylate/hydroxypyruvate reductase B
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__HerbieS:HSERO_RS07550 Length = 319 Score = 351 bits (901), Expect = e-101 Identities = 190/307 (61%), Positives = 226/307 (73%), Gaps = 3/307 (0%) Query: 4 IVAWKSLPEDVLAYLQQHAQVVQVDATQHDA---FVAALKDADGGIGSSVKITPAMLEGA 60 +V +K LPE ++ LQ + D D F+AAL A G IG+S+ IT AMLE A Sbjct: 5 VVVYKKLPEHLVQRLQAEFDLTLFDRITDDNRADFIAALATAHGMIGASLPITNAMLEAA 64 Query: 61 TRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEW 120 +LK +STISVG D FD+ +RG++LA+TP VLTE+TADT+F+LILASARRVVELAE+ Sbjct: 65 PQLKIVSTISVGVDNFDLDYFRQRGLMLAHTPGVLTEATADTIFALILASARRVVELAEY 124 Query: 121 VKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAE 180 VKAG W+ SIG A FGV+V GKTLG++G+GRIG AVARRA GF M +LY NR +P+AE Sbjct: 125 VKAGRWKGSIGEAQFGVNVHGKTLGLIGMGRIGSAVARRAHHGFGMPILYHNRRPDPEAE 184 Query: 181 EAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEK 240 GAR V +LLA ADFVC+ +PLTP+T+ + GA E MK+SAI INASRG VDE Sbjct: 185 RELGARYVSKEDLLAQADFVCVMLPLTPQTERMFGAPEFALMKRSAIFINASRGRIVDEA 244 Query: 241 ALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAEN 300 ALI ALQ+ TIHGAGLDVFE EPLP SPLLKL NVVALPHIGSATHETR AMA A N Sbjct: 245 ALIAALQDKTIHGAGLDVFEVEPLPLQSPLLKLPNVVALPHIGSATHETRLAMAELAVTN 304 Query: 301 LVAALDG 307 L+A L G Sbjct: 305 LIAGLRG 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: 292 Number of extensions: 6 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