Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate Ga0059261_2264 Ga0059261_2264 D-3-phosphoglycerate dehydrogenase
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__Korea:Ga0059261_2264 Length = 525 Score = 179 bits (454), Expect = 1e-49 Identities = 109/320 (34%), Positives = 173/320 (54%), Gaps = 6/320 (1%) Query: 2 KKIVAWKSLPEDVLAYLQQHAQVVQVDATQHDAFVAALKDADG-GIGSSVKITPAMLEGA 60 K +++ K P+ + ++ +V ++ + A + DG I S+ K+T +L+ A Sbjct: 3 KVLISDKMDPKAAQIFRERGVEVDEITGKTPEELKAIIGQYDGLAIRSATKVTKEILDAA 62 Query: 61 TRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVVELAEW 120 T LK + +G D D+ + + +G+V+ NTP + +TA+ +L+ A AR++ E Sbjct: 63 TNLKVVGRAGIGVDNVDIPNASAKGVVVMNTPFGNSITTAEHAIALMFALARQLPEANTQ 122 Query: 121 VKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRSANPQAE 180 +AG W + GV+V GKTLG++G G IG VA RA G MKV+ + +P+ Sbjct: 123 TQAGLWPKN---GFMGVEVTGKTLGLIGAGNIGSIVADRAH-GLRMKVVAYDPFLSPERA 178 Query: 181 EAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRGATVDEK 240 G +VEL +LLA ADF+ L PLT +T++++ A L KK +IN +RG +DE Sbjct: 179 VEMGVEKVELEQLLARADFITLHTPLTEQTRNILSAENLAKTKKGVRIINCARGGLIDEA 238 Query: 241 ALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMARNAAEN 300 AL + L +G + GA LDVF TEP + L N VA PH+G++T E + +A AE Sbjct: 239 ALKDLLDSGHVAGAALDVFVTEP-AKEHALFNTPNFVATPHLGASTSEAQVNVAIQVAEQ 297 Query: 301 LVAALDGTLTSNIVNREVLS 320 + L +N +N L+ Sbjct: 298 MADYLVNGGVTNALNMPSLT 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: 354 Number of extensions: 14 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: 525 Length adjustment: 31 Effective length of query: 290 Effective length of database: 494 Effective search space: 143260 Effective search space used: 143260 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 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