Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate Pf6N2E2_3932 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)
Query= reanno::BFirm:BPHYT_RS11290 (321 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3932 Length = 409 Score = 132 bits (331), Expect = 2e-35 Identities = 97/279 (34%), Positives = 140/279 (50%), Gaps = 11/279 (3%) Query: 45 GIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVF 104 GI S ++T + + A +L A+ +G +Q D+ RGI + N P T S A+ V Sbjct: 58 GIRSRTQLTEEIFDHAKKLVAVGCFCIGTNQVDLNAARERGIAVFNAPYSNTRSVAELVL 117 Query: 105 SLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGF 164 + + R + E G W I A +++GK LGIVG G IG ++ A G Sbjct: 118 AEAILLLRGIPEKNASCHRGGW---IKSAANSFEIRGKKLGIVGYGSIGTQLSVLAE-GL 173 Query: 165 NMKVLYTNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKK 224 M+V + + A L ELL +D V L VP T T+ +IG E++++KK Sbjct: 174 GMQVFFYDTVTKLPLGNATQVNN--LHELLGMSDIVTLHVPETAATQWMIGEKEIRAIKK 231 Query: 225 SAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPSD----SPLLKLANVVALP 280 ILINA+RG V AL +A+++ + GA +DVF EP +D SPL L NV+ P Sbjct: 232 GGILINAARGTVVKLDALADAIKDKHLIGAAIDVFPVEPRSNDDIFESPLRGLDNVILTP 291 Query: 281 HIGSATHETRHAMARNAAENLVAALD-GTLTSNIVNREV 318 HIG +T E + + AE LV D GT S++ EV Sbjct: 292 HIGGSTAEAQANIGLEVAEKLVKYSDNGTSVSSVNFPEV 330 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: 272 Number of extensions: 13 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: 409 Length adjustment: 29 Effective length of query: 292 Effective length of database: 380 Effective search space: 110960 Effective search space used: 110960 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: 49 (23.5 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