Align glycerone kinase (EC 2.7.1.29) (characterized)
to candidate H281DRAFT_02701 H281DRAFT_02701 dihydroxyacetone kinase, C-terminal domain
Query= BRENDA::P76014 (210 letters) >FitnessBrowser__Burk376:H281DRAFT_02701 Length = 208 Score = 102 bits (253), Expect = 7e-27 Identities = 64/205 (31%), Positives = 107/205 (52%), Gaps = 4/205 (1%) Query: 1 MSLSRTQIVNWLTRCGDIFSTESEYLTGLDREIGDADHGLNMNRGFSKVVEKLPAIAD-K 59 MS+S ++ LTR + ++ L LD +GD D G+ + G + VV L A+ D Sbjct: 1 MSVSNNELRELLTRALNALPAHADELRDLDAALGDGDLGITVRAGSAAVVNALAALPDGA 60 Query: 60 DIGFILKNTGMTLLSSVGGASGPLFGTFFIRAAQATQARQSLTLEELYQMFRDGADGVIS 119 + +L G ++ L G + AA+A Q + E + R A ++ Sbjct: 61 SLSDVLLAAGKAFSTANPSTFAALVGGGLLAAAKAVPGVQGVGRAEALAIGRAVAGRIVE 120 Query: 120 RGKAEPGDKTMCDVWVPVVESLRQSSEQNLSVPVALEAASSIAESAAQSTITMQARKGRA 179 RGK++ GDKT+ D +P +++L S + + L+A + A+ +T ++Q+RKGRA Sbjct: 121 RGKSQLGDKTVLDALLPSLDTLEASQGSAVEL---LDAMIATAQEGVAATASIQSRKGRA 177 Query: 180 SYLGERSIGHQDPGATSVMFMMQML 204 +++ ERSIGH DPGAT+ + +Q L Sbjct: 178 AWVQERSIGHADPGATAYVRFLQAL 202 Lambda K H 0.316 0.130 0.364 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: 104 Number of extensions: 7 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: 210 Length of database: 208 Length adjustment: 21 Effective length of query: 189 Effective length of database: 187 Effective search space: 35343 Effective search space used: 35343 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: 45 (21.9 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