Align glycerone kinase (EC 2.7.1.29) (characterized)
to candidate WP_012706470.1 NGR_RS02000 dihydroxyacetone kinase subunit DhaL
Query= BRENDA::P76014 (210 letters) >NCBI__GCF_000018545.1:WP_012706470.1 Length = 207 Score = 125 bits (315), Expect = 4e-34 Identities = 74/183 (40%), Positives = 104/183 (56%), Gaps = 12/183 (6%) Query: 15 CGDIFSTESEYLTGLDREIGDADHGLNMNRGFSKVVEKLPAIADKDIGFILKNTGMTLLS 74 C + + +++L+ LDR IGD DHG+NM RG V + +A+ + L+ G+TL+ Sbjct: 18 CREAIAANADHLSELDRAIGDGDHGINMRRGLEAVYAERNRLAELALPKALEEIGLTLVM 77 Query: 75 SVGGASGPLFGTFFIRAAQATQARQSLTLEELYQMFRDGADGVISRGKAEPGDKTMCDVW 134 SVGGA+GPL+GT I A Q + ++ + D V RG+A PGDKT+ DV Sbjct: 78 SVGGAAGPLYGTLLI--AIGRQLGGANGQQDFARALEHAIDAVARRGRASPGDKTLLDVL 135 Query: 135 VPV-VESLRQSSEQNLSVPVALEAASSIAESAAQSTITMQARKGRASYLGERSIGHQDPG 193 PV E +R++ L S AE AA T M+A +GRA++LG+RSIGH DPG Sbjct: 136 YPVHAEVVRRA---------GLAGISEQAERAASLTFGMRAMRGRAAFLGDRSIGHVDPG 186 Query: 194 ATS 196 A S Sbjct: 187 AKS 189 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: 112 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: 207 Length adjustment: 21 Effective length of query: 189 Effective length of database: 186 Effective search space: 35154 Effective search space used: 35154 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 Apr 09 2024. 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