Align glycerone kinase (EC 2.7.1.29) (characterized)
to candidate WP_164924037.1 NGR_RS01995 dihydroxyacetone kinase subunit DhaK
Query= BRENDA::P76014 (210 letters) >NCBI__GCF_000018545.1:WP_164924037.1 Length = 544 Score = 86.7 bits (213), Expect = 8e-22 Identities = 64/193 (33%), Positives = 97/193 (50%), Gaps = 17/193 (8%) Query: 15 CGDIFSTESEYLTGLDREIGDADHGLNMNRGFSKVVEKLPAIADKDIGFILKNTGMTLLS 74 C + S E+E L LD GD D G + G V+ ++ + KD+ L + G L + Sbjct: 364 CDHLLSLEAE-LNHLDARAGDGDTGSTVATGSRSVLAQIERLPLKDVAATLSSIGSILST 422 Query: 75 SVGGASGPLFGTFFIRAAQATQARQSLTLEELYQMFRDGADGVISRGKAEPGDKTMCDVW 134 S+GG+SG L FF AA+A L +++ G + + G A GD+TM D Sbjct: 423 SMGGSSGVLLSIFFTAAAKA-----YLDTKDMAGALLAGLERMTFYGGAGVGDRTMVDAL 477 Query: 135 VPVVESLRQSSEQNLSVPVALEAASSIAESAAQSTITM-QARKGRASYLGERSI-GHQDP 192 P + +L+ L AA+S A + A +T M +A+ GRASY+GER + G DP Sbjct: 478 DPALRALKAG---------GLAAAASAARAGADATRAMKKAKAGRASYVGERDLDGIPDP 528 Query: 193 GATSVMFMMQMLA 205 GA +V + ++ A Sbjct: 529 GAMAVAAVFEVAA 541 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: 224 Number of extensions: 8 Number of successful extensions: 2 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: 544 Length adjustment: 28 Effective length of query: 182 Effective length of database: 516 Effective search space: 93912 Effective search space used: 93912 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 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