Align glycerone kinase (EC 2.7.1.29) (characterized)
to candidate WP_010959411.1 MCA_RS00195 dihydroxyacetone kinase subunit L
Query= BRENDA::P76014 (210 letters) >NCBI__GCF_000008325.1:WP_010959411.1 Length = 212 Score = 141 bits (355), Expect = 1e-38 Identities = 77/190 (40%), Positives = 116/190 (61%), Gaps = 1/190 (0%) Query: 21 TESEYLTGLDREIGDADHGLNMNRGFSKVVEKLPAIADKDIGFILKNTGMTLLSSVGGAS 80 + +E ++ LD+ IGD DH +N+ RG + ++ ++A D L+ GMTL++SVGGAS Sbjct: 21 SHAEEVSALDQAIGDGDHVVNLQRGLEALSQQAESLAALDWPAALQKIGMTLMASVGGAS 80 Query: 81 GPLFGTFFIRAAQATQARQSLTLEELYQMFRDGADGVISRGKAEPGDKTMCDVWVPVVES 140 G L+GT FI +A + R+ + L L + F G + + +RGKA+ G+KTM DV +PV + Sbjct: 81 GSLYGTLFIAMGKAMKDRE-MNLANLAEAFGRGVEAMKARGKADRGEKTMLDVLIPVADV 139 Query: 141 LRQSSEQNLSVPVALEAASSIAESAAQSTITMQARKGRASYLGERSIGHQDPGATSVMFM 200 L+ ++E ++ E S AE+ +ST M A KGRAS+LGER+IGH D GA S M Sbjct: 140 LKSAAEHAIAPGQLAEEVSRAAEAGMESTRDMLATKGRASFLGERAIGHVDAGARSSQLM 199 Query: 201 MQMLALAAKE 210 + +A E Sbjct: 200 ISAIAEVVAE 209 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: 6 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: 212 Length adjustment: 21 Effective length of query: 189 Effective length of database: 191 Effective search space: 36099 Effective search space used: 36099 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 24 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