Align triokinase (EC 2.7.1.28); glycerone kinase (EC 2.7.1.29); FAD-AMP lyase (cyclizing) (EC 4.6.1.15) (characterized)
to candidate WP_012706475.1 NGR_RS02025 dihydroxyacetone kinase subunit DhaK
Query= BRENDA::Q3LXA3 (575 letters) >NCBI__GCF_000018545.1:WP_012706475.1 Length = 331 Score = 213 bits (541), Expect = 1e-59 Identities = 136/338 (40%), Positives = 194/338 (57%), Gaps = 15/338 (4%) Query: 4 KKLVNSVAGCADDALAGLVACNPNLQLL--QGHRVALRSDLDSLKGRVALLSGGGSGHEP 61 KK +N ++LAGLV+ + L G V RS G+V+L+SGGG+GHEP Sbjct: 2 KKFMNRAETLVAESLAGLVSAHERLVTFGADGKFVRRRS---LRPGKVSLISGGGAGHEP 58 Query: 62 AHAGFIGKGMLTGVIAGAVFTSPAVGSILAAIRAVAQAGTVGTLLIVKNYTGDRLNFGLA 121 H GF+G+GML G VFTSP I+AAIR + G LLIVKNY GD +NF +A Sbjct: 59 MHVGFVGRGMLDAACTGHVFTSPTPDQIVAAIRETDRGE--GCLLIVKNYDGDVMNFEMA 116 Query: 122 REQARAEGIPVEMVVIGDDSAFTVLKKAGRRGLCGTVLIHKVAGALAEAGVGLEEIAKQV 181 E AE +VV D + GRRG+ GTV++ K+ GA AEAG L+E++ Sbjct: 117 AELVAAEHRIATVVVRDDVDPGGSKRSQGRRGVAGTVVMEKLLGAAAEAGWRLDELSALG 176 Query: 182 NVVAKAMGTLGVSLSSCSVPGS-KPTFELSADEVELGLGIHGEAGVRRIKMATADEIVKL 240 + + T+GVSL +VP + + TF L DE+E+G+GIHGE G R+K ATADEIV+ Sbjct: 177 ESLNGRIRTMGVSLRGVTVPDTERETFVLPEDEMEIGVGIHGEPGRARVKFATADEIVET 236 Query: 241 MLDHMTNTTNASHVPVQPGSSVVMMVNNLGGLSFLELGIIADATVRSLEGRGVKIARALV 300 ML+ + + + +++M +N GG EL ++ ++ E G+ IAR LV Sbjct: 237 MLEAI-----LGELASERDENLLMFINGYGGTPASELYLVYNSAKAQCERLGLTIARPLV 291 Query: 301 GTFMSALEMPGISLTLLLVDEPLLKLIDA--ETTAAAW 336 GT++++L+M G+S+T+ + E L L DA +T A W Sbjct: 292 GTYVTSLDMAGLSITVARLAERELSLWDAPVDTAALRW 329 Lambda K H 0.315 0.130 0.365 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: 448 Number of extensions: 21 Number of successful extensions: 4 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: 575 Length of database: 331 Length adjustment: 32 Effective length of query: 543 Effective length of database: 299 Effective search space: 162357 Effective search space used: 162357 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 (21.6 bits) S2: 51 (24.3 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