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 H281DRAFT_05885 H281DRAFT_05885 dihydroxyacetone kinase DhaK subunit
Query= BRENDA::Q3LXA3 (575 letters) >FitnessBrowser__Burk376:H281DRAFT_05885 Length = 329 Score = 228 bits (581), Expect = 3e-64 Identities = 139/337 (41%), Positives = 198/337 (58%), Gaps = 15/337 (4%) Query: 4 KKLVNSVAGCADDALAGLVACNPNLQLLQGHRVALRSDLDSLKGRVALLSGGGSGHEPAH 63 KK +N V ++LAG A + +L +L V +R D G+VAL+SGGGSGHEP H Sbjct: 2 KKFINHVDDFLAESLAGFAAAHGDLVVLNREPVFVRRK-DLKPGKVALISGGGSGHEPLH 60 Query: 64 AGFIGKGMLTGVIAGAVFTSPAVGSILAAIRAVAQAGTVGTLLIVKNYTGDRLNFGLARE 123 +GF+G GML G +FTSP ++AA +AV G L IVKNY+GD +NF +A E Sbjct: 61 SGFVGHGMLDAACPGQIFTSPTPDQMMAAAKAVDTG--AGVLFIVKNYSGDLMNFEMASE 118 Query: 124 QARAEGIPVEMVVIGDDSAF-TVLKKAGRRGLCGTVLIHKVAGALAEAGVGLEEIAKQVN 182 + +P MV+I DD A GRRG+ G V++ K+ G+LAE+G L+E N Sbjct: 119 MSE---VPNAMVLINDDVAVENSSYTTGRRGVAGAVIVEKLVGSLAESGASLDECKAFGN 175 Query: 183 VVAKAMGTLGVSLSSCSVPGSKP-TFELSADEVELGLGIHGEAGVRRIKMATADEIVKLM 241 + K ++GV+ SSC+VP + TF++ DE+E+G+GIHGE G RR K A+AD I + Sbjct: 176 RINKRTASMGVAFSSCTVPAAGTLTFKIGDDEIEVGVGIHGEPGRRRAKFASADTIAAEL 235 Query: 242 LDHMTNTTNASHVPVQPGSSVVMMVNNLGGLSFLELGIIADATVRSLEGRGVKIARALVG 301 L T + G+ V+++VN LGG EL ++ ++T LE R +KIAR VG Sbjct: 236 L-----TAIVDDLKPAAGAGVLVLVNGLGGTPLGELYLLFNSTRAWLEKRDLKIARVQVG 290 Query: 302 TFMSALEMPGISLTLLLVDEPLLKLIDA--ETTAAAW 336 + ++LEM G S+TL ++DE + K D+ T A W Sbjct: 291 SLTTSLEMAGASITLCMLDEQMTKHWDSAVHTPALRW 327 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: 432 Number of extensions: 21 Number of successful extensions: 5 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: 329 Length adjustment: 32 Effective length of query: 543 Effective length of database: 297 Effective search space: 161271 Effective search space used: 161271 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 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