Align Triokinase/FMN cyclase; Bifunctional ATP-dependent dihydroxyacetone kinase/FAD-AMP lyase (cyclizing); EC 2.7.1.28; EC 2.7.1.29; EC 4.6.1.15 (characterized)
to candidate 3607105 Dshi_0527 Glycerone kinase (RefSeq)
Query= SwissProt::Q4KLZ6 (578 letters) >FitnessBrowser__Dino:3607105 Length = 333 Score = 216 bits (551), Expect = 9e-61 Identities = 134/337 (39%), Positives = 195/337 (57%), Gaps = 12/337 (3%) Query: 4 KKMVNSVEGCAGDALAGFVACNPDLQLLQGY--RVALRSDLDSLKGRVALLSGGGSGHEP 61 KK++N E + LAG +A +P+ L G +V R++ G+V +++GGGSGH P Sbjct: 2 KKILNKPEDYVDEMLAGLIAAHPEYYRLHGDTGKVVARAN-PGKDGKVGIVTGGGSGHLP 60 Query: 62 AHAGFIGKGMLTGVIAGAVFASPAVGSILAAIRAVAQAGTAGTLLIVKNYTGDRLNFGLA 121 G++G+G+L G VFASP+ + AIR VA +G AG L + NY GD +NF +A Sbjct: 61 VFTGYVGEGLLDACAIGDVFASPSAEQMADAIR-VADSG-AGVLRLYGNYGGDVMNFDMA 118 Query: 122 MEQAKAEGISVEMVVIEDDSAFTVLKKAG-RRGLCGTILIHKVAGALAEEGMGLEEITKK 180 E + + I+ V++ DD A +A RRG+ G + K+AGA AEEG L+ +T Sbjct: 119 GELVEFDDITCTTVLLADDVASAPPAEAEKRRGVAGMVYAFKIAGAAAEEGRDLDGVTAV 178 Query: 181 VSVIAKAIGTLGVSLSPCSVPGT-KPTFELAADEMELGLGIHGEAGVRRIKLVPVDQIVT 239 A A ++G +LSPC+VP KPTFE+A DEME+G+GIHGE GV R KL DQI Sbjct: 179 AQKAADACRSIGAALSPCTVPQAGKPTFEIAEDEMEMGMGIHGEPGVWRGKLQTADQIAE 238 Query: 240 LMLDHMTDTSNISHVPVKSGSSVVLMVNNLGGLSFLELGIIADAAIRLLEGRGVKVARAL 299 M+D + ++ +P+ +G V +MVN+LG EL I+ LE G ++ L Sbjct: 239 EMMDRL-----LADMPIGNGDRVSVMVNSLGATPPEELYILYRRVKARLEAAGARIVMPL 293 Query: 300 VGTFMSALEMRGVSLTLMLVDEPLLKLIDAETNAKAW 336 VG + +++EM GVS TL +D+ L KL+ A + W Sbjct: 294 VGRYATSMEMAGVSFTLCKLDDELEKLLLAPCDCAFW 330 Lambda K H 0.316 0.131 0.366 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: 422 Number of extensions: 29 Number of successful extensions: 6 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: 578 Length of database: 333 Length adjustment: 32 Effective length of query: 546 Effective length of database: 301 Effective search space: 164346 Effective search space used: 164346 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