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 SM_b20314 SM_b20314 glycerone kinase
Query= SwissProt::Q4KLZ6 (578 letters) >FitnessBrowser__Smeli:SM_b20314 Length = 330 Score = 179 bits (453), Expect = 2e-49 Identities = 109/334 (32%), Positives = 171/334 (51%), Gaps = 9/334 (2%) Query: 4 KKMVNSVEGCAGDALAGFVACNPDLQLLQGYRVALRSDLDSLKGRVALLSGGGSGHEPAH 63 ++ +N+ + D + GFV + D+ L + + + G+V +++GGGSGHEPA Sbjct: 2 QRFINNPDEVVEDTVKGFVKAHADIVRLGENPRVIVAKGAPVAGKVGVVTGGGSGHEPAF 61 Query: 64 AGFIGKGMLTGVIAGAVFASPAVGSILAAIRAVAQAGTAGTLLIVKNYTGDRLNFGLAME 123 G+ G+ ML V G +F+SP S AIR G G + + NY GD +N +A++ Sbjct: 62 IGYTGRNMLDAVAVGELFSSPTAKSFHDAIREAD--GGKGVVCLYGNYAGDNMNVKMAVK 119 Query: 124 QAKAEGISVEMVVIEDD-SAFTVLKKAGRRGLCGTILIHKVAGALAEEGMGLEEITKKVS 182 A GI V VV DD + ++ RRG+ G I + K+ GA A G LEE+ Sbjct: 120 LAAKAGIEVATVVANDDVCSAPPEEREKRRGVAGEIFMWKIGGAKAAAGASLEEVRAAAQ 179 Query: 183 VIAKAIGTLGVSLSPCSVPGT-KPTFELAADEMELGLGIHGEAGVRRIKLVPVDQIVTLM 241 ++GV L PC++P P F + ME+G+G HGE G+R L +++ M Sbjct: 180 KAIDNCRSIGVGLGPCTLPAVGHPNFRIEPGTMEVGIGHHGEPGLRVEALKTAEEVAVDM 239 Query: 242 LDHMTDTSNISHVPVKSGSSVVLMVNNLGGLSFLELGIIADAAIRLLEGRGVKVARALVG 301 + D ++ G+ V ++V+ LG EL I+ D R + RG+K+ R VG Sbjct: 240 CKIVLDDHDLPQ-----GTEVAVLVSGLGATPLNELYILNDTIEREITARGLKIYRTFVG 294 Query: 302 TFMSALEMRGVSLTLMLVDEPLLKLIDAETNAKA 335 + ++LEM G +LT+M +D+ L L+D E A Sbjct: 295 NYFTSLEMVGATLTVMALDDELKALLDVEVRCTA 328 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: 365 Number of extensions: 16 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: 578 Length of database: 330 Length adjustment: 32 Effective length of query: 546 Effective length of database: 298 Effective search space: 162708 Effective search space used: 162708 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