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 206411 DVU0979 DAK1 domain protein
Query= BRENDA::Q3LXA3 (575 letters) >MicrobesOnline__882:206411 Length = 354 Score = 234 bits (596), Expect = 6e-66 Identities = 140/348 (40%), Positives = 198/348 (56%), Gaps = 25/348 (7%) Query: 4 KKLVNSVAGCADDALAGLVACNPNLQLLQGHRVALRSDLDSLKGRVALLSGGGSGHEPAH 63 KKL+N+V + L G+ A +P L++ R+D+ G+VA++SGGGSGHEP H Sbjct: 2 KKLINAVENVVREQLQGMAAAHPELRVNIDPHYICRADIPD--GKVAIVSGGGSGHEPMH 59 Query: 64 AGFIGKGMLTGVIAGAVFTSPAVGSILAAIRAVAQAGTVGTLLIVKNYTGDRLNFGLARE 123 GF+G+GML G G VFTSP + +AV + G L IVKNYTGD +NF A E Sbjct: 60 GGFVGRGMLDGACPGEVFTSPTPDQMYECAKAVDRG--AGVLFIVKNYTGDVMNFETAAE 117 Query: 124 QARAEGIPVEMVVIGDDSAF-TVLKKAGRRGLCGTVLIHKVAGALAEAGVGLEEIAKQVN 182 A+GI V+ ++I DD A L AGRRG+ TVL K+ GA AEAG L+ A Sbjct: 118 LCHADGIKVQNILIDDDVAVKDSLYTAGRRGVGTTVLAEKIVGAAAEAGYDLDRCADLCR 177 Query: 183 VVAKAMGTLGVSLSSCSVPGS-KPTFELSADEVELGLGIHGEAGVRRIKMATADEIVKLM 241 V + ++G++L+SC+VP + KPTFEL+ DE+E+G+GIHGE G +R M T DE+V++M Sbjct: 178 KVNRYGRSMGMALTSCTVPAAGKPTFELAEDEIEIGIGIHGEPGTQRAAMMTVDELVEVM 237 Query: 242 ----LDHMTNT---------------TNASHVPVQPGSSVVMMVNNLGGLSFLELGIIAD 282 +D T + + P G V+ VN++GG EL Sbjct: 238 ATAIIDDPAYTRTVREFDRAAGDWVEKSLTDEPFAKGDRVIAFVNSMGGTPVSELYAAYR 297 Query: 283 ATVRSLEGRGVKIARALVGTFMSALEMPGISLTLLLVDEPLLKLIDAE 330 + RG+ I R L+G ++++LEM G S+TLL VD+ +L DA+ Sbjct: 298 KLAEICDRRGIVIVRNLIGPYITSLEMQGFSITLLKVDDEMLAFWDAK 345 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: 468 Number of extensions: 24 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: 575 Length of database: 354 Length adjustment: 33 Effective length of query: 542 Effective length of database: 321 Effective search space: 173982 Effective search space used: 173982 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