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 15322 b1200 putative dihydroxyacetone kinase (EC 2.7.1.2) (VIMSS)
Query= BRENDA::Q3LXA3 (575 letters) >FitnessBrowser__Keio:15322 Length = 356 Score = 225 bits (574), Expect = 2e-63 Identities = 144/356 (40%), Positives = 194/356 (54%), Gaps = 26/356 (7%) Query: 4 KKLVNSVAGCADDALAGLVACNPNLQLLQGHRVALRSDLDSLKGRVALLSGGGSGHEPAH 63 KKL+N V D+ LAGL +P+L L Q R+D + G+VALLSGGGSGHEP H Sbjct: 2 KKLINDVQDVLDEQLAGLAKAHPSLTLHQDPVYVTRADAP-VAGKVALLSGGGSGHEPMH 60 Query: 64 AGFIGKGMLTGVIAGAVFTSPAVGSILAAIRAVAQAGTVGTLLIVKNYTGDRLNFGLARE 123 G+IG+GML+G G +FTSP I A+ G G LLI+KNYTGD LNF A E Sbjct: 61 CGYIGQGMLSGACPGEIFTSPTPDKIFEC--AMQVDGGEGVLLIIKNYTGDILNFETATE 118 Query: 124 QARAEGIPVEMVVIGDDSAF-TVLKKAGRRGLCGTVLIHKVAGALAEAGVGLEEIAKQVN 182 G+ V VVI DD A L AGRRG+ TVLI K+ GA AE G L+ A+ Sbjct: 119 LLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGR 178 Query: 183 VVAKAMGTLGVSLSSCSVPGS-KPTFELSADEVELGLGIHGEAGVRRIKMATADEIVKLM 241 + ++G++L +C+VP + KP+F L+ +E+E G+GIHGE G+ R ++ D+ V M Sbjct: 179 KLNNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEM 238 Query: 242 LD--------HMT-----------NTTNASHVPVQPGSSVVMMVNNLGGLSFLELGIIAD 282 D H T + P+Q G V+ +VNNLG EL + + Sbjct: 239 FDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYN 298 Query: 283 ATVRSLEGRGVKIARALVGTFMSALEMPGISLTLLLVDEPLLKLIDA--ETTAAAW 336 + G+ I R L+G + ++L+M G S+TLL VD+ L L DA T A W Sbjct: 299 RLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNW 354 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: 463 Number of extensions: 17 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: 356 Length adjustment: 33 Effective length of query: 542 Effective length of database: 323 Effective search space: 175066 Effective search space used: 175066 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