Align glycerone kinase (EC 2.7.1.29) (characterized)
to candidate BWI76_RS24595 BWI76_RS24595 dihydroxyacetone kinase subunit DhaK
Query= BRENDA::P76015 (356 letters) >FitnessBrowser__Koxy:BWI76_RS24595 Length = 356 Score = 646 bits (1667), Expect = 0.0 Identities = 316/356 (88%), Positives = 334/356 (93%) Query: 1 MKKLINDVQDVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMH 60 MKKLIN V+DVL EQLAGLAKAHP L LHQDPVYVTRADAPVAGKVALLSGGGSGHEPMH Sbjct: 1 MKKLINRVEDVLSEQLAGLAKAHPELRLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMH 60 Query: 61 CGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELL 120 CGYIGQGMLSGACPGEIFTSPTPDK+FECAM +DGGEGVLLIIKNYTGDILNFETATELL Sbjct: 61 CGYIGQGMLSGACPGEIFTSPTPDKMFECAMNIDGGEGVLLIIKNYTGDILNFETATELL 120 Query: 121 HDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKL 180 H+SGVKVTTVV+DDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSL++CAELGRKL Sbjct: 121 HESGVKVTTVVVDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLESCAELGRKL 180 Query: 181 NNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFD 240 NN GHSIGIALGACTVPAAG+PSF L D+EMEFGVGIHGEPGIDRR F+SLD+TVDEMFD Sbjct: 181 NNLGHSIGIALGACTVPAAGQPSFELQDDEMEFGVGIHGEPGIDRRRFTSLDRTVDEMFD 240 Query: 241 TLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRL 300 TLL NG+Y RTLR WD +G+WQE QTKQ LQ GDRVIALVNNLGATPLSELYGVYNRL Sbjct: 241 TLLENGAYSRTLRHWDNVKGAWQEVAQTKQALQKGDRVIALVNNLGATPLSELYGVYNRL 300 Query: 301 TTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWGK 356 T RC++ G+ IERNLIG+YCTSLDM GFSITLLKVDDETLALWDAPVHTPALNWGK Sbjct: 301 TQRCEETGIVIERNLIGSYCTSLDMVGFSITLLKVDDETLALWDAPVHTPALNWGK 356 Lambda K H 0.317 0.136 0.406 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: 534 Number of extensions: 12 Number of successful extensions: 1 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: 356 Length of database: 356 Length adjustment: 29 Effective length of query: 327 Effective length of database: 327 Effective search space: 106929 Effective search space used: 106929 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: 49 (23.5 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