Align glycerone kinase (EC 2.7.1.29) (characterized)
to candidate 8501867 DvMF_2582 dihydroxyacetone kinase subunit DhaK (RefSeq)
Query= BRENDA::P76015 (356 letters) >FitnessBrowser__Miya:8501867 Length = 354 Score = 436 bits (1121), Expect = e-127 Identities = 214/355 (60%), Positives = 263/355 (74%), Gaps = 1/355 (0%) Query: 1 MKKLINDVQDVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMH 60 MKKLIN V++V+ EQL G+A AHP L ++ DP +V R + P GKVA++SGGGSGHEPMH Sbjct: 1 MKKLINAVENVVREQLQGMAAAHPELRVNIDPHFVCRKEIP-QGKVAIVSGGGSGHEPMH 59 Query: 61 CGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELL 120 G++G GML GACPGE+FTSPTPD+++ECA VD G GVL I+KNYTGD++NFETA EL Sbjct: 60 GGFVGHGMLDGACPGEVFTSPTPDQMYECAKAVDRGAGVLFIVKNYTGDVMNFETAAELC 119 Query: 121 HDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKL 180 H G+KV ++IDDDVAVKDSLYTAGRRGV TVL EK+VGAAAE G LD CA+L RK+ Sbjct: 120 HADGLKVQNILIDDDVAVKDSLYTAGRRGVGTTVLAEKIVGAAAEAGYDLDKCADLCRKV 179 Query: 181 NNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFD 240 N G S+G+AL CTVPAAGKP+F LA+NE+E G+GIHGEPG R P ++D+ V M Sbjct: 180 NQYGRSMGMALTPCTVPAAGKPTFELAENEIEIGIGIHGEPGTQRAPMKTVDELVQIMAT 239 Query: 241 TLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRL 300 T++ + +Y RT+R D G W ++ T P GD+VIA VN++G TP+SELY VY +L Sbjct: 240 TIIDDPAYTRTVRELDRVSGQWVDKSLTDAPFAKGDKVIAFVNSMGGTPVSELYAVYRKL 299 Query: 301 TTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWG 355 C G++I RNLIG Y TSL+M GFSITLLKVDDE L WDA TP L G Sbjct: 300 AEICGARGISIVRNLIGPYITSLEMQGFSITLLKVDDEILKFWDAKAITPGLRMG 354 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: 386 Number of extensions: 13 Number of successful extensions: 2 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: 354 Length adjustment: 29 Effective length of query: 327 Effective length of database: 325 Effective search space: 106275 Effective search space used: 106275 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