Align PTS-dependent dihydroxyacetone kinase 2, dihydroxyacetone-binding subunit DhaK; EC 2.7.1.121 (characterized)
to candidate GFF2361 PS417_12040 dihydroxyacetone kinase
Query= SwissProt::Q92EU2 (331 letters) >FitnessBrowser__WCS417:GFF2361 Length = 333 Score = 264 bits (675), Expect = 2e-75 Identities = 139/325 (42%), Positives = 204/325 (62%), Gaps = 3/325 (0%) Query: 1 MRRLVNDGYEAVEEMLAGYVAAQGKYVDFAENDKRVIVSKQMSEEPRVRIIVGGGSGHEP 60 M R++ND + VE+ML G + A + + E + RVIV + S RV I+ GGGSGHEP Sbjct: 1 MNRVINDPDQVVEDMLRGILVAHPELRQY-ETNPRVIVKAKPSGPGRVGIVTGGGSGHEP 59 Query: 61 LFLGYVGKDFADAAVVGNINTSPSPEPCYNAVKAVDSGKGCLYMYGNYAGDVMNFDMGAE 120 FLGYVG DA VG I +SP+ + ++A +A D G G +YGNYAGD MN + + Sbjct: 60 AFLGYVGPGLVDAVAVGEIFSSPTAKSFFDAFRAADHGAGVACLYGNYAGDNMNVKLAMK 119 Query: 121 MAADDGIRVETVLVTDDIYSAENVE--DRRGVAGDLIVFKAAASAAAKGLDLDAVKQAAE 178 MAA +R+ TV+ DD+ SA E RRGVAG++ ++K +AAA+ DLD V + A+ Sbjct: 120 MAASKDMRIRTVVANDDVASAPKAEIAKRRGVAGEIFMWKIGGAAAAQHYDLDGVIRVAQ 179 Query: 179 KANANTFSMGVALSSSTLPVTGKAIFEMKEGEMEVGMGIHGEPGIKRTSIEPADKVVDQI 238 K + S+G+ L+ T+ GK F++ +G+ME+G+G HGEPGI IEPA + +++ Sbjct: 180 KTVDHCRSIGIGLTPCTIAAVGKPNFQIPDGQMELGIGHHGEPGIDVIPIEPAAAMAERM 239 Query: 239 MGYLIEEMKLTAGEEVHVLINGLGGLPVMDQYICYRRVDEILKEKGVHIHSPLVGNYATS 298 + ++ + + V VL++GLG PVM+ YI Y V++ L KG+ IH VGNY TS Sbjct: 240 LAPILADRDFSQDNSVVVLVSGLGATPVMELYIFYAEVEKQLTAKGLKIHRCYVGNYFTS 299 Query: 299 MDMIGMSITLVRLDDELKDLLDTPC 323 ++M+G+++TL+ LD EL L+D PC Sbjct: 300 LEMMGVTLTLLGLDAELTTLIDQPC 324 Lambda K H 0.317 0.136 0.386 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: 284 Number of extensions: 11 Number of successful extensions: 3 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: 331 Length of database: 333 Length adjustment: 28 Effective length of query: 303 Effective length of database: 305 Effective search space: 92415 Effective search space used: 92415 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