Align PTS-dependent dihydroxyacetone kinase 2, dihydroxyacetone-binding subunit DhaK; EC 2.7.1.121 (characterized)
to candidate WP_017558945.1 C892_RS0121990 DAK2 domain-containing protein
Query= SwissProt::Q92EU2 (331 letters) >NCBI__GCF_000341205.1:WP_017558945.1 Length = 591 Score = 234 bits (597), Expect = 4e-66 Identities = 133/318 (41%), Positives = 185/318 (58%), Gaps = 5/318 (1%) Query: 14 EMLAGYVAAQGKYVDFAENDKRVIVSKQMSEEPRVRIIVGGGSGHEPLFLGYVGKDFADA 73 + L G+ A G+ V V V+++ +V +++GGG GH P F G VG AD Sbjct: 13 DWLDGFATAYGRTVRKVPGAYGV-VARERPRTGKVAVVIGGGCGHYPAFAGLVGPGLADG 71 Query: 74 AVVGNINTSPSPEPCYNAVKAVDSGKGCLYMYGNYAGDVMNFDMGAEMAADDGIRVETVL 133 AVVG++ TSPS E Y + D G G L+ YGNY GDV++F + A A +GI TVL Sbjct: 72 AVVGDVFTSPSAEQVYRTAREADDGGGVLFGYGNYQGDVLHFGLAARRLAAEGIDSRTVL 131 Query: 134 VTDDIYS--AENVEDRRGVAGDLIVFKAAASAAAKGLDLDAVKQAAEKANANTFSMGVAL 191 VTDD+ S AE RRGVAGD VFK A +AA +G DL V AAE+ANA T + GVA Sbjct: 132 VTDDVASGPAEQAGRRRGVAGDFFVFKVAGAAAERGDDLAGVHAAAERANAATRTFGVAF 191 Query: 192 SSSTLPVTGKAIFEMKEGEMEVGMGIHGEPGIKRTSIEPADKVVDQIMGYLIEEMKLTAG 251 TLP +F + +G ME+G+GIHGEPG++ A+++ D+++ L+ E L + Sbjct: 192 GGCTLPGADGPLFTVDDGAMELGLGIHGEPGVRTVGRLGAEELADELVDGLLPE--LPSQ 249 Query: 252 EEVHVLINGLGGLPVMDQYICYRRVDEILKEKGVHIHSPLVGNYATSMDMIGMSITLVRL 311 V VL+NGLG + + RV E L G+ G + TS+DM G+S++++ L Sbjct: 250 GRVAVLLNGLGRTKYEEMFTVCTRVHERLAGAGLLPVHTEAGEFVTSLDMAGLSLSVMVL 309 Query: 312 DDELKDLLDTPCDTPYFK 329 DDEL +L PCDTP ++ Sbjct: 310 DDELAELYAAPCDTPGYR 327 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: 481 Number of extensions: 28 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: 591 Length adjustment: 32 Effective length of query: 299 Effective length of database: 559 Effective search space: 167141 Effective search space used: 167141 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 24 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