Align PTS-dependent dihydroxyacetone kinase 2, dihydroxyacetone-binding subunit DhaK; EC 2.7.1.121 (characterized)
to candidate SM_b20767 SM_b20767 dihydroxyacetone kinase
Query= SwissProt::Q92EU2 (331 letters) >FitnessBrowser__Smeli:SM_b20767 Length = 572 Score = 221 bits (563), Expect = 3e-62 Identities = 125/316 (39%), Positives = 175/316 (55%), Gaps = 6/316 (1%) Query: 16 LAGYVAAQGKYVDFAENDKRVIVSKQMSEEPRVRIIVGGGSGHEPLFLGYVGKDFADAAV 75 LAG+ A + V + +V + +V ++VGGGSGH P F GYVG ADAAV Sbjct: 16 LAGFAAIYQRNVRLVKGG---VVRSTKVPKGKVAVVVGGGSGHYPAFAGYVGPGLADAAV 72 Query: 76 VGNINTSPSPEPCYNAVKAVDSGKGCLYMYGNYAGDVMNFDMGAEMAADDGIRVETVLVT 135 G++ SPS + D G G L +GNYAGDV+NF + AE +GI V + VT Sbjct: 73 AGDVFASPSTAAVARVCRHADQGGGVLLGFGNYAGDVLNFGVAAERLRSEGIDVRILPVT 132 Query: 136 DDIYS--AENVEDRRGVAGDLIVFKAAASAAAKGLDLDAVKQAAEKANANTFSMGVALSS 193 DD+ S AE RRG+AGDL+VFK A +AA G LD V++ A AN T S GVA Sbjct: 133 DDVASAPAETSAKRRGIAGDLVVFKIAGAAAEAGKSLDEVERLARHANDRTVSFGVAFGG 192 Query: 194 STLPVTGKAIFEMKEGEMEVGMGIHGEPGIKRTSIEPADKVVDQIMGYLIEEMKLTAGEE 253 TLP +F + +G+M +G+GIHGEPG+ +I A + + G L+ E + + Sbjct: 193 CTLPGAAGPLFTVPKGQMALGLGIHGEPGVSEETIATASDLAKLLTGKLLAE-RPEGSRK 251 Query: 254 VHVLINGLGGLPVMDQYICYRRVDEILKEKGVHIHSPLVGNYATSMDMIGMSITLVRLDD 313 V ++NGLG + ++ + V L + G+ I P G + TS+DM G S+TL+ LD+ Sbjct: 252 VAAVLNGLGSTKYEELFVLWTAVARQLNDAGLEIVDPECGEFVTSLDMQGCSLTLLWLDE 311 Query: 314 ELKDLLDTPCDTPYFK 329 EL+ L P D P + Sbjct: 312 ELEALWRAPTDAPVLR 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: 440 Number of extensions: 22 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: 572 Length adjustment: 32 Effective length of query: 299 Effective length of database: 540 Effective search space: 161460 Effective search space used: 161460 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