Align PTS-dependent dihydroxyacetone kinase 2, dihydroxyacetone-binding subunit DhaK; EC 2.7.1.121 (characterized)
to candidate AZOBR_RS23290 AZOBR_RS23290 dihydroxyacetone kinase subunit K
Query= SwissProt::Q92EU2 (331 letters) >FitnessBrowser__azobra:AZOBR_RS23290 Length = 332 Score = 265 bits (678), Expect = 9e-76 Identities = 146/332 (43%), Positives = 201/332 (60%), Gaps = 3/332 (0%) Query: 1 MRRLVNDGYEAVEEMLAGYVAAQGKYVDFAENDKRVIVSKQMSEEPRVRIIVGGGSGHEP 60 +++L+ND V+EML G AA + RVI + + +V I+ GGGSGH P Sbjct: 1 VKKLINDPAHYVDEMLDGLCAAHPSLMRDGPAG-RVIRRTEGARAGKVGIVTGGGSGHLP 59 Query: 61 LFLGYVGKDFADAAVVGNINTSPSPEPCYNAVKAVDSGKGCLYMYGNYAGDVMNFDMGAE 120 LF GYVG DA +GN+ P+ + C A+KA D G+G L +YGNY GD MNFDM E Sbjct: 60 LFTGYVGPGLVDACSIGNVFEGPTVDSCMAAIKAADGGRGVLRLYGNYGGDRMNFDMAGE 119 Query: 121 MAADDGIRVETVLVTDDIYSAENVE--DRRGVAGDLIVFKAAASAAAKGLDLDAVKQAAE 178 ++G+ + TVL TDDI SA E RRGVAG + +K A + A +G L V AA Sbjct: 120 FLEEEGLELSTVLGTDDIASAAPAERSKRRGVAGIVYAYKIAGARADEGASLAEVTAAAA 179 Query: 179 KANANTFSMGVALSSSTLPVTGKAIFEMKEGEMEVGMGIHGEPGIKRTSIEPADKVVDQI 238 KA T ++G ALSS +P + F + EME+G+GIHGEPGI R +++PAD V D++ Sbjct: 180 KAVERTRTIGCALSSCQIPGAAEPSFRIAPSEMEMGIGIHGEPGIWRDTLKPADAVADEM 239 Query: 239 MGYLIEEMKLTAGEEVHVLINGLGGLPVMDQYICYRRVDEILKEKGVHIHSPLVGNYATS 298 + L+ E +G V VL+N LG P+ + +I YRR+ E L + G+ + PLVG Y TS Sbjct: 240 VDRLLAERPEGSGNRVSVLVNSLGATPLEELFILYRRIAERLDKAGLAVVQPLVGPYVTS 299 Query: 299 MDMIGMSITLVRLDDELKDLLDTPCDTPYFKV 330 M+M G+S++L LDDEL+ LL P P++KV Sbjct: 300 MEMTGVSLSLCFLDDELERLLAAPASCPFWKV 331 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: 288 Number of extensions: 12 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: 332 Length adjustment: 28 Effective length of query: 303 Effective length of database: 304 Effective search space: 92112 Effective search space used: 92112 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