Align PTS-dependent dihydroxyacetone kinase 2, dihydroxyacetone-binding subunit DhaK; EC 2.7.1.121 (characterized)
to candidate H281DRAFT_02702 H281DRAFT_02702 dihydroxyacetone kinase DhaK subunit
Query= SwissProt::Q92EU2 (331 letters) >FitnessBrowser__Burk376:H281DRAFT_02702 Length = 336 Score = 303 bits (775), Expect = 5e-87 Identities = 149/331 (45%), Positives = 216/331 (65%), Gaps = 2/331 (0%) Query: 1 MRRLVNDGYEAVEEMLAGYVAAQGKYVDFAENDKRVIVSKQMSEEPRVRIIVGGGSGHEP 60 M++++N+ V+E++ G + A ++ A DKR +V K + RV I+ GGGSGH P Sbjct: 1 MKKIINEPDAFVDEIIEGLLIAHPAWIKSATADKRALVRKDAPKAGRVGIVTGGGSGHLP 60 Query: 61 LFLGYVGKDFADAAVVGNINTSPSPEPCYNAVKAVDSGKGCLYMYGNYAGDVMNFDMGAE 120 FLGYVG+ VGN+ +SPS E A KAV+ G G LY+YGNY GDV+NFD+ A+ Sbjct: 61 GFLGYVGEGLCSGVAVGNVFSSPSAEQILEATKAVNGGAGVLYVYGNYGGDVLNFDLAAD 120 Query: 121 MAADDGIRVETVLVTDDIYSA--ENVEDRRGVAGDLIVFKAAASAAAKGLDLDAVKQAAE 178 +A DGI ++TV++TDD+ SA E DRRGVAG L FK A +AA +G LD V + Sbjct: 121 LAEPDGIEIQTVVLTDDVASAPKERAADRRGVAGMLFAFKCAGAAAERGDSLDEVARICG 180 Query: 179 KANANTFSMGVALSSSTLPVTGKAIFEMKEGEMEVGMGIHGEPGIKRTSIEPADKVVDQI 238 KANAN +MGV LS + LP GK F + EGEME+G+GIHGEPG R ++E AD + ++I Sbjct: 181 KANANCRTMGVGLSPTILPAAGKPTFTLPEGEMEIGIGIHGEPGTHRGNLESADAIAERI 240 Query: 239 MGYLIEEMKLTAGEEVHVLINGLGGLPVMDQYICYRRVDEILKEKGVHIHSPLVGNYATS 298 +++++ G V +L+NGLG P+ + Y+ YRR ++ ++G+ + VG Y TS Sbjct: 241 TREILDDLDAEKGSRVALLVNGLGATPLEELYLLYRRSARLIADRGLKVARSYVGEYVTS 300 Query: 299 MDMIGMSITLVRLDDELKDLLDTPCDTPYFK 329 ++M G SIT++ LDDEL+ LL+ P ++P+F+ Sbjct: 301 LEMAGASITVMLLDDELQALLEAPANSPFFR 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: 315 Number of extensions: 11 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: 331 Length of database: 336 Length adjustment: 28 Effective length of query: 303 Effective length of database: 308 Effective search space: 93324 Effective search space used: 93324 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