Align PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK; EC 2.7.1.121 (characterized)
to candidate BWI76_RS24610 BWI76_RS24610 dihydroxyacetone kinase
Query= SwissProt::Q9CIV8 (332 letters) >FitnessBrowser__Koxy:BWI76_RS24610 Length = 549 Score = 188 bits (478), Expect = 2e-52 Identities = 117/328 (35%), Positives = 186/328 (56%), Gaps = 11/328 (3%) Query: 8 NQPQDVVSEMLDGLTYA--YGDL--IEKVPDFEIIQRKSPKSGKVALVSGGGSGHKPAHA 63 NQ ++V+++++G A + +L +E P ++ R+ VA++SGGGSGH+PAHA Sbjct: 7 NQRANLVNDVIEGTIIASPWNNLARLESDPAIRVVVRRDLDKNNVAVISGGGSGHEPAHA 66 Query: 64 GFVGEGMLSAAVCGAIFTSPTPDQIYEAIKSADEGAGVLLIIKNYLGDVMNFEMAREMAE 123 GFVG+GML+AAVCG +F SP+ D + AI++ AG LLI+KNY GD +NF +A E A Sbjct: 67 GFVGKGMLTAAVCGDLFASPSVDAVLTAIQAVTGDAGCLLIVKNYTGDRLNFGLAAEKAR 126 Query: 124 MEEIKVEQIIVDDDIAVENSLYTQGRRGVAGTVLVHKILGAAAHQEASLDEIKDLADKVV 183 VE +IV DDI++ ++ + RG+AGT+LVHK+ G A + +L + A Sbjct: 127 RMGYNVEMLIVGDDISLPDNKHP---RGIAGTILVHKVAGYFAERGHNLATVLREAQYAA 183 Query: 184 KNIKTIGLALSAATVPEVGKPGFVLDDNEIEYGVGIHSEPGYRREKMKTSYELATELVGK 243 + ++GLAL++ +P+ + ++ E G+GIH EPG + S E+ T + K Sbjct: 184 GHTFSLGLALASCHLPQDAETAPRHHADQAELGMGIHGEPGASVIATQNSAEIVTLMAEK 243 Query: 244 LKEEFKFEAGQKYGILVNGMGATPLMEQFIFMNDVAKLLTEENIEILFKKVGNYMTSIDM 303 L E G + +++N +G + E I ++A ++ I+ L + +T++DM Sbjct: 244 LSAALP-ETG-RLAVMINNLGGVSIAEMAILTRELAHTPLQQRIDWLIGP-ASLVTALDM 300 Query: 304 AGLSLTMIKLEDDQWLKNLNEDVKTISW 331 G SLT I LE + K L V+T W Sbjct: 301 KGFSLTAIVLE-ESIEKALLSAVETAGW 327 Lambda K H 0.315 0.135 0.375 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: 389 Number of extensions: 19 Number of successful extensions: 4 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: 332 Length of database: 549 Length adjustment: 32 Effective length of query: 300 Effective length of database: 517 Effective search space: 155100 Effective search space used: 155100 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: 42 (22.0 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