Align PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK; EC 2.7.1.121 (characterized)
to candidate BPHYT_RS32475 BPHYT_RS32475 dihydroxyacetone kinase
Query= SwissProt::Q9CIV8 (332 letters) >FitnessBrowser__BFirm:BPHYT_RS32475 Length = 567 Score = 263 bits (673), Expect = 6e-75 Identities = 142/332 (42%), Positives = 208/332 (62%), Gaps = 6/332 (1%) Query: 4 EKIINQPQDVVSEMLDGLTYAYGDLIEKVPDFEIIQRKSPKS----GKVALVSGGGSGHK 59 +K+IN+ VV +MLDGL A + + I+ R ++ G+VAL+SGGGSGH+ Sbjct: 2 KKLINEVSAVVPDMLDGLA-ALNPNLSLLQGGTIVVRADAEAAAARGEVALISGGGSGHE 60 Query: 60 PAHAGFVGEGMLSAAVCGAIFTSPTPDQIYEAIKSADEGAGVLLIIKNYLGDVMNFEMAR 119 PAH G+VG GMLSAAV G +FTSP+ D + +AI++ AG LLI+KNY GD NF +A Sbjct: 61 PAHGGYVGSGMLSAAVAGEVFTSPSTDAVLDAIRAVAGAAGALLIVKNYTGDRFNFGLAA 120 Query: 120 EMAEMEEIKVEQIIVDDDIAVENSLYTQGRRGVAGTVLVHKILGAAAHQEASLDEIKDLA 179 E+A E I E +IV DD+A+ S GRRG+AGTVL+HKI GAAA L E+ +A Sbjct: 121 EIARAEGIPTEMVIVADDVALTASGDHAGRRGLAGTVLIHKIAGAAAAAGRPLGEVAQIA 180 Query: 180 DKVVKNIKTIGLALSAATVPEVGKPGFVLDDNEIEYGVGIHSEPGYRREKMKTSYELATE 239 V ++ T+G+AL+A TVP GKPGF L D EIE+G+GIH EPG R ++ + + + Sbjct: 181 RDVAASLGTMGVALTACTVPAAGKPGFELADGEIEWGLGIHGEPGVERGALEPADAIVEK 240 Query: 240 LVGKLKEEFKFEAGQKYGILVNGMGATPLMEQFIFMNDVAKLLTEENIEILFKKVGNYMT 299 L+ K+ + + G++ +LVN +G TP E I + L + IE+ G +++ Sbjct: 241 LLAKIVGDLSLQTGERVALLVNNLGGTPSSELSIVAGSALRYLAKRGIEVERAWAGTFLS 300 Query: 300 SIDMAGLSLTMIKLEDDQWLKNLNEDVKTISW 331 +++MAG+SLT++++ DD+ L L+ T +W Sbjct: 301 ALEMAGVSLTLLRV-DDERLAWLDAATHTSAW 331 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: 444 Number of extensions: 19 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: 332 Length of database: 567 Length adjustment: 32 Effective length of query: 300 Effective length of database: 535 Effective search space: 160500 Effective search space used: 160500 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