Align PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK; EC 2.7.1.121 (characterized)
to candidate WP_010959412.1 MCA_RS00200 dihydroxyacetone kinase subunit DhaK
Query= SwissProt::Q9CIV8 (332 letters) >NCBI__GCF_000008325.1:WP_010959412.1 Length = 329 Score = 261 bits (666), Expect = 2e-74 Identities = 147/332 (44%), Positives = 206/332 (62%), Gaps = 8/332 (2%) Query: 4 EKIINQPQDVVSEMLDGLTYAYGDLIEKVPDFEIIQRKSP-KSGKVALVSGGGSGHKPAH 62 +K IN +D + E L G A+ D+++ P+ + RK+P + GKVALVSGGGSGH+P H Sbjct: 2 KKFINTVEDFLDESLRGFALAHADIVDFSPEPRFVSRKAPARPGKVALVSGGGSGHEPLH 61 Query: 63 AGFVGEGMLSAAVCGAIFTSPTPDQIYEAIKSADEGAGVLLIIKNYLGDVMNFEMAREMA 122 GFVG GML AA G +FTSPTPDQ+ A ++ D G GVL I+KNY GDVMNFE+A A Sbjct: 62 TGFVGLGMLDAACPGQVFTSPTPDQMLAAAQAVDHGGGVLFIVKNYAGDVMNFEIA---A 118 Query: 123 EMEEIKVEQIIVDDDIAVENSLYTQGRRGVAGTVLVHKILGAAAHQEASLDEIKDLADKV 182 EM +I + ++V DD+++ + GRRG+AGT +V KI+GAAA L K L ++V Sbjct: 119 EMLDIPHDSLLVHDDVSLPENR-GMGRRGIAGTTVVEKIVGAAADAGYDLAACKALGERV 177 Query: 183 VKNIKTIGLALSAATVPEVGKPGFVLDDNEIEYGVGIHSEPGYRREKMKTSYELATELVG 242 V ++G+AL++ TVP +GKP F L + E+E GVGIH E G R + ++ E+ + Sbjct: 178 VHATASMGIALTSCTVPALGKPMFELGEREMEMGVGIHGERGRERMALGSAGEIVDYIAA 237 Query: 243 KLKEEFKFEAGQKYGILVNGMGATPLMEQFIFMNDVAKLLTEENIEILFKKVGNYMTSID 302 + EE K AGQ + VNG G TPL+E + + + ++I VGNY TS+D Sbjct: 238 VIDEELKPRAGQPVLLHVNGFGGTPLIELHLVYGLAHRYWSGRGVDIARSLVGNYTTSLD 297 Query: 303 MAGLSLTMIKLEDDQWLKNLNEDVKT--ISWG 332 MAG SLT + L D++ L+ + V T + WG Sbjct: 298 MAGCSLT-LSLLDEEMLRLWDAPVHTAALRWG 328 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: 336 Number of extensions: 18 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: 332 Length of database: 329 Length adjustment: 28 Effective length of query: 304 Effective length of database: 301 Effective search space: 91504 Effective search space used: 91504 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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