Align PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121 (characterized)
to candidate BWI76_RS24605 BWI76_RS24605 dihydroxyacetone kinase subunit DhaM
Query= SwissProt::A0A0H3H456 (472 letters) >FitnessBrowser__Koxy:BWI76_RS24605 Length = 473 Score = 808 bits (2086), Expect = 0.0 Identities = 422/473 (89%), Positives = 439/473 (92%), Gaps = 1/473 (0%) Query: 1 MVNLVIVSHSARLGEGVGELARQMLMNDGCKLAIAAGIDDPASPIGTDPIKVMEAIESVA 60 MVNLVIVSHSARLGEGVGELARQMLMNDGCKLAIAAGIDDPASPIGTDPIKVMEAIESVA Sbjct: 1 MVNLVIVSHSARLGEGVGELARQMLMNDGCKLAIAAGIDDPASPIGTDPIKVMEAIESVA 60 Query: 61 DADHILVMMDIGSALLSAETALDLLDPAIAAKVRLCAAPLVEGTLAATVSAAAGAGIDKV 120 DADH+LVMMDIGSALLSAETALDLLDPAIAAKVRLCAAPLVEGTLAATVSAAAGA IDKV Sbjct: 61 DADHVLVMMDIGSALLSAETALDLLDPAIAAKVRLCAAPLVEGTLAATVSAAAGADIDKV 120 Query: 121 IEDAMNALEAKRVQLGLPSQPQHASLTAAPVDDRDARSVSVVIQNHNGLHVRPASKLVAA 180 IEDAMNALEAKRVQLGLPSQPQ SLTA DDRDARSVSVVIQN NGLHVRPASKLVAA Sbjct: 121 IEDAMNALEAKRVQLGLPSQPQPPSLTAELADDRDARSVSVVIQNPNGLHVRPASKLVAA 180 Query: 181 LAGFNADLVLEKGGKCVTPDSLNQIALLQVRRNDTLRLLARGPDADAALAAFQALAAENF 240 LAGFNADLVLEK GKCVTPDSLNQIALLQVRRNDTLRLLARGPDADAALAAFQALAAENF Sbjct: 181 LAGFNADLVLEKEGKCVTPDSLNQIALLQVRRNDTLRLLARGPDADAALAAFQALAAENF 240 Query: 241 GEPTEAAPARRPASADRVEGKVVLYPQPQDRISRETSAAIGQQQLRLKRAIDRTLEDLSA 300 GE TEA PA +P A R++G+VVLYP+PQ+ ++RE SAAIGQQQLRLKRAIDRTL+DLSA Sbjct: 241 GEQTEATPALQPTHAARIQGQVVLYPRPQNSVTREKSAAIGQQQLRLKRAIDRTLDDLSA 300 Query: 301 LTTLAEATFSADIAAIFSGHHTLLDDPDLYAAACDIIRDEQCSAAWAWQQVLSDLSQQYR 360 LT LAE +SADIAAIFSGHHTLLDDPDLY AACDI+RDEQCSA WAW QVLSDLSQQYR Sbjct: 301 LTALAEEKYSADIAAIFSGHHTLLDDPDLYTAACDIVRDEQCSAEWAWHQVLSDLSQQYR 360 Query: 361 HLDDAYLQARYIDIEDILHRTLRHLNERNEALPQFSAPSILVADDIFPSTVLQLNAEQVK 420 HLDDAYLQARYIDIEDILHRTLRHLNE +EALPQFS PSILVADDIFPSTV+QL+ QVK Sbjct: 361 HLDDAYLQARYIDIEDILHRTLRHLNESSEALPQFSTPSILVADDIFPSTVVQLDGRQVK 420 Query: 421 GICLQAGSELSHGAIIARQAGIAMLCQQSDAL-TLQDGENVILDIPGKRVIRG 472 GICLQ SE +HGAIIARQAGIAMLCQQ D L TLQ+GE V LDIPGKRVIRG Sbjct: 421 GICLQESSEHAHGAIIARQAGIAMLCQQRDVLTTLQNGETVTLDIPGKRVIRG 473 Lambda K H 0.318 0.132 0.372 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: 696 Number of extensions: 21 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: 472 Length of database: 473 Length adjustment: 33 Effective length of query: 439 Effective length of database: 440 Effective search space: 193160 Effective search space used: 193160 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 (21.7 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