Align PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121 (characterized)
to candidate Pf1N1B4_833 PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)
Query= SwissProt::A0A0H3H456 (472 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_833 Length = 844 Score = 115 bits (287), Expect = 8e-30 Identities = 96/322 (29%), Positives = 140/322 (43%), Gaps = 21/322 (6%) Query: 158 SVSVVIQNHNGLHVRPASKLVAALAGFNADLVLEKGGKCVTPDSLNQIALLQVRRNDTLR 217 S V + N NGLH RPA+ A GF A + L K SL I LQ D L+ Sbjct: 172 SKPVTLPNTNGLHARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTAHGDVLQ 231 Query: 218 LLARGPDADAALAAFQALAAENFGEPT------EAAPARRP---------ASADRVEGKV 262 + A G DA+ A+ L A GE E A+ AS G+V Sbjct: 232 VSAAGADAEVAIKTLAELLAAGCGEAVTLMAEVETVAAQVSSLTVLRGVCASPGAAFGQV 291 Query: 263 VLYPQPQDRISRETSAAIGQQQLRLKRAIDRTLEDLSALTTLAEATFSADIAAIFSGHHT 322 V + +S E+ + ++ L RA+ + + L L A ADI F H Sbjct: 292 VQIAEQTLEVS-ESGVSPQVEREHLSRALAKAVLALQQLRDKATGDAQADI---FKAHQE 347 Query: 323 LLDDPDLYAAACDIIRDEQCSAAWAWQQVLSDLSQQYRHLDDAYLQARYIDIEDILHRTL 382 LL+DP L A +I D SA +AW+ + ++ L +A L R D+ D+ R L Sbjct: 348 LLEDPGLLDQALALI-DAGKSAGFAWRAATESTATLFKKLGNALLAERAADLADVGQRVL 406 Query: 383 RHLNERNEALPQFSAPSILVADDIFPSTVLQLNAEQVKGICLQAGSELSHGAIIARQAGI 442 + + + + +IL+A+ + PS L+ +V G G SH AI+AR +G+ Sbjct: 407 KLILGVEDRAMELPDGAILIAEQLTPSQTAGLDTRKVLGFATVGGGATSHVAILARASGL 466 Query: 443 AMLC-QQSDALTLQDGENVILD 463 +C LTL +G V+LD Sbjct: 467 PAICGLPVQVLTLINGTRVLLD 488 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: 697 Number of extensions: 24 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: 844 Length adjustment: 38 Effective length of query: 434 Effective length of database: 806 Effective search space: 349804 Effective search space used: 349804 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: 54 (25.4 bits)
This GapMind analysis is from Apr 09 2024. 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