Align PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121 (characterized)
to candidate WP_086509381.1 BZY95_RS07800 phosphoenolpyruvate--protein phosphotransferase
Query= SwissProt::D4GL26 (473 letters) >NCBI__GCF_002151265.1:WP_086509381.1 Length = 963 Score = 126 bits (317), Expect = 3e-33 Identities = 111/360 (30%), Positives = 165/360 (45%), Gaps = 34/360 (9%) Query: 139 PPAHAASLPAQAPDSDARSVTVTIR--NHHGLHVRPASRLVAALAGMNADL---VLEKQG 193 P A AA++ A+ A + T R N HGLH RPA +LV A + + E G Sbjct: 262 PSADAATVLARLAGESAAAHTRLARVLNAHGLHARPAKQLVQAAREQGLPIQVRLAEGGG 321 Query: 194 QCVKPDSLNQIALLQVRCHDAVTLSASGPDAERALAAFESLAAEDFGEHP-------ESM 246 V SL ++ L R + SA G A++AL A A+ GEH E Sbjct: 322 AAVSASSLTKVINLGARRGQQLLFSAEGEGAQQALDAVCRAVADGLGEHVLPFDESRERS 381 Query: 247 ALKTSASTVEKVQ------------GKAVFYPLPLAQPA---RHPCSDVGQEERRLQQAI 291 + A+ VE + G A+ L P +D +++RRL+QA+ Sbjct: 382 MPQADAAPVEPLPDDVPHPGVAASPGLAIAPAFVLQTPRFDYPERAADPAEQQRRLRQAL 441 Query: 292 VDTLNDLNALAALAEKKYGASVAAIFSGHYTLLDDPDLFDAACKVIRNDSCCAESAWYQV 351 + L AL A G VA I S H +L DP+LF+AA + I+ + AESAW++ Sbjct: 442 AEGAAQLEALVRQAR---GGEVAQILSMHEEMLTDPELFEAAREGIQ-EGRSAESAWWEA 497 Query: 352 LMELSQQYQHLDDAYLQARFIDIEDILYRSLCHLKGRDIRLPTP-DVPAIIVADDIFPSA 410 + + + L D L R D+ D+ R L L +++LP P + P I+V DDI PS Sbjct: 498 IETAAHAQEMLADRLLAERAADLRDVGRRVLGVLC--EVQLPEPPETPYILVTDDIGPSD 555 Query: 411 VVNLNAQLVKGICLREGSTLSHAAIIAQQAGIAFICQQGAVLDIIQPEDRLLIDPAAQRV 470 V L+ Q V+G+ G +H+AI+A+ GI + G + + L++D RV Sbjct: 556 VARLDTQRVRGLLTARGGATAHSAILARALGIPAVVGAGERVLTLAGGQELILDGERGRV 615 Lambda K H 0.320 0.133 0.380 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: 961 Number of extensions: 44 Number of successful extensions: 5 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: 473 Length of database: 963 Length adjustment: 39 Effective length of query: 434 Effective length of database: 924 Effective search space: 401016 Effective search space used: 401016 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 54 (25.4 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