Align PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121 (characterized)
to candidate 206413 DVU0981 multiphosphoryl transfer protein, putative
Query= SwissProt::D4GL26 (473 letters) >MicrobesOnline__882:206413 Length = 854 Score = 292 bits (747), Expect = 3e-83 Identities = 197/507 (38%), Positives = 272/507 (53%), Gaps = 45/507 (8%) Query: 1 MVNLVIVSHSAMLGEGVEMLARQMLTGDNCRIAVAAGIDDPDHPIGTDPIKVMEAIEAVA 60 MV +V+V+HSA+LG+G+ LA QM G +AVA GIDDPDHPIGTDP++VM AIE V Sbjct: 1 MVGIVVVTHSAVLGQGLRELAEQMTQG-RVPLAVAGGIDDPDHPIGTDPVRVMTAIEEVQ 59 Query: 61 DTDHVLVMMDMGSALLSAETALDLLDPVIAEKVRLCAAPLVEGTLAATVSAAAGADIDTV 120 D VLV+MD+GSAL+SAETALDLL P +A +VRL AAPLVEG +AA V A+ GAD+ V Sbjct: 60 QGDGVLVLMDLGSALMSAETALDLLPPEVASQVRLSAAPLVEGLMAAAVLASTGADLGAV 119 Query: 121 IDVAMNALAAKQAQLGITPPAHAASLPAQAPDSDARS------------VTVTIRNHHGL 168 + A +ALAAK+ LG PA A ++P+ P+ S +T+ + N GL Sbjct: 120 AEEAQSALAAKRELLGAAAPA-APAMPSAHPEGARDSTVPSSAMPAGEELTLVVPNRLGL 178 Query: 169 HVRPASRLVAALAGMNADLVLEKQGQCVKPDSLNQIALLQVRCHDAVTLSASGPDAERAL 228 H RPA+R+V AL AD+ L + + V S+N+IA L VR + VT A G DA AL Sbjct: 179 HARPAARIVTALGPFAADVQLVRGDRVVSARSVNRIATLAVRGGETVTFRAVGGDAALAL 238 Query: 229 AAFESLAAEDFGEHPESMA------------------------------LKTSASTVEKV 258 A E+LAA FG+ PE+ + L+ +A++ Sbjct: 239 RAIEALAAAHFGDAPEAPSKGEAPSPAEAPKDGDMAEAAVSADVQGGGVLRGAAASPGLT 298 Query: 259 QGKAVFYPLPLAQPARHP-CSDVGQEERRLQQAIVDTLNDLNALAALAEKKYGASVAAIF 317 G AV+Y P P D E RL A+ +L L G A IF Sbjct: 299 VGNAVWYRPAFDAPDVAPLADDPATEVTRLDAALGAARTELVELERRTVAAAGRKEAEIF 358 Query: 318 SGHYTLLDDPDLFDAACKVIRNDSCCAESAWYQVLMELSQQYQHLDDAYLQARFIDIEDI 377 + H LLDD + AA + I + AESAWY+V+ + + ++ L + Y++ R D+ D+ Sbjct: 359 AMHRLLLDDVTIAGAARQRIMDRREAAESAWYEVISDAAATFRQLPEGYMREREADMVDV 418 Query: 378 LYRSLCHLKGRDIRLPTPDVPAIIVADDIFPSAVVNLNAQLVKGICLREGSTLSHAAIIA 437 R L L G P P++++A D+ PS + L+ LV GI +G SHAAI+A Sbjct: 419 GARVLRLLTGVAAVGPRLGGPSVLLATDLGPSDMATLDPSLVIGIVTVQGGATSHAAILA 478 Query: 438 QQAGIAFICQQGAVLDIIQPEDRLLID 464 + GI + G L + D + +D Sbjct: 479 RSLGIPAVAGLGPALQGVGEGDIVALD 505 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: 862 Number of extensions: 37 Number of successful extensions: 4 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: 854 Length adjustment: 38 Effective length of query: 435 Effective length of database: 816 Effective search space: 354960 Effective search space used: 354960 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 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