Align PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121 (characterized)
to candidate 8501869 DvMF_2584 phosphoenolpyruvate-protein phosphotransferase (RefSeq)
Query= SwissProt::D4GL26 (473 letters) >FitnessBrowser__Miya:8501869 Length = 846 Score = 292 bits (748), Expect = 3e-83 Identities = 196/487 (40%), Positives = 270/487 (55%), Gaps = 39/487 (8%) Query: 1 MVNLVIVSHSAMLGEGVEMLARQMLTGDNCRIAVAAGIDDPDHPIGTDPIKVMEAIEAVA 60 MV +V+V+HSA+LG+GV+ L QM G +AVA GIDDP+HPIGTDP++VM AIE V Sbjct: 1 MVGIVVVTHSAVLGQGVKELVEQMTQG-RVPLAVAGGIDDPEHPIGTDPMRVMAAIEEVQ 59 Query: 61 DTDHVLVMMDMGSALLSAETALDLLDPVIAEKVRLCAAPLVEGTLAATVSAAAGADIDTV 120 D VLV+MD+GSAL+SAETALDLL P +A +VRL APLVEG +AA V A+ GAD+DTV Sbjct: 60 QGDGVLVLMDLGSALMSAETALDLLPPEVAAQVRLRPAPLVEGVMAAAVQASIGADLDTV 119 Query: 121 IDVAMNALAAKQAQLGITPPA------HAASLPAQAPDSDARSVTVTIRNHHGLHVRPAS 174 + A +ALAAK LG+ P AA A A + + +T+ + N GLH RPA+ Sbjct: 120 LREAQSALAAKAELLGMALPQDGGGVDEAAPPAAGATPAASHELTLMVPNRLGLHARPAA 179 Query: 175 RLVAALAGMNADLVLEKQGQCVKPDSLNQIALLQVRCHDAVTLSASGPDAERALAAFESL 234 R+V AL AD+ L + + V S+N+IA L VR + +T A+G DAE+AL A L Sbjct: 180 RIVTALGPFVADVQLARGERVVSARSVNRIATLAVRGGETITFRAAGTDAEQALKALADL 239 Query: 235 AAEDFGEHPESMALKTSAST-VE-----KVQGKAVFYPLPLAQ----------------- 271 AAE+FG+ P+ A K+S T VE QG+A +P A+ Sbjct: 240 AAENFGDLPD--ATKSSGRTGVEGPEGPGEQGRAGVAGVPAAKGGVPASPGIAVGPAVWH 297 Query: 272 -------PARHPCSDVGQEERRLQQAIVDTLNDLNALAALAEKKYGASVAAIFSGHYTLL 324 P D E RL A+ +L AL G A IF H LL Sbjct: 298 RPAFDAPPPDLAAGDPDSEAARLDGALDAARKELAALERRTAAMAGKQEAEIFVMHRLLL 357 Query: 325 DDPDLFDAACKVIRNDSCCAESAWYQVLMELSQQYQHLDDAYLQARFIDIEDILYRSLCH 384 DD + A + I AE+AWY V+ + ++ ++ L + Y++ R D+ D+ R L Sbjct: 358 DDATIAGDARQRIAERREPAEAAWYAVIDQAAESFRQLPEGYMRERAADLVDVGARVLRL 417 Query: 385 LKGRDIRLPTPDVPAIIVADDIFPSAVVNLNAQLVKGICLREGSTLSHAAIIAQQAGIAF 444 L G P + P++++A D+ PS + +L+ LV GI +G SHAAI+A+ GI Sbjct: 418 LTGAPPSGPRLERPSVLLAADLGPSDMAHLDPALVLGIVTAQGGATSHAAILARSMGIPA 477 Query: 445 ICQQGAV 451 + GA+ Sbjct: 478 VAGAGAL 484 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: 895 Number of extensions: 42 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: 846 Length adjustment: 38 Effective length of query: 435 Effective length of database: 808 Effective search space: 351480 Effective search space used: 351480 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