Align PEP-dependent dihydroxyacetone kinase, phosphoryl donor subunit DhaM; Dihydroxyacetone kinase subunit M; EC 2.7.1.121 (characterized)
to candidate AO356_17540 AO356_17540 PTS N-acetyl-D-glucosamine transporter
Query= SwissProt::A0A0H3H456 (472 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_17540 Length = 837 Score = 118 bits (296), Expect = 7e-31 Identities = 103/325 (31%), Positives = 150/325 (46%), Gaps = 19/325 (5%) Query: 161 VVIQNHNGLHVRPASKLVAALAGFNADLVLEKGGKCVTPDSLNQIALLQVRRNDTLRLLA 220 V I + GLH RPA+ + GF + L GK + DS+ + L + + + Sbjct: 176 VRIAHRGGLHARPAALVRQTAQGFKSRSQLHFSGKSASCDSVMGMMGLAITEQAQVHVSC 235 Query: 221 RGPDADAALAAFQALAAENFGEPTEA-APARRPASADRVEGKVV-------LYPQPQDRI 272 RG DA+AAL A + E A AP P A+ EG + L P R+ Sbjct: 236 RGSDAEAALQALLTTLSTALVEEAHASAPPPEPPRANAEEGVLHGVCAAPGLVTGPLVRL 295 Query: 273 SRET------SAAIGQQQLRLKRAIDRTLEDLSALTTLAEATFSADIAAIFSGHHTLLDD 326 S AI +Q+ RL A+ + ++ A A D AIFS H LL+D Sbjct: 296 SGIQLPEDIGGHAIEEQRQRLSDALAQVRGEIHLTLEHARARQHRDEEAIFSAHLALLED 355 Query: 327 PDLYAAACDIIRDEQCSAAWAWQQVLSDLSQQYRHLDDAYLQARYIDIEDILHRTLRHLN 386 P L AA D+ ++ +A AW + + Q + L L R D+ D+ R LR L Sbjct: 356 PVLLDAA-DLFIEQGSAAPHAWSRSIDTQCQVLQQLGSTLLAERANDLRDLRQRVLRVL- 413 Query: 387 ERNEALP-QFSAPSILVADDIFPSTVLQLNAEQVKGICLQAGSELSHGAIIARQAGIAML 445 EA +A +I+ A ++ PS +LQL+A+ V G+C+ G SH AI+AR G+ L Sbjct: 414 -LGEAWQFDVAAGAIVAAQELTPSDLLQLSAQGVAGVCMVEGGATSHVAILARGKGLPCL 472 Query: 446 CQQSDALTLQD-GENVILDIPGKRV 469 D L Q+ G+ V+LD G R+ Sbjct: 473 VALGDELLAQEQGQAVVLDADGGRL 497 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: 777 Number of extensions: 46 Number of successful extensions: 3 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: 837 Length adjustment: 38 Effective length of query: 434 Effective length of database: 799 Effective search space: 346766 Effective search space used: 346766 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 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