Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate WP_084544831.1 H566_RS22940 fructokinase
Query= metacyc::MONOMER-19002 (326 letters) >NCBI__GCF_000482785.1:WP_084544831.1 Length = 334 Score = 68.6 bits (166), Expect = 2e-16 Identities = 54/196 (27%), Positives = 85/196 (43%), Gaps = 35/196 (17%) Query: 84 GTIEFAPNLPWKGVLPLASMFEERLGIPTALTNDANAAAVGEMTYGAARGMKDFIMITLG 143 G I P W+ + GIP D N AA+GE +GAARG+ +F+ IT+G Sbjct: 85 GRITATPKPGWRDADVAGVLRAALPGIPLGFDTDVNGAALGEQRWGAARGLAEFVYITMG 144 Query: 144 TGVGSGIVINGQVVYGHDGFAGELGHVIVRR---DGRICGCGRKG-CLETYCSATGVA-R 198 TG+G+G + G++++G E+GH+ + R DG C G C E CS +A R Sbjct: 145 TGIGAGGMAGGRLLHGL--VHPEMGHMRLPRLAGDGFAGVCSFHGDCWEGLCSGPAIAAR 202 Query: 199 TAREFLAARTDASLLRNIPAESIVSKDVYDAAVQGDKLAQEIFEFTGNILGEALADAIAF 258 T R PA+ + + ++ + A+ + + Sbjct: 203 TGR---------------PADELPAD-------------HPVWALLADTTALAIGNLVCV 234 Query: 259 SSPEAIILFGGLAKSG 274 SP +IL G + K+G Sbjct: 235 LSPRRVILGGSVRKAG 250 Lambda K H 0.318 0.138 0.399 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: 268 Number of extensions: 22 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 326 Length of database: 334 Length adjustment: 28 Effective length of query: 298 Effective length of database: 306 Effective search space: 91188 Effective search space used: 91188 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: 49 (23.5 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