Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_086509236.1 BZY95_RS06985 amino-acid N-acetyltransferase
Query= BRENDA::Q9X2A4 (282 letters) >NCBI__GCF_002151265.1:WP_086509236.1 Length = 437 Score = 121 bits (303), Expect = 3e-32 Identities = 86/285 (30%), Positives = 141/285 (49%), Gaps = 13/285 (4%) Query: 2 RIDTVNVLLEALPYIKEFYGKTFVIKFGGSAMKQENAKKAFIQDIILLKYTGIKPIIVHG 61 R V+ + PYI G+TFVI G AM + ++ IQD+ LL G++ ++V G Sbjct: 4 RFPFVDWFRNSSPYINAHRGRTFVILIEGEAMARGRGEQ-LIQDLALLHTLGVRLVVVFG 62 Query: 62 GGPAISQMMKDLGIEPVFKNGHRVTDEKTMEIVEMVLVGK---INKEIVM---NLNLHGG 115 P + Q + + GI P NG V DE M VE V + + + N LHG Sbjct: 63 IRPQVEQALNEAGIVPRRHNGRWVADEAIMACVERVAAEQRLWLEARFSLGLPNTPLHGV 122 Query: 116 RAVGICGKDSKLIVAEK-ETKHG-DIGYVGKVKKVNPEILHALIENDYIPVIAPVGIGED 173 + G L++A+ + G D + G+V++V + L++ + ++ P+G Sbjct: 123 ELTAVSGN---LVMAKPLGVREGIDYDHSGEVRRVRVSAVQGLLDRGSLVLLPPLGFSST 179 Query: 174 GHSYNINADTAAAEIAKSLMAEKLILLTDVDGVL-KDGKLISTLTPDEAEELIRDGTVTG 232 G ++++A A A +L A+KLIL+ + G+ ++G L L+PDEAE L+ Sbjct: 180 GEVFDLDAAEVAQHAAMALAADKLILMGEEPGLYDENGALQRQLSPDEAEPLLSQAEPGS 239 Query: 233 GMIPKVECAVSAVRGGVGAVHIINGGLEHAILLEIFSRKGIGTMI 277 + A +A R GV H+++ A+L E+F+R G+GTMI Sbjct: 240 EQARHIAAACAAARHGVARTHLLSWHDHDALLGELFTRDGVGTMI 284 Lambda K H 0.318 0.140 0.393 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: 273 Number of extensions: 12 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: 282 Length of database: 437 Length adjustment: 29 Effective length of query: 253 Effective length of database: 408 Effective search space: 103224 Effective search space used: 103224 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 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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