Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_014148273.1 MEALZ_RS08785 amino-acid N-acetyltransferase
Query= BRENDA::Q9X2A4 (282 letters) >NCBI__GCF_000968535.2:WP_014148273.1 Length = 445 Score = 128 bits (322), Expect = 2e-34 Identities = 84/281 (29%), Positives = 147/281 (52%), Gaps = 8/281 (2%) Query: 4 DTVNVLLEALPYIKEFYGKTFVIKFGGSAMKQENAKKAFIQDIILLKYTGIKPIIVHGGG 63 D VN ++ PYI +TFV+ FGG A+ ++ + D LL GI+ ++VHG Sbjct: 14 DFVNWFRDSSPYIHAHRNRTFVVSFGGEAV-YDSGFAHHVHDFALLNSLGIRLVLVHGIR 72 Query: 64 PAISQMMKDLGIEPVFKNGHRVTDEKTMEIV-EMVLVGKINKEIVMNLNLHGGRAVG--I 120 P I ++ I P F RVTDE ++ V E + ++ E ++++ L G I Sbjct: 73 PQIDTCLRKQNIAPRFHKNLRVTDELALQCVKEAAGLVRVETEALLSMGLANSPMAGAKI 132 Query: 121 CGKDSKLIVAEK--ETKHGDIGYVGKVKKVNPEILHALIENDYIPVIAPVGIGEDGHSYN 178 ++A+ D G+ G+V++++ + +H ++ + + +I+PVG G ++N Sbjct: 133 RVVSGNFVIAKPIGVIDGVDYGHTGEVRRIDSQAIHQQLDMNSVVLISPVGYSPSGEAFN 192 Query: 179 INADTAAAEIAKSLMAEKLILLTDVD-GVLKDGKLISTLTPDEAEELI-RDGTVTGGMIP 236 ++A+ A EIA +L AEKL+LLT+ + G I +T E ++ I R + + Sbjct: 193 LSAEKVATEIAIALKAEKLLLLTEQSINHPESGDKIQQMTTVETQQFINRFPDIEQSISL 252 Query: 237 KVECAVSAVRGGVGAVHIINGGLEHAILLEIFSRKGIGTMI 277 ++ A+ + GV VH++N + +LLE+FSR G GT+I Sbjct: 253 PLQAAIHGCQSGVERVHLVNRHQDGGLLLELFSRDGTGTLI 293 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: 282 Number of extensions: 16 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: 445 Length adjustment: 29 Effective length of query: 253 Effective length of database: 416 Effective search space: 105248 Effective search space used: 105248 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