Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_052473176.1 SUTH_RS03725 amino-acid N-acetyltransferase
Query= BRENDA::Q9X2A4 (282 letters) >NCBI__GCF_000828635.1:WP_052473176.1 Length = 447 Score = 139 bits (350), Expect = 1e-37 Identities = 94/275 (34%), Positives = 145/275 (52%), Gaps = 9/275 (3%) Query: 11 EALPYIKEFYGKTFVIKFGGSAMKQENAKKAFIQDIILLKYTGIKPIIVHGGGPAISQMM 70 +A PYI F G+TFVI FGG + + A +A I DI LL GI+ ++VHG P I M Sbjct: 22 QAAPYIHAFRGRTFVIAFGGEVL-EAGAAQALIHDIALLDSMGIRLVLVHGARPQIDAEM 80 Query: 71 KDLGIEPVFKNGHRVTDEKTMEIVEMVL-VGKINKEIVMNLNL----HGGRAVGICGKDS 125 G+ P F G RVTD +E V+ + V +I E +++ L G + + G + Sbjct: 81 HARGLVPKFHKGLRVTDAAALECVKRAMGVTRIEIEALLSQGLPNTPMAGAFLRVTGGNF 140 Query: 126 KLIVAEKETKHGDIGYVGKVKKVNPEILHALIENDYIPVIAPVGIGEDGHSYNINADTAA 185 D Y G ++KV E + A + + + +I P+G G +N+ + AA Sbjct: 141 ITARPVGVVDGIDFQYTGAIRKVIAEEIQADLAQENVVLITPIGASPTGEIFNLAWEEAA 200 Query: 186 AEIAKSLMAEKLILLTDVDGVLK-DGKLISTLTPDEAEELI-RDGTVTGGMIPKV-ECAV 242 +A S+ A+KLI L D G++ G LI LT DEA++L R+ + I +V A+ Sbjct: 201 EAVAVSIGADKLIYLCDAPGLVNGKGALIDALTADEAQKLAGRNLNLQAPEIARVLPSAI 260 Query: 243 SAVRGGVGAVHIINGGLEHAILLEIFSRKGIGTMI 277 A R G+G VH ++ + A+L+E F+R G+GT++ Sbjct: 261 RACRSGIGRVHFLDARADGAMLMEFFTRDGVGTVM 295 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: 277 Number of extensions: 14 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: 447 Length adjustment: 29 Effective length of query: 253 Effective length of database: 418 Effective search space: 105754 Effective search space used: 105754 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 09 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