Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_092997128.1 BLP65_RS11060 acetylglutamate kinase
Query= BRENDA::Q87EL2 (421 letters) >NCBI__GCF_900102855.1:WP_092997128.1 Length = 298 Score = 135 bits (339), Expect = 2e-36 Identities = 99/301 (32%), Positives = 147/301 (48%), Gaps = 43/301 (14%) Query: 3 SAKEISQ---YLKRFSQLDAKRFAVVKVGGAVLRDDV--DALTSSLSFLQEVGLTPIVLH 57 SAK +S+ Y++RFS + V+K GG + DD + ++ VG+ P+V+H Sbjct: 11 SAKVLSEALPYIRRFSG----KTLVIKYGGNAMVDDALKTGFARDVVLMKLVGMNPVVVH 66 Query: 58 GAGPQLDEELTAVGIQKKTVNGFRVTLPETMAIVRKVFHA-TNLQLIEALQRNGARATSI 116 G GPQ+ E L +G + + V G RVT ETM +V V N +++ + RNG RA + Sbjct: 67 GGGPQIGELLERIGKESRFVEGMRVTDSETMDVVEMVLGGLVNKEIVSLINRNGGRAVGL 126 Query: 117 TGGVFEAHYLDQETY---------------GLVGGISAVNIAPIEASLRAASIPVIASLG 161 TG + + + T+ G VG + +N ++ + IPV+A +G Sbjct: 127 TGKDGDLIHARKMTFTRSAPEMNTPEIIDIGHVGEVEHINAEVVDMLIHGDFIPVVAPIG 186 Query: 162 ETPSGQILNINADVAANELVHVLQPYKIIFLTGTGGLLDADGKIINSINLSTEYEQLIQQ 221 GQ NINADV A +L L K+I LT T GLLD + +++ ++ ST ++LI Sbjct: 187 VGRDGQSYNINADVVAGKLAEGLGAEKLILLTNTAGLLDKEEEVLTGLS-STRVDELIAD 245 Query: 222 PWVYGGMKLKIEQIKHLLDRLPLESSVSITR---------PADLAKELFTHKGSGTLIRR 272 ++GGM KI R LE+ S R P L E+FT G GTLI Sbjct: 246 GTIHGGMLPKI--------RCALEAVQSGVRTAHIIDGRVPHALLLEIFTDAGVGTLIEN 297 Query: 273 G 273 G Sbjct: 298 G 298 Lambda K H 0.320 0.136 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: 288 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: 421 Length of database: 298 Length adjustment: 29 Effective length of query: 392 Effective length of database: 269 Effective search space: 105448 Effective search space used: 105448 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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