Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_038125948.1 N746_RS0109530 acetylglutamate kinase
Query= BRENDA::Q87EL2 (421 letters) >NCBI__GCF_000711195.1:WP_038125948.1 Length = 304 Score = 119 bits (297), Expect = 2e-31 Identities = 86/289 (29%), Positives = 146/289 (50%), Gaps = 34/289 (11%) Query: 6 EISQYLKRFSQLDAKRFAVVKVGGAVLRDD--VDALTSSLSFLQEVGLTPIVLHGAGPQL 63 E Y++RF A + VVK GG + +D + + + ++ VG+ P+V+HG GPQ+ Sbjct: 23 EALPYIQRF----AGKTIVVKYGGNAMTEDDLMASFARDIVLMKLVGMNPVVVHGGGPQI 78 Query: 64 DEELTAVGIQKKTVNGFRVTLPETMAIVRKVFHA-TNLQLIEALQRNGARATSITGG--- 119 + L VG + + + G RVT ETM IV V N +++ + ++G + +TG Sbjct: 79 GDLLKRVGKESEFIQGMRVTDTETMDIVEMVLGGLVNKEIVNLIHQHGGNSVGLTGKDGN 138 Query: 120 --VFEAHYLDQETYGL----------VGGISAVNIAPIEASLRAASIPVIASLGETPSGQ 167 + + + ++T G+ VG + +N I+ ++ IPVIA +G G Sbjct: 139 MIMAKKLKVTKQTPGMDVPEIIDIGHVGEVERINTGVIDMLIKGDFIPVIAPVGVDAEGN 198 Query: 168 ILNINADVAANELVHVLQPYKIIFLTGTGGLLDADGKIINSINLSTEYEQLIQQPWVYGG 227 NINAD+ A ++ LQ K++ LT T GLL+ G+++ +N + ++LI +YGG Sbjct: 199 SYNINADLVAGKVAEALQAEKLMLLTNTPGLLNKQGELLTGLN-AKMVDELIADGTIYGG 257 Query: 228 MKLKIEQIKHLLDRLPLESSVSITRPAD------LAKELFTHKGSGTLI 270 M + +I+ LD ++ V D + E+FT +G GTLI Sbjct: 258 M---LPKIQCALD--AVQGGVKAVHIVDGRVSHAVMLEVFTDEGVGTLI 301 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: 254 Number of extensions: 11 Number of successful extensions: 2 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: 304 Length adjustment: 29 Effective length of query: 392 Effective length of database: 275 Effective search space: 107800 Effective search space used: 107800 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 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