Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_019867255.1 METMI_RS0115735 acetylglutamate kinase
Query= BRENDA::Q87EL2 (421 letters) >NCBI__GCF_000384075.1:WP_019867255.1 Length = 299 Score = 117 bits (293), Expect = 5e-31 Identities = 90/284 (31%), Positives = 141/284 (49%), Gaps = 24/284 (8%) Query: 6 EISQYLKRFSQLDAKRFAVVKVGGAVLRDDV--DALTSSLSFLQEVGLTPIVLHGAGPQL 63 E Y++RF + VVK GG + D+ ++ + ++ VG PIV+HG GPQ+ Sbjct: 16 EALPYIQRFKG----KTVVVKFGGNAMVDESLKNSFARDIVLMKLVGFNPIVVHGGGPQI 71 Query: 64 DEELTAVGIQKKTVNGFRVTLPETMAIVRKVFHA-TNLQLIEALQRNGARATSITG--GV 120 + L +G V+G R+T ETM +V V N +++ + NG +A +TG G Sbjct: 72 GQLLEKLGKTTGFVDGMRITDSETMDVVEMVLGGLVNKEIVNLINMNGGKAVGLTGKDGD 131 Query: 121 F--------EAHYLDQET-----YGLVGGISAVNIAPIEASLRAASIPVIASLGETPSGQ 167 F + LD E G VG +S+++ + +E R+ IPVIA +G G Sbjct: 132 FIRAKKINLKRSSLDAEASEIIDLGHVGEVSSIDPSVVEMLGRSDFIPVIAPIGVGADGH 191 Query: 168 ILNINADVAANELVHVLQPYKIIFLTGTGGLLDADGKIINSINLSTEYEQLIQQPWVYGG 227 NINAD+ A ++ VL+ K+I LT T G+LD G ++ +++ T+ + LI + GG Sbjct: 192 SYNINADLVAGKIAEVLKAEKLILLTNTAGILDKQGSLLTGLSV-TDIDSLIADGTISGG 250 Query: 228 MKLKIEQIKHLLDRLPLESSVSITRPAD-LAKELFTHKGSGTLI 270 M K L+ + R A + ELFT +G GTL+ Sbjct: 251 MIPKTRCATDALNGGVHSVHIIDGRVAHAVLLELFTDQGVGTLL 294 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: 259 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: 421 Length of database: 299 Length adjustment: 29 Effective length of query: 392 Effective length of database: 270 Effective search space: 105840 Effective search space used: 105840 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