Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_086509007.1 BZY95_RS05700 acetylglutamate kinase
Query= BRENDA::Q87EL2 (421 letters) >NCBI__GCF_002151265.1:WP_086509007.1 Length = 306 Score = 122 bits (306), Expect = 1e-32 Identities = 90/299 (30%), Positives = 146/299 (48%), Gaps = 44/299 (14%) Query: 6 EISQYLKRFSQLDAKRFAVVKVGGAVLRDD--VDALTSSLSFLQEVGLTPIVLHGAGPQL 63 E Y++RFS + VVK GG + +D +D+ ++ ++EVG+ P+V+HG GPQ+ Sbjct: 17 EALPYIQRFSG----KTVVVKYGGNAMTEDTLIDSFARNMVLMKEVGINPVVVHGGGPQI 72 Query: 64 DEELTAVGIQKKTVNGFRVTLPETMAIVRKVFHA-TNLQLIEALQRNGARATSIT---GG 119 + L + I+ + VNG RVT ETM +V V N +++ + + G +A +T G Sbjct: 73 GDLLAKLKIESRFVNGMRVTDSETMDVVEMVLGGLVNKEIVNLINQCGGKAIGLTGKDGA 132 Query: 120 VFEAHYLDQE------------TYGLVGGISAVNIAPIEASLRAASIPVIASLGETPSGQ 167 A L E G VG + V+ IE IPVIA +G G Sbjct: 133 QIRARQLKVEHQTPEMTAPEIIDIGHVGEVEHVSTDLIEMLAERDFIPVIAPIGVDAKGN 192 Query: 168 ILNINADVAANELVHVLQPYKIIFLTGTGGLLDADGKIINSINLSTEYEQLIQQPWVYGG 227 NINAD+ A ++ L K++ LT GL++A+G+++ + + + + LI ++GG Sbjct: 193 SYNINADLVAGKVAEALGAEKLMLLTNVAGLMNAEGEVLTGLT-TAQVDALIADGTIHGG 251 Query: 228 MKLKIE----------QIKHLLD-RLPLESSVSITRPADLAKELFTHKGSGTLIRRGER 275 M KI + H++D R+P + + E+FT+ G GTLI +R Sbjct: 252 MLPKIRCALDAVKGGVRSAHIIDGRVPHATLL----------EIFTNAGVGTLITDADR 300 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: 293 Number of extensions: 13 Number of successful extensions: 3 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: 306 Length adjustment: 29 Effective length of query: 392 Effective length of database: 277 Effective search space: 108584 Effective search space used: 108584 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