Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_078716082.1 B5D49_RS02490 acetylglutamate kinase
Query= BRENDA::Q87EL2 (421 letters) >NCBI__GCF_900167125.1:WP_078716082.1 Length = 325 Score = 106 bits (265), Expect = 9e-28 Identities = 87/292 (29%), Positives = 142/292 (48%), Gaps = 41/292 (14%) Query: 6 EISQYLKRFSQLDAKRFAVVKVGGAVLRDDVDALTSSLS--FLQEVGLTPIVLHGAGPQL 63 E Y+++F K+ V+K GG + D+ + +L+ L+ +G+ P+++HG GPQ+ Sbjct: 21 EALPYIRKFY----KKTIVIKYGGHAMVDEQLKKSFALNVILLKYIGINPVIVHGGGPQI 76 Query: 64 DEELTAVGIQKKTVNGFRVTLPETMAIVRKVFHA-TNLQLIEALQRNGARATSITG---- 118 + L+A+ I G RVT TM +V V N Q++ + NG +A ++G Sbjct: 77 GKMLSALHIPSTFREGHRVTDQATMDVVEMVLVGKVNKQIVNLINLNGGKALGLSGKDGW 136 Query: 119 ---------GVFEAHYLDQET-YGLVGGISAVNIAPIEASLRAASIPVIASLGETPSGQI 168 V + H + G VG +SAVN+ + + LR IPVIA +G +G+ Sbjct: 137 LIRAEKKELAVSKEHATPELIDLGKVGQVSAVNVDLLNSLLRQDIIPVIAPVGVDTNGET 196 Query: 169 LNINADVAANELVHVLQPYKIIFLTGTGGLLDADGKIINSINLSTEYEQLIQQPWVYGGM 228 NINAD A+ + + ++ LT GLLD +G+++ S+ + +E I+ GGM Sbjct: 197 YNINADSVASAVAAAVGAKRLHLLTDVEGLLDKEGRLLQSLTVPEAFE-AIETGVATGGM 255 Query: 229 KLKIEQI----------KHLLDRLPLESSVSITRPADLAKELFTHKGSGTLI 270 K+ H+LD LE++V + ELFT +G GT I Sbjct: 256 IPKLHACLEAVTAGVDKAHILDG-RLENAVLL--------ELFTDEGIGTAI 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: 315 Number of extensions: 19 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: 325 Length adjustment: 30 Effective length of query: 391 Effective length of database: 295 Effective search space: 115345 Effective search space used: 115345 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