Align amino-acid N-acetyltransferase (EC 2.3.1.1); acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_073039490.1 BUB04_RS11045 acetylglutamate kinase
Query= BRENDA::Q0ASS9 (441 letters) >NCBI__GCF_900129305.1:WP_073039490.1 Length = 303 Score = 113 bits (282), Expect = 9e-30 Identities = 85/286 (29%), Positives = 144/286 (50%), Gaps = 28/286 (9%) Query: 24 EIREYLHRFSGIDQERFAVIKVGGAVIQDDL--PGLASALAFLQTVGLTPVVVHGGGPQL 81 E Y+ +FSG + VIK GG ++D+ A + ++ +G+ PVVVHGGGPQ+ Sbjct: 10 EALPYIRQFSG----KTIVIKYGGHAMKDEALKESFAKDVVLMKYIGIHPVVVHGGGPQI 65 Query: 82 DAALEAADIPTERVDGLRVTRDEAIPIIRDTLT-QANLALVDAIRDAGGRAAAVPRGVFE 140 LE ++ G+RVT ++ + ++ L + N +V I GGRA + + Sbjct: 66 GRMLERVGKKSDFRAGMRVTDEDTMDVVEMVLAGKVNKEIVALINRHGGRAIGLSGK--D 123 Query: 141 ADIVDADKL-----------------GRVGEPRHIHLDLVGSAARAGQAAILACLGETPD 183 +++A K+ G VGE R I+++++ ++ ++A +G PD Sbjct: 124 GQLIEARKMHLYRYQGDDQPPEIIDIGLVGEVRRINVEILKVLEQSRVIPVIAPVGVGPD 183 Query: 184 GTLVNINADVAVRALVHALQPYKVVFLTGTGGLLDEDGDILSSINLATDFGDLMQADWVN 243 G NINAD+ ++ AL K++ +T G+LD G ++SS+ +A + DLMQ + + Sbjct: 184 GETYNINADLVAGSVASALNAEKLLLMTDVPGVLDGAGQLISSMTVA-EAADLMQDETLK 242 Query: 244 GGMRLKLE-EIKRLLDDLPLSSSVSITRPSELARELFTHAGSGTLI 288 GGM K++ I + + + V P + ELFT +G GT I Sbjct: 243 GGMIPKVQCAIDAVQAGVRKVAIVDGRIPHSVLLELFTDSGIGTEI 288 Lambda K H 0.320 0.139 0.411 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: 299 Number of extensions: 16 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: 441 Length of database: 303 Length adjustment: 30 Effective length of query: 411 Effective length of database: 273 Effective search space: 112203 Effective search space used: 112203 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