Align Amino-acid acetyltransferase; EC 2.3.1.1; N-acetylglutamate synthase; AGS; NAGS (uncharacterized)
to candidate WP_089322531.1 CHB58_RS02525 acetylglutamate kinase
Query= curated2:Q8XZZ5 (451 letters) >NCBI__GCF_900188395.1:WP_089322531.1 Length = 292 Score = 130 bits (326), Expect = 7e-35 Identities = 84/281 (29%), Positives = 145/281 (51%), Gaps = 15/281 (5%) Query: 31 PYIHAFRDKTFVIGFGGE-LVKAGMLGALVNDIALLHAMGMHIVLVHGSRPQVEEQLALR 89 PYI F KT VI +GG +V + + D+ LL +G++ V+VHG PQ+ E L Sbjct: 16 PYIKRFYGKTVVIKYGGNAMVDDELKRSFAEDVVLLKYIGINPVIVHGGGPQIGEFLKKL 75 Query: 90 HVQTQFVDGIRVTDNAALESAKEAS-GELRLDIEATFSQALPNTPMAGARISVVSGNFVT 148 ++T+F+ G+RVTD + + G++ +I + N +S GN + Sbjct: 76 DIKTRFIGGMRVTDKETMNIVEMVLVGKVNKEIVKLINSHGGNA----VGLSGKDGNLIE 131 Query: 149 ARPVGI---------VNGVDFQHTGLVRKIDAESIQHSLSNRKIVLLSPLGFSPTGQAFN 199 AR + +D G V K++ + L ++ I +++P+G +A+N Sbjct: 132 ARKIDYKKYLSEVKATEIIDLGFVGEVEKVNPAIVFKLLESKFIPVIAPVGVGKDYEAYN 191 Query: 200 LSMEDVATNTATALKADKLIFITEVPGIMDRVGKLQQELSMESAIERLREGRLSADTAYY 259 ++ + VA A ALKA+KLI +T++ GI D+ G L LS + + + +G +S Sbjct: 192 INADIVAGEVAAALKAEKLIMLTDIEGIKDKNGDLMSVLSKDDIPQLIEDGTISGGMIPK 251 Query: 260 LQHIVKAMRGGVRRAHLIPFALDGSILLELFLHDGVGTMVS 300 ++ A+ GGV++AH+I + ++LLE+F +GVGT +S Sbjct: 252 VKACQIALGGGVKKAHIIDGRVKHAVLLEIFTKEGVGTEIS 292 Lambda K H 0.322 0.138 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: 351 Number of extensions: 16 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: 451 Length of database: 292 Length adjustment: 29 Effective length of query: 422 Effective length of database: 263 Effective search space: 110986 Effective search space used: 110986 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 (21.9 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