Align Amino-acid acetyltransferase; EC 2.3.1.1; N-acetylglutamate synthase; AGS; NAGS (uncharacterized)
to candidate WP_083441686.1 NITAL_RS16990 acetylglutamate kinase
Query= curated2:Q8XZZ5 (451 letters) >NCBI__GCF_000969705.1:WP_083441686.1 Length = 323 Score = 126 bits (317), Expect = 9e-34 Identities = 90/293 (30%), Positives = 153/293 (52%), Gaps = 15/293 (5%) Query: 26 LRAVAPYIHAFRDKTFVIGFGGE-LVKAGMLGALVNDIALLHAMGMHIVLVHGSRPQVEE 84 LR P+I F +T VI +GG +V + + D+ALLH +G+ V+VHG PQ+ + Sbjct: 20 LREALPWITRFHGQTVVIKYGGNAMVDEELKRSFAADVALLHFVGLRPVIVHGGGPQIGQ 79 Query: 85 QLALRHVQTQFVDGIRVTDNAALESAKEA-SGELRLDIEATFSQA-LPNTPMAGARISVV 142 A + ++FV G+RVTD A ++ + A G++ ++ A P+ +AG Sbjct: 80 LAAQMGLTSRFVGGLRVTDAAMMDVVRMALLGQVNPEVVGLVQDAGAPSVGVAG-----T 134 Query: 143 SGNFVTARPVGIVNGVDFQHTGLVRKIDAESIQHSLSNRKIVLLSPLGFSPTGQAFNLSM 202 + RP G D G V +D + L + +++ +G G N++ Sbjct: 135 DAGLLQVRPAVGPEGEDLGFVGEVEHVDTSYLTELLEGEFLPVVATVGRDAGGVERNVNA 194 Query: 203 EDVATNTATALKADKLIFITEVPGIMDRVGKLQQELSMESAIERLREGRLSADTAY---- 258 + A A AL A K + +T+VPG+ G+ +Q L E ++++L+ L+AD + Sbjct: 195 DLAAGAIAAALGASKFVCLTDVPGLYQDFGRDEQSLMSEVSVKQLQH-MLAADELHAGMR 253 Query: 259 -YLQHIVKAMRGGVRRAHLIPFALDGSILLELFLHDGVGTMVSHTDLEYLREA 310 ++ IV A+RGGV +AH++ + ++L+E+F +GVGTMV+ T E LR+A Sbjct: 254 PKIRSIVDAVRGGVPQAHILDGRVLHAVLIEIFTDEGVGTMVT-TGGETLRDA 305 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: 344 Number of extensions: 14 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: 451 Length of database: 323 Length adjustment: 30 Effective length of query: 421 Effective length of database: 293 Effective search space: 123353 Effective search space used: 123353 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: 50 (23.9 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