Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate WP_011885443.1 N-acetylglutamate synthase
Query= curated2:B2V7Y5 (299 letters) >NCBI__GCF_000016205.1:WP_011885443.1 Length = 459 Score = 139 bits (350), Expect = 1e-37 Identities = 85/286 (29%), Positives = 147/286 (51%), Gaps = 19/286 (6%) Query: 16 PFIRNFRGKTFVIKYGGNAMDKADLRDAFAQDIIMLKYIGINPVIVHGGGPQIGQYLKKM 75 P+I FR TFV+ +GG + + L +A DI +L+ +GI V+VHG PQ+ + L Sbjct: 39 PYIHKFRNSTFVVGFGGEVVQQG-LLNALVSDIALLQAMGIQIVLVHGSRPQVEEQLSLH 97 Query: 76 GLESKFVGGLRVTDKETMDIVEMVLGGL---VNKSIVQLINSYSGGHVKAVGITGKDGCL 132 G+ES+F GLR+TD ++ + G + + +I Q + + H ++G Sbjct: 98 GVESEFSHGLRITDARALESAKEAAGEVRLDIEAAISQGLPNSPMAHAHISVVSGNFVTA 157 Query: 133 IKAKKLDAEEYFRSIGDYRPTELLDLGHVGEVEEVNPELLIHLDEDNYIPVIAPIGFDAE 192 LD +D H G V +++ E + H + +++P+GF Sbjct: 158 RPVGILDG---------------VDFAHTGIVRKIDAESIRHSLASRKLVLLSPLGFSPT 202 Query: 193 GNAYNINADFVAAAIAGALKAEKVLFLTDIEGLKDENGNTLSSATVSQINQMIKDGVIKG 252 G A+N++ + VA+A A AL+A+K++FLT+ G+ D+ G + ++ +++ G I+G Sbjct: 203 GEAFNLSMEDVASAAAIALRADKIIFLTEAPGIVDDEGELVREMSLDAAAELLDSGNIQG 262 Query: 253 GMIPKVKACIQALEKGVNKAHILDGRLPHCILLEIFTKKGVGTEIT 298 +K I+A GV +AH++ L +LLE+F GVGT I+ Sbjct: 263 DDAFFLKHSIRACRGGVTRAHLIPQSLDGSMLLELFLHDGVGTMIS 308 Lambda K H 0.319 0.141 0.398 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: 285 Number of extensions: 11 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: 299 Length of database: 459 Length adjustment: 30 Effective length of query: 269 Effective length of database: 429 Effective search space: 115401 Effective search space used: 115401 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 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