Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate WP_029908055.1 P166_RS0101440 amino-acid N-acetyltransferase
Query= curated2:Q97GH8 (295 letters) >NCBI__GCF_000711315.1:WP_029908055.1 Length = 432 Score = 79.7 bits (195), Expect = 1e-19 Identities = 59/195 (30%), Positives = 91/195 (46%), Gaps = 5/195 (2%) Query: 15 LTQYSGKTFVIKYGGSIMKNKKAEEAFIKDVKYLRKLGINIVIVHGGGPEISRWLELSGI 74 + + GKT VI G +++ F KD+ L LGI +V+ G +I L+L+G Sbjct: 19 IATHRGKTLVIYLPGEMLQVSDHLLQFAKDIVLLNNLGIKVVLTLGASVQIDDALKLAGH 78 Query: 75 ESRFVDGLRVTDEKVIEIVQMVLSGKINKKLSLQFNIDGVNAVG-LSGVDNKLIEATKKY 133 + RVT +E +Q + G + KL F+ LS V + A K Sbjct: 79 QWETHQFCRVTQTDHVETIQKTI-GWVRSKLEAVFSQACAEQHSPLSLVSGNWVIAKPKG 137 Query: 134 VYKGNETIDIGYVGKVTKVNSEFIKELLKGGQVPVIAPIGCDNKGNVYNINADYAAAFIS 193 V G ID + G + K+NS I L QV ++ P+ G V+N+N A +S Sbjct: 138 VING---IDFQHTGSLRKINSSAINACLNNNQVCLLTPLAYSLTGEVFNLNTLEQAFAVS 194 Query: 194 SALDAEKLIILTDVE 208 AL+A+KLI+ +D + Sbjct: 195 QALNADKLIVYSDTD 209 Lambda K H 0.317 0.139 0.391 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: 254 Number of extensions: 10 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: 295 Length of database: 432 Length adjustment: 29 Effective length of query: 266 Effective length of database: 403 Effective search space: 107198 Effective search space used: 107198 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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