Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate WP_011801563.1 PNAP_RS10915 amino-acid N-acetyltransferase
Query= curated2:A1ATU7 (292 letters) >NCBI__GCF_000015505.1:WP_011801563.1 Length = 450 Score = 118 bits (295), Expect = 3e-31 Identities = 85/285 (29%), Positives = 144/285 (50%), Gaps = 16/285 (5%) Query: 16 PYIRRFAGKTFVIKYGGHAMSDEKLKESFALDVIMLRSLGINAVIVHGGGPQINQTLKRY 75 PYI +F +TFV+ G A++ KL A D+ M++S+G+ V+VHG PQ+N+ L+ Sbjct: 18 PYIHKFRNQTFVVAVCGEAIAAGKLPH-LAQDLAMIQSMGVKVVLVHGFRPQVNEQLRAK 76 Query: 76 GIVSQFVKGMRVTDSETMAVVEMVLVGQVNKEVVGYLNQHGGRAVGLSGKDGTLLLSKKL 135 G +++ GMR+TD + + GQ+ E+ +Q G ++G ++ + Sbjct: 77 GHQARYSHGMRITDEVALDCAQEA-AGQLRYEIEAAFSQ-GLPNTPMAGSTIRVISGNFI 134 Query: 136 LQDVVGDDGTTEQVDMGYVGDVVKVNTDLLKALENGNYLPVIAPVGVGPQGESYNINADL 195 VG + VD + G V KV+ + + + +++P G P GE++N+ + Sbjct: 135 TARPVG---IVDGVDFQHSGLVRKVDVAGITRTLDMGAMVLLSPFGFSPTGEAFNLTMEE 191 Query: 196 VAGRVAAALNAEKLILLTDIEGVKDKAGQLLSSIAVADMH-RLIREEAITGGMIPK---- 250 VA V+ AL A+KLI +T++ G++ K G+ S D L E + P Sbjct: 192 VATSVSIALQADKLIFVTEVPGIRLKPGEPASEDNPIDTELPLAAAEELLSKAPPSQRPT 251 Query: 251 -----VVCCADALEEGVKKAHIIDGRVEHAVLLEIFTDVGIGTEI 290 + C A + GV+++HII V+ A+LLEI+ GIGT + Sbjct: 252 DTAFYLQHCVKACKAGVERSHIIPFAVDGALLLEIYVHDGIGTMV 296 Lambda K H 0.318 0.138 0.380 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: 301 Number of extensions: 9 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: 292 Length of database: 450 Length adjustment: 29 Effective length of query: 263 Effective length of database: 421 Effective search space: 110723 Effective search space used: 110723 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 (21.7 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