Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_029133645.1 A3GO_RS0112310 acetylglutamate kinase
Query= BRENDA::A0A0H2X8L7 (447 letters) >NCBI__GCF_000428045.1:WP_029133645.1 Length = 298 Score = 123 bits (308), Expect = 9e-33 Identities = 94/286 (32%), Positives = 142/286 (49%), Gaps = 26/286 (9%) Query: 27 EISQYLKRFSQLDAKRFAVVKVGG-AVLRDDL-EALTSSLSFLQEVGLTPIVLHGAGPQL 84 E Y++RF + V+K GG A+ DL + + ++ VG+ P+V+HG GPQ+ Sbjct: 17 EALPYIQRFRG----KTVVIKYGGNAMTEADLKDGFARDVVLMKLVGINPVVVHGGGPQI 72 Query: 85 DAELSAAGIEKQTVNGLRVTSPHALAIVRKVFQAS-NLKLVEALQQNGARATSITG---G 140 L G E + V G+RVT + +V V N ++V L Q+G A +TG G Sbjct: 73 GNLLGRLGKESEFVQGMRVTDSETMDVVEMVLGGQVNKEIVNLLNQHGGSAVGLTGKDGG 132 Query: 141 VFEAE--YLNRDT----------YGLVGEVKAVNLAPIEASLQAGSIPVITSLGETPSGQ 188 + A L R + G VGEV ++N A ++ + IPVI +G G+ Sbjct: 133 LIHARKLMLKRTSPELQAPEIIDVGHVGEVASINKAVVDMLVSGNFIPVIAPIGVGEDGR 192 Query: 189 ILNVNADFAANELVQELQPYKIIFLTGTGGLLDAEGKLIDSINLSTEYDHLMQQPWINGG 248 N+NAD A ++ + LQ K+I LT T GLLD +G L+ + + D L+ I+GG Sbjct: 193 SYNINADLVAGKMAEVLQAEKLILLTNTAGLLDKQGGLLTGLT-AGRVDELIADGTIHGG 251 Query: 249 MRVKIEQIKDLLDRLPLESSVSITRPADLA--KELFTHKGSGTLVR 292 M KI D ++ + SSV + A ELFT +G GTL++ Sbjct: 252 MLPKIRCALDAVN-AGVNSSVIVDGRVKHAVLLELFTDQGIGTLIK 296 Lambda K H 0.318 0.134 0.383 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: 302 Number of extensions: 10 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: 447 Length of database: 298 Length adjustment: 29 Effective length of query: 418 Effective length of database: 269 Effective search space: 112442 Effective search space used: 112442 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