Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_012973152.1 AZL_RS02775 acetylglutamate kinase
Query= BRENDA::A0A0H2X8L7 (447 letters) >NCBI__GCF_000010725.1:WP_012973152.1 Length = 299 Score = 114 bits (284), Expect = 5e-30 Identities = 88/290 (30%), Positives = 138/290 (47%), Gaps = 23/290 (7%) Query: 22 MASAKEISQYLKRFSQLDAKRFAVVKVGGAVLRDD--LEALTSSLSFLQEVGLTPIVLHG 79 +A A+ +S+ L + F V+K GG + D E + L++VG+ P+V+HG Sbjct: 10 LAKARTLSEALPYMRRYAGSTF-VIKYGGHAMGDASLAELFARDIVLLKQVGINPVVVHG 68 Query: 80 AGPQLDAELSAAGIEKQTVNGLRVTSPHALAIVRKVFQAS-NLKLVEALQQNGARATSIT 138 GPQ+ L I+ ++GLRVT + +V V S N ++V A+ G RA ++ Sbjct: 69 GGPQIGQMLERLKIKSSFIDGLRVTDKETVEVVEMVLAGSINKQIVAAINSAGGRAVGLS 128 Query: 139 GG------VFEAEYLNRDT---------YGLVGEVKAVNLAPIEASLQAGSIPVITSLGE 183 G E + RD G VGE VN + A Q+ IPVI +G Sbjct: 129 GKDSNLITARRLERVQRDPDSNIEKVLDLGFVGEPYKVNPQILHAMAQSDIIPVIAPVGF 188 Query: 184 TPSGQILNVNADFAANELVQELQPYKIIFLTGTGGLLDAEGKLIDSINLSTEYDHLMQQP 243 G N+NAD AA + ++ + LT G+LD E KLI+ ++L + + Sbjct: 189 DVKGDTYNINADTAAGAVAAAVKAARFFLLTDVAGVLDKEKKLIERMSLE-DAQRAIADG 247 Query: 244 WINGGMRVKIEQIKDLLDRLPLESSVSITR--PADLAKELFTHKGSGTLV 291 +GGM KIE +++ +E++V + P L E+FT G+GTL+ Sbjct: 248 TASGGMIPKIETCIGAVEQ-GVEAAVILDGRVPHALLLEIFTEGGAGTLI 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: 273 Number of extensions: 14 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: 447 Length of database: 299 Length adjustment: 30 Effective length of query: 417 Effective length of database: 269 Effective search space: 112173 Effective search space used: 112173 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 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