Align amino-acid N-acetyltransferase (EC 2.3.1.1); acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_011386705.1 AMB_RS22045 acetylglutamate kinase
Query= BRENDA::Q0ASS9 (441 letters) >NCBI__GCF_000009985.1:WP_011386705.1 Length = 300 Score = 107 bits (267), Expect = 5e-28 Identities = 78/223 (34%), Positives = 114/223 (51%), Gaps = 19/223 (8%) Query: 42 VIKVGG-AVIQDDLPGL-ASALAFLQTVGLTPVVVHGGGPQLDAALEAADIPTERVDGLR 99 VIK GG A+ DDL L A + L+ VG+ PVVVHGGGPQ+DA L+ DI T RVDGLR Sbjct: 39 VIKFGGHAMESDDLARLFARDVVLLKQVGINPVVVHGGGPQIDAMLKRLDIQTPRVDGLR 98 Query: 100 VTRDEAIPIIRDTLT-QANLALVDAIRDAGG-------------RAAAVPRGVFEAD--I 143 T + + ++ L + N +V AI +AGG RA + R + D I Sbjct: 99 FTDEATVEVVEMILAGKINKQIVSAINEAGGFAVGLSGKDGHLIRARKLRRTKKDPDSNI 158 Query: 144 VDADKLGRVGEPRHIHLDLVGSAARAGQAAILACLGETPDGTLVNINADVAVRALVHALQ 203 LG VGEP I+ ++ ++ ++A +G G NINAD A A+ A Sbjct: 159 EKVLDLGFVGEPAEINPHILDQFKKSDTIPVIAPVGMGGAGETYNINADTAAGAIAGATN 218 Query: 204 PYKVVFLTGTGGLLDEDGDILSSINLATDFGDLMQADWVNGGM 246 +++ LT G+LD+ G+++ + A + ++GGM Sbjct: 219 AKRLLMLTDVAGVLDKSGNLIPEMTAAQVHAYIADGT-ISGGM 260 Lambda K H 0.320 0.139 0.411 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: 280 Number of extensions: 11 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: 441 Length of database: 300 Length adjustment: 29 Effective length of query: 412 Effective length of database: 271 Effective search space: 111652 Effective search space used: 111652 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 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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