Align N-acetylglutamate synthase (EC 2.3.1.1) (characterized)
to candidate WP_028314121.1 G491_RS0107340 GNAT family N-acetyltransferase
Query= reanno::DvH:207038 (154 letters) >NCBI__GCF_000429905.1:WP_028314121.1 Length = 149 Score = 148 bits (373), Expect = 4e-41 Identities = 76/147 (51%), Positives = 98/147 (66%), Gaps = 2/147 (1%) Query: 5 IRKATVPDVKRIHAILMECAGQRLLLPRSLNDLYSRIRDFVVVDADEGGAILGCCALSIT 64 IRKATV D+K+IH IL + Q LLPRSL LY +RDF V EG ++GCC L I Sbjct: 2 IRKATVADMKQIHRILQIFSAQGTLLPRSLMALYDHVRDFCVYA--EGEDVIGCCGLQIC 59 Query: 65 WEDIAEIRSLVVLESLRGQGWGRRLVEACMSDAVTLGLYRVFTLTYQVEFFNKLGYSVVG 124 WED+AEIRSL V + + G L+E M +A+ + ++FTLTY +FF G++VV Sbjct: 60 WEDMAEIRSLAVKPEHQHKKIGSHLLEFSMEEALKFKIKKLFTLTYVPQFFELHGFAVVD 119 Query: 125 KEVLPQKVWADCIHCPQFPECDETAML 151 K LPQK+WADCI+C +FP+CDE AML Sbjct: 120 KSELPQKIWADCINCVKFPDCDEIAML 146 Lambda K H 0.327 0.142 0.445 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: 90 Number of extensions: 3 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: 154 Length of database: 149 Length adjustment: 17 Effective length of query: 137 Effective length of database: 132 Effective search space: 18084 Effective search space used: 18084 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 42 (20.8 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