Align N-acetylglutamate synthase (EC 2.3.1.1) (characterized)
to candidate WP_011305618.1 MBAR_RS03180 GNAT family N-acetyltransferase
Query= reanno::DvH:207038 (154 letters) >NCBI__GCF_000195895.1:WP_011305618.1 Length = 159 Score = 141 bits (356), Expect = 4e-39 Identities = 68/147 (46%), Positives = 96/147 (65%), Gaps = 2/147 (1%) Query: 5 IRKATVPDVKRIHAILMECAGQRLLLPRSLNDLYSRIRDFVVVDADEGGAILGCCALSIT 64 IRKA V DV + I+ + + L+L RSL+++Y IRD+ V + D G ++GCCAL + Sbjct: 10 IRKARVNDVVVMKQIINTYSKEELMLARSLSEMYENIRDYYVCEID--GEVMGCCALHVV 67 Query: 65 WEDIAEIRSLVVLESLRGQGWGRRLVEACMSDAVTLGLYRVFTLTYQVEFFNKLGYSVVG 124 WED+AEI +L V + +G G +LV AC+ DA LG+ VF LTY FF L + VV Sbjct: 68 WEDLAEILALAVNPACARKGIGTKLVSACLEDAKNLGMKEVFALTYVPGFFETLDFKVVD 127 Query: 125 KEVLPQKVWADCIHCPQFPECDETAML 151 K LP+K+WA C+ CP+FP+C+E A+L Sbjct: 128 KNTLPRKIWAGCLRCPKFPDCNEVAVL 154 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: 83 Number of extensions: 2 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: 159 Length adjustment: 17 Effective length of query: 137 Effective length of database: 142 Effective search space: 19454 Effective search space used: 19454 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: 43 (21.2 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