Align N-acetylglutamate synthase (EC 2.3.1.1) (characterized)
to candidate WP_027178996.1 G496_RS0108995 GNAT family N-acetyltransferase
Query= reanno::DvH:207038 (154 letters) >NCBI__GCF_000429985.1:WP_027178996.1 Length = 157 Score = 167 bits (424), Expect = 5e-47 Identities = 82/153 (53%), Positives = 105/153 (68%), Gaps = 1/153 (0%) Query: 1 MAPFIRKATVPDVKRIHAILMECAGQRLLLPRSLNDLYSRIRDFVVVDADEGGAILGCCA 60 MA I KAT+ D K +HA+++E A ++LPR L+ +Y +RDF V DE G I GCCA Sbjct: 1 MAVTIEKATMTDAKALHAMIVESARTAMVLPRPLSKVYGHLRDFFVAK-DESGKIFGCCA 59 Query: 61 LSITWEDIAEIRSLVVLESLRGQGWGRRLVEACMSDAVTLGLYRVFTLTYQVEFFNKLGY 120 LSITW+++AE+RSLVV RG G G+ LV AC+ +A L + VF LT FF KLG+ Sbjct: 60 LSITWDNLAEVRSLVVHPDSRGSGIGKELVRACLDEAFKLDINTVFVLTNIDGFFAKLGF 119 Query: 121 SVVGKEVLPQKVWADCIHCPQFPECDETAMLIE 153 K +LPQKVWADCI+CPQFP+CDE M+IE Sbjct: 120 KATDKGILPQKVWADCINCPQFPDCDEIPMVIE 152 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: 94 Number of extensions: 4 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: 157 Length adjustment: 17 Effective length of query: 137 Effective length of database: 140 Effective search space: 19180 Effective search space used: 19180 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