Align Serine acetyltransferase; SAT; EC 2.3.1.30 (uncharacterized)
to candidate WP_011382553.1 AMB_RS00535 N-acetyltransferase
Query= curated2:Q65PC9 (216 letters) >NCBI__GCF_000009985.1:WP_011382553.1 Length = 159 Score = 46.2 bits (108), Expect = 3e-10 Identities = 36/130 (27%), Positives = 55/130 (42%), Gaps = 28/130 (21%) Query: 66 GIEIHPGAKIGRRFFIDHGMGVVIGETCEIGNNVTVFQGVTLG----------------- 108 G I KIG F++ G IG C+I ++ V +GVT+ Sbjct: 25 GCSIGDETKIGA--FVEIQGGATIGARCKISSHSFVCEGVTIEDEVFVGHGVMFTNDVYP 82 Query: 109 ---------GTGKEKGKRHPTIEDDALISTGAKVLGSITVGRGAKIGAGSVVLHDVPECS 159 T + ++ A I +GA +L ++T+G A + AG+VV DVP + Sbjct: 83 RATTPDGALATAADWTCSPTVVKRRASIGSGATILPNLTIGENALVAAGAVVTKDVPANA 142 Query: 160 TVVGIPGRVV 169 V G+P VV Sbjct: 143 IVAGVPAVVV 152 Lambda K H 0.323 0.142 0.416 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: 110 Number of extensions: 8 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 216 Length of database: 159 Length adjustment: 19 Effective length of query: 197 Effective length of database: 140 Effective search space: 27580 Effective search space used: 27580 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 44 (21.6 bits)
This GapMind analysis is from Apr 09 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