Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate WP_069665046.1 BCR25_RS18255 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase
Query= BRENDA::A0A0H2UNY1 (205 letters) >NCBI__GCF_001730305.1:WP_069665046.1 Length = 233 Score = 55.8 bits (133), Expect = 6e-13 Identities = 39/120 (32%), Positives = 59/120 (49%), Gaps = 2/120 (1%) Query: 67 IHPGAQIDSGVFIDHGSGLVIGETAIVEKGVLLYHGVTLGGTGKDCGKRHPTVRKGALIS 126 I+ GA I G ID G+ ++G A V K + G L G + + + LI Sbjct: 115 INIGAVIGEGTMIDMGA--ILGGRATVGKQCHIGAGTVLAGVVEPPSAQPVIIEDNVLIG 172 Query: 127 AHAQVIGPVEIGENAKVGAAAVVVADVPSDVTVVGIPAKIVRLHGKKDEPVIHEVEEKRE 186 A+A V+ V +GE A V A A+VV DV V G+PA+ ++ +K + +EE R+ Sbjct: 173 ANAVVLEGVRVGEGAVVAAGAIVVDDVAPYTVVAGVPARKIKDIDEKTKSKTTMLEELRK 232 Lambda K H 0.319 0.137 0.418 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: 101 Number of extensions: 9 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: 205 Length of database: 233 Length adjustment: 22 Effective length of query: 183 Effective length of database: 211 Effective search space: 38613 Effective search space used: 38613 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 (21.7 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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