Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; EC 2.3.1.89; Tetrahydrodipicolinate N-acetyltransferase; THP acetyltransferase; Tetrahydropicolinate acetylase (uncharacterized)
to candidate WP_086508134.1 BZY95_RS00955 serine O-acetyltransferase
Query= curated2:Q5HPE5 (240 letters) >NCBI__GCF_002151265.1:WP_086508134.1 Length = 288 Score = 70.9 bits (172), Expect = 3e-17 Identities = 44/125 (35%), Positives = 62/125 (49%), Gaps = 9/125 (7%) Query: 114 MMGATINIGAIVGEGTMID--MNATLGGRATTGKNVHVGAGAVLAGVIEPPSASPVVIED 171 + G I+ GA +G ID M +G A G +V + G L G +ED Sbjct: 63 LTGIEIHPGAKIGRRFFIDHGMGVVIGETAEVGDDVTLYQGVTLGGTSWNKGKRHPTLED 122 Query: 172 NVLIGANAVILEGVRVGAGAIVAAGAIVTQDVPAGAVVAGTPAKVIKQTS-------EVQ 224 V++GA A IL VG GA + + A+VT++VPAGA V G P K++K+ EV Sbjct: 123 GVIVGAGAKILGPFTVGTGAKIGSNAVVTKEVPAGATVVGIPGKIVKRADPDAAEVLEVD 182 Query: 225 DSKRE 229 +RE Sbjct: 183 PERRE 187 Score = 26.9 bits (58), Expect = 4e-04 Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 1/64 (1%) Query: 107 IEDGAVVMMGATINIGAIVGEGTMIDMNATLGGRATTGKNVHVGAGAVLAGVIEPPSASP 166 +EDG +V GA I VG G I NA + G V VG + +P +A Sbjct: 120 LEDGVIVGAGAKILGPFTVGTGAKIGSNAVVTKEVPAGATV-VGIPGKIVKRADPDAAEV 178 Query: 167 VVIE 170 + ++ Sbjct: 179 LEVD 182 Lambda K H 0.315 0.132 0.364 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: 111 Number of extensions: 7 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 240 Length of database: 288 Length adjustment: 25 Effective length of query: 215 Effective length of database: 263 Effective search space: 56545 Effective search space used: 56545 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 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