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_089299603.1 CHB84_RS01395 acyltransferase
Query= curated2:Q8TY70 (245 letters) >NCBI__GCF_900188115.1:WP_089299603.1 Length = 163 Score = 53.9 bits (128), Expect = 2e-12 Identities = 38/111 (34%), Positives = 52/111 (46%), Gaps = 14/111 (12%) Query: 133 IGDGTMVDMNAVV---GSRAEVGKNVHIGAGAVI-----------AGVLEPPSAKPVVIE 178 IG+GT + V+ G +G I AGA I + + V I Sbjct: 32 IGEGTWIGAFTVLDGGGGLLRIGDGCDIAAGAQIYTHSSMRRCVSGRAYDAVDREAVSIG 91 Query: 179 DDVVIGANAVILEGVRVGKGAVVAAGAVVTEDVPPSKVVAGVPARVVKDVD 229 + V IG + ++ GV VG A V AG+VVT DV +VAGVPAR + +D Sbjct: 92 NHVFIGPHVTVMPGVSVGDSAAVLAGSVVTGDVAARSLVAGVPARPIGHLD 142 Lambda K H 0.315 0.136 0.375 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: 1 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: 245 Length of database: 163 Length adjustment: 21 Effective length of query: 224 Effective length of database: 142 Effective search space: 31808 Effective search space used: 31808 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: 42 (22.0 bits) S2: 45 (21.9 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