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_086508764.1 BZY95_RS04320 acetyltransferase
Query= curated2:Q8TY70 (245 letters) >NCBI__GCF_002151265.1:WP_086508764.1 Length = 225 Score = 76.3 bits (186), Expect = 5e-19 Identities = 40/125 (32%), Positives = 66/125 (52%), Gaps = 8/125 (6%) Query: 103 IEPGAIIREKVKLGKGVVVMMGAVINIGAKIGDGTMVDMNAVVGSRAEVGKNVHIGAGAV 162 I P A++ +LG G + + G ++N + G+GT+++ A VG +G+ VH+ GA Sbjct: 91 IHPAAMVSRYAELGMGTLAVAGCIVNAFTRCGEGTIINTGATVGHDCLLGQGVHVAPGAN 150 Query: 163 IAGVLEPPSAKPVVIEDDVVIGANAVILEGVRVGKGAVVAAGAVVTEDVPPSKVVAGVPA 222 +AG VV+ +G A +++ V +GKG + AGA V V + V G PA Sbjct: 151 LAG--------HVVVGAYTWVGIGARVIQCVTIGKGVFIGAGATVIGSVRDGEKVVGTPA 202 Query: 223 RVVKD 227 R ++D Sbjct: 203 RPLRD 207 Score = 37.7 bits (86), Expect = 2e-07 Identities = 25/67 (37%), Positives = 32/67 (47%) Query: 99 EDVRIEPGAIIREKVKLGKGVVVMMGAVINIGAKIGDGTMVDMNAVVGSRAEVGKNVHIG 158 E I GA + LG+GV V GA + +G T V + A V +GK V IG Sbjct: 123 EGTIINTGATVGHDCLLGQGVHVAPGANLAGHVVVGAYTWVGIGARVIQCVTIGKGVFIG 182 Query: 159 AGAVIAG 165 AGA + G Sbjct: 183 AGATVIG 189 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: 129 Number of extensions: 8 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 245 Length of database: 225 Length adjustment: 23 Effective length of query: 222 Effective length of database: 202 Effective search space: 44844 Effective search space used: 44844 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: 46 (22.3 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