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_083763388.1 AMB_RS00270 hypothetical protein
Query= curated2:Q5HPE5 (240 letters) >NCBI__GCF_000009985.1:WP_083763388.1 Length = 243 Score = 77.4 bits (189), Expect = 2e-19 Identities = 41/124 (33%), Positives = 68/124 (54%), Gaps = 8/124 (6%) Query: 95 IEPGAFIREQAIIEDGAVVMMGATINIGAIVGEGTMIDMNATLGGRATTGKNVHVGAGAV 154 I+P A + ++ G +M A +++ A+VG+ +++ AT+ V +G GA Sbjct: 118 IDPTAMVSAGVVLGTGLQMMPFALVHVDAVVGDQCIVNTRATVEHDCVLADGVEIGPGAT 177 Query: 155 LAGVIEPPSASPVVIEDNVLIGANAVILEGVRVGAGAIVAAGAIVTQDVPAGAVVAGTPA 214 L G + + + IGA A +L + +GA +IV AGA+VT+D+P VVAG PA Sbjct: 178 LCGRVH--------VGRDTWIGAGATVLPRLAIGANSIVGAGAVVTRDIPDNVVVAGNPA 229 Query: 215 KVIK 218 KV++ Sbjct: 230 KVLR 233 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: 108 Number of extensions: 9 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 240 Length of database: 243 Length adjustment: 23 Effective length of query: 217 Effective length of database: 220 Effective search space: 47740 Effective search space used: 47740 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: 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