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 7025324 Shewana3_2484 hexapaptide repeat-containing transferase (RefSeq)
Query= curated2:Q9K9H8 (240 letters) >FitnessBrowser__ANA3:7025324 Length = 185 Score = 60.5 bits (145), Expect = 2e-14 Identities = 36/99 (36%), Positives = 53/99 (53%), Gaps = 10/99 (10%) Query: 128 TMIDM-NVVLGGRATVGKNCHIGAGSVLAGVIEPPS------AKPVVVEDDVVIGANCVI 180 T++D+ V +G G N I S I+P + KP+ + V +G N + Sbjct: 86 TILDVCQVTIGNHVMFGPNVLI---STATHPIDPIARLTTEFGKPIHIGHHVWLGGNVSV 142 Query: 181 LEGVTVGKGAVVAAGAVVTEDVPPNTVVAGTPARVIKEI 219 L GVT+G V+ AG+VV +D+P N+V G P RVIK+I Sbjct: 143 LPGVTIGDNCVIGAGSVVNKDIPANSVAVGNPCRVIKQI 181 Score = 26.6 bits (57), Expect = 4e-04 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%) Query: 100 IRDQVEIGDNAVIMMGASINIGSVIGEGTMIDMNVVLGGRATVGKNCHI 148 I V +G N ++ G +I VIG G++++ ++ A VG C + Sbjct: 130 IGHHVWLGGNVSVLPGVTIGDNCVIGAGSVVNKDIPANSVA-VGNPCRV 177 Lambda K H 0.314 0.135 0.372 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: 109 Number of extensions: 6 Number of successful extensions: 3 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: 240 Length of database: 185 Length adjustment: 21 Effective length of query: 219 Effective length of database: 164 Effective search space: 35916 Effective search space used: 35916 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 (21.9 bits) S2: 45 (21.9 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