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_019867370.1 METMI_RS0116315 colanic acid biosynthesis acetyltransferase WcaF
Query= curated2:A8F8L8 (238 letters) >NCBI__GCF_000384075.1:WP_019867370.1 Length = 175 Score = 60.8 bits (146), Expect = 2e-14 Identities = 41/132 (31%), Positives = 69/132 (52%), Gaps = 7/132 (5%) Query: 90 FNARVEPGAVIRDLVKIGDGAVIMMGAIINVGAVIGEKTMIDM--NAVIGGRAIIGRNCH 147 F AR+ +I+ V+I +++G + IGE ID IG + + + Sbjct: 45 FGARIGNDVIIKPRVRIKFPWRLVIGCY----SWIGEAVWIDNLDQVTIGSNTCLSQGVY 100 Query: 148 IGAGAVIAGVIE-PPSATPVVIEDNVMVGANAVVLEGVKVGKGSVVAAGAVVVSDVDPYT 206 + G+ G IE PVVIED V + A A++ G V +G+++ G++ ++DP+T Sbjct: 101 VCTGSHDWGKIEFNLIVKPVVIEDQVWIAAKAILSPGTVVRQGAILTMGSMASKELDPWT 160 Query: 207 VVAGIPAKFIKK 218 + AGIPAK I++ Sbjct: 161 IYAGIPAKPIRE 172 Lambda K H 0.319 0.138 0.382 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: 75 Number of extensions: 5 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: 238 Length of database: 175 Length adjustment: 21 Effective length of query: 217 Effective length of database: 154 Effective search space: 33418 Effective search space used: 33418 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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