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 209274 DVU0340 acetyltransferase, CysE/LacA/LpxA/NodL family
Query= curated2:A8F8L8 (238 letters) >MicrobesOnline__882:209274 Length = 197 Score = 82.8 bits (203), Expect = 4e-21 Identities = 46/111 (41%), Positives = 67/111 (60%), Gaps = 15/111 (13%) Query: 123 VIGEKTMIDMNAVI---GGRAIIGRNCHIGAGAVIAGV------IEPP------SATPVV 167 V+GE +++N V+ GG IG + +G G VI ++ P VV Sbjct: 82 VMGENAALNINVVVDADGGTVRIGAHATVGPGTVIRAANHRFDRLDTPIMFQGHEYGEVV 141 Query: 168 IEDNVMVGANAVVLEGVKVGKGSVVAAGAVVVSDVDPYTVVAGIPAKFIKK 218 I+D+V + AN V+ GV +G+G+VV AGAVV DV+PYTVVAG+PA+FI++ Sbjct: 142 IDDDVWIAANCTVVPGVHIGRGAVVGAGAVVTKDVEPYTVVAGVPARFIRR 192 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: 121 Number of extensions: 10 Number of successful extensions: 3 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: 197 Length adjustment: 22 Effective length of query: 216 Effective length of database: 175 Effective search space: 37800 Effective search space used: 37800 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 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