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 SMa0772 SMa0772 NodL Nod factor acetyltransferase
Query= curated2:C4L2D4 (235 letters) >FitnessBrowser__Smeli:SMa0772 Length = 183 Score = 68.6 bits (166), Expect = 8e-17 Identities = 48/134 (35%), Positives = 64/134 (47%), Gaps = 22/134 (16%) Query: 93 IEPGSFIRD--HVQIGNNAVVMMGAVVNIGAVIGDGSMVDMNAVIGARGTLGKNVHLGAG 150 + PG+ IR H G N + A +N VI D + V T+G +G Sbjct: 58 VGPGAVIRPPFHCDYGFNISIGAHAYMNFNCVILDVAKV----------TIGDGTAIGPA 107 Query: 151 AVVAGVLEPPSKD----------PVIIEDGVMIGANAVILEGVRVGENAVVAAGSVVTQD 200 + P + PV I V IG A+IL GV +G++AVV AGSVVT+D Sbjct: 108 VQIYTADHPDDPEQRQAGLQLGRPVRIGKHVWIGGGAIILPGVTIGDHAVVGAGSVVTRD 167 Query: 201 VPPGVVVAGTPARI 214 VPPG V G+PAR+ Sbjct: 168 VPPGAKVMGSPARV 181 Lambda K H 0.315 0.133 0.360 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: 84 Number of extensions: 4 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: 235 Length of database: 183 Length adjustment: 21 Effective length of query: 214 Effective length of database: 162 Effective search space: 34668 Effective search space used: 34668 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: 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