Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; Tetrahydrodipicolinate N-acetyltransferase; THP acetyltransferase; Tetrahydropicolinate acetylase; EC 2.3.1.89 (characterized)
to candidate 6936989 Sama_1163 acetyltransferase (RefSeq)
Query= SwissProt::O34981 (236 letters) >FitnessBrowser__SB2B:6936989 Length = 204 Score = 79.3 bits (194), Expect = 5e-20 Identities = 52/134 (38%), Positives = 71/134 (52%), Gaps = 14/134 (10%) Query: 94 IEPGAIIRDQVEIGDNAVIMMGASINIGSVIGEGTMIDMNVVLGGRATVGKNCHIGAGSV 153 I G I VE+GD I G+S++ G V + +G R + N I A + Sbjct: 79 IAAGVFIHGPVEMGDEVAINHGSSLDGGRV---------GINIGSRTRIANNVTIYAFNH 129 Query: 154 LAGVIEP-----PSAKPVVIEDDVVIGANAVVLEGVTVGKGAVVAAGAIVVNDVEPYTVV 208 EP S+K +VI +DV IGA A +++GVT+G AVV GAIV DV PY++V Sbjct: 130 GMAPDEPIYTQKVSSKGIVIGEDVWIGAQAGIVDGVTIGNHAVVGMGAIVTRDVAPYSIV 189 Query: 209 AGTPAKKIKDIDEK 222 AG PA+ I D +K Sbjct: 190 AGNPARPIGDRRDK 203 Lambda K H 0.313 0.134 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: 123 Number of extensions: 10 Number of successful extensions: 4 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: 236 Length of database: 204 Length adjustment: 22 Effective length of query: 214 Effective length of database: 182 Effective search space: 38948 Effective search space used: 38948 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 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