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 3610758 Dshi_4144 transferase hexapeptide repeat containing protein (RefSeq)
Query= curated2:Q5HPE5 (240 letters) >FitnessBrowser__Dino:3610758 Length = 190 Score = 69.3 bits (168), Expect = 5e-17 Identities = 49/143 (34%), Positives = 71/143 (49%), Gaps = 11/143 (7%) Query: 83 IPLKDLT-NTNARIEPGAFIREQAIIEDGAVVMMGATINIGAIVGEGTMIDMNATLGGRA 141 IP + L + R+ P A IE G V +GA + A G G + +G A Sbjct: 48 IPRRSLRLGRDVRLSPNAAFSNPERIEIGDRVSIGAHCTLWAGPGTGRI-----EIGADA 102 Query: 142 TTGKNVHVGAGAVLAGVIEPPSA-----SPVVIEDNVLIGANAVILEGVRVGAGAIVAAG 196 G V V A P +A + VVI +V +GA A+++ G R+G GAI+ AG Sbjct: 103 LFGPEVFVTAAGYRFNEGSPVTAQAMDEADVVIGRDVWLGARAMVMPGARIGDGAIIGAG 162 Query: 197 AIVTQDVPAGAVVAGTPAKVIKQ 219 A+V ++PAGA+ G PA+V+ Q Sbjct: 163 ALVRGEIPAGAIAVGVPARVVGQ 185 Score = 21.9 bits (45), Expect = 0.009 Identities = 14/38 (36%), Positives = 18/38 (47%) Query: 76 MDRRNSAIPLKDLTNTNARIEPGAFIREQAIIEDGAVV 113 MD + I A + PGA I + AII GA+V Sbjct: 128 MDEADVVIGRDVWLGARAMVMPGARIGDGAIIGAGALV 165 Lambda K H 0.315 0.132 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: 90 Number of extensions: 8 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 240 Length of database: 190 Length adjustment: 22 Effective length of query: 218 Effective length of database: 168 Effective search space: 36624 Effective search space used: 36624 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: 41 (21.6 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