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 7025668 Shewana3_2818 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase (RefSeq)
Query= curated2:Q8TY70 (245 letters) >FitnessBrowser__ANA3:7025668 Length = 274 Score = 104 bits (259), Expect = 2e-27 Identities = 71/187 (37%), Positives = 98/187 (52%), Gaps = 34/187 (18%) Query: 90 VPL--ADYSEF----EDVRIEPGAIIREKVKLGKGVVVMMGAVINIGAKIGDGTMVDMNA 143 VPL A+Y E E +R+ P A +R+ +GK V +M + +N+GA + +GTMVD A Sbjct: 86 VPLKFAEYDEARFKAEAIRVVPSATVRKGSFIGKNTV-LMPSYVNLGAYVDEGTMVDTWA 144 Query: 144 VVGSRAEVGKNVHIGAGAVIAGVLEPPSAKPVVIEDDVVIGANAVILEGVRVGKGAVVAA 203 VGS A++GKNVH+ G I GVLEP A P +IED+ IGA + I+EGV V +G+V++ Sbjct: 145 TVGSCAQIGKNVHLSGGVGIGGVLEPLQAGPTIIEDNCFIGARSEIVEGVVVEEGSVISM 204 Query: 204 GAVVTED---------------VPPSKVVAG------------VPARVVKDVDKKTEAKT 236 G + + VP VV A +VK VD KT K Sbjct: 205 GVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPSACGKYSLYAAIIVKKVDAKTRGKV 264 Query: 237 QIVDALR 243 I + LR Sbjct: 265 GINELLR 271 Lambda K H 0.315 0.136 0.375 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: 136 Number of extensions: 9 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: 245 Length of database: 274 Length adjustment: 24 Effective length of query: 221 Effective length of database: 250 Effective search space: 55250 Effective search space used: 55250 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: 47 (22.7 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