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 Ac3H11_2296 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117)
Query= curated2:B1L0V4 (236 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2296 Length = 277 Score = 99.0 bits (245), Expect = 9e-26 Identities = 66/179 (36%), Positives = 92/179 (51%), Gaps = 31/179 (17%) Query: 87 DMLKINARIEPGAIIRDKVIIGENSVIMMGAVINIGAEIGEGTMVDMNAVVGARGKLGKN 146 +M R+ P A+ R I + + I+M + +NIGA +GEGTMVD A VG+ ++G N Sbjct: 99 EMKATGVRVVPPAVARRGSFIAKGA-ILMPSYVNIGAYVGEGTMVDTWATVGSCAQIGSN 157 Query: 147 VHLGAGAVVAGVLEPPSSDPCTIEDNVLIGANAVILEGIKIGKGSVV------------- 193 VHL G + GVLEP + P IEDN IGA + ++EG+ + + SV+ Sbjct: 158 VHLSGGVGIGGVLEPLQAGPTIIEDNCFIGARSEVVEGVVVEENSVLGMGVYLGQSTPIF 217 Query: 194 --AAGSIVTTDVPENVVVA----------GAP-----AKIIKEVDVKTKDKTKLLDDLR 235 A G I VP VV GAP A I+K+VD +T+ KT + D LR Sbjct: 218 NRATGEISYGRVPSGSVVVSGNLPKTAANGAPYSMYAAIIVKQVDAQTRSKTSINDLLR 276 Lambda K H 0.315 0.137 0.374 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: 144 Number of extensions: 10 Number of successful extensions: 2 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: 277 Length adjustment: 24 Effective length of query: 212 Effective length of database: 253 Effective search space: 53636 Effective search space used: 53636 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