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 WP_013820661.1 METME_RS20550 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= curated2:Q8TY70 (245 letters) >NCBI__GCF_000214665.1:WP_013820661.1 Length = 272 Score = 99.4 bits (246), Expect = 7e-26 Identities = 73/207 (35%), Positives = 102/207 (49%), Gaps = 39/207 (18%) Query: 68 EVLESEDSVEYYHKELDHRNRAVPLADYSEFE----DVRIEPGAIIREKVKLGKGVVVMM 123 +V+ES D V YY K YSE E VR+ P A+ R + G + +M Sbjct: 73 KVIESGD-VRYYDKV------PTKFGQYSEDEFAKAGVRVVPNAVARYGSYVAPGAI-LM 124 Query: 124 GAVINIGAKIGDGTMVDMNAVVGSRAEVGKNVHIGAGAVIAGVLEPPSAKPVVIEDDVVI 183 + +NIGA + GTMVD VGS A++GKNVH+ G I GVLEP A P +I D+ I Sbjct: 125 PSYVNIGAYVDSGTMVDTWVTVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIGDNCFI 184 Query: 184 GANAVILEGVRVGKGAVVAAGAVVTED---------------VPPSKVV--AGVPAR--- 223 GA + I+EGV V VV+ G + + +P VV +P++ Sbjct: 185 GARSEIVEGVIVEDNCVVSMGVYIGQSTKIFNRMTGEISYGRIPAGSVVVSGNLPSKDGS 244 Query: 224 -------VVKDVDKKTEAKTQIVDALR 243 ++K VD+KT +KT I + LR Sbjct: 245 HSLYCAVIIKQVDEKTRSKTGINELLR 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: 139 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: 245 Length of database: 272 Length adjustment: 24 Effective length of query: 221 Effective length of database: 248 Effective search space: 54808 Effective search space used: 54808 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 10 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