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 6936962 Sama_1136 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase (RefSeq)
Query= curated2:Q8TY70 (245 letters) >FitnessBrowser__SB2B:6936962 Length = 274 Score = 105 bits (261), Expect = 1e-27 Identities = 69/182 (37%), Positives = 96/182 (52%), Gaps = 32/182 (17%) Query: 93 ADYSEF----EDVRIEPGAIIREKVKLGKGVVVMMGAVINIGAKIGDGTMVDMNAVVGSR 148 ADY E E +R+ P A +R+ +GK V +M + +N+GA + +GTMVD A VGS Sbjct: 91 ADYDEARFRAEAIRVVPPAAVRKGSFIGKNTV-LMPSYVNLGAYVDEGTMVDTWATVGSC 149 Query: 149 AEVGKNVHIGAGAVIAGVLEPPSAKPVVIEDDVVIGANAVILEGVRVGKGAVVAAGAVVT 208 A++GKNVH+ G I GVLEP A P +IED+ IGA + I+EGV V +G+V++ G + Sbjct: 150 AQIGKNVHLSGGVGIGGVLEPLQAGPTIIEDNCFIGARSEIVEGVVVEEGSVISMGVYIG 209 Query: 209 ED---------------VPPSKVVAG------------VPARVVKDVDKKTEAKTQIVDA 241 + VP VV A +VK VD+KT K I + Sbjct: 210 QSTRIYDRETGEIHYGRVPAGSVVVSGTLPSSCGKYNLYAAIIVKKVDEKTRGKVGINEL 269 Query: 242 LR 243 LR Sbjct: 270 LR 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: 140 Number of extensions: 7 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