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 Ga0059261_1374 Ga0059261_1374 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Query= curated2:Q8TY70 (245 letters) >FitnessBrowser__Korea:Ga0059261_1374 Length = 272 Score = 108 bits (269), Expect = 1e-28 Identities = 71/166 (42%), Positives = 93/166 (56%), Gaps = 28/166 (16%) Query: 105 PGAIIREKVKLGKGVVVMMGAVINIGAKIGDGTMVDMNAVVGSRAEVGKNVHIGAGAVIA 164 PG+++R + K VV +M + +NIGA +G+G+MVD A VGS A++G+NVH+ G I Sbjct: 107 PGSVVRHGAFISKNVV-LMPSFVNIGAYVGEGSMVDGWATVGSCAQIGRNVHLSGGVGIG 165 Query: 165 GVLEPPSAKPVVIEDDVVIGANAVILEGVRVGKGAVV---------------AAGAVVTE 209 GVLEP A PV+I D IGA A + EGVRVG+GAV+ A G V Sbjct: 166 GVLEPLQADPVIIGDGAFIGARAEVAEGVRVGEGAVLSMGVYLGASTKIVDRATGEVHRG 225 Query: 210 DVPPSKVVA--------GVP----ARVVKDVDKKTEAKTQIVDALR 243 VPP VV G P A +VK VD +T +KT I + LR Sbjct: 226 VVPPYSVVVPGTLPGKDGGPGLYCAVIVKTVDAQTRSKTGINELLR 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: 155 Number of extensions: 7 Number of successful extensions: 4 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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