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_083780027.1 BTUS_RS04450 NeuD/PglB/VioB family sugar acetyltransferase
Query= curated2:B1L0V4 (236 letters) >NCBI__GCF_000092905.1:WP_083780027.1 Length = 257 Score = 77.4 bits (189), Expect = 2e-19 Identities = 44/135 (32%), Positives = 72/135 (53%), Gaps = 8/135 (5%) Query: 93 ARIEPGAIIRDKVIIGENSVIMMGAVINIGAEIGEGTMVDMNAVVGARGKLGKNVHLGAG 152 A I+P + V IGE S+I G ++ + IG+ +V++ + + KLG + G Sbjct: 131 ALIDPDIDVHRSVNIGEGSIICPGVILTVNVVIGKFVIVNVASSISHESKLGDFSSVMTG 190 Query: 153 AVVAGVLEPPSSDPCTIEDNVLIGANAVILEGIKIGKGSVVAAGSIVTTDVPENVVVAGA 212 ++G C I IG+ AV+L+G +G+ +VV AG++VT DV VV G Sbjct: 191 VRISG--------NCRIGHGAYIGSGAVVLQGRAVGEAAVVGAGAVVTRDVEPRVVSVGI 242 Query: 213 PAKIIKEVDVKTKDK 227 PA+I + ++VK D+ Sbjct: 243 PARIQRWIEVKPDDR 257 Score = 23.5 bits (49), Expect = 0.004 Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 6/40 (15%) Query: 92 NARIEPGAIIRDKVIIGENSVIMMGAVINIGAEIGEGTMV 131 N RI GA IG +V++ G + A +G G +V Sbjct: 196 NCRIGHGA------YIGSGAVVLQGRAVGEAAVVGAGAVV 229 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: 187 Number of extensions: 13 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 236 Length of database: 257 Length adjustment: 24 Effective length of query: 212 Effective length of database: 233 Effective search space: 49396 Effective search space used: 49396 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: 46 (22.3 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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