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_086511385.1 BZY95_RS18610 acetyltransferase
Query= curated2:Q8TY70 (245 letters) >NCBI__GCF_002151265.1:WP_086511385.1 Length = 244 Score = 81.6 bits (200), Expect = 1e-20 Identities = 48/121 (39%), Positives = 68/121 (56%), Gaps = 8/121 (6%) Query: 103 IEPGAIIREKVKLGKGVVVMMGAVINIGAKIGDGTMVDMNAVVGSRAEVGKNVHIGAGAV 162 + P A I +LG G VV+ GAV+N A++G+G +V+ A VG +G VH+ GA Sbjct: 94 VHPRATISPLARLGPGCVVVAGAVVNAFAELGEGCIVNTCASVGHDCRLGACVHVAPGAN 153 Query: 163 IAGVLEPPSAKPVVIEDDVVIGANAVILEGVRVGKGAVVAAGAVVTEDVPPSKVVAGVPA 222 +AG +E I IGA A + +G+ +G+G +V AGA V V +VV GVPA Sbjct: 154 VAGDVE--------IGRTSWIGAGAAVRQGMTIGEGVMVGAGAAVVASVGDRQVVGGVPA 205 Query: 223 R 223 R Sbjct: 206 R 206 Score = 35.0 bits (79), Expect = 1e-06 Identities = 25/81 (30%), Positives = 37/81 (45%), Gaps = 6/81 (7%) Query: 101 VRIEPGAIIREKVKLGKGVVVMMGAVINIGAKIGDGTMVDMNAV----VGSRAEVG--KN 154 V + PGA + V++G+ + GA + G IG+G MV A VG R VG Sbjct: 146 VHVAPGANVAGDVEIGRTSWIGAGAAVRQGMTIGEGVMVGAGAAVVASVGDRQVVGGVPA 205 Query: 155 VHIGAGAVIAGVLEPPSAKPV 175 + + AG + P A P+ Sbjct: 206 RPLSPSSTDAGPADNPDADPL 226 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: 149 Number of extensions: 12 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 245 Length of database: 244 Length adjustment: 24 Effective length of query: 221 Effective length of database: 220 Effective search space: 48620 Effective search space used: 48620 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 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