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_086511395.1 BZY95_RS18660 aminotransferase class V-fold PLP-dependent enzyme
Query= curated2:Q9K9H8 (240 letters) >NCBI__GCF_002151265.1:WP_086511395.1 Length = 583 Score = 75.9 bits (185), Expect = 2e-18 Identities = 46/147 (31%), Positives = 67/147 (45%), Gaps = 25/147 (17%) Query: 93 RIEPGAIIRDQVEIGDNAVIMMGASINIGSVIGEGTMIDMNVVLGGRATVGKNCHI---- 148 +I P AI+ EIG+++ + + G+ IG G + NV +G R +G C + Sbjct: 14 QIHPSAIVDAGAEIGESSYVWHFVHVCGGARIGRGVSLGQNVFIGNRVVIGDGCRVQNNV 73 Query: 149 --------------GAGSVLAGVIEPPSA-------KPVVVEDDVVIGANCVILEGVTVG 187 G V V P S + +V + +GANC I+ GVT+G Sbjct: 74 SVYDNVTLEAGVFCGPSMVFTNVYNPRSTVDRKSEYRDTLVREGATLGANCTIVCGVTIG 133 Query: 188 KGAVVAAGAVVTEDVPPNTVVAGTPAR 214 + A V AGAVV DVP ++ G PAR Sbjct: 134 RYAFVGAGAVVNRDVPDFALMLGVPAR 160 Lambda K H 0.314 0.135 0.372 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: 300 Number of extensions: 13 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: 240 Length of database: 583 Length adjustment: 30 Effective length of query: 210 Effective length of database: 553 Effective search space: 116130 Effective search space used: 116130 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 (21.9 bits) S2: 49 (23.5 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