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 8501162 DvMF_1896 transferase hexapeptide repeat containing protein (RefSeq)
Query= curated2:Q9K9H8 (240 letters) >FitnessBrowser__Miya:8501162 Length = 223 Score = 77.4 bits (189), Expect = 2e-19 Identities = 52/127 (40%), Positives = 70/127 (55%), Gaps = 28/127 (22%) Query: 106 IGDNAVIMMGASINIGSV---IGEGTMIDMNVVLGGRATVGKNCHIGAGSVLAGVIEPPS 162 +GD V M G +I S IG+GTMI G NC I A PP Sbjct: 111 VGDG-VTMNGTAITARSRTIRIGKGTMI------------GPNCVITDSDFHAPW--PPE 155 Query: 163 AK----------PVVVEDDVVIGANCVILEGVTVGKGAVVAAGAVVTEDVPPNTVVAGTP 212 + V + D+V +G C++L+GVT+G GA+VAAG+VVT DVPP T+VAGTP Sbjct: 156 TRLTTPAFERDRDVTIGDNVWLGMRCIVLKGVTIGDGAIVAAGSVVTRDVPPATLVAGTP 215 Query: 213 ARVIKEI 219 ARV++++ Sbjct: 216 ARVVRQL 222 Score = 25.4 bits (54), Expect = 0.001 Identities = 14/51 (27%), Positives = 28/51 (54%), Gaps = 7/51 (13%) Query: 91 KARIEPGAIIRDQ-VEIGDN------AVIMMGASINIGSVIGEGTMIDMNV 134 + R+ A RD+ V IGDN +++ G +I G+++ G+++ +V Sbjct: 155 ETRLTTPAFERDRDVTIGDNVWLGMRCIVLKGVTIGDGAIVAAGSVVTRDV 205 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: 129 Number of extensions: 9 Number of successful extensions: 4 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: 240 Length of database: 223 Length adjustment: 23 Effective length of query: 217 Effective length of database: 200 Effective search space: 43400 Effective search space used: 43400 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: 46 (22.3 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