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 8501167 DvMF_1901 transferase hexapeptide repeat containing protein (RefSeq)
Query= curated2:A8F8L8 (238 letters) >FitnessBrowser__Miya:8501167 Length = 212 Score = 30.8 bits (68), Expect = 2e-05 Identities = 34/103 (33%), Positives = 41/103 (39%), Gaps = 19/103 (18%) Query: 77 ARNSALPMADITKFNARV---EPGAVIR--DLVKIGDGAVIMMG---------AIINVGA 122 AR AL MA+ N V G IR V +G G VI I+ G Sbjct: 83 ARTGALEMAENAALNVNVVVDADGGHIRMGAHVTVGPGTVIRAANHNFDRTDVPIMFQGH 142 Query: 123 VIGEKTMID-----MNAVIGGRAIIGRNCHIGAGAVIAGVIEP 160 GE T+ D N I IGR +GAGAV+ +EP Sbjct: 143 EYGEVTIEDDVWIAANCTITPGVHIGRGAVVGAGAVVTKDVEP 185 Lambda K H 0.319 0.138 0.382 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: 143 Number of extensions: 14 Number of successful extensions: 1 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: 238 Length of database: 212 Length adjustment: 22 Effective length of query: 216 Effective length of database: 190 Effective search space: 41040 Effective search space used: 41040 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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