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 8501107 DvMF_1843 acetyltransferase (RefSeq)
Query= curated2:A7HJ58 (249 letters) >FitnessBrowser__Miya:8501107 Length = 222 Score = 69.3 bits (168), Expect = 6e-17 Identities = 51/155 (32%), Positives = 70/155 (45%), Gaps = 35/155 (22%) Query: 116 VEIGNNAVIM--MGAVINLGAIIGEGTMID-------MNTVIGARARIGKYCHIGAGS-- 164 V G N I+ I G+ IG+ T I+ + VIG R +G+ I AG Sbjct: 14 VSFGKNVQILGLANVAIGQGSAIGDDTWINVCDRDDRLRLVIGQRVLVGRQSMISAGGEL 73 Query: 165 -------------------VIAGVVEPPSAQ-----PVIIEDNVVIGANAVILEGVRVGE 200 V+ + P S Q V++E+N +G N VI + VG Sbjct: 74 EIGDFCLFAPRVFVSDADHVVDNISRPYSEQGFTRGKVVVEENCWLGINTVITGSITVGR 133 Query: 201 HSVVAAGAVVVEDVPPYTVVAGVPAKVIKKVDEKT 235 VVAA AVV DVPP++VVAGVPA ++K + T Sbjct: 134 GCVVAANAVVTRDVPPFSVVAGVPAVILKMFNPAT 168 Lambda K H 0.318 0.137 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: 118 Number of extensions: 5 Number of successful extensions: 2 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: 249 Length of database: 222 Length adjustment: 23 Effective length of query: 226 Effective length of database: 199 Effective search space: 44974 Effective search space used: 44974 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: 41 (21.6 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