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 SMc00232 SMc00232 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase
Query= curated2:B1L0V4 (236 letters) >FitnessBrowser__Smeli:SMc00232 Length = 456 Score = 55.5 bits (132), Expect = 2e-12 Identities = 40/126 (31%), Positives = 66/126 (52%), Gaps = 9/126 (7%) Query: 93 ARIEPGAIIRDKVIIGENSVIMMGAVINIGAEIGEGTMVDMNAVVGARGKLGKNVHLGAG 152 AR+ PGA + K +G N + A I GA++ T + +A VGA G N+ GAG Sbjct: 315 ARLRPGADLGAKSKVG-NFCEVKNAEIGAGAKVNHLTYIG-DAFVGA----GSNI--GAG 366 Query: 153 AVVAGVLEPPSSDPCTIEDNVLIGANAVILEGIKIGKGSVVAAGSIVTTDVPENVVVAGA 212 + + + I N +G+N+ ++ + IG G++VA+GS++T DVP + V G Sbjct: 367 TITCNY-DGVNKHVTRIGANAFVGSNSSLVAPVSIGDGALVASGSVITEDVPADAVAFGR 425 Query: 213 PAKIIK 218 + +K Sbjct: 426 ARQDVK 431 Lambda K H 0.315 0.137 0.374 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: 244 Number of extensions: 22 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 236 Length of database: 456 Length adjustment: 28 Effective length of query: 208 Effective length of database: 428 Effective search space: 89024 Effective search space used: 89024 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: 48 (23.1 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