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_013452079.1 CALNI_RS10005 colanic acid biosynthesis acetyltransferase WcaF
Query= curated2:A7HJ58 (249 letters) >NCBI__GCF_000183405.1:WP_013452079.1 Length = 183 Score = 57.0 bits (136), Expect = 3e-13 Identities = 50/157 (31%), Positives = 72/157 (45%), Gaps = 17/157 (10%) Query: 88 IAHNSAIPLSDISKFNARIEPGAIIREYVEIGNNAVIMMGAVINLGAIIGEGTMIDMNTV 147 I + S I + + F A+I +I+ V I + +G + IGE ID T Sbjct: 35 IPYPSKIKVLLLRIFGAKIGKNVVIKPCVNIKYPWFLKIGDNV----WIGENVWIDNLTT 90 Query: 148 IGARARIGKYCHIGAGSVIAGVVEPPSAQ-------PVIIEDNVVIGANAVILEGVRVGE 200 + IG I G+ I Q PVIIED V IGA A++ GVR Sbjct: 91 V----EIGNNVCISQGAYIFTGNHNYKTQSFDLIIKPVIIEDGVWIGAKAIVCPGVRCKS 146 Query: 201 HSVVAAGAVVVEDVPPYTVVAGVPAKVIKK--VDEKT 235 HS+++ G+V +D+ YTV G PA +K +D+ T Sbjct: 147 HSILSVGSVATKDLEEYTVYQGNPAVPKRKRIIDDGT 183 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: 129 Number of extensions: 7 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: 183 Length adjustment: 22 Effective length of query: 227 Effective length of database: 161 Effective search space: 36547 Effective search space used: 36547 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: 45 (21.9 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