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_013644330.1 METBO_RS03705 N-acetyltransferase
Query= curated2:B1L0V4 (236 letters) >NCBI__GCF_000191585.1:WP_013644330.1 Length = 203 Score = 69.3 bits (168), Expect = 5e-17 Identities = 41/123 (33%), Positives = 62/123 (50%), Gaps = 4/123 (3%) Query: 98 GAIIRDKVIIGENSVIMMGAVINIGAEIGEGTMVDMNAVVGARGKLGKNVHLGAGAVVAG 157 G ++R+K IG+N +I +++ IG + + + + NV +G A Sbjct: 67 GVVVREKTYIGDNVLIGTNSIVEGYTSIGNDVNIQSSVYIPKNSLIEDNVFIGPCACFTN 126 Query: 158 VLEPPSSD----PCTIEDNVLIGANAVILEGIKIGKGSVVAAGSIVTTDVPENVVVAGAP 213 P D I IG+N+ L I+IGKG++VAAG+IVT DVPE + GAP Sbjct: 127 DKYPLRIDYDLKGPVIRTGASIGSNSTFLSDIEIGKGAMVAAGAIVTIDVPEYFLAIGAP 186 Query: 214 AKI 216 A+I Sbjct: 187 ARI 189 Score = 23.1 bits (48), Expect = 0.004 Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 15/89 (16%) Query: 118 VINIGAEIGEGTMVDMNAVVGARGK-------LGKNVHLGAGAVVAGVLEPPSSDPCTIE 170 ++N EI E + N ++G K +GKN + + V+ + I Sbjct: 8 LLNHQDEIVEKGNNNKNIILGVEYKSKSELPVIGKNSFIRSNTVIY--------NDVNIG 59 Query: 171 DNVLIGANAVILEGIKIGKGSVVAAGSIV 199 DN G V+ E IG ++ SIV Sbjct: 60 DNFTTGHGVVVREKTYIGDNVLIGTNSIV 88 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: 156 Number of extensions: 15 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 5 Number of HSP's successfully gapped: 2 Length of query: 236 Length of database: 203 Length adjustment: 22 Effective length of query: 214 Effective length of database: 181 Effective search space: 38734 Effective search space used: 38734 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: 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