Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; Tetrahydrodipicolinate N-acetyltransferase; THP acetyltransferase; Tetrahydropicolinate acetylase; EC 2.3.1.89 (characterized)
to candidate WP_013451920.1 CALNI_RS09110 N-acetyltransferase
Query= SwissProt::O34981 (236 letters) >NCBI__GCF_000183405.1:WP_013451920.1 Length = 216 Score = 67.8 bits (164), Expect = 2e-16 Identities = 45/147 (30%), Positives = 67/147 (45%), Gaps = 25/147 (17%) Query: 94 IEPGAIIRDQVEIGDNAVI------MMGASINIGSVIGEGTMIDMNVVLGGRATVGKNCH 147 + + + + VEIGD I + G I G+ M+ NV++G V N Sbjct: 5 VHSSSFVDENVEIGDGTKIWHFCHILPGTRIGKNCSFGQNCMVGPNVIVGNNVKVQNNVS 64 Query: 148 I------------GAGSVLAGVIEPPSA-------KPVVIEDDVVIGANAVVLEGVTVGK 188 I G VL V P S + V++ IGANA ++ G+TVG+ Sbjct: 65 IYEGLIIEDDVFLGPSCVLTNVTNPRSQVNRKNFYEKTVLKRGCTIGANATIVCGITVGR 124 Query: 189 GAVVAAGAIVVNDVEPYTVVAGTPAKK 215 A ++AGA+VV DV Y ++ G PAK+ Sbjct: 125 YAFISAGAVVVKDVPDYALMVGVPAKQ 151 Lambda K H 0.313 0.134 0.364 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: 132 Number of extensions: 13 Number of successful extensions: 5 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: 236 Length of database: 216 Length adjustment: 22 Effective length of query: 214 Effective length of database: 194 Effective search space: 41516 Effective search space used: 41516 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 46 (22.3 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