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_013259869.1 DEBA_RS15385 acetyltransferase
Query= curated2:Q9K9H8 (240 letters) >NCBI__GCF_000143965.1:WP_013259869.1 Length = 255 Score = 81.3 bits (199), Expect = 2e-20 Identities = 58/147 (39%), Positives = 84/147 (57%), Gaps = 17/147 (11%) Query: 84 LLDLKNIKARIEPGAIIRDQVEIGDNAVIMM-GASINIGSVIGEG--TMI----DMNVVL 136 +LD +N + R +P I+ D V + ++ +I S+ IG G G T+I D VV+ Sbjct: 106 ILDARNPQ-RHDP-LILGDDVNLSNDVMISCKNGSVRIGERTGVGARTIIHSADDNPVVV 163 Query: 137 GGRATVGKNCHI-GAGSVLAGVIEPPSAKP-------VVVEDDVVIGANCVILEGVTVGK 188 G A +G C+I G G+ ++ P + VV+EDDV +GAN +L+GV +GK Sbjct: 164 GADAAIGPMCYIVGGGNYNIDRLDAPMSMQGVRRTGGVVIEDDVWLGANVTVLDGVRMGK 223 Query: 189 GAVVAAGAVVTEDVPPNTVVAGTPARV 215 GAV AAGAV+T+D PP + G PARV Sbjct: 224 GAVGAAGAVLTKDAPPLAICMGVPARV 250 Lambda K H 0.314 0.135 0.372 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: 210 Number of extensions: 16 Number of successful extensions: 4 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: 240 Length of database: 255 Length adjustment: 24 Effective length of query: 216 Effective length of database: 231 Effective search space: 49896 Effective search space used: 49896 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 (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