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_013258062.1 DEBA_RS06195 gamma carbonic anhydrase family protein
Query= curated2:Q5HPE5 (240 letters) >NCBI__GCF_000143965.1:WP_013258062.1 Length = 179 Score = 67.4 bits (163), Expect = 2e-16 Identities = 51/145 (35%), Positives = 74/145 (51%), Gaps = 19/145 (13%) Query: 95 IEPGAFIREQAIIEDGAVVMMGATI--NIGAI-VGEGTMIDMNATL-----GGRATTGKN 146 + P A + + + D V G I ++GAI VG + I + L G G++ Sbjct: 18 VAPSALVAGEVDLADEVSVWYGCVIRGDVGAIAVGARSNIQDMSVLHVSRGGPPCLVGRD 77 Query: 147 VHVGAGAVLAGVIEPPSASPVVIEDNVLIGANAVILEGVRVGAGAIVAAGAIVTQD--VP 204 V VG AVL G IED IG A+IL+G RVGAGA++AAG +V +P Sbjct: 78 VLVGHRAVLHGCS---------IEDEAFIGIGAIILDGARVGAGAMIAAGGLVPPGALIP 128 Query: 205 AGAVVAGTPAKVIKQTSEVQDSKRE 229 GA+ G+PAKV +Q S + ++ + Sbjct: 129 PGALAMGSPAKVKRQLSSEEMARNQ 153 Lambda K H 0.315 0.132 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: 92 Number of extensions: 7 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 240 Length of database: 179 Length adjustment: 21 Effective length of query: 219 Effective length of database: 158 Effective search space: 34602 Effective search space used: 34602 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