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 SMc01732 SMc01732 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase
Query= curated2:A7HJ58 (249 letters) >FitnessBrowser__Smeli:SMc01732 Length = 296 Score = 107 bits (268), Expect = 2e-28 Identities = 71/184 (38%), Positives = 97/184 (52%), Gaps = 34/184 (18%) Query: 96 LSDISKFNARIEPGAIIREYVEIGNNAVIMMGAVINLGAIIGEGTMIDMNTVIGARARIG 155 +++ K R P ++R I NAV+M + +NLGA +GEGTM+D +G+ A+IG Sbjct: 113 VNEFEKAGFRAVPNCVVRRSAYIAPNAVLMP-SFVNLGAYVGEGTMVDTWATVGSCAQIG 171 Query: 156 KYCHIGAGSVIAGVVEPPSAQPVIIEDNVVIGANAVILEGVRVGEHSVV----------- 204 K H+ G I GV+EP A P IIEDN IGA + ++EG V E SV+ Sbjct: 172 KNVHLSGGVGIGGVLEPMQAGPTIIEDNCFIGARSEVVEGCIVREGSVLGMGVFIGKSTK 231 Query: 205 ----AAGAVVVEDVPPYTVVA------------GVPAK------VIKKVDEKTISKTQLI 242 A G V+ +VPPY+VV G PA ++K+VDEKT SKT + Sbjct: 232 IVDRATGEVMYGEVPPYSVVVAGSMASGSTMANGQPAPNLYCAVIVKRVDEKTRSKTGIN 291 Query: 243 EELR 246 E LR Sbjct: 292 ELLR 295 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: 179 Number of extensions: 11 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: 249 Length of database: 296 Length adjustment: 25 Effective length of query: 224 Effective length of database: 271 Effective search space: 60704 Effective search space used: 60704 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 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