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 Ga0059261_3663 Ga0059261_3663 UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase
Query= curated2:Q8TY70 (245 letters) >FitnessBrowser__Korea:Ga0059261_3663 Length = 451 Score = 57.8 bits (138), Expect = 4e-13 Identities = 42/125 (33%), Positives = 61/125 (48%), Gaps = 9/125 (7%) Query: 102 RIEPGAIIREKVKLGKGVVVMMGAVINIGAKIGDGTMVDMNAVVGSRAEVGKNVHIGAGA 161 R+ PG ++ EK K+G V V+ GAK T + AEVG +IGAG Sbjct: 318 RLRPGTVVGEKAKIGNFVETKK-TVLGKGAKANHLTYL-------GDAEVGAGANIGAGT 369 Query: 162 VIAGVLEPPSAKPVVIEDDVVIGANAVILEGVRVGKGAVVAAGAVVTEDVPPSKVVAGVP 221 + + I IG+N+ ++ V +G+GA+VAAGAVVT+DV + P Sbjct: 370 ITCNY-DGFFKYGTRIGAGAFIGSNSALVAPVAIGEGAIVAAGAVVTKDVEADALALVRP 428 Query: 222 ARVVK 226 +V K Sbjct: 429 EQVAK 433 Lambda K H 0.315 0.136 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: 244 Number of extensions: 13 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: 245 Length of database: 451 Length adjustment: 28 Effective length of query: 217 Effective length of database: 423 Effective search space: 91791 Effective search space used: 91791 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: 49 (23.5 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