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 352470 BT2943 putative hexapeptide transferase family protein (NCBI ptt file)
Query= curated2:A7HJ58 (249 letters) >FitnessBrowser__Btheta:352470 Length = 552 Score = 84.3 bits (207), Expect = 5e-21 Identities = 54/147 (36%), Positives = 70/147 (47%), Gaps = 20/147 (13%) Query: 99 ISKFNARIEPGAIIREYVEIGNNAVIMMGAVINLGAIIGEGTMIDMNTVIGARARIGKYC 158 + ++ IEPG VI+ GA I IG+GT I+ +TVI RIG+YC Sbjct: 96 VGGYDNTIEPGV------------VILSGATITCNVSIGQGTFINKSTVISHDVRIGRYC 143 Query: 159 HIGAGSVIAGVVEPPSAQPVIIEDNVVIGANAVILEGVRVGEHSVVAAGAVVVEDVPPYT 218 + G+ + G II D IGANAVIL V VG + AGAVV ++ +T Sbjct: 144 EVSPGAKVLG--------RAIIGDRTEIGANAVILPDVIVGADCKIGAGAVVTRNIDSHT 195 Query: 219 VVAGVPAKVIKKVDEKTISKTQLIEEL 245 VAGVPA+ I K I L Sbjct: 196 TVAGVPARSITKSSNNAFKLKSKIRNL 222 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: 327 Number of extensions: 26 Number of successful extensions: 7 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: 552 Length adjustment: 30 Effective length of query: 219 Effective length of database: 522 Effective search space: 114318 Effective search space used: 114318 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: 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