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 CA265_RS05165 CA265_RS05165 hypothetical protein
Query= curated2:A8F8L8 (238 letters) >FitnessBrowser__Pedo557:CA265_RS05165 Length = 211 Score = 80.5 bits (197), Expect = 2e-20 Identities = 44/120 (36%), Positives = 64/120 (53%), Gaps = 8/120 (6%) Query: 100 IRDLVKIGDGAVIMMGAIINVGAVIGEKTMIDMNAVIGGRAIIGRNCHIGAGAVIAGVIE 159 I +KIG+G I G +IN IG +++ N I I+ I G IAG + Sbjct: 99 ISSSIKIGEGNCIAPGCVINANVRIGNHCIVNSNCNISHDCILENYVTISPGVTIAGNVH 158 Query: 160 PPSATPVVIEDNVMVGANAVVLEGVKVGKGSVVAAGAVVVSDVDPYTVVAGIPAKFIKKV 219 I + V +G+ A V+ G+ +GKG+ VAAGA V DV P+ +VAG+PA+ K+V Sbjct: 159 --------IHEGVFIGSGATVIPGISIGKGAYVAAGACVTKDVPPHVMVAGVPARVKKEV 210 Score = 24.3 bits (51), Expect = 0.002 Identities = 13/43 (30%), Positives = 19/43 (44%) Query: 94 VEPGAVIRDLVKIGDGAVIMMGAIINVGAVIGEKTMIDMNAVI 136 + PG I V I +G I GA + G IG+ + A + Sbjct: 147 ISPGVTIAGNVHIHEGVFIGSGATVIPGISIGKGAYVAAGACV 189 Lambda K H 0.319 0.138 0.382 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: 112 Number of extensions: 9 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 238 Length of database: 211 Length adjustment: 22 Effective length of query: 216 Effective length of database: 189 Effective search space: 40824 Effective search space used: 40824 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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