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 5210546 Shew_2974 hexapaptide repeat-containing transferase (RefSeq)
Query= curated2:Q9K9H8 (240 letters) >FitnessBrowser__PV4:5210546 Length = 180 Score = 71.6 bits (174), Expect = 1e-17 Identities = 61/183 (33%), Positives = 83/183 (45%), Gaps = 33/183 (18%) Query: 53 EWSEIDAALKANEAKIKDVVVENDRR----NSAIPLLDLKNI-----------KARIEPG 97 E++ +D L++ + E +RR N +P LD K + + P Sbjct: 15 EYNCLDGELQSRWQARQQANAEMNRRGEVDNELLPHLDAKAVVKLPLYISYGQNLHVAPQ 74 Query: 98 AIIRDQVEIGDNAVIMMGASINIGSVIGEGTMIDMNVVLGGRATVGKNCHIGAGSVLAGV 157 I V + DNA I IG TMI NV N + A G Sbjct: 75 VFINVNVTLQDNAPI----------TIGRQTMIGPNV-----QCYTANHPLDAARRCQGW 119 Query: 158 IEPPSAKPVVVEDDVVIGANCVILEGVTVGKGAVVAAGAVVTEDVPPNTVVAGTPARVIK 217 A+ + + + V IG +IL GVT+G AVVAAGAVVT+DVPP TVV G PARVI+ Sbjct: 120 ---ELAEAIHIGERVWIGGGAIILPGVTIGDEAVVAAGAVVTKDVPPKTVVGGNPARVIR 176 Query: 218 EID 220 ++ Sbjct: 177 HLE 179 Lambda K H 0.314 0.135 0.372 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: 114 Number of extensions: 10 Number of successful extensions: 4 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: 240 Length of database: 180 Length adjustment: 21 Effective length of query: 219 Effective length of database: 159 Effective search space: 34821 Effective search space used: 34821 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 (21.9 bits) S2: 45 (21.9 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