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 3608125 Dshi_1530 transferase hexapeptide repeat containing protein (RefSeq)
Query= curated2:Q032G9 (257 letters) >FitnessBrowser__Dino:3608125 Length = 174 Score = 67.8 bits (164), Expect = 1e-16 Identities = 47/151 (31%), Positives = 77/151 (50%), Gaps = 19/151 (12%) Query: 112 NARIEPGAIIRDQVMIGDNAVIMMGAII---NIGAEIGEGTMIDMGAVL----GGRATVG 164 N + P A + +V++ + + + GA + N +G G+ I VL G T+G Sbjct: 17 NYWVAPDANLIGKVVLEEASSVWFGATLRGDNEEIRLGTGSNIQEACVLHTDMGFPLTIG 76 Query: 165 KNSHIGAGAVLAGVIEPASAEPVRVGDNVLVGANAVVIEGVQVGSGSVVAAGAIVTQ--D 222 N IG A+L G +GD LVG A ++ G ++G G ++ AGA+VT+ + Sbjct: 77 TNCTIGHKAILHGCT---------IGDGSLVGMGATILNGARIGKGCLIGAGALVTESKE 127 Query: 223 VPENVVVAGVPARTIKEIDEKTAQKTALEDA 253 +P+ +V G P + ++ +DE TAQ LE A Sbjct: 128 IPDFSLVMGAPGKVVRTLDE-TAQAGLLESA 157 Lambda K H 0.316 0.134 0.368 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: 15 Number of successful extensions: 6 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: 257 Length of database: 174 Length adjustment: 21 Effective length of query: 236 Effective length of database: 153 Effective search space: 36108 Effective search space used: 36108 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: 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