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 350000 BT0472 putative acyltransferase in colanic acid biosynthesis (NCBI ptt file)
Query= curated2:Q9K9H8 (240 letters) >FitnessBrowser__Btheta:350000 Length = 252 Score = 70.5 bits (171), Expect = 3e-17 Identities = 43/130 (33%), Positives = 70/130 (53%), Gaps = 15/130 (11%) Query: 104 VEIGDNAVIMMGASINI--------GSVIGEGTMIDMN---VVLGGRATVGKNCHIGAGS 152 V++ N+V+ G+ I GSV+G+ +++D + +G + N + G Sbjct: 106 VKMEKNSVLYYGSEIRAPWMLMIGKGSVVGDNSILDARRGGIYIGENVNIASNVSLWTGG 165 Query: 153 VLAGVIEPPSAK----PVVVEDDVVIGANCVILEGVTVGKGAVVAAGAVVTEDVPPNTVV 208 S K P+ +++ V IG N IL VT+G+GAV+AAGAVVT+D+PP T+ Sbjct: 166 HDYNDPYFRSMKTNRGPIYIKNRVWIGPNVTILHSVTIGEGAVIAAGAVVTKDIPPFTIC 225 Query: 209 AGTPARVIKE 218 G PA+V+ + Sbjct: 226 GGIPAKVLAQ 235 Score = 26.2 bits (56), Expect = 6e-04 Identities = 11/35 (31%), Positives = 21/35 (60%) Query: 100 IRDQVEIGDNAVIMMGASINIGSVIGEGTMIDMNV 134 I+++V IG N I+ +I G+VI G ++ ++ Sbjct: 185 IKNRVWIGPNVTILHSVTIGEGAVIAAGAVVTKDI 219 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: 132 Number of extensions: 14 Number of successful extensions: 4 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: 240 Length of database: 252 Length adjustment: 24 Effective length of query: 216 Effective length of database: 228 Effective search space: 49248 Effective search space used: 49248 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: 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