Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; Tetrahydrodipicolinate N-acetyltransferase; THP acetyltransferase; Tetrahydropicolinate acetylase; EC 2.3.1.89 (characterized)
to candidate GFF460 Psest_0465 Acetyltransferase (isoleucine patch superfamily)
Query= SwissProt::O34981 (236 letters) >FitnessBrowser__psRCH2:GFF460 Length = 234 Score = 65.1 bits (157), Expect = 1e-15 Identities = 43/134 (32%), Positives = 62/134 (46%), Gaps = 16/134 (11%) Query: 99 IIRDQVEIGDNAVIMMGASINIGSVIGEGTMIDMNVVLGGRATVGKNCHIGAGS------ 152 ++ + V +GD A+ I + I G + ++ + G ++G+ IG S Sbjct: 36 VVEENVRLGDVAIKARDLRIGAYTYIRSGLLQSVSEI-GRFCSIGQEVQIGLSSDAHPLY 94 Query: 153 ---------VLAGVIEPPSAKPVVIEDDVVIGANAVVLEGVTVGKGAVVAAGAIVVNDVE 203 + AG+ I DV IGA +L GVTVG GAV+A GA+V V Sbjct: 95 WLTTHPVHDIAAGLKYDTQKAHARIGHDVWIGAGVKILSGVTVGDGAVIATGAVVTRHVA 154 Query: 204 PYTVVAGTPAKKIK 217 PY +V G PAK IK Sbjct: 155 PYEIVGGNPAKHIK 168 Score = 22.3 bits (46), Expect = 0.009 Identities = 10/43 (23%), Positives = 23/43 (53%) Query: 155 AGVIEPPSAKPVVIEDDVVIGANAVVLEGVTVGKGAVVAAGAI 197 AG+ ++ VV+E++V +G A+ + +G + +G + Sbjct: 24 AGLASLTASAQVVVEENVRLGDVAIKARDLRIGAYTYIRSGLL 66 Lambda K H 0.313 0.134 0.364 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: 111 Number of extensions: 13 Number of successful extensions: 3 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: 236 Length of database: 234 Length adjustment: 23 Effective length of query: 213 Effective length of database: 211 Effective search space: 44943 Effective search space used: 44943 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 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