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 WP_057508416.1 ABB28_RS09435 acyltransferase
Query= SwissProt::O34981 (236 letters) >NCBI__GCF_001431535.1:WP_057508416.1 Length = 201 Score = 72.8 bits (177), Expect = 5e-18 Identities = 51/140 (36%), Positives = 71/140 (50%), Gaps = 18/140 (12%) Query: 103 QVEIGDNAVIMM-----GASINIGSVIGEGTMIDMNVVLGGRATV--GKNCHIGAGSVLA 155 +V +G + + M G + IG +I+ V L GR V G N ++ + + Sbjct: 47 KVAVGQDTHVSMRWFVTGYPVRANVTIGNNCVINREVYLDGRVGVHIGNNVNVSFQTCIL 106 Query: 156 GVIEPPSA-------KPVVIEDDVVIGANAVVLEGVTVGKGAVVAAGAIVVNDVEPYTVV 208 + ++ V I+D V IGA A +L GVTVG+GAV+AAGA+V DV Y VV Sbjct: 107 SLHHDHNSPDFIAVGSAVTIQDHVWIGARATILPGVTVGEGAVIAAGAVVARDVPAYDVV 166 Query: 209 AGTPAKKI----KDIDEKTK 224 G PAKKI +DI TK Sbjct: 167 GGVPAKKIGERNRDIRYLTK 186 Score = 28.9 bits (63), Expect = 8e-05 Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 4/43 (9%) Query: 100 IRDQVEIGDNAVIMMGASINIGSVIGEGTMIDMNV----VLGG 138 I+D V IG A I+ G ++ G+VI G ++ +V V+GG Sbjct: 126 IQDHVWIGARATILPGVTVGEGAVIAAGAVVARDVPAYDVVGG 168 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: 108 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 236 Length of database: 201 Length adjustment: 22 Effective length of query: 214 Effective length of database: 179 Effective search space: 38306 Effective search space used: 38306 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: 45 (21.9 bits)
This GapMind analysis is from Apr 10 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