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 14480 b0342 galactoside O-acetyltransferase (NCBI)
Query= curated2:B1IMX1 (236 letters) >FitnessBrowser__Keio:14480 Length = 203 Score = 68.6 bits (166), Expect = 9e-17 Identities = 53/161 (32%), Positives = 79/161 (49%), Gaps = 23/161 (14%) Query: 75 EQDRRKSAIP-LLDMLKVNARIEPGAIIR--DKVLIGEN--AVIMMGAVINIGAEIGEGT 129 E ++R+S I + + NA +EP + IG N A + V + IG+ Sbjct: 43 EVEKRESLIKEMFATVGENAWVEPPVYFSYGSNIHIGRNFYANFNLTIVDDYTVTIGDNV 102 Query: 130 MVDMNAVVGARG-----KLGKNVHLGAGAVVAGVLEPPSSDPCTIEDNVLIGANAVILEG 184 ++ N + G +L KN + S P TI +NV IG++ VI G Sbjct: 103 LIAPNVTLSVTGHPVHHELRKNGEM-------------YSFPITIGNNVWIGSHVVINPG 149 Query: 185 VKIGKGSVVAAGSIVTTDVPENVVVAGAPAKIIKEVDVKTK 225 V IG SV+ AGSIVT D+P NVV AG P ++I+E++ + K Sbjct: 150 VTIGDNSVIGAGSIVTKDIPPNVVAAGVPCRVIREINDRDK 190 Lambda K H 0.315 0.136 0.375 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: 133 Number of extensions: 13 Number of successful extensions: 3 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: 236 Length of database: 203 Length adjustment: 22 Effective length of query: 214 Effective length of database: 181 Effective search space: 38734 Effective search space used: 38734 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 (22.0 bits) S2: 45 (21.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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