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 WP_013451244.1 CALNI_RS05615 gamma carbonic anhydrase family protein
Query= curated2:B1L0V4 (236 letters) >NCBI__GCF_000183405.1:WP_013451244.1 Length = 178 Score = 57.0 bits (136), Expect = 2e-13 Identities = 40/133 (30%), Positives = 69/133 (51%), Gaps = 27/133 (20%) Query: 103 DKVIIGENSVIMMGAVINIGAEIGEGTMVDMNAVVGARGKLGKNVHLGAGAVVAGVLEPP 162 ++V IGE S + G VI++ D + +GKNV +G A + G Sbjct: 49 ERVEIGECSNVQDGTVIHVTK--------DKYPTI-----IGKNVTIGHNATLHG----- 90 Query: 163 SSDPCTIEDNVLIGANAVILEGIKIGKGSVVAAGSIVTTD--VPENVVVAGAPAKIIKEV 220 C I+DNVL+G A+IL+ I + +++AAG++V + P N ++ G+P K++K + Sbjct: 91 ----CKIKDNVLVGIGAIILDNTVISENTIIAAGTLVPPNKTFPPNSLIMGSPGKVVKTL 146 Query: 221 DVKTKDKTKLLDD 233 T ++ K + D Sbjct: 147 ---TGEEIKSITD 156 Score = 29.6 bits (65), Expect = 4e-05 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 7/57 (12%) Query: 98 GAIIRDKVIIGENSVIMMGAVINIGAEIGEGTMVDMN-------AVVGARGKLGKNV 147 G I+D V++G ++I+ VI+ I GT+V N ++G+ GK+ K + Sbjct: 90 GCKIKDNVLVGIGAIILDNTVISENTIIAAGTLVPPNKTFPPNSLIMGSPGKVVKTL 146 Lambda K H 0.315 0.137 0.374 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: 136 Number of extensions: 9 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: 236 Length of database: 178 Length adjustment: 21 Effective length of query: 215 Effective length of database: 157 Effective search space: 33755 Effective search space used: 33755 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 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