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_013645859.1 METBO_RS11340 gamma carbonic anhydrase family protein
Query= curated2:B1L0V4 (236 letters) >NCBI__GCF_000191585.1:WP_013645859.1 Length = 161 Score = 68.2 bits (165), Expect = 9e-17 Identities = 48/130 (36%), Positives = 67/130 (51%), Gaps = 18/130 (13%) Query: 98 GAIIRDKVIIGENSVIMMGAVINIGAE---IGEGTMVDMNAVV----GARGKLGKNVHLG 150 G+++ V I E S + AVI E IG+ + V N V+ G +G V +G Sbjct: 13 GSVVNGNVSIDEKSSVWYNAVIRGDIEPIKIGKCSNVQDNCVLHSSKGYPLTIGNKVSVG 72 Query: 151 AGAVVAGVLEPPSSDPCTIEDNVLIGANAVILEGIKIGKGSVVAAGSIVTT--DVPENVV 208 AV+ G C IEDN LIG NA +L G I K S+V AG++VT + PEN + Sbjct: 73 HAAVLHG---------CDIEDNCLIGMNATVLNGALIRKNSIVGAGALVTENHEFPENSL 123 Query: 209 VAGAPAKIIK 218 + G PAK ++ Sbjct: 124 ILGVPAKAVR 133 Score = 30.8 bits (68), Expect = 2e-05 Identities = 29/109 (26%), Positives = 50/109 (45%), Gaps = 8/109 (7%) Query: 29 EGELSNCDFTNIEKFNSGDLYILFGESEEILVIIEKNKDKIKNCRIEQDRRKSAIPLLDM 88 EG + N + + EK + ++ G+ E I I K + NC + + PL Sbjct: 12 EGSVVNGNVSIDEKSSVWYNAVIRGDIEPIK--IGKCSNVQDNCVLHSSK---GYPLTIG 66 Query: 89 LKIN---ARIEPGAIIRDKVIIGENSVIMMGAVINIGAEIGEGTMVDMN 134 K++ A + G I D +IG N+ ++ GA+I + +G G +V N Sbjct: 67 NKVSVGHAAVLHGCDIEDNCLIGMNATVLNGALIRKNSIVGAGALVTEN 115 Score = 23.9 bits (50), Expect = 0.002 Identities = 12/44 (27%), Positives = 25/44 (56%), Gaps = 6/44 (13%) Query: 88 MLKINARIEPGAIIRDKVIIGENSVIMMGAVINIGAEIGEGTMV 131 ++ +NA + GA+IR +NS++ GA++ E E +++ Sbjct: 87 LIGMNATVLNGALIR------KNSIVGAGALVTENHEFPENSLI 124 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: 125 Number of extensions: 9 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 236 Length of database: 161 Length adjustment: 20 Effective length of query: 216 Effective length of database: 141 Effective search space: 30456 Effective search space used: 30456 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: 44 (21.6 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