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 Dsui_2684 Dsui_2684 UDP-3-O-(3-hydroxymyristoyl) glucosamine N-acyltransferase
Query= curated2:B1L0V4 (236 letters) >FitnessBrowser__PS:Dsui_2684 Length = 328 Score = 51.2 bits (121), Expect = 2e-11 Identities = 37/111 (33%), Positives = 52/111 (46%), Gaps = 15/111 (13%) Query: 95 IEPGAIIRDKVIIGENSVIMMGAVINIGAEIGEGTMVDMNAVVGARGKLGKNVHLGAGAV 154 + P ++ V +GE VI G VI GA IG+G+++ N V A ++GK + AGAV Sbjct: 102 VHPSVVLGQDVQLGEGVVIHAGCVIGDGASIGDGSVLHPNVTVYAGCRIGKRALIHAGAV 161 Query: 155 VA-----------GVLEPPSSDPCTIEDNVLIGANAVI----LEGIKIGKG 190 + L+ P I D+V IGAN I +E IG G Sbjct: 162 IGADGFGFAKDGEAWLKIPQVGRVIIGDDVEIGANTTIDRGAIEDTVIGDG 212 Score = 36.6 bits (83), Expect = 6e-07 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 8/74 (10%) Query: 129 TMVDMNAVVGARGKLGKNVHLGAGAVVAGVLEPPSSDPCTIEDNVLIGANAVILEGIKIG 188 T V + V+G +LG+ V + AG V+ D +I D ++ N + G +IG Sbjct: 100 TPVHPSVVLGQDVQLGEGVVIHAGCVIG--------DGASIGDGSVLHPNVTVYAGCRIG 151 Query: 189 KGSVVAAGSIVTTD 202 K +++ AG+++ D Sbjct: 152 KRALIHAGAVIGAD 165 Score = 33.9 bits (76), Expect = 4e-06 Identities = 27/103 (26%), Positives = 45/103 (43%), Gaps = 24/103 (23%) Query: 100 IIRDKVIIGENSVIMMGA----VINIGAEIGEGTMVDMNAVVG------------ARGKL 143 II D V IG N+ I GA VI G ++ V N V+G ++ Sbjct: 186 IIGDDVEIGANTTIDRGAIEDTVIGDGVKLDNQIQVGHNVVIGDHAAMAGCVGIAGSARI 245 Query: 144 GKNVHLGAGAVVAGVLEPPSSDPCTIEDNVLIGANAVILEGIK 186 G+ +G GA++ G LE + D+V + + ++ + +K Sbjct: 246 GRRCTVGGGAIILGHLE--------LGDDVHVSSGTLVAKSLK 280 Score = 33.1 bits (74), Expect = 7e-06 Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 4/76 (5%) Query: 87 DMLKINARIEPGAIIRDKVIIGENSVIMMGAVINIGAEIGEGTMVDMNAVVGARGKLGKN 146 D +K++ +I+ G V+IG+++ + I A IG V A++ +LG + Sbjct: 211 DGVKLDNQIQVG----HNVVIGDHAAMAGCVGIAGSARIGRRCTVGGGAIILGHLELGDD 266 Query: 147 VHLGAGAVVAGVLEPP 162 VH+ +G +VA L+ P Sbjct: 267 VHVSSGTLVAKSLKQP 282 Score = 23.5 bits (49), Expect = 0.005 Identities = 12/42 (28%), Positives = 20/42 (47%) Query: 162 PSSDPCTIEDNVLIGANAVILEGIKIGKGSVVAAGSIVTTDV 203 P + +V +G VI G IG G+ + GS++ +V Sbjct: 101 PVHPSVVLGQDVQLGEGVVIHAGCVIGDGASIGDGSVLHPNV 142 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: 221 Number of extensions: 27 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 7 Number of HSP's successfully gapped: 5 Length of query: 236 Length of database: 328 Length adjustment: 25 Effective length of query: 211 Effective length of database: 303 Effective search space: 63933 Effective search space used: 63933 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: 47 (22.7 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