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_013450742.1 CALNI_RS03095 serine O-acetyltransferase
Query= curated2:Q8TY70 (245 letters) >NCBI__GCF_000183405.1:WP_013450742.1 Length = 219 Score = 69.3 bits (168), Expect = 6e-17 Identities = 40/108 (37%), Positives = 60/108 (55%), Gaps = 2/108 (1%) Query: 122 MMGAVINIGAKIGDGTMVD--MNAVVGSRAEVGKNVHIGAGAVIAGVLEPPSAKPVVIED 179 + G I+ GAKIG +D M V+G AE+G +V I G + GV + I + Sbjct: 65 LTGIEIHPGAKIGKRFFIDHGMGVVIGETAEIGDDVTIYHGVTLGGVSLNKGKRHPTIGN 124 Query: 180 DVVIGANAVILEGVRVGKGAVVAAGAVVTEDVPPSKVVAGVPARVVKD 227 VVIG+ A +L +VG GA + + +VV ++VP + V G+P RVV + Sbjct: 125 GVVIGSGAKVLGPFKVGDGAKIGSNSVVIKEVPENATVVGIPGRVVTE 172 Score = 44.7 bits (104), Expect = 2e-09 Identities = 36/121 (29%), Positives = 52/121 (42%), Gaps = 20/121 (16%) Query: 101 VRIEPGAIIREKVKLGKGVVVMMGAVINIGAKIGDGTMVDMNAVVGS--------RAEVG 152 + I PGA I ++ + G MG VI A+IGD + +G +G Sbjct: 68 IEIHPGAKIGKRFFIDHG----MGVVIGETAEIGDDVTIYHGVTLGGVSLNKGKRHPTIG 123 Query: 153 KNVHIGAGAVIAGVLEPPSAKPVVIEDDVVIGANAVILEGVRVGKGAVVAAGAVVTEDVP 212 V IG+GA + G P + D IG+N+V+++ V V G VVTE Sbjct: 124 NGVVIGSGAKVLG--------PFKVGDGAKIGSNSVVIKEVPENATVVGIPGRVVTESSR 175 Query: 213 P 213 P Sbjct: 176 P 176 Score = 29.6 bits (65), Expect = 5e-05 Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 5/66 (7%) Query: 115 LGKGVVVMMGAVINIGAKIGDGTMVDMNAVVGSRAEVGKNVHIGAGAVIAGVLEPPSAKP 174 +G GVV+ GA + K+GDG + N+VV EV +N + I G + S++P Sbjct: 122 IGNGVVIGSGAKVLGPFKVGDGAKIGSNSVV--IKEVPENATV---VGIPGRVVTESSRP 176 Query: 175 VVIEDD 180 E D Sbjct: 177 QDFEHD 182 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: 146 Number of extensions: 10 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: 245 Length of database: 219 Length adjustment: 23 Effective length of query: 222 Effective length of database: 196 Effective search space: 43512 Effective search space used: 43512 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: 46 (22.3 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