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_051622996.1 P166_RS0105490 acetyltransferase
Query= curated2:Q8TY70 (245 letters) >NCBI__GCF_000711315.1:WP_051622996.1 Length = 224 Score = 80.1 bits (196), Expect = 3e-20 Identities = 53/174 (30%), Positives = 94/174 (54%), Gaps = 16/174 (9%) Query: 59 VIGEHDDVVEVLESEDSVEYYHKELDHRNRAVPLADYSEFEDVR------IEPGAIIREK 112 VIG D + E+L++ + +++H AV + +++ + + + P A + Sbjct: 48 VIGTDDHLSELLKTTQNCVITVGQIEHA--AVRKSLFAKVKKLGGQLPSIVSPLARVARS 105 Query: 113 VKLGKGVVVMMGAVINIGAKIGDGTMVDMNAVVGSRAEVGKNVHIGAGAVIAGVLEPPSA 172 +LG+GVVVM A++N A IGD ++++ A+V A VGK+ HI A + G +E Sbjct: 106 ARLGEGVVVMHHAIVNHFASIGDNSIINHKALVEHGALVGKHCHISTSATLNGDVE---- 161 Query: 173 KPVVIEDDVVIGANAVILEGVRVGKGAVVAAGAVVTEDVPPSKVVAGVPARVVK 226 + D+ +G+ AV+++GV + + ++V AGAVVT + V G PA + K Sbjct: 162 ----VSDECFVGSGAVLVQGVMIPENSLVGAGAVVTHHLQTPGVYVGCPAVLKK 211 Score = 22.3 bits (46), Expect = 0.008 Identities = 11/44 (25%), Positives = 22/44 (50%) Query: 163 IAGVLEPPSAKPVVIEDDVVIGANAVILEGVRVGKGAVVAAGAV 206 I G++E P A+ + VIG + + E ++ + V+ G + Sbjct: 29 IVGIVEAPGAETKSLLGYPVIGTDDHLSELLKTTQNCVITVGQI 72 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: 123 Number of extensions: 12 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 245 Length of database: 224 Length adjustment: 23 Effective length of query: 222 Effective length of database: 201 Effective search space: 44622 Effective search space used: 44622 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