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_051335378.1 METAC_RS0104650 bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU
Query= curated2:Q9K9H8 (240 letters) >NCBI__GCF_000427445.1:WP_051335378.1 Length = 456 Score = 41.2 bits (95), Expect = 4e-08 Identities = 37/157 (23%), Positives = 60/157 (38%), Gaps = 34/157 (21%) Query: 94 IEPGAIIRDQVEIGDNAVIMMGASINIGSVIGEGTMIDMNVVLGGRATVGKNCHIG---- 149 +EP + V + + AVI + + G+V+G T I L +G N HIG Sbjct: 288 VEPHVVFGLGVSVAEGAVIRSFSHLE-GAVVGPKTTIGPFARLRPGTDLGPNVHIGNFVE 346 Query: 150 -----------------AGSVLAGVIEPPSAKPVV------------VEDDVVIGANCVI 180 G + G A + + + IG+N + Sbjct: 347 LKAAKVEAGAKINHLSYIGDAVIGAKTNIGAGTITCNYDGFGKFRTEIGEGAFIGSNSAL 406 Query: 181 LEGVTVGKGAVVAAGAVVTEDVPPNTVVAGTPARVIK 217 + V +G GA V +G+V+T DV P+ + G +V K Sbjct: 407 VAPVKIGAGAYVGSGSVITADVAPDALALGRAVQVEK 443 Score = 37.4 bits (85), Expect = 5e-07 Identities = 26/84 (30%), Positives = 36/84 (42%), Gaps = 18/84 (21%) Query: 92 ARIEPGAIIRDQVEIGDNAVIMMGASINIGS---------------VIGEGTMIDMNVVL 136 A++E GA I IGD + GA NIG+ IGEG I N L Sbjct: 350 AKVEAGAKINHLSYIGDAVI---GAKTNIGAGTITCNYDGFGKFRTEIGEGAFIGSNSAL 406 Query: 137 GGRATVGKNCHIGAGSVLAGVIEP 160 +G ++G+GSV+ + P Sbjct: 407 VAPVKIGAGAYVGSGSVITADVAP 430 Lambda K H 0.314 0.135 0.372 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: 249 Number of extensions: 21 Number of successful extensions: 3 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: 240 Length of database: 456 Length adjustment: 28 Effective length of query: 212 Effective length of database: 428 Effective search space: 90736 Effective search space used: 90736 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 (21.9 bits) S2: 49 (23.5 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