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_084275459.1 B8779_RS05065 acyl-ACP--UDP-N-acetylglucosamine O-acyltransferase
Query= curated2:A7HJ58 (249 letters) >NCBI__GCF_900176045.1:WP_084275459.1 Length = 257 Score = 53.1 bits (126), Expect = 5e-12 Identities = 36/111 (32%), Positives = 56/111 (50%), Gaps = 3/111 (2%) Query: 118 IGNNAVIMMGAVINLGAIIGEG-TMIDMNTVIGARARIGKYCHIGAGSVIAGVVEPPSAQ 176 IG N +I IN G G G T+I N ++ A + C IG ++A A Sbjct: 80 IGKNNIIREFCFINPGTEGGGGKTVIGDNNLLMAYVHVAHDCIIGNNCILANAAT--LAG 137 Query: 177 PVIIEDNVVIGANAVILEGVRVGEHSVVAAGAVVVEDVPPYTVVAGVPAKV 227 V + D VVIG I + V +G+++++A + V +D+PPY + G AK+ Sbjct: 138 HVELGDFVVIGGMTPIHQFVHIGDYAMIAGASAVSQDIPPYCLAEGNRAKL 188 Score = 37.7 bits (86), Expect = 2e-07 Identities = 26/108 (24%), Positives = 49/108 (45%), Gaps = 2/108 (1%) Query: 106 IEPGAIIREYVEIGNNAVIMMGAVINLGAIIGEGTMIDMNTVIGARARIGKYCHIGAGSV 165 I P AI++ +IG N I A ++ A+I + I +I + RIG+ + +V Sbjct: 2 IHPTAIVKPGAQIGKNVNIGAYAFVSKDAVIEDEVTIMQGAIIDGKTRIGEGTKVFYNAV 61 Query: 166 IAGVVEPPSAQPVIIEDNVVIGANAVILEGVRVGEHSVVAAGAVVVED 213 + + + + +E ++IG N +I E + + G V+ D Sbjct: 62 VGSIPQDLKFKGEEVE--LIIGKNNIIREFCFINPGTEGGGGKTVIGD 107 Score = 28.5 bits (62), Expect = 1e-04 Identities = 25/82 (30%), Positives = 33/82 (40%), Gaps = 20/82 (24%) Query: 129 VINLGAIIGEGTMIDMNTVIGARARIGKYCHIGAGSVIAGVVEPPSAQPVIIEDNVVIGA 188 +I+ AI+ G I N IGA A + K +IED V I Sbjct: 1 MIHPTAIVKPGAQIGKNVNIGAYAFVSK--------------------DAVIEDEVTIMQ 40 Query: 189 NAVILEGVRVGEHSVVAAGAVV 210 A+I R+GE + V AVV Sbjct: 41 GAIIDGKTRIGEGTKVFYNAVV 62 Score = 27.3 bits (59), Expect = 3e-04 Identities = 14/58 (24%), Positives = 28/58 (48%) Query: 111 IIREYVEIGNNAVIMMGAVINLGAIIGEGTMIDMNTVIGARARIGKYCHIGAGSVIAG 168 ++ YV + ++ +I ++ A + + VIG I ++ HIG ++IAG Sbjct: 110 LLMAYVHVAHDCIIGNNCILANAATLAGHVELGDFVVIGGMTPIHQFVHIGDYAMIAG 167 Lambda K H 0.318 0.137 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: 211 Number of extensions: 25 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 7 Number of HSP's successfully gapped: 4 Length of query: 249 Length of database: 257 Length adjustment: 24 Effective length of query: 225 Effective length of database: 233 Effective search space: 52425 Effective search space used: 52425 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: 41 (21.6 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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