Align Homoserine O-acetyltransferase; HAT; EC 2.3.1.31; Homoserine transacetylase; HTA (uncharacterized)
to candidate WP_012046107.1 BBTA_RS29210 hypothetical protein
Query= curated2:B3QZ51 (378 letters) >NCBI__GCF_000015165.1:WP_012046107.1 Length = 363 Score = 86.3 bits (212), Expect = 1e-21 Identities = 62/185 (33%), Positives = 95/185 (51%), Gaps = 22/185 (11%) Query: 30 GGTLPEYRVAYRSWGKLNKSGDNAILICHALTGSADADIWWAP----LFGEGKTFDETKD 85 G TLPE ++ Y + G+ +L+ H TG + A + AP LFG+ + D TK Sbjct: 52 GETLPELKLHYTTVGEPT---GQPVLVLHG-TGGSGASMLVAPFAGELFGKDQPLDATKY 107 Query: 86 FIVCSNVLGSCYGTTGPASINPETGKRFGPDFPSFTIRDMVRVQRSLLN-ALGVKKLKMV 144 +I+ + +G +G + S +TG FP++ DMV Q LL LG+K L++V Sbjct: 108 YIIIPDSIG--HGKSSKPSDGLKTG------FPAYDYADMVDAQHRLLTEGLGIKHLRLV 159 Query: 145 IGGSLGGMQALEWCAMYPDFVETQVTIASSGKHSA---WCIGLSEAQRQAICADENWNGG 201 IG S+GGM + W YPDF++ V +AS A W L + I D +++GG Sbjct: 160 IGNSMGGMHSWVWATRYPDFMDIAVPMASQPTEMAARNWM--LRRIMLETIRNDPDYSGG 217 Query: 202 HYTPE 206 +YT + Sbjct: 218 NYTTQ 222 Lambda K H 0.320 0.135 0.411 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: 327 Number of extensions: 15 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 378 Length of database: 363 Length adjustment: 30 Effective length of query: 348 Effective length of database: 333 Effective search space: 115884 Effective search space used: 115884 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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