Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_086511565.1 BZY95_RS19555 homoserine acetyltransferase
Query= SwissProt::D3P9D1 (377 letters) >NCBI__GCF_002151265.1:WP_086511565.1 Length = 410 Score = 226 bits (576), Expect = 9e-64 Identities = 135/374 (36%), Positives = 204/374 (54%), Gaps = 16/374 (4%) Query: 7 GLVKTKYVTFKDDFYFESGRILSPITVAYETYGKLNEKKDNAILICHALTGSAHAAGYNS 66 GLV+ K V D++ G ++P+ + +E YG LNE++DN ILI H +G++HAAG + Sbjct: 42 GLVE-KQVFELDEYTTVGGDTIAPVRIGWEAYGTLNEERDNVILITHFFSGTSHAAGRYT 100 Query: 67 PDDQKPGWWDDMIGPGKAFDTDKYFIICSNFLGSC------YGTTGPASIDPSTGKPYGL 120 DD PG+WD +IGPGK DTD+Y+II S+ L + TTGPA+ +P TG+P+G Sbjct: 101 EDDAAPGYWDAIIGPGKPLDTDEYYIISSDTLVNLNVHDPNVTTTGPATPNPETGEPWGT 160 Query: 121 KFPVFTVKDMVKLQKKLIDYLGIEKLLCVAGGSMGGMQALEWAVTFPEKTYSIIPIATAG 180 FP+ T++D V++QK L++ GIE+L V G SMG +QA EWA T+PE+ +IP+ G Sbjct: 161 DFPLVTIRDFVEVQKALLESQGIERLHAVMGPSMGALQAYEWASTYPERVERLIPVIGGG 220 Query: 181 RITPMAIAFNTIGRFAIMKDPNWMNGDYYGKTFPRDGL-----AIARMAGHITYMSDKSF 235 P +A + I D NW GDYY P DGL + A H + ++++F Sbjct: 221 VADPWLLATLSAWAAPIRLDANWNEGDYYDSEPPLDGLREALKLVTLNANHWLW-ANETF 279 Query: 236 HKKFGRRYATFGGIYDFFGYFEVENYLRYNGYKFTERFDANSYLYIIKAMDIFDLSYGYG 295 + + A + + +E L E DAN LY++KA F +G G Sbjct: 280 DRSWADEDA--DPTRELDARYAIEQTLDDIAAARAELADANHLLYLVKANQSFIAGHG-G 336 Query: 296 SYEEAIGRIEADSLFITFTSDFLFPSYQTEEIVNIMKNHGKNPEWVNIESDYGHDAFLLE 355 S EE +GRIEA +L + +D +F + ++++ G + E V +E GH +L Sbjct: 337 SLEEGLGRIEAPTLILYSENDLVFAPEGVRQTAELIEDGGADVELVTLEGKRGHLDGILA 396 Query: 356 FDTQTSCIKEFLSK 369 D I+ FL++ Sbjct: 397 IDQAGERIRAFLAE 410 Lambda K H 0.321 0.140 0.432 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: 402 Number of extensions: 23 Number of successful extensions: 4 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: 377 Length of database: 410 Length adjustment: 31 Effective length of query: 346 Effective length of database: 379 Effective search space: 131134 Effective search space used: 131134 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: 50 (23.9 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