Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_084143800.1 METAC_RS0119490 hypothetical protein
Query= SwissProt::C4XNQ9 (397 letters) >NCBI__GCF_000427445.1:WP_084143800.1 Length = 395 Score = 122 bits (307), Expect = 1e-32 Identities = 109/359 (30%), Positives = 162/359 (45%), Gaps = 42/359 (11%) Query: 33 VESGRALGPVVLAYETCGQLNERADNAVLVLHALTGDSHAAGYYEPGDAKPGWWDLMIGP 92 +E+G A+ + LAY T G+L+ DNA+L +G + +GP Sbjct: 71 LEAGGAIRGLKLAYVTFGKLSPGKDNAILFPTWYSGTTKNLE------------QAYVGP 118 Query: 93 GKPIDTDRYYVICSNVIGGCMGSTGPSSLDPATGQPYGLT-FPVITIGDMVRAQKRL-VE 150 G+ +D +Y++I N IG + S+ PS+ P P+ FP IGD VRAQ RL VE Sbjct: 119 GRALDPSKYFIILVNQIGNGLSSS-PSTAPP----PFNAARFPRARIGDDVRAQHRLIVE 173 Query: 151 HLGVTKLLSVVGGSMGGMQALEWSVRYPDMVRTAVPLATTTKHSALAIAFNEVARQAIMA 210 GV +L V+G SMG Q EW+VR+PD V A P+A TT+ S + AI + Sbjct: 174 RFGVERLALVLGASMGAQQTYEWAVRFPDAVARAAPIAGTTRTSPHNRLLLDNFIAAIAS 233 Query: 211 DPNWNGGNYYDGVPPAHGLAVGRMIGHITYLSDEAMRQKFDRRLQDRCENSFVLEEPDFQ 270 DP W+GG Y D GL + + + + Q R+L FV +E DF Sbjct: 234 DPAWDGGWYADASAVHRGLRRHARLFALNGFTPDLYAQALWRKL------GFVSDE-DFL 286 Query: 271 ---VESYLRYQGQKFVDRFDANSFLYITKAADYFNLEASHGCGSAVAAFAKAKCRYLVAS 327 VE + Q D N +++ + ++ + G G +A A+ K R V + Sbjct: 287 TGFVEGHFLPQ--------DPNDLIFLARKWRDNDVSRAGG-GDKASALARIKARTFVIA 337 Query: 328 FSSDWLYPTYQSRSMVQAMKKNGLDVSFVELEAKWGHDAFLLPNARLSGMIARFLDRAL 386 D +P + ++A +K + L +KWGH A L + I FL L Sbjct: 338 IEEDGFFPL----ADIEAEQKLIANSELKTLSSKWGHLALLGVDPGYDARIDAFLKELL 392 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: 387 Number of extensions: 21 Number of successful extensions: 5 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: 397 Length of database: 395 Length adjustment: 31 Effective length of query: 366 Effective length of database: 364 Effective search space: 133224 Effective search space used: 133224 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