Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_028489154.1 Q394_RS0109900 homoserine O-succinyltransferase
Query= SwissProt::A0A1D3PDD4 (309 letters) >NCBI__GCF_000621325.1:WP_028489154.1 Length = 361 Score = 148 bits (374), Expect = 2e-40 Identities = 111/337 (32%), Positives = 164/337 (48%), Gaps = 43/337 (12%) Query: 7 MPIKIPDHLPAKEILLKENIFIMDESRAYTQDIRPLKICILNLMPTKQ--ETETQLLRLL 64 MP+ LP E L +E ++ E A+ QDIR L I LN+MP TE Q RL+ Sbjct: 1 MPLVAHTALPTFERLRQEGQTVLSEDYAFNQDIRELHIGFLNMMPDAALAATERQFFRLV 60 Query: 65 GNTPLQVDVSLLHPSTHS--PRNTSKE-HLNLFYKTIDEVKQQKFDGMIITGAPVETLPF 121 G + L + HP T PR+ + +++ Y+ +++++Q D +IITGA Sbjct: 61 GESNLIAQFHI-HPFTLDSLPRSDKAQAYIDQHYEKFEDLRKQGLDALIITGANPSAAHL 119 Query: 122 HDVNYWNEMTSILDWTTTNVTSTLHICWGAQAGLYHHYGIKKKPLTTKLFGVYSHKLEVK 181 D +W + + W NVTSTL C + A + H +GI+++PL K +GVYSH + + Sbjct: 120 EDEPFWEGLCEVAAWAMENVTSTLCSCLASHALVQHLWGIRRRPLGFKRWGVYSHAVTMP 179 Query: 182 NVNLLRGFDDVFYAPHSRHTTVSREDIERVDELIVLSSSEEAGVYIASSKDGKR-VFVMG 240 L+ + F PHSR + R +E V + VL S+EAGV++A S D R +F+ G Sbjct: 180 EHPLVNDLNTRFDVPHSRFNQIDRVQLEAVG-VQVLVESDEAGVHMAVSPDLFRMIFLQG 238 Query: 241 HSEYDAHTLKQEYERDVKR---GIACD-PPF--NY------------------------- 269 H EYD +L +EY R+ R G D PPF NY Sbjct: 239 HPEYDQVSLLKEYRRETMRWFEGAREDYPPFPENYLRPKAKAILNEYRLTQRLAKRQGKP 298 Query: 270 ---FPEGNVDALPPLQWRAHSNLLFSNWLNYYVYQET 303 FPE + ++ WR + + +SNW+ VYQ T Sbjct: 299 LPDFPEALLLSMLHNTWRDTAKVFYSNWIG-KVYQIT 334 Lambda K H 0.319 0.136 0.416 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: 325 Number of extensions: 21 Number of successful extensions: 4 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: 309 Length of database: 361 Length adjustment: 28 Effective length of query: 281 Effective length of database: 333 Effective search space: 93573 Effective search space used: 93573 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