Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_058932725.1 AU252_RS03655 homoserine O-acetyltransferase
Query= SwissProt::Q4ZZ78 (379 letters) >NCBI__GCF_001484605.1:WP_058932725.1 Length = 369 Score = 277 bits (708), Expect = 4e-79 Identities = 156/344 (45%), Positives = 209/344 (60%), Gaps = 13/344 (3%) Query: 24 LALACGRSLPAYDLIYETYGQLNAARSNAVLICHALSGHHHAAGFHSADDRKPGWWDSCI 83 L L G LP L YET+G LNA SNAVLI HAL+G H D +PGWW+ Sbjct: 22 LELEAGGYLPEVTLGYETWGTLNADGSNAVLIEHALTGSTHVT---RGDSDEPGWWEQLA 78 Query: 84 GPGKPIDTTKFFVVSLNNLGGCNGSTGPSSIDPDTGKPFGANFPVVTVEDWVNSQARLAD 143 GPG P+DT +FFVVS+N +GGC GSTGPSS+ PD GKP+G+ FP+VT+ D ++ARLAD Sbjct: 79 GPGAPVDTDRFFVVSINIVGGCYGSTGPSSVAPD-GKPWGSRFPLVTLRDTTAAEARLAD 137 Query: 144 LLGIDTWAAVIGGSLGGMQALQWTISYPNRVRHCLAIASAPKLSAQNIAFNEVARQAILT 203 LGI +W AV+GGS+GG +AL+W ++YP RV+ C I+ +A+ IAF + AI Sbjct: 138 QLGIPSWYAVLGGSMGGARALEWAVTYPERVQRCAVISIGAASTAEQIAFAQAQTLAIRQ 197 Query: 204 DPEFHGGSFQERGVIPKRGLMLARMVGHITYLSDDSMGEKFGRGLKSEKLNYDFHSV--- 260 D F+ G + G +P+ GL LAR + HITY S + +FGR + + + ++ Sbjct: 198 DSNFNDGDYY-GGPLPEDGLALARRIAHITYRSAEEFHGRFGRSAQHPESPFQAAALGER 256 Query: 261 -EFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAANFNDDLAKTFANATARFCVMS 319 +QVESYL +QG++ RFDAN+Y+ +T AL D L + ATARF V + Sbjct: 257 GRYQVESYLDHQGKKLVRRFDANSYIAITDALMSHD-VCRGRGSLNEALGRATARFFVAA 315 Query: 320 FTTDWRFSPARSRELVDALMAARKDVCYLEIDAPQGHDAFLIPI 363 +D + P++SREL DAL DV I+AP GHD FL I Sbjct: 316 VDSDRLYFPSQSRELADALPG---DVDVHVIEAPIGHDGFLTEI 356 Lambda K H 0.321 0.137 0.428 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: 368 Number of extensions: 25 Number of successful extensions: 7 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: 379 Length of database: 369 Length adjustment: 30 Effective length of query: 349 Effective length of database: 339 Effective search space: 118311 Effective search space used: 118311 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 (21.9 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