Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_068170716.1 HTA01S_RS10920 homoserine O-acetyltransferase
Query= SwissProt::B7X2B6 (409 letters) >NCBI__GCF_001592305.1:WP_068170716.1 Length = 391 Score = 588 bits (1516), Expect = e-173 Identities = 292/395 (73%), Positives = 328/395 (83%), Gaps = 20/395 (5%) Query: 4 IATPQFMHFDEPLPLQSGGSIADYDLAFETYGQLNADKSNAIVVCHALNASHHVAGSY-- 61 I TPQ FD PLPL+SG ++ Y+L ETYG LNAD+SNA++VCHALNASHHVAG + Sbjct: 2 IVTPQTFRFDTPLPLKSGATLPAYELVVETYGTLNADRSNAVLVCHALNASHHVAGWHAD 61 Query: 62 -EGQP--KSEGWWDNMIGPGKPVDTDKFFVIGINNLGSCFGSTGPMHTNPATGKPYGADF 118 GQP +SEGWW +MIGP K VDTDK+FVIG+NNLGSCFGSTGP HTNPATG+P+GADF Sbjct: 62 ANGQPLPRSEGWWHSMIGPSKAVDTDKWFVIGVNNLGSCFGSTGPTHTNPATGQPWGADF 121 Query: 119 PVVTVEDWVDAQARLLDRLGIQTLAAVLGGSLGGMQALSWSLRYPERMRHAVVVASAPNL 178 PVVTVEDWV+AQARLLD +GI+ LAAV+GGSLGGMQ LSW+L+YPER+RHA+VVASAPNL Sbjct: 122 PVVTVEDWVNAQARLLDVMGIEQLAAVMGGSLGGMQTLSWTLQYPERVRHAIVVASAPNL 181 Query: 179 NAENIAFNEVARRAIVTDPDFNGGHFYEHGVVPARGLRIARMVGHITYLSDDVMNQKFGR 238 AENIAFNEVARRAIVTDPDF+GGH+ G +P RGLRIARM+GHITYLSDDVMN+KFGR Sbjct: 182 TAENIAFNEVARRAIVTDPDFHGGHYLREGTLPRRGLRIARMIGHITYLSDDVMNEKFGR 241 Query: 239 SLRAPTLPAARGSLPPEGTDPTRGGPASDRRDYLYSTQDVEFQIESYLRYQGEKFSGYFD 298 SLR G DP + Y Y+TQDVEFQIESYLRYQG+KFS YFD Sbjct: 242 SLRT-----------ANGDDPADTAELA----YRYTTQDVEFQIESYLRYQGDKFSEYFD 286 Query: 299 ANTYLLITRALDYFDPARCHDGDLTRALAVAKARFLLVSFTTDWRFAPARSREIVKSLLE 358 ANTYLLITRALDYFDPAR H G L+ ALA AKARFLLVSFTTDWRF+PARSRE+VK+LLE Sbjct: 287 ANTYLLITRALDYFDPAREHGGSLSAALARAKARFLLVSFTTDWRFSPARSREMVKALLE 346 Query: 359 NNRDVSYAEIDAPHGHDAFLLDDPRYMSVMRSYFE 393 N RDVSYAEIDAPHGHDAFLLDDPRY +R+YFE Sbjct: 347 NGRDVSYAEIDAPHGHDAFLLDDPRYHQAVRAYFE 381 Lambda K H 0.320 0.137 0.417 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: 671 Number of extensions: 21 Number of successful extensions: 3 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: 409 Length of database: 391 Length adjustment: 31 Effective length of query: 378 Effective length of database: 360 Effective search space: 136080 Effective search space used: 136080 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