Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_013521130.1 ALIDE2_RS23390 homoserine O-acetyltransferase
Query= SwissProt::B7X2B6 (409 letters) >NCBI__GCF_000204645.1:WP_013521130.1 Length = 376 Score = 627 bits (1618), Expect = 0.0 Identities = 309/398 (77%), Positives = 339/398 (85%), Gaps = 25/398 (6%) Query: 1 MSFIATPQFMHFDEPLPLQSGGSIADYDLAFETYGQLNADKSNAIVVCHALNASHHVAGS 60 MSFIATPQ MHF E LPL SG SI DY LA+ETYG+LNA+ +NA++VCHALNASHHVAG Sbjct: 1 MSFIATPQSMHFAEALPLSSGASIRDYTLAYETYGRLNAEGTNAVLVCHALNASHHVAGV 60 Query: 61 YEGQPKSEGWWDNMIGPGKPVDTDKFFVIGINNLGSCFGSTGPMHTNPATGKPYGADFPV 120 YEGQP+SEGWWDNMIGPGKPVDT++FFVIG+NNLGSCFGSTGPMH NP TG+ YGADFPV Sbjct: 61 YEGQPRSEGWWDNMIGPGKPVDTNRFFVIGVNNLGSCFGSTGPMHANPDTGEVYGADFPV 120 Query: 121 VTVEDWVDAQARLLDRLGIQTLAAVLGGSLGGMQALSWSLRYPERMRHAVVVASAPNLNA 180 VTVEDWV+AQARLLDRLG+ LAAV+GGSLGGMQALSW+L+YPERMRHAVVVASAPNL A Sbjct: 121 VTVEDWVNAQARLLDRLGVGQLAAVMGGSLGGMQALSWTLQYPERMRHAVVVASAPNLTA 180 Query: 181 ENIAFNEVARRAIVTDPDFNGGHFYEHGVVPARGLRIARMVGHITYLSDDVMNQKFGRSL 240 ENIAFNEVARRAIVTDPDF+GGHFY HG +P RGLRIARM+GHITYLSDDVMN+KFGR L Sbjct: 181 ENIAFNEVARRAIVTDPDFHGGHFYRHGTIPKRGLRIARMIGHITYLSDDVMNEKFGRQL 240 Query: 241 RAPTLPAARGSLPPEGTDPTRGGPASDRRDYLYSTQDVEFQIESYLRYQGEKFSGYFDAN 300 R EG D YSTQD+EFQIESYLRYQG+KFS YFDAN Sbjct: 241 R-------------EGI------------DLKYSTQDIEFQIESYLRYQGDKFSEYFDAN 275 Query: 301 TYLLITRALDYFDPARCHDGDLTRALAVAKARFLLVSFTTDWRFAPARSREIVKSLLENN 360 TYLLITRALDYFDPA + G L +ALAVA+ARFLLVSFTTDWRF+P RSREIV +LLEN Sbjct: 276 TYLLITRALDYFDPALRYGGSLAQALAVARARFLLVSFTTDWRFSPRRSREIVHALLENR 335 Query: 361 RDVSYAEIDAPHGHDAFLLDDPRYMSVMRSYFEGIAKE 398 RDVSYAEIDAPHGHDAFLLDD RYM V+RSYF+ IA+E Sbjct: 336 RDVSYAEIDAPHGHDAFLLDDVRYMGVVRSYFDNIAQE 373 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: 645 Number of extensions: 18 Number of successful extensions: 2 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: 376 Length adjustment: 31 Effective length of query: 378 Effective length of database: 345 Effective search space: 130410 Effective search space used: 130410 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