Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_020564901.1 A3OW_RS0118260 homoserine O-succinyltransferase
Query= SwissProt::G3ISL7 (354 letters) >NCBI__GCF_000372865.1:WP_020564901.1 Length = 354 Score = 618 bits (1594), Expect = 0.0 Identities = 294/354 (83%), Positives = 322/354 (90%) Query: 1 MPLVAHTDLPTFQRLREEGEEILDPDRASNQDIREMHIGLLNMMPDAALEATERQFFRLV 60 MPLVAHT+LPTFQRLREEGE IL PDRAS+QDIREMHIGLLN+MPDAALEATERQFFRLV Sbjct: 1 MPLVAHTELPTFQRLREEGETILAPDRASHQDIREMHIGLLNIMPDAALEATERQFFRLV 60 Query: 61 GACNQIVQFHVHPFTIEGLKRSPEAQAHIAKYYESFEQIKRDGLDALIISGANVSHPRLP 120 GACNQI QFHVHPFTI+GL RS A+AHIAKYYE FE+IK DGLDALIISGANV+ P L Sbjct: 61 GACNQIAQFHVHPFTIDGLPRSDAAKAHIAKYYEPFEKIKEDGLDALIISGANVTRPHLQ 120 Query: 121 EEDFWQPLSEVFFWAKENVTSILCSCLATHALIQYCYGIERTRLPAKRWGVFSHKLTDRT 180 EEDFW PL+EVF WAKENVTS+LCSCLATHALIQYCYGIERTRLP KRWGVFSHKLTDRT Sbjct: 121 EEDFWMPLTEVFSWAKENVTSVLCSCLATHALIQYCYGIERTRLPGKRWGVFSHKLTDRT 180 Query: 181 HPLVAEINTRFDVPHSRFNEIFQSDMERHGLKVLAVSKEAGVHLAVSPDGFRIVFFQGHP 240 HPLVAEINTRFDVPHSRFNEIFQ+DMER GLKVLAVSKEAGVHLAVS DGFRIVFFQGHP Sbjct: 181 HPLVAEINTRFDVPHSRFNEIFQADMERKGLKVLAVSKEAGVHLAVSSDGFRIVFFQGHP 240 Query: 241 EYDDISLLKEYKREILRFYRAERDDYPPFPENYFNDVVQQILVDYEQRVRSAKQSGQRLE 300 EYD+ISLLKEYKRE+LR+YR E +DYPPFPENYFN+ +QI Y V SA+++G+ LE Sbjct: 241 EYDEISLLKEYKREVLRYYRREIEDYPPFPENYFNEEARQIFTVYRDHVVSARRNGRELE 300 Query: 301 EFPESLILEHIDNTWSDTAKAVFNNWLGKIYQLTHQERGLPFMDGVDPNNPLGL 354 FPE+ +LEHIDNTW DTAKAVFNNWLGK+YQLT+Q+R LPFM+G+DP+NPLGL Sbjct: 301 PFPENRVLEHIDNTWRDTAKAVFNNWLGKVYQLTNQDRRLPFMEGIDPDNPLGL 354 Lambda K H 0.322 0.138 0.424 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: 608 Number of extensions: 17 Number of successful extensions: 1 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: 354 Length of database: 354 Length adjustment: 29 Effective length of query: 325 Effective length of database: 325 Effective search space: 105625 Effective search space used: 105625 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: 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