Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate Ac3H11_4277 Homoserine O-acetyltransferase (EC 2.3.1.31)
Query= SwissProt::B7X2B6 (409 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4277 Length = 401 Score = 705 bits (1819), Expect = 0.0 Identities = 339/400 (84%), Positives = 365/400 (91%) Query: 1 MSFIATPQFMHFDEPLPLQSGGSIADYDLAFETYGQLNADKSNAIVVCHALNASHHVAGS 60 MSF ATPQ +HF E LPLQSG S+ DY LA+ETYG LNAD+SNA++VCHALNASHHVAG Sbjct: 1 MSFFATPQSLHFPEVLPLQSGASLRDYHLAYETYGTLNADRSNAVLVCHALNASHHVAGV 60 Query: 61 YEGQPKSEGWWDNMIGPGKPVDTDKFFVIGINNLGSCFGSTGPMHTNPATGKPYGADFPV 120 Y GQ KSEGWWDNMIGPGKPVDTD+FFVIG+NNLGSCFGSTGPMH +P TG+ YGADFPV Sbjct: 61 YAGQDKSEGWWDNMIGPGKPVDTDRFFVIGVNNLGSCFGSTGPMHNHPDTGEVYGADFPV 120 Query: 121 VTVEDWVDAQARLLDRLGIQTLAAVLGGSLGGMQALSWSLRYPERMRHAVVVASAPNLNA 180 VTVEDWV+AQARLLDRLGI LAAVLGGSLGGMQALSW+L+YPERMRHAVVVASAPNL A Sbjct: 121 VTVEDWVNAQARLLDRLGITQLAAVLGGSLGGMQALSWTLQYPERMRHAVVVASAPNLTA 180 Query: 181 ENIAFNEVARRAIVTDPDFNGGHFYEHGVVPARGLRIARMVGHITYLSDDVMNQKFGRSL 240 ENIAFNEVARRAIVTDPDF+GGHFY HGV+P RGLRIARM+GHITYLSDDVMN+KFGRSL Sbjct: 181 ENIAFNEVARRAIVTDPDFHGGHFYRHGVIPKRGLRIARMIGHITYLSDDVMNEKFGRSL 240 Query: 241 RAPTLPAARGSLPPEGTDPTRGGPASDRRDYLYSTQDVEFQIESYLRYQGEKFSGYFDAN 300 RAPTLPAARGSLPPEG P RGGPA D RDYLYSTQD+EFQIESYLRYQG+KFS YFDAN Sbjct: 241 RAPTLPAARGSLPPEGAGPARGGPAPDLRDYLYSTQDIEFQIESYLRYQGDKFSDYFDAN 300 Query: 301 TYLLITRALDYFDPARCHDGDLTRALAVAKARFLLVSFTTDWRFAPARSREIVKSLLENN 360 TYLLITRALDYFDPAR H G+LTRALA A A+FLLVSFTTDWRF+P RSREIVK+LL+N Sbjct: 301 TYLLITRALDYFDPARAHGGNLTRALARATAKFLLVSFTTDWRFSPQRSREIVKALLDNR 360 Query: 361 RDVSYAEIDAPHGHDAFLLDDPRYMSVMRSYFEGIAKELK 400 R VSYAEIDAPHGHDAFLLDD RYM VMRSYF+ IAKEL+ Sbjct: 361 RRVSYAEIDAPHGHDAFLLDDARYMGVMRSYFDSIAKELQ 400 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: 719 Number of extensions: 18 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: 409 Length of database: 401 Length adjustment: 31 Effective length of query: 378 Effective length of database: 370 Effective search space: 139860 Effective search space used: 139860 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 09 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