Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_012399486.1 BPHY_RS00305 homoserine O-acetyltransferase
Query= SwissProt::Q2T284 (381 letters) >NCBI__GCF_000020045.1:WP_012399486.1 Length = 381 Score = 704 bits (1818), Expect = 0.0 Identities = 336/381 (88%), Positives = 364/381 (95%) Query: 1 MESIGVVAPHTMHFAEPLRLQSGSVLGNYQLVVETYGELNAARSNAVLVCHALNASHHVA 60 MESIG+V+P TMHF+EPLRLQ+GS L NY LVVETYG+LNAARSNAVLVCHALNASHHVA Sbjct: 1 MESIGIVSPQTMHFSEPLRLQNGSSLANYDLVVETYGKLNAARSNAVLVCHALNASHHVA 60 Query: 61 GVYADDPRSTGWWDNMVGPGKPLDTNRFFVIGVNNLGSCFGSTGPMSIDPATGTPYGARF 120 GVYADDP++ GWWDNMVGPGKPLDTNRFFVIGVNNLGSCFGSTGPMSIDP+TG PYGA F Sbjct: 61 GVYADDPKNVGWWDNMVGPGKPLDTNRFFVIGVNNLGSCFGSTGPMSIDPSTGRPYGASF 120 Query: 121 PVVTVEDWVHAQARVADAFGIERFAAVMGGSLGGMQALAWSLLYPERVAHCIDIASTPKL 180 PVVTVEDWV+AQARVAD FGIE+FAAVMGGSLGGMQALAWS++YP+R+ HCI +ASTPKL Sbjct: 121 PVVTVEDWVNAQARVADEFGIEKFAAVMGGSLGGMQALAWSMMYPDRLEHCIVVASTPKL 180 Query: 181 SAQNIAFNEVARSAILSDPDFHGGDYYAHGVKPRRGLRVARMIGHITYLSDDDMAEKFGR 240 SAQNIAFNEVARS+ILSDPDFHGGDYYAHGVKP+RGLRVARMIGHITYLSDDDMA KFGR Sbjct: 181 SAQNIAFNEVARSSILSDPDFHGGDYYAHGVKPKRGLRVARMIGHITYLSDDDMAAKFGR 240 Query: 241 ALRRADGALDAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFNG 300 ALRRA+GA AYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKA++G Sbjct: 241 ALRRAEGAEKAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAYDG 300 Query: 301 NLSAALAHTKAKYLVASFTTDWRFAPARSREIVKALLDNRRSVSYAEIDAPHGHDAFLLD 360 +L+AALAHTKAKYL+ASFTTDWRFAPARSRE+VKALLD++R V+Y EIDAPHGHDAFLLD Sbjct: 301 DLTAALAHTKAKYLIASFTTDWRFAPARSRELVKALLDHKRQVTYGEIDAPHGHDAFLLD 360 Query: 361 DARYHNLVRAYYERIAEEVGA 381 DARYHNL+RAYYERIA EV A Sbjct: 361 DARYHNLMRAYYERIAAEVNA 381 Lambda K H 0.322 0.136 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: 631 Number of extensions: 20 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: 381 Length of database: 381 Length adjustment: 30 Effective length of query: 351 Effective length of database: 351 Effective search space: 123201 Effective search space used: 123201 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 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