Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate WP_011654184.1 RL_RS28060 homoserine O-acetyltransferase
Query= SwissProt::H8L374 (367 letters) >NCBI__GCF_000009265.1:WP_011654184.1 Length = 391 Score = 173 bits (438), Expect = 8e-48 Identities = 113/355 (31%), Positives = 185/355 (52%), Gaps = 10/355 (2%) Query: 18 RGGQ-LQGARLAYETWGRLSPGCDNAVLILTGLSPSAHAAS-HPDGDTSPGWWEGMLGPG 75 RGG+ + RL YET+G L+ DNA+LI S ++HAA + + D S G+W+ ++G G Sbjct: 36 RGGRTVPEMRLGYETYGTLNDAKDNAILIPHYFSGNSHAAGKYKEADVSAGYWDAIIGSG 95 Query: 76 KAIDTDRWYVICVNS---LGSDKGS---TGPASPDPATGAPYRLSFPELALEDVASAAHD 129 K +DTD+++V+ V++ LG++ + TGPA+ +P TG P+ + FP + + D Sbjct: 96 KPVDTDKYFVVSVDTPVNLGANDPNVITTGPATTNPKTGKPWGMDFPIMTIGDFVDTQKG 155 Query: 130 LVKALGIARLACLIGCSMGGMSALAYMLQYEGEVEAHISVDTAPQAQPFAIAIRSLQREA 189 L++ LGI + ++G SMGG+ + + +Y ++E I V ++ A IA + Sbjct: 156 LMEQLGIGKWHAVMGASMGGLQSYEWAARYPDKLERVIPVISSGWADANLIAWLDVWASP 215 Query: 190 IRLDPNWQDGHYTDAAYPETGMAMARKLGVITYRSAMEWNGRFARIRLDGDQRPDEPFAR 249 I+LDPNW G Y P G+A A K + SA +G F R P + +A Sbjct: 216 IKLDPNWNGGDYYTGQAPNAGLAQAMKTLTLQANSAEWTDGTFGRDWASEGADPGQSWAN 275 Query: 250 EFQVESYLEHHAQRFVRRFDPACYLYLTRASDWFDVAEYGEGSVMQGLARIHVRRALVIG 309 +++V + L V + D +LYL RA+ F VA + S+ +GL I V ++I Sbjct: 276 DYKVVTKLNEAGAARVAQSDANHFLYLARANQLF-VAGQPKDSLYKGLLNIDV-PVMLIY 333 Query: 310 VSTDILFPLEQQQQIAEGLQAAGAEVDFVALDSPQGHDAFLVDIENYSAAIGGFL 364 D++FP + + +++ G V+FV L+ +GH L+ I I FL Sbjct: 334 TDEDLIFPGDAVRGTGTIIKSDGTPVEFVELEGTRGHMDGLLSIAQAGERIRAFL 388 Lambda K H 0.320 0.136 0.421 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: 387 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 367 Length of database: 391 Length adjustment: 30 Effective length of query: 337 Effective length of database: 361 Effective search space: 121657 Effective search space used: 121657 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 Jul 25 2024. The underlying query database was built on Jul 25 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