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_086510438.1 BZY95_RS13465 homoserine O-acetyltransferase
Query= SwissProt::S2KHP1 (367 letters) >NCBI__GCF_002151265.1:WP_086510438.1 Length = 385 Score = 241 bits (615), Expect = 2e-68 Identities = 137/355 (38%), Positives = 197/355 (55%), Gaps = 6/355 (1%) Query: 13 PVRMYRGGELPSVTIAYETWGELRGQGDNALLLFTGLSPSAHAAS--SMADPSPGWWEYM 70 P+ + G LP+ + YET+G L + NA+L+ LS HAA + PGWW+ Sbjct: 22 PLALACGRTLPAYDLVYETYGTLNAERSNAVLICHALSGHHHAAGYHDADERKPGWWDAH 81 Query: 71 IGPGKPIDTERFFVIAINSLGSCFGSTGPASINPATGQPYRLDFPKLSVEDIVAAARGAC 130 IGPGK IDT RFFV+++N+LG C GSTGP S NPATG+ + DFP ++V D V + Sbjct: 82 IGPGKSIDTNRFFVVSLNNLGGCHGSTGPISTNPATGRQWGPDFPMVTVSDWVHSQARLA 141 Query: 131 RALGIDHVHTVAGASLGGMDALAYAVMYPGTYRDIISISAAAHATPFTIALRSIQREAVR 190 LGI+ G SLGGM L + +YP + + I+A + IA + R+A+R Sbjct: 142 DRLGIERFAAAIGGSLGGMQVLQWTRLYPERVANAVIIAATPKLSAQNIAFNEVARQAIR 201 Query: 191 ADPAWAGGNYAP-GEGPKDGMRVARQLGILTYRSAEEWLQRFDRERLEGSDDSANPFAMA 249 +DP + G YA G P+ G+++AR +G +TY S + +F R+ S+D + + Sbjct: 202 SDPDFHDGWYAEHGTAPRRGLKLARMVGHITYLSEDAMGSKFGRDL--RSEDLNFGYDVE 259 Query: 250 FQVQSYMEANARKFADRFDANCYLYLSQAMDLFDMAEHGDGSLEAAVRRIDAKRALVAGV 309 FQV+SY+ F+ FDAN YL +++A+D FD A G L AV LV Sbjct: 260 FQVESYLRYQGDTFSTAFDANTYLLMTKALDYFDPAAEHGGVLAEAVAPCQGP-FLVVSF 318 Query: 310 TTDWLFPLWQQRQVAELLEHAGVAVSYHELGSIQGHDAFLVDSERFAPMVAEFLA 364 T+DW FP + R++A L AG VSY + S GHDAFL+ R+ + A F++ Sbjct: 319 TSDWRFPPSRSRELANALIRAGKRVSYVNIDSPHGHDAFLLPEPRYQAVFAAFMS 373 Lambda K H 0.320 0.135 0.414 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: 414 Number of extensions: 29 Number of successful extensions: 4 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: 367 Length of database: 385 Length adjustment: 30 Effective length of query: 337 Effective length of database: 355 Effective search space: 119635 Effective search space used: 119635 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