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_013521130.1 ALIDE2_RS23390 homoserine O-acetyltransferase
Query= SwissProt::S2KHP1 (367 letters) >NCBI__GCF_000204645.1:WP_013521130.1 Length = 376 Score = 261 bits (666), Expect = 3e-74 Identities = 142/347 (40%), Positives = 201/347 (57%), Gaps = 4/347 (1%) Query: 19 GGELPSVTIAYETWGELRGQGDNALLLFTGLSPSAHAASSMADP--SPGWWEYMIGPGKP 76 G + T+AYET+G L +G NA+L+ L+ S H A S GWW+ MIGPGKP Sbjct: 21 GASIRDYTLAYETYGRLNAEGTNAVLVCHALNASHHVAGVYEGQPRSEGWWDNMIGPGKP 80 Query: 77 IDTERFFVIAINSLGSCFGSTGPASINPATGQPYRLDFPKLSVEDIVAAARGACRALGID 136 +DT RFFVI +N+LGSCFGSTGP NP TG+ Y DFP ++VED V A LG+ Sbjct: 81 VDTNRFFVIGVNNLGSCFGSTGPMHANPDTGEVYGADFPVVTVEDWVNAQARLLDRLGVG 140 Query: 137 HVHTVAGASLGGMDALAYAVMYPGTYRDIISISAAAHATPFTIALRSIQREAVRADPAWA 196 + V G SLGGM AL++ + YP R + +++A + T IA + R A+ DP + Sbjct: 141 QLAAVMGGSLGGMQALSWTLQYPERMRHAVVVASAPNLTAENIAFNEVARRAIVTDPDFH 200 Query: 197 GGN-YAPGEGPKDGMRVARQLGILTYRSAEEWLQRFDRERLEGSDDSANPFAMAFQVQSY 255 GG+ Y G PK G+R+AR +G +TY S + ++F R+ EG D + + FQ++SY Sbjct: 201 GGHFYRHGTIPKRGLRIARMIGHITYLSDDVMNEKFGRQLREGIDLKYSTQDIEFQIESY 260 Query: 256 MEANARKFADRFDANCYLYLSQAMDLFDMAEHGDGSLEAAVRRIDAKRALVAGVTTDWLF 315 + KF++ FDAN YL +++A+D FD A GSL A+ + R L+ TTDW F Sbjct: 261 LRYQGDKFSEYFDANTYLLITRALDYFDPALRYGGSLAQAL-AVARARFLLVSFTTDWRF 319 Query: 316 PLWQQRQVAELLEHAGVAVSYHELGSIQGHDAFLVDSERFAPMVAEF 362 + R++ L VSY E+ + GHDAFL+D R+ +V + Sbjct: 320 SPRRSREIVHALLENRRDVSYAEIDAPHGHDAFLLDDVRYMGVVRSY 366 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: 374 Number of extensions: 16 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: 376 Length adjustment: 30 Effective length of query: 337 Effective length of database: 346 Effective search space: 116602 Effective search space used: 116602 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: 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