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_011386326.1 AMB_RS20100 homoserine O-acetyltransferase
Query= SwissProt::S2KHP1 (367 letters) >NCBI__GCF_000009985.1:WP_011386326.1 Length = 393 Score = 253 bits (646), Expect = 6e-72 Identities = 143/357 (40%), Positives = 194/357 (54%), Gaps = 12/357 (3%) Query: 13 PVRMYRGGELPSVTIAYETWGELRGQGDNALLLFTGLSPSAHAASSMADP-----SPGWW 67 P+R+ G EL + +AY+T+G L NA+L+ L+ + +ADP PGWW Sbjct: 26 PIRLDCGVELGPIQVAYQTYGRLNADKSNAILICHALTGDHY----VADPHPITAKPGWW 81 Query: 68 EYMIGPGKPIDTERFFVIAINSLGSCFGSTGPASINPATGQPYRLDFPKLSVEDIVAAAR 127 ++GPG+ DT+R+F+I N LG C G+TGP NPATGQ + LDFP +++ D+V Sbjct: 82 HELVGPGRVFDTDRYFLICSNVLGGCMGTTGPVDENPATGQAWGLDFPVITIGDMVKVQA 141 Query: 128 GACRALGIDHVHTVAGASLGGMDALAYAVMYPGTYRDIISISAAAHATPFTIALRSIQRE 187 LGID + V G S+GGM L +A +YP I I++AA + IA + R+ Sbjct: 142 RLVDHLGIDQLFCVVGGSMGGMQVLKWAQVYPERVFSAIPIASAARHSAQNIAFHEVGRQ 201 Query: 188 AVRADPAWAGGNY-APGEGPKDGMRVARQLGILTYRSAEEWLQRFDRERLEGSDDSANPF 246 A+ ADP W GNY G+ P G+ VAR +TY S Q+F R L+ D F Sbjct: 202 AIMADPDWCEGNYLQEGKRPHRGLAVARMAAHITYLSEPALHQKFGR-NLQNRDTVTYGF 260 Query: 247 AMAFQVQSYMEANARKFADRFDANCYLYLSQAMDLFDMAEHGDGSLEAAVRRIDAKRALV 306 FQV+SY+ F DRFDAN YLY+++AMD FD+A G L A R R V Sbjct: 261 DADFQVESYLRHQGNTFVDRFDANSYLYITRAMDYFDLAAESGGVLANAFRG-TRTRFCV 319 Query: 307 AGVTTDWLFPLWQQRQVAELLEHAGVAVSYHELGSIQGHDAFLVDSERFAPMVAEFL 363 T+DWLFP + R V L VS+ E+ S +GHDAFL+D F + FL Sbjct: 320 VSFTSDWLFPTPESRAVVHALNAVAANVSFVEIKSDKGHDAFLLDEPEFHATLTGFL 376 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: 409 Number of extensions: 22 Number of successful extensions: 5 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: 393 Length adjustment: 30 Effective length of query: 337 Effective length of database: 363 Effective search space: 122331 Effective search space used: 122331 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