Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate Ga0059261_2301 Ga0059261_2301 homoserine O-acetyltransferase (EC 2.3.1.31)
Query= SwissProt::S2KHP1 (367 letters) >FitnessBrowser__Korea:Ga0059261_2301 Length = 371 Score = 280 bits (717), Expect = 3e-80 Identities = 149/359 (41%), Positives = 208/359 (57%), Gaps = 3/359 (0%) Query: 6 RFIELPGPVRMYRGGELPSVTIAYETWGELRGQGDNALLLFTGLSPSAHAASSM-ADPSP 64 R + LPGP+R+ G L V IAYET+G L G NA+L+ L+ H AS P Sbjct: 11 RHVTLPGPLRLDGGVLLSPVEIAYETYGTLAPDGGNAILICHALTGDQHVASPHPVTGKP 70 Query: 65 GWWEYMIGPGKPIDTERFFVIAINSLGSCFGSTGPASINPATGQPYRLDFPKLSVEDIVA 124 GWW M+GPGKP+D +R F++ N LGSC GS+GPA++NPATG+P+ +DFP +++ D+V Sbjct: 71 GWWTRMVGPGKPVDPDRHFIVCANVLGSCMGSSGPATVNPATGRPWGMDFPVITIRDMVR 130 Query: 125 AARGACRALGIDHVHTVAGASLGGMDALAYAVMYPGTYRDIISISAAAHATPFTIALRSI 184 A LG+ + V G S+GGM AL++ +P ++ I++ A + IA + Sbjct: 131 AQAMLLDHLGVGRLKAVVGGSMGGMQALSWPATFPDRVDAVVVIASTARHSAQNIAFHEV 190 Query: 185 QREAVRADPAWAGGNYAPGEGPKDGMRVARQLGILTYRSAEEWLQRFDRERLEGSDDSAN 244 R+AV ADP W GG Y G+ P G+ VAR +TY S ++F R RL+ + + Sbjct: 191 GRQAVMADPRWNGGAYYDGDPPAAGLAVARMAAHITYLSEAGLTEKFGR-RLQAREAKSF 249 Query: 245 PFAMAFQVQSYMEANARKFADRFDANCYLYLSQAMDLFDMAEHGDGSLEAAVRRIDAKRA 304 F FQ++SY+ F DRFDAN YLY+++AMD FD+AE G L A R A+ Sbjct: 250 GFDADFQIESYLRHQGLSFVDRFDANAYLYITRAMDYFDLAEEHGGLLANAFRETRARFC 309 Query: 305 LVAGVTTDWLFPLWQQRQVAELLEHAGVAVSYHELGSIQGHDAFLVDSERFAPMVAEFL 363 LV+ TDWL+P R + L AG VS+ EL S GHDAFL+++ +V FL Sbjct: 310 LVS-FDTDWLYPTRDSRAIVHALNAAGAPVSFVELSSPFGHDAFLLEAPELNRVVDGFL 367 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: 441 Number of extensions: 28 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: 371 Length adjustment: 30 Effective length of query: 337 Effective length of database: 341 Effective search space: 114917 Effective search space used: 114917 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 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