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_066919752.1 ACG33_RS06625 homoserine O-acetyltransferase
Query= SwissProt::S2KHP1 (367 letters) >NCBI__GCF_001579945.1:WP_066919752.1 Length = 365 Score = 423 bits (1088), Expect = e-123 Identities = 210/363 (57%), Positives = 268/363 (73%), Gaps = 1/363 (0%) Query: 1 MPDARRFIELPGPVRMYRGGELPSVTIAYETWGELRGQGDNALLLFTGLSPSAHAASSMA 60 M AR+ ++L P M+RGG L V IAYETWG+ +GDNA+L+FTGL+PSAHAASS + Sbjct: 1 MNAARKILKLDRPFEMHRGGTLQGVEIAYETWGDPAHRGDNAILIFTGLTPSAHAASSES 60 Query: 61 DPSPGWWEYMIGPGKPIDTERFFVIAINSLGSCFGSTGPASINPATGQPYRLDFPKLSVE 120 DPSPGWWE MIGPG+PIDT RFFVI +NSLGS FGST P SINPATG+ YRL FP L+VE Sbjct: 61 DPSPGWWEDMIGPGRPIDTRRFFVICVNSLGSPFGSTSPVSINPATGRAYRLTFPVLTVE 120 Query: 121 DIVAAARGACRALGIDHVHTVAGASLGGMDALAYAVMYPGTYRDIISISAAAHATPFTIA 180 DI A +LGI+ + V G SLGGM LAY ++PG R ++SISAAA + PF IA Sbjct: 121 DIAHAGHEVVVSLGIEKLLAVVGPSLGGMTVLAYCALFPGAARSVVSISAAARSLPFAIA 180 Query: 181 LRSIQREAVRADPAWAGGNYAPGEGPKDGMRVARQLGILTYRSAEEWLQRFDRERLEGSD 240 LRS+QRE +R D AW G+YA P +GMR+AR+LG++TYRSA+EW RF RER + Sbjct: 181 LRSLQREIIRRDSAWREGDYAADAIPVEGMRLARKLGMITYRSAKEWGLRFGRERADLQR 240 Query: 241 DSANPFAMAFQVQSYMEANARKFADRFDANCYLYLSQAMDLFDMAEHGDGSLEAAVRRID 300 +PF + F+V+SY+E +A KF ++D NCYLY+S+AMDLFD+A+HG GS+ A+RR Sbjct: 241 RPGDPFGIDFEVESYLENHAEKFTGQYDPNCYLYISRAMDLFDLADHG-GSVNEALRRFT 299 Query: 301 AKRALVAGVTTDWLFPLWQQRQVAELLEHAGVAVSYHELGSIQGHDAFLVDSERFAPMVA 360 +RALV GV TD LFP+ QQ+++AE L G V++ L S+QGHD+FLVD +RF P++A Sbjct: 300 VERALVIGVETDLLFPIEQQQELAEGLAAGGREVTFVRLPSLQGHDSFLVDMDRFRPVIA 359 Query: 361 EFL 363 EFL Sbjct: 360 EFL 362 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: 497 Number of extensions: 24 Number of successful extensions: 2 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: 365 Length adjustment: 30 Effective length of query: 337 Effective length of database: 335 Effective search space: 112895 Effective search space used: 112895 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