Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate AZOBR_RS14580 AZOBR_RS14580 homoserine O-acetyltransferase
Query= SwissProt::S2KHP1 (367 letters) >FitnessBrowser__azobra:AZOBR_RS14580 Length = 398 Score = 182 bits (461), Expect = 2e-50 Identities = 112/356 (31%), Positives = 189/356 (53%), Gaps = 13/356 (3%) Query: 19 GGELPSVTIAYETWGELRGQGDNALLLFTGLSPSAHAASS--MADPSPGWWEYMIGPGKP 76 GG + +V I +E++G+L DN +L+ S ++HAA M DP+PG+W+ +IGPGKP Sbjct: 45 GGTIKNVRIGWESYGKLNDARDNVILVTHFFSGNSHAAGKYKMEDPAPGYWDSIIGPGKP 104 Query: 77 IDTERFFVIAINSLGSC------FGSTGPASINPATGQPYRLDFPKLSVEDIVAAARGAC 130 +DT++FF+I+ ++L + +TGPAS+NP TG+PY + FP +++ D V + Sbjct: 105 LDTDKFFIISSDTLVNLSPKDPTVTTTGPASVNPDTGKPYGMSFPVVTIRDFVNVQKALL 164 Query: 131 RALGIDHVHTVAGASLGGMDALAYAVMYPGTYRDIISISAAAHATPFTIALRSIQREAVR 190 +L + +H V G S+G + AL + +P + ++++ A A PF I ++ +R Sbjct: 165 DSLNVKSLHAVMGGSMGSLQALEWGATHPEMVKRVVAVIGGAEADPFLIGWLNLWAAPIR 224 Query: 191 ADPAWAGGNYAPGEGPKDGMRVARQLGILTYRSAEEWLQRFDRERLEGSDDSANPFAMAF 250 DP W GG+Y PK G+ A +L L R + F R E D A + Sbjct: 225 VDPNWQGGDYYGKAEPKAGLTEALKLVTLHARHWKWADATFGRGWAEEGKDPAASMNNQY 284 Query: 251 QVQSYMEANARKFADRFDANCYLYLSQAMDLFDMAEHGDGSLEAAVRRIDAKRALVAGVT 310 ++++++ A A DAN +LYL +A F + G GSL+ + +I A L+ Sbjct: 285 AIEAWLDKAAAARAAVSDANHFLYLVKANQTFLVG--GGGSLDEGLAKIKAPVLLIPS-A 341 Query: 311 TDWLFPLWQ-QRQVAELLEHAGVAVSYHE-LGSIQGHDAFLVDSERFAPMVAEFLA 364 D +FP + R + E LE G+AV+Y + + + GH + + + ++ F+A Sbjct: 342 DDLVFPPERAMRPLKERLEKQGIAVTYTDAITTSLGHLDGIANIAKAGDAISAFMA 397 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: 415 Number of extensions: 18 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: 398 Length adjustment: 30 Effective length of query: 337 Effective length of database: 368 Effective search space: 124016 Effective search space used: 124016 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