Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate CA265_RS08175 CA265_RS08175 homoserine O-acetyltransferase
Query= SwissProt::S2KHP1 (367 letters) >FitnessBrowser__Pedo557:CA265_RS08175 Length = 352 Score = 171 bits (432), Expect = 4e-47 Identities = 107/352 (30%), Positives = 183/352 (51%), Gaps = 25/352 (7%) Query: 15 RMYRGGELPSVTIAYETWGELRGQGDNALLLFTGLSPSAHAASSMADPSPGWWEYMIGPG 74 ++ G ++ ++ IAY+T+G+L DN + + HA ++ AD WWE + G Sbjct: 14 KLESGKKIRNLQIAYQTYGKLNANKDNVIWV-------CHALTANADVFE-WWEGLFGQN 65 Query: 75 KPIDTERFFVIAINSLGSCFGSTGPASINPATGQPYRLDFPKLSVEDIVAAARGACRALG 134 + E +++ N LGS +GS+ P S NP TG PY L FP+ ++ D+V+A + LG Sbjct: 66 SLFNPEEHYIVCANVLGSHYGSSNPLSTNPVTGLPYYLSFPQFTIRDLVSAHQLLASHLG 125 Query: 135 IDHVHTVAGASLGGMDALAYAVMYPGTYRDIISISAAAHATPFTIALRSIQREAVRADPA 194 ID++ + G SLGG A+ +++ P ++I I+ A +P+ IA QR A+ D Sbjct: 126 IDYIKLLIGGSLGGQQAVEWSISEPNKIENLILIATNAAHSPWGIAFNESQRLAITTDRT 185 Query: 195 WAGGNYAPGEGPKDGMRVARQLGILTYRSAEEWLQRFDRERLEGSDDSANPFAMAFQVQS 254 + P G K G++ AR + +L+YR+ + ++E +D + F+ S Sbjct: 186 FYANQ--PNGGSK-GLKTARSIALLSYRT----YSAYGSTQVESVNDKTD----NFRSSS 234 Query: 255 YMEANARKFADRFDANCYLYLSQAMDLFDMAEHGDGSLEAAVRRIDAKRALVAGVTTDWL 314 Y K +RF+A Y YL++AMD ++ + S+ A++ I A LV G+ D L Sbjct: 235 YQNYQGEKLINRFNAYSYYYLTKAMDSHNVGRNRK-SIADALKLITA-NTLVIGIENDVL 292 Query: 315 FPLWQQRQVAELLEHAGVAVSYHELGSIQGHDAFLVDSERFAPMVAEFLAHS 366 FPL +Q+ +A+ + A + L S GHD FL++++ ++ F+ S Sbjct: 293 FPLSEQKYLADHIPGA----EFSALHSDYGHDGFLIETDALTNVIGNFIKES 340 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: 280 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: 352 Length adjustment: 29 Effective length of query: 338 Effective length of database: 323 Effective search space: 109174 Effective search space used: 109174 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