Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate Ac3H11_4277 Homoserine O-acetyltransferase (EC 2.3.1.31)
Query= SwissProt::S2KHP1 (367 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4277 Length = 401 Score = 248 bits (632), Expect = 3e-70 Identities = 147/383 (38%), Positives = 208/383 (54%), Gaps = 29/383 (7%) Query: 8 IELPGPVRMYRGGELPSVTIAYETWGELRGQGDNALLLFTGLSPSAHAASSMA--DPSPG 65 + P + + G L +AYET+G L NA+L+ L+ S H A A D S G Sbjct: 10 LHFPEVLPLQSGASLRDYHLAYETYGTLNADRSNAVLVCHALNASHHVAGVYAGQDKSEG 69 Query: 66 WWEYMIGPGKPIDTERFFVIAINSLGSCFGSTGPASINPATGQPYRLDFPKLSVEDIVAA 125 WW+ MIGPGKP+DT+RFFVI +N+LGSCFGSTGP +P TG+ Y DFP ++VED V A Sbjct: 70 WWDNMIGPGKPVDTDRFFVIGVNNLGSCFGSTGPMHNHPDTGEVYGADFPVVTVEDWVNA 129 Query: 126 ARGACRALGIDHVHTVAGASLGGMDALAYAVMYPGTYRDIISISAAAHATPFTIALRSIQ 185 LGI + V G SLGGM AL++ + YP R + +++A + T IA + Sbjct: 130 QARLLDRLGITQLAAVLGGSLGGMQALSWTLQYPERMRHAVVVASAPNLTAENIAFNEVA 189 Query: 186 REAVRADPAWAGGN-YAPGEGPKDGMRVARQLGILTYRSAEEWLQRFDRE-------RLE 237 R A+ DP + GG+ Y G PK G+R+AR +G +TY S + ++F R Sbjct: 190 RRAIVTDPDFHGGHFYRHGVIPKRGLRIARMIGHITYLSDDVMNEKFGRSLRAPTLPAAR 249 Query: 238 GS--DDSANPFA----------------MAFQVQSYMEANARKFADRFDANCYLYLSQAM 279 GS + A P + FQ++SY+ KF+D FDAN YL +++A+ Sbjct: 250 GSLPPEGAGPARGGPAPDLRDYLYSTQDIEFQIESYLRYQGDKFSDYFDANTYLLITRAL 309 Query: 280 DLFDMAEHGDGSLEAAVRRIDAKRALVAGVTTDWLFPLWQQRQVAELLEHAGVAVSYHEL 339 D FD A G+L A+ R AK LV+ TTDW F + R++ + L VSY E+ Sbjct: 310 DYFDPARAHGGNLTRALARATAKFLLVS-FTTDWRFSPQRSREIVKALLDNRRRVSYAEI 368 Query: 340 GSIQGHDAFLVDSERFAPMVAEF 362 + GHDAFL+D R+ ++ + Sbjct: 369 DAPHGHDAFLLDDARYMGVMRSY 391 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: 423 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: 401 Length adjustment: 30 Effective length of query: 337 Effective length of database: 371 Effective search space: 125027 Effective search space used: 125027 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