Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate Echvi_3285 Echvi_3285 homoserine O-acetyltransferase
Query= SwissProt::S2KHP1 (367 letters) >FitnessBrowser__Cola:Echvi_3285 Length = 351 Score = 182 bits (461), Expect = 2e-50 Identities = 115/344 (33%), Positives = 176/344 (51%), Gaps = 26/344 (7%) Query: 19 GGELPSVTIAYETWGELRGQGDNALLLFTGLSPSAHAASSMADPSPGWWEYMIGPGKPID 78 G LP I+Y T G L + DN + + L+ A+ WW ++G K D Sbjct: 28 GESLPGFEISYTTQGHLTPKKDNVIWILHALTGDANVHE--------WWSGLVGEDKFFD 79 Query: 79 TERFFVIAINSLGSCFGSTGPASINPATGQPYRLDFPKLSVEDIVAAARGACRALGIDHV 138 ++F++ N LGSC+GST P S NP TG+PY DFP LS D+ A + LGI + Sbjct: 80 PTKYFIVCANLLGSCYGSTQPLSDNPKTGKPYYYDFPNLSTRDMAKAFDRLRQHLGIQQI 139 Query: 139 HTVAGASLGGMDALAYAVMYPGTYRDIISISAAAHATPFTIALRSIQREAVRADPAWAGG 198 T+ G SLGG AL ++ + I +++ A +P+TI QR A+ +D W G Sbjct: 140 DTIIGGSLGGQVALEWSYNLQEQVKKTIIVASNAKTSPWTIGFNEAQRMAIESDSTW--G 197 Query: 199 NYAPGEGPKDGMRVARQLGILTYRSAEEWLQRFDRERLEGSDDSANPFAMAFQVQSYMEA 258 +P G K G+ AR +G+L+YR ++ E E +D F+V SY+ Sbjct: 198 QNSPDAG-KKGLEAARAIGMLSYRH-QDIFHASQAETEEKTDH--------FRVSSYLRY 247 Query: 259 NARKFADRFDANCYLYLSQAMDLFDMAEHGDGSLEAAVRRIDAKRALVAGVTTDWLFPLW 318 +K ++RF+A Y L++AMD D+ G G A+ I AK L G+ TD LF Sbjct: 248 QGQKLSNRFNALSYWVLTKAMDSHDLG-RGRGGTAKALSAIKAK-VLSIGINTDLLFTKE 305 Query: 319 QQRQVAELLEHAGVAVSYHELGSIQGHDAFLVDSERFAPMVAEF 362 + + +++ + + +Y E+ SI GHDAFLV++E+ ++ F Sbjct: 306 ESQFISKNVPNG----TYREISSIYGHDAFLVENEQLNYILTSF 345 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: 291 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: 351 Length adjustment: 29 Effective length of query: 338 Effective length of database: 322 Effective search space: 108836 Effective search space used: 108836 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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