Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate BPHYT_RS01595 BPHYT_RS01595 homoserine O-acetyltransferase
Query= SwissProt::S2KHP1 (367 letters) >FitnessBrowser__BFirm:BPHYT_RS01595 Length = 381 Score = 267 bits (682), Expect = 4e-76 Identities = 149/349 (42%), Positives = 207/349 (59%), Gaps = 7/349 (2%) Query: 13 PVRMYRGGELPSVTIAYETWGELRGQGDNALLLFTGLSPSAHAASSMADPSP--GWWEYM 70 P+++ G L + ET+G L NA+L+ L+ S H A AD GWW+ M Sbjct: 17 PLQLQNGSSLAGYDLMVETYGTLNAARSNAVLVCHALNASHHVAGVYADNPKDIGWWDNM 76 Query: 71 IGPGKPIDTERFFVIAINSLGSCFGSTGPASINPATGQPYRLDFPKLSVEDIVAAARGAC 130 +GPGKP+DT++FFVI +N+LGSCFGSTGP SI+PATG PY FP ++VED V A Sbjct: 77 VGPGKPLDTDKFFVIGVNNLGSCFGSTGPMSIDPATGNPYGAAFPVVTVEDWVNAQARVA 136 Query: 131 RALGIDHVHTVAGASLGGMDALAYAVMYPGTYRDIISISAAAHATPFTIALRSIQREAVR 190 GI V G SLGGM ALA+++MYP I +++ + IA + R A+ Sbjct: 137 DQFGITRFAAVMGGSLGGMQALAWSMMYPERVGHCIVVASTPKLSAQNIAFNEVARSAIL 196 Query: 191 ADPAWAGGN-YAPGEGPKDGMRVARQLGILTYRSAEEWLQRFDR--ERLEGSDDSAN-PF 246 +DP + GGN YA PK G+RVAR +G +TY S ++ ++F R R EG+ D+ N F Sbjct: 197 SDPDFHGGNYYAHNVKPKRGLRVARMIGHITYLSDDDMAEKFGRSLRRAEGAVDAYNFNF 256 Query: 247 AMAFQVQSYMEANARKFADRFDANCYLYLSQAMDLFDMAEHGDGSLEAAVRRIDAKRALV 306 + F+V+SY+ KFAD FDAN YL +++A+D FD A+ DG L AAV AK L+ Sbjct: 257 DVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFDGDLTAAVAHTTAK-YLI 315 Query: 307 AGVTTDWLFPLWQQRQVAELLEHAGVAVSYHELGSIQGHDAFLVDSERF 355 A +TDW F + R++ + L V+Y E+ + GHDAFL+D R+ Sbjct: 316 ASFSTDWRFAPARSRELVKALLDHKRTVTYAEIDAPHGHDAFLLDDARY 364 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: 389 Number of extensions: 18 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: 381 Length adjustment: 30 Effective length of query: 337 Effective length of database: 351 Effective search space: 118287 Effective search space used: 118287 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