Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate N515DRAFT_2885 N515DRAFT_2885 homoserine O-acetyltransferase
Query= SwissProt::H8L374 (367 letters) >FitnessBrowser__Dyella79:N515DRAFT_2885 Length = 368 Score = 590 bits (1522), Expect = e-173 Identities = 294/366 (80%), Positives = 321/366 (87%), Gaps = 2/366 (0%) Query: 3 DARRYHALPSPFPMKRGGQLQGARLAYETWGRLSPGCDNAVLILTGLSPSAHAASHPDGD 62 DARRY +LPSPFPMKRGG+L GAR+A+ETWG LS DNA+LILTGLSPSAHAAS+ + D Sbjct: 4 DARRYFSLPSPFPMKRGGELHGARVAFETWGALSDARDNALLILTGLSPSAHAASN-EQD 62 Query: 63 TSPGWWEGMLGPGKAIDTDRWYVICVNSLGSDKGSTGPASPDPATGAPYRLSFPELALED 122 SPGWWE M+GPGKAIDTDRW+VICVNSLGSDKGST PAS DPATG PYRLSFPELALED Sbjct: 63 PSPGWWEAMIGPGKAIDTDRWFVICVNSLGSDKGSTCPASIDPATGEPYRLSFPELALED 122 Query: 123 VASAAHDLVKALGIARLACLIGCSMGGMSALAYMLQYEGEVEAHISVDTAPQAQPFAIAI 182 VA+AAH V +LGI +LACL+GCSMGGMSALAYML + G V HISVDTAPQAQPFAIAI Sbjct: 123 VANAAHAAVSSLGIEQLACLVGCSMGGMSALAYMLLHPGSVRTHISVDTAPQAQPFAIAI 182 Query: 183 RSLQREAIRLDPNWQDGHYTDAAYPETGMAMARKLGVITYRSAMEWNGRFARIRLDGDQR 242 RSLQREAIRLDP W +G Y DA YPETGM++ARKLGVITYRSAMEWNGRFARIRLD +QR Sbjct: 183 RSLQREAIRLDPQWNNGRYDDAHYPETGMSIARKLGVITYRSAMEWNGRFARIRLDAEQR 242 Query: 243 PDE-PFAREFQVESYLEHHAQRFVRRFDPACYLYLTRASDWFDVAEYGEGSVMQGLARIH 301 D+ PF EFQVESYLE HAQRFVR FDP YLYL+RASDWFD++EYGEGS+ GL RI Sbjct: 243 DDDVPFGFEFQVESYLEGHAQRFVRTFDPNSYLYLSRASDWFDISEYGEGSIQAGLKRIR 302 Query: 302 VRRALVIGVSTDILFPLEQQQQIAEGLQAAGAEVDFVALDSPQGHDAFLVDIENYSAAIG 361 V +ALVIGVSTDILFPLEQQ+QIAEGL+AAGA V+FVALDSPQGHDAFLVDIENYS AIG Sbjct: 303 VEQALVIGVSTDILFPLEQQEQIAEGLEAAGAAVEFVALDSPQGHDAFLVDIENYSRAIG 362 Query: 362 GFLRTL 367 GFL L Sbjct: 363 GFLGRL 368 Lambda K H 0.320 0.136 0.421 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: 581 Number of extensions: 20 Number of successful extensions: 3 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: 368 Length adjustment: 30 Effective length of query: 337 Effective length of database: 338 Effective search space: 113906 Effective search space used: 113906 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