Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate WP_013834891.1 THICY_RS01725 homoserine O-acetyltransferase
Query= SwissProt::S2KHP1 (367 letters) >NCBI__GCF_000214825.1:WP_013834891.1 Length = 377 Score = 243 bits (620), Expect = 6e-69 Identities = 139/352 (39%), Positives = 195/352 (55%), Gaps = 7/352 (1%) Query: 8 IELPGPVRMYRGGELPSVTIAYETWGELRGQGDNALLLFTGLSPSAHAASSM-ADPSPGW 66 +++ P+++ G ELPS + YET+GEL NA+L+ LS H D PGW Sbjct: 12 LQVSMPLQLVSGAELPSYDLVYETYGELNADASNAVLICHALSGDHHVTGYYEGDTKPGW 71 Query: 67 WEYMIGPGKPIDTERFFVIAINSLGSCFGSTGPASINPATGQPYRLDFPKLSVEDIVAAA 126 W IGPGKP+DT FFV+ N+LG C GS+GPAS+NPATG+ Y DFP ++ D V + Sbjct: 72 WSDYIGPGKPVDTNEFFVVCSNNLGGCRGSSGPASLNPATGKVYGPDFPIVTCRDWVNSQ 131 Query: 127 RGACRALGIDHVHTVAGASLGGMDALAYAVMYPGTYRDIISISAAAHATPFTIALRSIQR 186 + LGI+ V G S+GGM + +A+ +P R + I+AA + IA + R Sbjct: 132 NTLRQHLGIEQWAAVIGGSMGGMQVMQWAIDHPDKLRHALVIAAAPKLSAQNIAFNEVAR 191 Query: 187 EAVRADPAWAGGNY-APGEGPKDGMRVARQLGILTYRSAEEWLQRFDRERLEGSDDSANP 245 A+ DP + GG + G PK G+ +AR LG LTY S + +F RE S+ Sbjct: 192 RAIMTDPEFNGGRFIEAGTTPKGGLALARMLGHLTYLSDDMMGAKFGREL--RSESLKYS 249 Query: 246 FAMAFQVQSYMEANARKFADR--FDANCYLYLSQAMDLFDMAEHGDGSLEAAVRRIDAKR 303 F + FQV+SY+ KFA + FDAN YL +++A+D FD A D +L AA + A Sbjct: 250 FDVEFQVESYLRYQGEKFATKQNFDANTYLLMTKALDYFDPAAEFDNNLSAAFAQTQAS- 308 Query: 304 ALVAGVTTDWLFPLWQQRQVAELLEHAGVAVSYHELGSIQGHDAFLVDSERF 355 LV T+DW F + R++ L AVSY E+ S GHDAFL+ + + Sbjct: 309 FLVVSFTSDWRFSPTRSREIVRALLDNDRAVSYAEIESEHGHDAFLLPNTHY 360 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: 388 Number of extensions: 21 Number of successful extensions: 6 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: 377 Length adjustment: 30 Effective length of query: 337 Effective length of database: 347 Effective search space: 116939 Effective search space used: 116939 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 10 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