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_086511565.1 BZY95_RS19555 homoserine acetyltransferase
Query= SwissProt::S2KHP1 (367 letters) >NCBI__GCF_002151265.1:WP_086511565.1 Length = 410 Score = 172 bits (437), Expect = 1e-47 Identities = 114/357 (31%), Positives = 179/357 (50%), Gaps = 17/357 (4%) Query: 19 GGELPSVTIAYETWGELRGQGDNALLLFTGLSPSAHAASSMA--DPSPGWWEYMIGPGKP 76 G + V I +E +G L + DN +L+ S ++HAA D +PG+W+ +IGPGKP Sbjct: 59 GDTIAPVRIGWEAYGTLNEERDNVILITHFFSGTSHAAGRYTEDDAAPGYWDAIIGPGKP 118 Query: 77 IDTERFFVIAINSLGSC------FGSTGPASINPATGQPYRLDFPKLSVEDIVAAARGAC 130 +DT+ +++I+ ++L + +TGPA+ NP TG+P+ DFP +++ D V + Sbjct: 119 LDTDEYYIISSDTLVNLNVHDPNVTTTGPATPNPETGEPWGTDFPLVTIRDFVEVQKALL 178 Query: 131 RALGIDHVHTVAGASLGGMDALAYAVMYPGTYRDIISISAAAHATPFTIALRSIQREAVR 190 + GI+ +H V G S+G + A +A YP +I + A P+ +A S +R Sbjct: 179 ESQGIERLHAVMGPSMGALQAYEWASTYPERVERLIPVIGGGVADPWLLATLSAWAAPIR 238 Query: 191 ADPAWAGGNYAPGEGPKDGMRVARQLGILTYRSAEEWL---QRFDRERLEGSDDSANPFA 247 D W G+Y E P DG+R A +L L +A WL + FDR + D Sbjct: 239 LDANWNEGDYYDSEPPLDGLREALKLVTL---NANHWLWANETFDRSWADEDADPTRELD 295 Query: 248 MAFQVQSYMEANARKFADRFDANCYLYLSQAMDLFDMAEHGDGSLEAAVRRIDAKRALVA 307 + ++ ++ A A+ DAN LYL +A F +A HG GSLE + RI+A L+ Sbjct: 296 ARYAIEQTLDDIAAARAELADANHLLYLVKANQSF-IAGHG-GSLEEGLGRIEAP-TLIL 352 Query: 308 GVTTDWLFPLWQQRQVAELLEHAGVAVSYHELGSIQGHDAFLVDSERFAPMVAEFLA 364 D +F RQ AEL+E G V L +GH ++ ++ + FLA Sbjct: 353 YSENDLVFAPEGVRQTAELIEDGGADVELVTLEGKRGHLDGILAIDQAGERIRAFLA 409 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: 404 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: 410 Length adjustment: 30 Effective length of query: 337 Effective length of database: 380 Effective search space: 128060 Effective search space used: 128060 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 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