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_007472882.1 CMTB2_RS00345 homoserine O-acetyltransferase
Query= SwissProt::S2KHP1 (367 letters) >NCBI__GCF_000170735.1:WP_007472882.1 Length = 368 Score = 228 bits (581), Expect = 2e-64 Identities = 136/353 (38%), Positives = 201/353 (56%), Gaps = 7/353 (1%) Query: 13 PVRMYRGGELPSVTIAYETWGELRGQGDNALLLFTGLSPSAHAAS-SMADPSPGWWEYMI 71 P+ + G L I YET+GEL NA+L+ LS S HAA D PGWW+ +I Sbjct: 13 PLYLESGRILEPWQIIYETYGELNEDKSNAILITHALSGSHHAAGWYKGDRKPGWWDGLI 72 Query: 72 GPGKPIDTERFFVIAINSLGSCFGSTGPAS-INPATGQPYRLDFPKLSVEDIVAAARGAC 130 G K IDT ++FVI N +GSCFGST P S I P + + YRL FP ++++D+V A + Sbjct: 73 GDSKAIDTTKYFVICTNVIGSCFGSTSPMSPIYPGSNERYRLKFPVITIKDMVKAQKILL 132 Query: 131 RALGIDHVHTVAGASLGGMDALAYAVMYPGTYRDIISISAAAHATPFTIALRSIQREAVR 190 +LGI + V G S+GGM AL + V +PG +II I+ P+ IA+ EA+R Sbjct: 133 DSLGIKKLKAVVGGSMGGMQALRFGVDFPGFVENIIPIATTYQTRPYVIAINKSMIEAIR 192 Query: 191 ADPAWAGGNYAPGEGPKDGMRVARQLGILTYRSAEEWLQRFDRERLEGSDDSANPFAMAF 250 AD + GNY G+ K G+ VAR +G L Y S + + ++F RE ++ D F Sbjct: 193 ADCEFKNGNYEIGKELK-GLAVARMIGYLNYISPKTFDKKFGREYVK--TDGMFELFGRF 249 Query: 251 QVQSYMEANARKFADRFDANCYLYLSQAMDLFDMAEHGDGSLEAAVRRIDAKRALVAGVT 310 QV+SY+E N F FDA Y+YL +A+ LFD+ G SL+ A I K L++ + Sbjct: 250 QVESYLEYNGAMFPKWFDALSYIYLLKAISLFDIG-RGFNSLDEAFSNIKDKLFLIS-FS 307 Query: 311 TDWLFPLWQQRQVAELLEHAGVAVSYHELGSIQGHDAFLVDSERFAPMVAEFL 363 D LF + R++ + ++ G Y+E+ S GHD+FLV+ ++F+ ++++ L Sbjct: 308 GDTLFFPEEMREIKKYMDKVGGRCQYYEIDSDYGHDSFLVEIDKFSDLISDIL 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: 327 Number of extensions: 16 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: 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 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