Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_012471501.1 GLOV_RS17225 homoserine O-acetyltransferase
Query= SwissProt::S2L5R8 (390 letters) >NCBI__GCF_000020385.1:WP_012471501.1 Length = 367 Score = 321 bits (823), Expect = 2e-92 Identities = 164/369 (44%), Positives = 229/369 (62%), Gaps = 4/369 (1%) Query: 14 SVGLVAPQTAHFDVPLALACGKTLQSYDLVYETYGKLNASRSNAVLICHALSGHHHAAGY 73 S+G+V QT F+ + L G+ L LVYE YG +NA SN +++ HA +G H AG Sbjct: 2 SIGVVHEQTITFEAGIRLESGRILAPITLVYELYGTMNADCSNVIMVEHAWTGDAHLAGK 61 Query: 74 HSREDRKPGWWDAHIGPGKSIDTDRFFVISLNNLGGCHGSTGPCAINPDTGRQWGPDFPM 133 +D KPGWWDA +GPG+ +DTDR+ V+ N +G C+GSTGP +INP TG+++ FP+ Sbjct: 62 RREDDPKPGWWDAIVGPGRLLDTDRYCVLCSNVIGSCYGSTGPASINPRTGKRYNLSFPV 121 Query: 134 MTVGDWVHSQARLADRLGIERFAAVIGGSLGGMQVLQWSLAYPERIANAVVIAATPKLSA 193 +TV D V +Q L D LGI R V+GGS+GGMQ L+W+ YPER+A+ V +A TP+ S Sbjct: 122 ITVRDMVRAQELLLDHLGIRRLLCVMGGSMGGMQALEWATQYPERVASVVALATTPRPSP 181 Query: 194 QNIAFNEVARQAIRSDPDFYDGWYAEHDTLPRRGLKLARMVGHITYLSEDAMGSKFGRDL 253 Q I+ N VAR AI +DP + G Y + P+ GL LAR +GHIT+LS+++M KF R Sbjct: 182 QAISLNAVARWAIYNDPTWKKGEYKHN---PKDGLALARGIGHITFLSDESMWQKFERRF 238 Query: 254 RSDDLNFGYDVEFQVESYLRYQGDTFSTSFDANTYLLMTKALDYFDPAAAHDGDLAAAVA 313 + D F + +F+VE YL Y G F FDAN +L + KALD +D A ++ + A + Sbjct: 239 SAKDGLFDFFGQFEVERYLNYNGYNFVDRFDANCFLYLAKALDLYDVAWGYE-SMTDAFS 297 Query: 314 PASCPFLVVSFSTDWRFPPSRSRELVDALIRAGKPVSYVCIDSPHGHDAFLLPETRYQAI 373 + P +FS+DW +PP ++ E+V L GK V Y I S +GHDAFLL + + Sbjct: 298 RITAPIQFFAFSSDWLYPPYQTEEMVTCLQGLGKEVEYHLIQSAYGHDAFLLEHETFTPM 357 Query: 374 FASFMGRVA 382 S + RVA Sbjct: 358 VRSLLERVA 366 Lambda K H 0.321 0.136 0.428 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: 393 Number of extensions: 15 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: 390 Length of database: 367 Length adjustment: 30 Effective length of query: 360 Effective length of database: 337 Effective search space: 121320 Effective search space used: 121320 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